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US20130267443A1 - ncRNA AND USES THEREOF - Google Patents

ncRNA AND USES THEREOF Download PDF

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Publication number
US20130267443A1
US20130267443A1 US13/797,106 US201313797106A US2013267443A1 US 20130267443 A1 US20130267443 A1 US 20130267443A1 US 201313797106 A US201313797106 A US 201313797106A US 2013267443 A1 US2013267443 A1 US 2013267443A1
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cancer
expression
sample
rna
prostate
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Arul Chinnaiyan
John Prensner
Matthew Iyer
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University of Michigan System
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University of Michigan System
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Priority claimed from US13/299,000 external-priority patent/US20150284802A1/en
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Priority to US13/797,106 priority Critical patent/US20130267443A1/en
Assigned to THE REGENTS OF THE UNIVERSITY OF MICHIGAN reassignment THE REGENTS OF THE UNIVERSITY OF MICHIGAN ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: IYER, MATTHEW, PRENSNER, JOHN
Assigned to HOWARD HUGHES MEDICAL INSTITUTE ("HHMI") reassignment HOWARD HUGHES MEDICAL INSTITUTE ("HHMI") ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CHINNAIYAN, ARUL
Assigned to THE REGENTS OF THE UNIVERSITY OF MICHIGAN reassignment THE REGENTS OF THE UNIVERSITY OF MICHIGAN ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: HOWARD HUGHES MEDICAL INSTITUTE ("HHMI")
Assigned to NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT reassignment NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT CONFIRMATORY LICENSE (SEE DOCUMENT FOR DETAILS). Assignors: UNIVERSITY OF MICHIGAN
Publication of US20130267443A1 publication Critical patent/US20130267443A1/en
Priority to US15/156,936 priority patent/US10407735B2/en
Priority to US16/523,008 priority patent/US12270080B2/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
    • A61K31/4164—1,3-Diazoles
    • A61K31/4184—1,3-Diazoles condensed with carbocyclic rings, e.g. benzimidazoles
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers.
  • the present invention relates to ncRNAs as diagnostic markers and clinical targets for prostate, lung, breast and pancreatic cancer.
  • a central aim in cancer research is to identify altered genes that are causally implicated in oncogenesis.
  • Several types of somatic mutations have been identified including base substitutions, insertions, deletions, translocations, and chromosomal gains and losses, all of which result in altered activity of an oncogene or tumor suppressor gene.
  • base substitutions e.g., base substitutions, insertions, deletions, translocations, and chromosomal gains and losses, all of which result in altered activity of an oncogene or tumor suppressor gene.
  • Epithelial tumors which are much more common and contribute to a relatively large fraction of the morbidity and mortality associated with human cancer, comprise less than 1% of the known, disease-specific chromosomal rearrangements (Mitelman, Mutat Res 462: 247 (2000)). While hematological malignancies are often characterized by balanced, disease-specific chromosomal rearrangements, most solid tumors have a plethora of non-specific chromosomal aberrations. It is thought that the karyotypic complexity of solid tumors is due to secondary alterations acquired through cancer evolution or progression.
  • chromosomal rearrangements Two primary mechanisms of chromosomal rearrangements have been described.
  • promoter/enhancer elements of one gene are rearranged adjacent to a proto-oncogene, thus causing altered expression of an oncogenic protein.
  • This type of translocation is exemplified by the apposition of immunoglobulin (IG) and T-cell receptor (TCR) genes to MYC leading to activation of this oncogene in B- and T-cell malignancies, respectively (Rabbitts, Nature 372: 143 (1994)).
  • IG immunoglobulin
  • TCR T-cell receptor
  • the present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers.
  • the present invention relates to ncRNAs as diagnostic markers and clinical targets for cancer (e.g., prostate, lung, breast and pancreatic cancer).
  • Embodiments of the present invention provide compositions, kits, and methods useful in the detection and screening of a cancer. Experiments conducted during the course of development of embodiments of the present invention identified upreguation of one or more non-coding RNAs in cancer. Some embodiments of the present invention provide compositions and methods for detecting expression levels of such ncRNAs. Identification of ncRNAs finds use in screening, diagnostic and research uses.
  • the present invention provides a method of screening for the presence of a cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of one or more non-coding RNAs (ncRNA); and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of a cancer in the subject.
  • the cancer is a prostate cancer.
  • the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample.
  • the control sample may comprise one or more normal cells.
  • the normal cells are normal prostate cells.
  • the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point. Alternatively, the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level.
  • the ncRNAs are described by SEQ ID NOs: 1-9.
  • the non-coding RNAs comprise one or more PCAT transcripts. In some embodiments, the non-coding RNAs are selected from the group comprising PCAT1, PCAT14, PCAT43 and PCAT 109.
  • the sample is tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions or prostate cells.
  • detecting the level of expression of the ncRNA comprises one or more in vitro assays.
  • the detection is carried out utilizing a sequencing technique, a nucleic acid hybridization technique, a nucleic acid amplification technique, or an immunoassay.
  • the invention is not limited to the technique employed.
  • the nucleic acid amplification technique is polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification or nucleic acid sequence based amplification.
  • the prostate cancer is localized prostate cancer or metastatic prostate cancer.
  • the reagent is a pair of amplification oligonucleotides or an oligonucleotide probe.
  • Additional embodiments provide a method of screening for the presence of a cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of two or more (e.g., 10 or more, 25 or more, 50 or more, 100 or more or all 121) non-coding RNAs (ncRNA); and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of cancer in the subject.
  • the cancer is a prostate cancer.
  • the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample.
  • the control sample may comprise one or more normal cells.
  • the normal cells are normal prostate cells.
  • the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point.
  • the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level.
  • At least one of the two or more ncRNAs are selected from a group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59,
  • the two or more ncRNAs are selected from the group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, P
  • RNAs selected from, for example, PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48,
  • ncRNA non-coding RNAs
  • the present invention provides a method for screening for the presence of a cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of one or more non-coding RNAs; and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of cancer in the subject.
  • the cancer is a lung cancer.
  • the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample.
  • the control sample may comprise one or more normal cells. In some instances, the normal cells are normal lung cells.
  • the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point.
  • the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level.
  • the one or more non-coding RNAs are selected from the group comprising M41 and ENST-75.
  • detecting the level of expression of the ncRNA comprises one or more in vitro assays.
  • the present invention provides a method for screening for the presence of a cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of one or more non-coding RNAs; and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of cancer in the subject.
  • the cancer is a breast cancer.
  • the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample.
  • the control sample may comprise one or more normal cells. In some instances, the normal cells are normal breast cells.
  • the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point.
  • the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level.
  • the one or more ncRNAs are selected from the group comprising TU0011194, TU0019356 and TU0024146.
  • detecting the level of expression of the ncRNA comprises one or more in vitro assays.
  • the present invention provides a method for screening for the presence of cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of one or more non-coding RNAs; and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of cancer in the subject.
  • the cancer is a pancreatic cancer.
  • the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample.
  • the control sample may comprise one or more normal cells. In some instances, the normal cells are normal pancreatic cells.
  • the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point.
  • the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level.
  • the one or more ncRNAs are selected from the group comprising TU0011194, TU0019356 and TU0024146.
  • detecting the level of expression of the ncRNA comprises one or more in vitro assays.
  • the present invention provides a method of screening for the presence of a cancer in a subject, comprising (a) contacting a biological sample from a subject with a gene expression detection assay, wherein the gene expression detection assay comprises a gene expression informative reagent for identification of the level of expression of SChLAP-1; (b) detecting the level of expression of SChLAP-1 in the sample; and (c) diagnosing cancer in the subject when an increased level of expression of SChLAP-1 in the sample is detected.
  • the cancer is a prostate cancer.
  • the increased level of expression of SChLAP-1 in the sample is relative to the level of SChLAP-1 in a control sample.
  • the control sample may comprise one or more normal cells.
  • the normal cells are normal prostate cells.
  • the increased level of expression of SChLAP-1 in the sample is relative to the level of expression of SChLAP-1 in a sample from a prior time point.
  • the increased level of expression of SChLAP-1 in the sample is relative to a pre-established threshold level.
  • detecting the level of expression of SChLAP-1 comprises one or more in vitro assays.
  • the gene expression detection assay further comprises a gene expression informative reagent for identification of the level of expression of one or more ncRNAs.
  • the present invention provides a method of identifying subjects at risk of cancer metastatis, comprising (a) contacting a biological sample from a subject with a gene expression detection assay, wherein the gene expression detection assay comprises a gene expression informative reagent for identification of the level of expression of SChLAP-1; (b) detecting the level of expression of SChLAP-1 in the sample using an in vitro assay; and (c)
  • the subject is at increased risk of lethal prostate cancer when an increased level of expression of SChLAP-1 in the sample is detected.
  • the cancer is a prostate cancer.
  • the increased level of expression of SChLAP-1 in the sample is relative to the level of SChLAP-1 in a control sample.
  • the control sample may comprise one or more normal cells.
  • the normal cells are normal prostate cells.
  • the increased level of expression of SChLAP-1 in the sample is relative to the level of expression of SChLAP-1 in a sample from a prior time point.
  • the increased level of expression of SChLAP-1 in the sample is relative to a pre-established threshold level.
  • detecting the level of expression of SChLAP-1 comprises one or more in vitro assays.
  • the gene expression detection assay further comprises a gene expression informative reagent for identification of the level of expression of one or more ncRNAs.
  • Such systems may comprise (a) a probe set may comprise a plurality of probes, wherein the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; and (b) a computer model or algorithm for analyzing an expression level and/or expression profile of a target molecule hybridized to the probe in a sample from a subject suffering from a cancer.
  • the PCAT may be selected from the group may comprise PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT
  • the system may further comprise an electronic memory for capturing and storing an expression profile.
  • the system may further comprise a computer-processing device, optionally connected to a computer network.
  • the system may further comprise a software module executed by the computer-processing device to analyze an expression profile.
  • the system may further comprise a software module executed by the computer-processing device to compare the expression profile to a standard or control.
  • the system may further comprise a software module executed by the computer-processing device to determine the expression level of the target.
  • the system may further comprise a machine to isolate the target molecule or the probe from the sample.
  • the system may further comprise a machine to sequence the target molecule or the probe.
  • the system may further comprise a machine to amplify the target molecule or the probe.
  • the system may further comprise a label that specifically binds to the target molecule the probe, or a combination thereof.
  • the system may further comprise a software module executed by the computer-processing device to transmit an analysis of the expression profile to the subject or a medical professional treating the subject.
  • the system may further comprise a software module executed by the computer-processing device to transmit a diagnosis or prognosis to the subject or a medical professional treating the subject.
  • kits comprising (a) a probe set may comprise a plurality of probes, wherein the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; and (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the target molecules in a sample.
  • the kit may further comprise a computer model or algorithm for correlating the expression level or expression profile with disease state or outcome.
  • the kit may further comprise a computer model or algorithm for designating a treatment modality for the subject.
  • the kit may further comprise a computer model or algorithm for normalizing expression level or expression profile of the target molecules.
  • the kit may further comprise a computer model or algorithm may comprise a robust multichip average (RMA), probe logarithmic intensity error estimation (PLIER), non-linear fit (NLFIT) quantile-based, nonlinear normalization, or a combination thereof.
  • RMA robust multichip average
  • PIER probe logarithmic intensity error estimation
  • NLFIT non-linear fit
  • Methods for analyzing a cancer in a subject in need thereof may comprise (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile comprises one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; and (b) comparing the expression profile from the sample to an expression profile of a control or standard.
  • Such methods for diagnosing cancer in a subject in need thereof may comprise (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile may comprise one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; (b) comparing the expression profile from the sample to an expression profile of a control or standard; and (c) diagnosing a cancer in the subject if the expression profile of the sample (i) deviates from the control or standard from a healthy subject or population of healthy subjects, or (ii) matches the control or standard from a subject or population of subjects who have or have had the cancer.
  • Such methods for predicting whether a subject may be susceptible to developing a cancer may comprise (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile may comprise one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; (b) comparing the expression profile from the sample to an expression profile of a control or standard; and (c) predicting the susceptibility of the subject for developing a cancer based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • Such methods for predicting a subject's response to a treatment regimen for a cancer may comprise: (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile may comprise one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; (b) comparing the expression profile from the sample to an expression profile of a control or standard; and (c) predicting the subject's response to a treatment regimen based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • treating or determining a treatment regimen for cancer may comprise: (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile may comprise one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; (b) comparing the expression profile from the sample to an expression profile of a control or standard; and (c) treating or determining a treatment regimen for cancer based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • the method may further comprise a software module executed by a computer-processing device to compare the expression profiles.
  • the method may further comprise providing diagnostic or prognostic information to the subject about the cancer based on the comparison.
  • the method may further comprise diagnosing the subject with a cancer if the expression profile of the sample (a) deviates from the control or standard from a healthy subject or population of healthy subjects, or (b) matches the control or standard from a subject or population of subjects who have or have had the cancer.
  • the method may further comprise predicting the susceptibility of the subject for developing a cancer based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (b) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • the method may further comprise prescribing a treatment regimen based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (b) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • the method may further comprise altering a treatment regimen prescribed or administered to the subject based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (b) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • the method may further comprise predicting the subject's response to a treatment regimen based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (b) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • the method may further comprise using a machine to isolate the one or more target molecules, one or more probes, or one or more probe hybridized target molecules from the sample.
  • the method may further comprise contacting the sample with a label that specifically binds to the target molecule, the probe, or a combination thereof.
  • the method may further comprise contacting the sample with a label that specifically binds to one or more target molecules.
  • the method may further comprise amplifying at least a portion of the target molecule, the probe, or any combination thereof.
  • the method may further comprise sequencing at least a portion of the target molecule, the probe, or any combination thereof.
  • a probe set for assessing a cancer status of a subject may comprise a plurality of probes, wherein the probes in the probe set may be capable of detecting an expression level of one or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9, wherein The expression level of the one or more target molecules may determine the cancer status of the subject with at least 40% accuracy.
  • the methods, systems, compositions and kits may comprise a plurality of probes.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of two or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of three or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of four or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of five or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of ten or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise and SEQ ID NOs: 1-9.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise PCAT1, PCAT14, PCAT43 and PCAT 109.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules may comprise SChLAP-1.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57,
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise M41 and ENST-75.
  • the cancer may be a lung cancer.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise TU0011194, TU0019356 and TU0024146.
  • the cancer may be a breast cancer.
  • the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise TU0011194, TU0019356 and TU0024146.
  • the cancer may be a pancreatic cancer.
  • the probes may be between about 15 nucleotides and about 500 nucleotides in length.
  • the probes may be between about 15 nucleotides and about 450 nucleotides in length.
  • the probes may be between about 15 nucleotides and about 400 nucleotides in length.
  • the probes may be between about 15 nucleotides and about 350 nucleotides in length.
  • the probes may be between about 15 nucleotides and about 300 nucleotides in length.
  • the probes may be between about 15 nucleotides and about 250 nucleotides in length.
  • the probes may be between about 15 nucleotides and about 200 nucleotides in length.
  • the probes may be at least 15 nucleotides in length.
  • the probes may be at least 25 nucleotides in length.
  • the cancer may be selected from the group may comprise prostate, lung, breast, and pancreatic cancer.
  • Assessing the cancer status may comprise assessing cancer recurrence risk. Assessing the cancer status may comprise determining a treatment modality. Assessing the cancer status may comprise determining the efficacy of treatment.
  • Obtaining an expression profile may comprise hybridizing one or more probes to the one or more target molecules to produce one or more probe hybridized target molecules.
  • the deviation may be the expression level of one or more targets from the sample may be greater than the expression level of one or more targets from a control or standard derived from a healthy subject or population of healthy subjects.
  • the deviation may be the expression level of one or more targets from the sample may be at least about 30% greater than the expression level of one or more targets from a control or standard derived from a healthy subject or population of healthy subjects.
  • the deviation may be the expression level of one or more targets from the sample may be less than the expression level of one or more targets from a control or standard derived from a healthy subject or population of healthy subjects.
  • the expression level of the one or more target molecules may determine the cancer status of the subject with at least 50% accuracy.
  • the expression level of the one or more target molecules may determine the cancer status of the subject with at least 60% accuracy.
  • the expression level of the one or more target molecules may determine the cancer status of the subject with at least 65% accuracy.
  • the expression level of the one or more target molecules may determine the cancer status of the subject with at least 70% accuracy.
  • the expression level of the one or more target molecules may determine the cancer status of the subject with at least 75% accuracy.
  • the expression level of the one or more target molecules may determine the cancer status of the subject with at least 80% accuracy.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 50% specificity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 60% specificity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 65% specificity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 70% specificity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 75% specificity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 80% specificity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 85% specificity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 50% sensitivity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 60% sensitivity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 65% sensitivity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 70% sensitivity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 75% sensitivity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 80% sensitivity.
  • the plurality of probes may determine the expression level of the one or more target molecules with at least about 85% sensitivity.
  • FIG. 1 shows that prostate cancer transcriptome sequencing reveals dysregulation of exemplary transcripts identified herein.
  • a A global overview of transcription in prostate cancer.
  • b A line graph showing the cumulative fraction of genes that are expressed at a given RPKM level.
  • c Conservation analysis comparing unannotated transcripts to known genes and intronic controls shows a low but detectable degree of purifying selection among intergenic and intronic unannotated transcripts.
  • FIG. 2 shows that unannotated intergenic transcripts differentiate prostate cancer and benign prostate samples.
  • a A histogram plotting the genomic distance between an unannotated ncRNA and the nearest protein-coding gene.
  • b A Circos plot displaying the location of annotated transcripts and unannotated transcripts on Chr15q.
  • c A heatmap of differentially expressed or outlier unannotated intergenic transcripts clusters benign samples, localized tumors, and metastatic cancers by unsupervised clustering analyses.
  • COPA Cancer outlier profile analysis
  • FIG. 3 shows validation of tissue-specific prostate cancer-associated non-coding RNAs.
  • a-c Quantitative real-time PCR was performed on a panel of prostate and non-prostate samples to measure expression levels of three nominated non-coding RNAs (ncRNAs), PCAT-43, PCAT-109, and PCAT-14, upregulated in prostate cancer compared to normal prostate tissues.
  • ncRNAs nominated non-coding RNAs
  • PCAT-43 is a 20 kb ncRNA located 40 kb upstream of PMEPA1 on chr20q13.31.
  • PCAT-109 located in a large, 0.5 Mb gene desert region on chr2q31.3 displays widespread transcription in prostate tissues, particularly metastases.
  • PCAT-14 a genomic region on chr22q11.23 encompassing a human endogenous retrovirus exhibits marked upregulation in prostate tumors but not metastases.
  • FIG. 4 shows that prostate cancer ncRNAs populate the Chr8q24 gene desert.
  • a A schematic of the chr8q24 region.
  • b Comprehensive analysis of the chr8q24 region by RNA-Seq and ChIP-Seq reveals numerous transcripts supported by histone modifications, such as Acetyl-H3 and H3K4me3, demarcating active chromatin.
  • c RT-PCR and Sanger sequencing validation of the PCAT-1 exon-exon junction.
  • d The genomic location of PCAT-1 determined by 5′ and 3′ RACE.
  • PCAT-1 is a viral long terminal repeat (LTR) promoter splicing to a marniner family transposase that has been bisected by an Alu repeat.
  • LTR viral long terminal repeat
  • qPCR on a panel of prostate and non-prostate samples shows prostate-specific expression and upregulation in prostate cancers and metastases compared to benign prostate samples.
  • Four matched tumor/normal pairs included in the analysis in e. demonstrate somatic upregulation of PCAT-1 in matched cancer samples.
  • FIG. 5 shows that ncRNAs serve as urine biomarkers for prostate cancer.
  • a-c Three ncRNAs displaying biomarker status in prostate cancer tissues were evaluated on a cohort of urine samples from 77 patients with prostate cancer and 31 controls with negative prostate biopsy results and absence of the TMPRSS2-ERG fusion transcript.
  • PCA3 (a); PCAT-1 (b); and PCAT-14 (c).
  • d Scatter plots demonstrating distinct patient subsets scoring positively for PCA3, PCAT-1, or PCAT-14 expression.
  • e. A heatmap displaying patients positive and negative for several different prostate cancer biomarkers in urine sediment samples.
  • f. A table displaying the statistical significance of the ncRNA signature.
  • g. A model for non-coding RNA (ncRNA) activation in prostate cancer.
  • FIG. 6 shows Ab initio assembly of the prostate cancer transcriptome.
  • FIG. 7 shows classification tree results for Chromosome 1.
  • the recursive regression and partitioning trees (rpart) machine learning algorithm was used to predict expressed transcripts versus background signal.
  • FIG. 8 shows transcript assembly of known genes. ab initio transcript assembly on prostate transcriptome sequencing data was used to reconstruct the known prostate transcriptome. a. SPINK1, a biomarker for prostate cancer. b. PRUNE2 with the PCA3 non-coding RNA within its intronic regions. c. NFKB1. d. COL9A2.
  • FIG. 9 shows analysis of EST support for exemplary transcripts.
  • ESTs from the UCSC database table “Human ESTs” were used to evaluate the amount of overlap between ESTs and novel transcripts.
  • a. A line graph showing the fraction of genes whose transcripts are supported by a particular fraction of ESTs.
  • b. A table displaying the number of ESTs supporting each class of transcripts
  • FIG. 10 shows analysis of coding potential of unannotated transcripts.
  • DNA sequences for each transcript were extracted and searched for open reading frames (ORFs) using the txCdsPredict program from the UCSC source tool set.
  • ORFs open reading frames
  • FIG. 11 shows repetitive content of novel transcripts. The percentage of repetitive sequences was assessed in all transcripts by calculating the percentage of repeatmasked nucleotides in each sequence.
  • FIG. 12 shows distinct ChIP-Seq signatures for repeat-associated and nonrepeat novel ncRNAs. Unannotated transcripts were divided into two groups, repeat-associated and non-repeat, and intersected with ChIP-Seq data for Acetyl-H3 and H3K4me3, two histone modifications strongly associated with transcriptional start sites (TSS), in two prostate cancer cell lines.
  • a Acetyl-H3 in LNCaP cells.
  • H3K4me3 in LNCaP cells c.
  • H3K4me3 in VCaP cells aP cells.
  • FIG. 13 shows overlap of unannotated transcripts with ChIP-Seq data in VCaP cells.
  • Previously published ChIP-Seq data for VCaP prostate cancer cells were intersected with unannotated prostate cancer transcripts and annotated control genes.
  • a. H3K4me1 b. H3K36me3.
  • FIG. 14 shows overlap of unannotated transcripts with ChIP-Seq data in LNCaP cells.
  • ChIP-Seq data for LNCaP prostate cancer cells were intersected with unannotated transcripts and annotated control genes.
  • ncRNAs were divided into intergenic and intronic. a. H3K4me1 b. H3K4me2 c. H3K4me3 d. Acetyl-H3 e. H3K36me3 f. RNA polymerase II.
  • FIG. 15 shows validation of a novel transcript on chromosome 15.
  • a Coverage maps showing the average expression levels (RPKM) across the benign, localized tumor, and metastatic samples shows upregulation of a novel transcript downstream of TLE3.
  • b Several predicted isoforms of this transcript were nominated which retained common exons 1 and 2.
  • c The exon-exon boundary between exons 1 and 2, as well as an internal portion of exon 3, was validated by RT-PCR in prostate cell line models.
  • FIG. 16 shows clustering of prostate cancer with outliers. Transcripts with outlier profile scores in the top 10% were clustered using hierarchical trees.
  • FIG. 17 shows validation of novel transcripts in prostate cell lines. 11/14 unannotated transcripts selected for validation by RT-PCR and qPCR were confirmed in cell line models.
  • a RT-PCR gels showing expected bands for the 11 transcripts that validated.
  • b Representative qPCR results using primers selected from a. The primers used in b are indicated by a red asterisk in a.
  • FIG. 18 shows that PCAT-14 is upregulated by androgen signaling.
  • VCaP and LNCaP cells were treated 5 nM R1881 or vehicle (ethanol) control.
  • FIG. 19 shows that PCAT-14 is upregulated in matched tumor tissues.
  • Four matched tumor-normal patient tissue samples were assayed for PCAT-14 expression by qPCR.
  • FIG. 20 shows analysis of PCAT-14 transcript structure.
  • a Representative 5′RACE results using a 3′ primer confirms the presence of the sense transcript PCAT-14. Predicted novel transcripts are displayed above the RACE results.
  • b DNA sequence analysis of PCAT-14 indicates expected splice donor sites, splice acceptor sites, and a polyadenylation site.
  • FIG. 21 shows analysis of PCAT-1 transcript structure. 5′ and 3′ RACE experiments showed a ncRNA transcript containing two exons.
  • FIG. 22 shows that knockdown of PCAT-1 does not affect invasion or proliferation of VCaP cells.
  • VCaP cells were transfected with custom-made siRNAs targeting PCAT-1 or non-targeting controls.
  • b.-d. siRNAs 2-4 were tested for functional effect due to their higher efficiency of knockdown.
  • b. A cell proliferation assay performed with a Coulter counter shows no significant difference in cell proliferation following knockdown of PCAT-1.
  • a WST-1 assay indicates no change in VCaP cell viability following PCAT-1 knockdown.
  • a transmembrane invasion assay shows no change in VCaP cell invasiveness following PCAT-1 knockdown.
  • FIG. 23 shows transcription of two Alu elements in a CACNA1D intron.
  • a Coverage maps representing average expression in RPKM in benign samples, localized tumors, and prostate metastases.
  • b RPKM expression values for the CACNA1D Alu transcript across the prostate transcriptome sequencing cohort.
  • c RT-PCR validation of the Alu transcript in cell line models.
  • d Sanger sequencing confirmation of RT-PCR fragments verifies the presence of AluSp transcript sequence.
  • e Raw sequencing data of a portion of the AluSp sequence.
  • FIG. 24 shows transcription of numerous repeat elements at the SChLAP1 locus.
  • a Coverage maps representing repeat elements transcribed at the chr2q31.3 locus.
  • b RPKM expression expression values for the LINE-1 repeat region on chr2q31.3 across the prostate transcriptome sequencing cohort.
  • c RTPCR validation of the LINE-1 repetitive element in cell line models. A 402 bp fragment was amplified.
  • FIG. 25 shows a heatmap of repeats clusters prostate cancer samples. Unannotated transcripts that contained repeat elements were used to cluster prostate cancer samples in an unsupervised manner.
  • FIG. 26 shows that the SChLAP1 locus spans >500 kb. Visualization of transcriptome sequencing data in the UCSC genome browser indicates that a large, almost 1 Mb section of chromosome 2 is highly activated in cancer, contributing to many individual transcripts regulated in a coordinated fashion.
  • FIG. 27 shows that the SChLAP1 locus is associated with ETS positive tumors.
  • FIG. 28 shows the sequence of PCAT-1 and PCAT-14.
  • FIG. 29 shows that PCAT-1 expression sensitizes prostate cancer cells to treatment with PARP-1 inhibitors.
  • (a-d) treatment with the PARP 1 inhibitor olaparib (e-h) treatment with the PARP1 inhibitor ABT-888.
  • Stable PCAT-1 knockdown in LNCAP prostate cells reduces sensitivity to olaparib (a) and ABT-888 (e).
  • Stable overexpression in Du145 prostate cancer and RWPE benign prostate cells increases sensitivity to olaparib (b,c) and ABT-888 (f,g).
  • Overexpression of PCAT-1 in MCF7 breast cancer cells does not recapitulate this effect (d,h).
  • FIG. 30 shows that PCAT-1 expression sensitizes prostate cancer cells to radiation treatment.
  • Stable PCAT-1 knockdown in LNCAP prostate cells reduces sensitivity to radiation.
  • Stable overexpression in Du145 prostate cancer and RWPE benign prostate cells increases sensitivity to radiation.
  • Stable overexpression in MCF7 breast cancer cells does not recapitulate this effect.
  • FIG. 31 shows that unannotated intergenic transcripts differentiate prostate cancer and benign samples.
  • SChLAP-1 The genomic location and exon structure of SChLAP-1.
  • SChLAP-1 is located on chromosome 2 in a previously unannotated region.
  • Cell fractionation into nuclear and cytoplasmic fractions demonstrates that SChLAP-1 is predominantly nuclear in its localization.
  • SChLAP-1 is a prostate cancer outlier associated with cancers.
  • FIG. 32 shows that SChLAP-1 is required for prostate cancer cell invasion and proliferation.
  • Prostate and non-prostate cancer cell lines were treated with SChLAP-1 siRNAs.
  • prostate and non-prostate cell lines were assayed for cell proliferation following SChLAP-1 knockdown.
  • the three most abundant isoforms of SChLAP-1 were cloned and overexpressed in RWPE benign immortalized prostate cells at levels similar to LNCaP cancer cells.
  • RWPE cells overexpressing SChLAP-1 isoforms show an increased ability to invade through Matrigel in Boyden chamber assays.
  • FIG. 33 shows that deletion analysis of SChLAP-1 identifies a region essential for its function.
  • RWPE cells overexpressing SChLAP-1 deletion constructs or full-length isoform #1 were generated as shown in the schematic of the constructs.
  • RWPE cells overexpressing SChLAP-1 deletion constructs demonstrated an impaired ability to invade through Matrigel, while the other deletion constructs showed no reduction in their ability to induce RWPE cell invasion compared to the wild type SChLAP-1.
  • FIG. 34 shows detection of prostate cancer RNAs in patient urine samples.
  • (a-e). (a) PCA3 (b) PCAT-14 (c) PCAT-1 (d) SChLAP-1 (e) PDLIM5
  • FIG. 35 shows multiplexing urine SChLAP-1 measurements with serum PSA improves prostate cancer risk stratification.
  • FIG. 36 shows analysis of the lung cancer transcriptome.
  • FIG. 37 shows discovery of M41 and ENST-75 in lung cancer.
  • M41 The genomic location of M41, which resides in an intron of DSCAM. M41 is poorly conserved across species.
  • qPCR of M41 demonstrates outlier expression in 15-20% of lung adenocarcinomas as well as high expression in breast cells.
  • ENST-75 The genomic location of ENST-75, which demonstrates high conservation across species.
  • qPCR of ENST-75 shows up-regulation in lung cancer but not breast or prostate cancers. High expression is observed in normal testis.
  • FIG. 38 shows lncRNAs are drivers and biomarkers in lung cancer.
  • Knockdown of ENST-75 in H1299 cells impairs cell proliferation. Error bars represent s.e.m.
  • (c) ENST-75 expression in lung adenocarcinomas stratifies patient overall survival.
  • FIG. 39 shows nomination of cancer-associated lncRNAs in breast and pancreatic cancer.
  • (a-c) (a) TU0011194 (b) TU0019356 (c) TU0024146 (d-f) Three novel pancreatic cancer lncRNAs nominated from RNA-Seq data. All show outlier expression patterns in pancreatic cancer samples but not benign samples.
  • FIG. 40 shows discovery of SChLAP-1 as a prostate cancer lncRNA.
  • COPA Cancer outlier profile analysis
  • FIG. 40 shows discovery of SChLAP-1 as a prostate cancer lncRNA.
  • COPA Cancer outlier profile analysis
  • FIG. 40 shows discovery of SChLAP-1 as a prostate cancer lncRNA.
  • COPA Cancer outlier profile analysis
  • FIG. 40 shows discovery of SChLAP-1 as a prostate cancer lncRNA.
  • COPA Cancer outlier profile analysis
  • lncRNA outliers nominated by COPA including their location, frequency in clinical samples, their expression in tissues and cell lines, and whether they occur in metastatic prostate samples.
  • SChLAP-1 may consist of up to seven exons on Chr2q31.3.
  • (d) A schematic summarizing the observed SChLAP-1 isoforms.
  • FIG. 41 shows that SChLAP-1 coordinates prostate cancer cell invasion.
  • siRNA knockdown of SChLAP-1 in vitro (b) Overexpression of SChLAP-1 in RWPE cells.
  • FIG. 42 shows that SChLAP-1 antagonizes SWI/SNF complex function.
  • GSEA Gene set enrichment analysis
  • HNCaP and 22Rv1 cells treated with SChLAP-1 siRNAs Heatmap results for SChLAP-1 or SWI/SNF knockdown in LNCaP and 22Rv1 cells.
  • GSEA analysis of SChLAP-1 and SWI/SNF knockdowns GSEA analysis of SChLAP-1 and SWI/SNF knockdowns.
  • RIP RNA immunoprecipitation
  • SNF5 and AR demonstrates SChLAP-1 binding to SNF5 in 22Rv1 and LNCaP cells.
  • FIG. 43 shows that SChLAP-1 expression characterizes aggressive prostate cancer.
  • (c) clinical progression to systemic disease
  • e prostate cancer-specific mortality
  • f A model of SChLAP-1 activity in prostate cancer.
  • FIG. 44 shows that chromosome 2 region contains prostate cancer-associated transcripts.
  • FIG. 45 shows the structure and sequence of SChLAP1.
  • FIG. 46 shows expression of SChLAP-1 across cancers.
  • the terms “detect”, “detecting” or “detection” may describe either the general act of discovering or discerning or the specific observation of a composition.
  • Detecting a composition may comprise determining the presence or absence of a composition.
  • Detecting may comprise quantifying a composition.
  • detecting comprises determining the expression level of a composition.
  • the composition may comprise a nucleic acid molecule.
  • the composition may comprise at least a portion of the ncRNAs disclosed herein.
  • the composition may be a detectably labeled composition.
  • the term “subject” refers to any organisms that are screened using the diagnostic methods described herein. Such organisms preferably include, but are not limited to, mammals (e.g., murines, simians, equines, bovines, porcines, canines, felines, and the like), and most preferably includes humans. Alternatively, the organism is an avian, amphibian, reptile or fish.
  • mammals e.g., murines, simians, equines, bovines, porcines, canines, felines, and the like
  • the organism is an avian, amphibian, reptile or fish.
  • diagnosis refers to the recognition of a disease by its signs and symptoms, or genetic analysis, pathological analysis, histological analysis, and the like.
  • a “subject suspected of having cancer” encompasses an individual who has received an initial diagnosis (e.g., a CT scan showing a mass or increased PSA level) but for whom the stage of cancer or presence or absence of ncRNAs indicative of cancer is not known. The term further includes people who once had cancer (e.g., an individual in remission). In some embodiments, “subjects” are control subjects that are suspected of having cancer or diagnosed with cancer.
  • the term “characterizing cancer in a subject” refers to the identification of one or more properties of a cancer sample in a subject, including but not limited to, the presence of benign, pre-cancerous or cancerous tissue, the stage of the cancer, and the subject's prognosis. Cancers may be characterized by the identification of the expression of one or more cancer marker genes, including but not limited to, the ncRNAs disclosed herein.
  • the term “characterizing prostate tissue in a subject” refers to the identification of one or more properties of a prostate tissue sample (e.g., including but not limited to, the presence of cancerous tissue, the presence or absence of ncRNAs, the presence of pre-cancerous tissue that is likely to become cancerous, and the presence of cancerous tissue that is likely to metastasize).
  • tissues are characterized by the identification of the expression of one or more cancer marker genes, including but not limited to, the cancer markers disclosed herein.
  • stage of cancer refers to a qualitative or quantitative assessment of the level of advancement of a cancer. Criteria used to determine the stage of a cancer include, but are not limited to, the size of the tumor and the extent of metastases (e.g., localized or distant).
  • nucleic acid molecule refers to any nucleic acid containing molecule, including but not limited to, DNA or RNA.
  • the nucleic acid molecule may comprise one or more nucleotides.
  • the term encompasses sequences that include any of the known base analogs of DNA and RNA including, but not limited to, 4-acetylcytosine, 8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine, 5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-
  • gene refers to a nucleic acid (e.g., DNA) sequence that comprises coding sequences necessary for the production of a polypeptide, precursor, or RNA (e.g., rRNA, tRNA).
  • the polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragments are retained.
  • the term also encompasses the coding region of a structural gene and the sequences located adjacent to the coding region on both the 5′ and 3′ ends for a distance of about 1 kb or more on either end such that the gene corresponds to the length of the full-length mRNA. Sequences located 5′ of the coding region and present on the mRNA are referred to as 5′ non-translated sequences. Sequences located 3′ or downstream of the coding region and present on the mRNA are referred to as 3′ non-translated sequences.
  • the term “gene” encompasses both cDNA and genomic forms of a gene.
  • a genomic form or clone of a gene contains the coding region interrupted with non-coding sequences termed “introns” or “intervening regions” or “intervening sequences.”
  • Introns are segments of a gene that are transcribed into nuclear RNA (hnRNA); introns may contain regulatory elements such as enhancers. Introns are removed or “spliced out” from the nuclear or primary transcript; introns therefore are absent in the messenger RNA (mRNA) transcript.
  • mRNA messenger RNA
  • oligonucleotide refers to a short length of single-stranded polynucleotide chain. Oligonucleotides are typically less than 200 residues long (e.g., between 15 and 100), however, as used herein, the term is also intended to encompass longer polynucleotide chains. Oligonucleotides are often referred to by their length. For example a 24 residue oligonucleotide is referred to as a “24-mer”. Oligonucleotides can form secondary and tertiary structures by self-hybridizing or by hybridizing to other polynucleotides. Such structures can include, but are not limited to, duplexes, hairpins, cruciforms, bends, and triplexes.
  • the terms “complementary” or “complementarity” are used in reference to polynucleotides (i.e., a sequence of nucleotides) related by the base-pairing rules. For example, the sequence “5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.”
  • Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, as well as detection methods that depend upon binding between nucleic acids.
  • a partially complementary sequence is a nucleic acid molecule that at least partially inhibits a completely complementary nucleic acid molecule from hybridizing to a target nucleic acid is “substantially homologous.”
  • the inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or Northern blot, solution hybridization and the like) under conditions of low stringency.
  • a substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous nucleic acid molecule to a target under conditions of low stringency.
  • low stringency conditions are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction.
  • the absence of non-specific binding may be tested by the use of a second target that is substantially non-complementary (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second non-complementary target.
  • hybridization is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is impacted by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, the T m of the formed hybrid, and the G:C ratio within the nucleic acids. A single molecule that contains pairing of complementary nucleic acids within its structure is said to be “self-hybridized.”
  • stringency is used in reference to the conditions of temperature, ionic strength, and the presence of other compounds such as organic solvents, under which nucleic acid hybridizations are conducted.
  • low stringency conditions a nucleic acid sequence of interest will hybridize to its exact complement, sequences with single base mismatches, closely related sequences (e.g., sequences with 90% or greater homology), and sequences having only partial homology (e.g., sequences with 50-90% homology).
  • intermediate stringency conditions a nucleic acid sequence of interest will hybridize only to its exact complement, sequences with single base mismatches, and closely relation sequences (e.g., 90% or greater homology).
  • a nucleic acid sequence of interest will hybridize only to its exact complement, and (depending on conditions such a temperature) sequences with single base mismatches. In other words, under conditions of high stringency the temperature can be raised so as to exclude hybridization to sequences with single base mismatches.
  • isolated when used in relation to a nucleic acid, as in “an isolated oligonucleotide” or “isolated polynucleotide” refers to a nucleic acid sequence that is identified and separated from at least one component or contaminant with which it is ordinarily associated in its natural source. Isolated nucleic acid is such present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids as nucleic acids such as DNA and RNA found in the state they exist in nature.
  • a given DNA sequence e.g., a gene
  • RNA sequences such as a specific mRNA sequence encoding a specific protein
  • isolated nucleic acid encoding a given protein includes, by way of example, such nucleic acid in cells ordinarily expressing the given protein where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature.
  • the isolated nucleic acid, oligonucleotide, or polynucleotide may be present in single-stranded or double-stranded form.
  • the oligonucleotide or polynucleotide will contain at a minimum the sense or coding strand (i.e., the oligonucleotide or polynucleotide may be single-stranded), but may contain both the sense and anti-sense strands (i.e., the oligonucleotide or polynucleotide may be double-stranded).
  • the term “purified” or “to purify” refers to the removal of components (e.g., contaminants) from a sample.
  • antibodies are purified by removal of contaminating non-immunoglobulin proteins; they are also purified by the removal of immunoglobulin that does not bind to the target molecule.
  • the removal of non-immunoglobulin proteins and/or the removal of immunoglobulins that do not bind to the target molecule results in an increase in the percent of target-reactive immunoglobulins in the sample.
  • recombinant polypeptides are expressed in bacterial host cells and the polypeptides are purified by the removal of host cell proteins; the percent of recombinant polypeptides is thereby increased in the sample.
  • sample is used in its broadest sense. In one sense, it is meant to include a specimen or culture obtained from any source, as well as biological and environmental samples. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues, and gases. Biological samples include blood products, such as plasma, serum and the like. Such examples are not however to be construed as limiting the sample types applicable to the present invention.
  • the present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers.
  • the present invention relates to ncRNAs as diagnostic markers and clinical targets for cancer.
  • ncRNAs may be used as diagnostic markers and clinical targets for prostate, lung, breast and pancreatic cancer.
  • RNA-Seq analyses of tissue samples and ab initio transcriptome assembly were utilized to predict the complete polyA+ transcriptome of prostate cancer. 6,144 novel ncRNAs found in prostate cancer were identified, including 121 ncRNAs that associated with disease progression ( FIGS. 1 , 2 , 16 and 25 ). These data demonstrate the global utility of RNA-Seq in defining functionally-important elements of the genome.
  • RNAs are activated in prostate cancer, enabling the transcription of numerous disease-specific and tissue-specific ncRNAs ( FIG. 5 g ).
  • these ncRNA signatures are suitable for urine-based assays to detect and diagnose prostate cancer in a non-invasive manner (See e.g., Example 1). It is further contemplated that specific ncRNA signatures occur universally in all disease states and applying these methodologies to other diseases reveals clinically important biomarkers, particularly for diseases that currently lack good protein biomarkers.
  • SChLAP1 locus which represents a >500 kb stretch of coordinately regulated expression
  • chr8q24 locus which contains a prostate specific region with the prostate cancer biomarker PCAT-1.
  • the fact that the SChLAP 1 locus is almost exclusively expressed in prostate cancers harboring an ETS gene fusion further confirms the capacity of ncRNAs to identify patient disease subtypes.
  • these analyses reveal novel cancer-specific drivers of tumorigenesis.
  • the long ncRNA HOTAIR is known to direct cancer-promoting roles for EZH2 in breast cancer (Gupta et al., Nature 464 (7291), 1071 (2010)), while in the PC3 prostate cancer cell line a similar role has been proposed for the ANRIL ncRNA (Yap et al., Mol Cell 38 (5), 662 (2010)).
  • ncRNAs include, but are not limited to, PCAT-1, PCAT-14, PCAT-43 and PCAT-109; SChLAP-1; and SEQ ID NOs: 1-9. Exemplary, non-limiting methods are described herein.
  • the sample may be tissue (e.g., a biopsy sample, a prostate biopsy sample or a tissue sample obtained by prostatectomy), blood, urine, semen, prostatic secretions or a fraction thereof (e.g., plasma, serum, urine supernatant, urine cell pellet, cells or prostate cells).
  • a urine sample may be collected immediately following an attentive digital rectal examination (DRE), which causes prostate cells from the prostate gland to shed into the urinary tract.
  • DRE attentive digital rectal examination
  • the patient sample is subjected to preliminary processing designed to isolate or enrich the sample for the ncRNAs or cells that contain the ncRNAs.
  • preliminary processing designed to isolate or enrich the sample for the ncRNAs or cells that contain the ncRNAs.
  • a variety of techniques known to those of ordinary skill in the art may be used for this purpose, including but not limited to: centrifugation; immunocapture; cell lysis; nucleic acid amplification; and, nucleic acid target capture (See, e.g., EP Pat. No. 1 409 727, herein incorporated by reference in its entirety).
  • ncRNAs may be detected along with other markers in a multiplex or panel format. Markers may be selected for their predictive value alone or in combination with the gene fusions.
  • Exemplary prostate cancer markers include, but are not limited to: AMACR/P504S (U.S. Pat. No. 6,262,245); PCA3 (U.S. Pat. No. 7,008,765); PCGEM1 (U.S. Pat. No. 6,828,429); prostein/P501S, P503S, P504S, P509S, P510S, prostase/P703P, P710P (U.S. Publication No. 20030185830); RAS/KRAS (Bos, Cancer Res.
  • multiplex or array formats are utilized to detect multiple markers in combination.
  • the level of expression of one or more, 2 or more, 3 or more, 4 or more, 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more or all 121) non-coding RNAs (ncRNAs) is utilized in the research, screening, diagnostic and prognositic compositions and methods described herein.
  • the one or more ncRNAs may be selected from the group comprising SChLAP-1, PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT
  • ncRNAs of the present invention are detected using a variety of nucleic acid techniques known to those of ordinary skill in the art, including but not limited to: nucleic acid sequencing; nucleic acid hybridization; and, nucleic acid amplification.
  • the methods, compositions and kits may comprise one or more ncRNAs.
  • the methods, compositions and kits may comprise 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 40 or more, 45 or more, 50 or more, 55 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more, 150 or more ncRNAs.
  • the one or more ncRNAs may be selected from the group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61,
  • the one or more ncRNAs of the present invention may comprise one or more prostate cancer-associated ncRNA transcripts (PCATs).
  • the one or more PCATs may be selected from the group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53
  • the ncRNAs of the present invention may comprise SChLAP-1.
  • the ncRNAs may comprise M41, ENST-75, or a combination thereof.
  • the ncRNAs may comprise TU0011194, TU0019356, TU0024146, or a combination thereof.
  • the ncRNAs may comprise TU0009141, TU0062051, TU0021861 or a combination thereof.
  • the ncRNAs may comprise any one of SEQ ID NOs: 1-9 or a combination thereof.
  • nucleic acid sequencing techniques include, but are not limited to, chain terminator (Sanger) sequencing and dye terminator sequencing.
  • chain terminator Sanger
  • dye terminator sequencing Those of ordinary skill in the art will recognize that because RNA is less stable in the cell and more prone to nuclease attack experimentally RNA is usually reverse transcribed to DNA before sequencing.
  • Chain terminator sequencing uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. Extension is initiated at a specific site on the template DNA by using a short radioactive, or other labeled, oligonucleotide primer complementary to the template at that region.
  • the oligonucleotide primer is extended using a DNA polymerase, standard four deoxynucleotide bases, and a low concentration of one chain terminating nucleotide, most commonly a di-deoxynucleotide. This reaction is repeated in four separate tubes with each of the bases taking turns as the di-deoxynucleotide.
  • the DNA polymerase Limited incorporation of the chain terminating nucleotide by the DNA polymerase results in a series of related DNA fragments that are terminated only at positions where that particular di-deoxynucleotide is used.
  • the fragments are size-separated by electrophoresis in a slab polyacrylamide gel or a capillary tube filled with a viscous polymer. The sequence is determined by reading which lane produces a visualized mark from the labeled primer as you scan from the top of the gel to the bottom.
  • Dye terminator sequencing alternatively labels the terminators. Complete sequencing can be performed in a single reaction by labeling each of the di-deoxynucleotide chain-terminators with a separate fluorescent dye, which fluoresces at a different wavelength.
  • nucleic acid sequencing methods are contemplated for use in the methods of the present disclosure including, for example, chain terminator (Sanger) sequencing, dye terminator sequencing, and high-throughput sequencing methods. Many of these sequencing methods are well known in the art. See, e.g., Sanger et al., Proc. Natl. Acad. Sci. USA 74:5463-5467 (1997); Maxam et al., Proc. Natl. Acad. Sci. USA 74:560-564 (1977); Drmanac, et al., Nat. Biotechnol. 16:54-58 (1998); Kato, Int. J. Clin. Exp. Med.
  • the methods disclosed herein can comprise transcriptome sequencing (e.g., RNA-Seq).
  • Sequencing can comprise platforms such as the Illumina Genome Analyzer platform, ABI Solid Sequencing or Life Science's 454 Sequencing.
  • sequencing comprises Helicos' Direct RNA Sequencing (DRSTM) technology.
  • the sequencing reactions may comprise capillary sequencing, next generation sequencing, Sanger sequencing, sequencing by synthesis, single molecule nanopore sequencing, sequencing by ligation, sequencing by hybridization, sequencing by nanopore current restriction, or a combination thereof.
  • Sequencing by synthesis may comprise reversible terminator sequencing, processive single molecule sequencing, sequential nucleotide flow sequencing, or a combination thereof.
  • Sequential nucleotide flow sequencing may comprise pyrosequencing, pH-mediated sequencing, semiconductor sequencing or a combination thereof. Conducting one or more sequencing reactions comprises whole genome sequencing or exome sequencing.
  • nucleic acid hybridization techniques include, but are not limited to, in situ hybridization (ISH), microarray, and Southern or Northern blot.
  • In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA or RNA strand as a probe to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough, the entire tissue (whole mount ISH).
  • DNA ISH can be used to determine the structure of chromosomes.
  • RNA ISH is used to measure and localize mRNAs and other transcripts (e.g., ncRNAs) within tissue sections or whole mounts.
  • ISH x-ray fluorescence microscopy
  • ISH can also use two or more probes, labeled with radioactivity or the other non-radioactive labels, to simultaneously detect two or more transcripts.
  • ncRNAs are detected using fluorescence in situ hybridization (FISH).
  • FISH assays utilize bacterial artificial chromosomes (BACs). These have been used extensively in the human genome sequencing project (see Nature 409: 953-958 (2001)) and clones containing specific BACs are available through distributors that can be located through many sources, e.g., NCBI. Each BAC clone from the human genome has been given a reference name that unambiguously identifies it. These names can be used to find a corresponding GenBank sequence and to order copies of the clone from a distributor.
  • BACs bacterial artificial chromosomes
  • the present invention further provides a method of performing a FISH assay on the patient sample.
  • the methods disclosed herein may comprise performing a FISH assay on one or more cells, tissues, organs, or fluids surrounding such cells, tissues and organs.
  • the methods disclosed herein further comprise performing a FISH assay on human prostate cells, human prostate tissue or on the fluid surrounding said human prostate cells or human prostate tissue.
  • the methods disclosed herein comprise performing a FISH assay on breast cells, lung cells, pancreatic cells, liver cells, breast tissue, lung tissue, pancreatic tissue, liver tissue, or on the fluid surrounding the cells or tissues. Specific protocols are well known in the art and can be readily adapted for the present invention.
  • kits that are commercially available and that provide protocols for performing FISH assays (available from e.g., Oncor, Inc., Gaithersburg, Md.).
  • Patents providing guidance on methodology include U.S. Pat. Nos. 5,225,326; 5,545,524; 6,121,489 and 6,573,043. All of these references are hereby incorporated by reference in their entirety and may be used along with similar references in the art and with the information provided in the Examples section herein to establish procedural steps convenient for a particular laboratory.
  • the one or more ncRNAs may be detected by conducting one or more hybridization reactions.
  • the one or more hybridization reactions may comprise one or more hybridization arrays, hybridization reactions, hybridization chain reactions, isothermal hybridization reactions, nucleic acid hybridization reactions, or a combination thereof.
  • the one or more hybridization arrays may comprise hybridization array genotyping, hybridization array proportional sensing, DNA hybridization arrays, macroarrays, microarrays, high-density oligonucleotide arrays, genomic hybridization arrays, comparative hybridization arrays, or a combination thereof.
  • DNA microarrays e.g., cDNA microarrays and oligonucleotide microarrays
  • protein microarrays e.g., cDNA microarrays and oligonucleotide microarrays
  • tissue microarrays e.g., tissue microarrays
  • transfection or cell microarrays e.g., cell microarrays
  • chemical compound microarrays e.g., antibody microarrays.
  • a DNA microarray commonly known as gene chip, DNA chip, or biochip, is a collection of microscopic DNA spots attached to a solid surface (e.g., glass, plastic or silicon chip) forming an array for the purpose of expression profiling or monitoring expression levels for thousands of genes simultaneously.
  • the affixed DNA segments are known as probes, thousands of which can be used in a single DNA microarray.
  • Microarrays can be used to identify disease genes or transcripts (e.g., ncRNAs) by comparing gene expression in disease and normal cells.
  • Microarrays can be fabricated using a variety of technologies, including but not limiting: printing with fine-pointed pins onto glass slides; photolithography using pre-made masks; photolithography using dynamic micromirror devices; ink-jet printing; or, electrochemistry on microelectrode arrays.
  • the methods disclosed herein may comprise conducting one or more amplification reactions.
  • Nucleic acids e.g., ncRNAs
  • Conducting one or more amplification reactions may comprise one or more PCR-based amplifications, non-PCR based amplifications, or a combination thereof.
  • nucleic acid amplification techniques include, but are not limited to, polymerase chain reaction (PCR), reverse transcription polymerase chain reaction (RT-PCR), nested PCR, linear amplification, multiple displacement amplification (MDA), real-time SDA, rolling circle amplification, circle-to-circle amplification transcription-mediated amplification (TMA), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence based amplification (NASBA).
  • PCR polymerase chain reaction
  • RT-PCR reverse transcription polymerase chain reaction
  • MDA multiple displacement amplification
  • TMA circle-to-circle amplification transcription-mediated amplification
  • LCR ligase chain reaction
  • SDA strand displacement amplification
  • NASBA nucleic acid sequence based amplification
  • RNA be reversed transcribed to DNA prior to amplification e.g., RT-PCR
  • other amplification techniques directly amplify RNA (e.g., TMA and NASBA).
  • PCR The polymerase chain reaction (U.S. Pat. Nos. 4,683,195, 4,683,202, 4,800,159 and 4,965,188, each of which is herein incorporated by reference in its entirety), commonly referred to as PCR, uses multiple cycles of denaturation, annealing of primer pairs to opposite strands, and primer extension to exponentially increase copy numbers of a target nucleic acid sequence.
  • RT-PCR reverse transcriptase (RT) is used to make a complementary DNA (cDNA) from mRNA, and the cDNA is then amplified by PCR to produce multiple copies of DNA.
  • cDNA complementary DNA
  • TMA Transcription mediated amplification
  • a target nucleic acid sequence autocatalytically under conditions of substantially constant temperature, ionic strength, and pH in which multiple RNA copies of the target sequence autocatalytically generate additional copies.
  • TMA optionally incorporates the use of blocking moieties, terminating moieties, and other modifying moieties to improve TMA process sensitivity and accuracy.
  • the ligase chain reaction (Weiss, R., Science 254: 1292 (1991), herein incorporated by reference in its entirety), commonly referred to as LCR, uses two sets of complementary DNA oligonucleotides that hybridize to adjacent regions of the target nucleic acid.
  • the DNA oligonucleotides are covalently linked by a DNA ligase in repeated cycles of thermal denaturation, hybridization and ligation to produce a detectable double-stranded ligated oligonucleotide product.
  • Strand displacement amplification (Walker, G. et al., Proc. Natl. Acad. Sci. USA 89: 392-396 (1992); U.S. Pat. Nos. 5,270,184 and 5,455,166, each of which is herein incorporated by reference in its entirety), commonly referred to as SDA, uses cycles of annealing pairs of primer sequences to opposite strands of a target sequence, primer extension in the presence of a dNTP ⁇ S to produce a duplex hemiphosphorothioated primer extension product, endonuclease-mediated nicking of a hemimodified restriction endonuclease recognition site, and polymerase-mediated primer extension from the 3′ end of the nick to displace an existing strand and produce a strand for the next round of primer annealing, nicking and strand displacement, resulting in geometric amplification of product.
  • Thermophilic SDA (tSDA) uses thermophilic endonucleases and polymer
  • amplification methods include, for example: nucleic acid sequence based amplification (U.S. Pat. No. 5,130,238, herein incorporated by reference in its entirety), commonly referred to as NASBA; one that uses an RNA replicase to amplify the probe molecule itself (Lizardi et al., BioTechnol. 6: 1197 (1988), herein incorporated by reference in its entirety), commonly referred to as Q ⁇ replicase; a transcription based amplification method (Kwoh et al., Proc. Natl. Acad. Sci. USA 86:1173 (1989)); and, self-sustained sequence replication (Guatelli et al., Proc. Natl. Acad. Sci.
  • Non-amplified or amplified nucleic acids can be detected by any conventional means.
  • the ncRNAs can be detected by hybridization with a detectably labeled probe and measurement of the resulting hybrids.
  • the ncRNAs can be detected by sequencing. Illustrative non-limiting examples of detection methods are described herein.
  • Hybridization Protection Assay involves hybridizing a chemiluminescent oligonucleotide probe (e.g., an acridinium ester-labeled (AE) probe) to the target sequence, selectively hydrolyzing the chemiluminescent label present on unhybridized probe, and measuring the chemiluminescence produced from the remaining probe in a luminometer.
  • a chemiluminescent oligonucleotide probe e.g., an acridinium ester-labeled (AE) probe
  • AE acridinium ester-labeled
  • Another illustrative detection method provides for quantitative evaluation of the amplification process in real-time.
  • Evaluation of an amplification process in “real-time” involves determining the amount of amplicon in the reaction mixture either continuously or periodically during the amplification reaction, and using the determined values to calculate the amount of target sequence initially present in the sample.
  • a variety of methods for determining the amount of initial target sequence present in a sample based on real-time amplification are well known in the art. These include methods disclosed in U.S. Pat. Nos. 6,303,305 and 6,541,205, each of which is herein incorporated by reference in its entirety.
  • Another method for determining the quantity of target sequence initially present in a sample, but which is not based on a real-time amplification is disclosed in U.S. Pat. No. 5,710,029, herein incorporated by reference in its entirety.
  • Amplification products may be detected in real-time through the use of various self-hybridizing probes, most of which have a stem-loop structure.
  • Such self-hybridizing probes are labeled so that they emit differently detectable signals, depending on whether the probes are in a self-hybridized state or an altered state through hybridization to a target sequence.
  • “molecular torches” are a type of self-hybridizing probe that includes distinct regions of self-complementarity (referred to as “the target binding domain” and “the target closing domain”) which are connected by a joining region (e.g., non-nucleotide linker) and which hybridize to each other under predetermined hybridization assay conditions.
  • molecular torches contain single-stranded base regions in the target binding domain that are from 1 to about 20 bases in length and are accessible for hybridization to a target sequence present in an amplification reaction under strand displacement conditions.
  • hybridization of the two complementary regions, which may be fully or partially complementary, of the molecular torch is favored, except in the presence of the target sequence, which will bind to the single-stranded region present in the target binding domain and displace all or a portion of the target closing domain.
  • the target binding domain and the target closing domain of a molecular torch include a detectable label or a pair of interacting labels (e.g., luminescent/quencher) positioned so that a different signal is produced when the molecular torch is self-hybridized than when the molecular torch is hybridized to the target sequence, thereby permitting detection of probe:target duplexes in a test sample in the presence of unhybridized molecular torches.
  • a detectable label or a pair of interacting labels e.g., luminescent/quencher
  • Molecular beacons include nucleic acid molecules having a target complementary sequence, an affinity pair (or nucleic acid arms) holding the probe in a closed conformation in the absence of a target sequence present in an amplification reaction, and a label pair that interacts when the probe is in a closed conformation. Hybridization of the target sequence and the target complementary sequence separates the members of the affinity pair, thereby shifting the probe to an open conformation. The shift to the open conformation is detectable due to reduced interaction of the label pair, which may be, for example, a fluorophore and a quencher (e.g., DABCYL and EDANS).
  • Molecular beacons are disclosed in U.S. Pat. Nos. 5,925,517 and 6,150,097, herein incorporated by reference in its entirety.
  • probe binding pairs having interacting labels such as those disclosed in U.S. Pat. No. 5,928,862 (herein incorporated by reference in its entirety) might be adapted for use in the present invention.
  • Probe systems used to detect single nucleotide polymorphisms (SNPs) might also be utilized in the present invention.
  • Additional detection systems include “molecular switches,” as disclosed in U.S. Publ. No. 20050042638, herein incorporated by reference in its entirety.
  • Other probes, such as those comprising intercalating dyes and/or fluorochromes are also useful for detection of amplification products in the present invention.
  • Additional detection methods may include microarrays and electrophoresis (e.g., gel electrophoresis). Detection methods can be quantitative or semi-quantitative. Detection methods may also comprise the use of one or more labels (e.g., radioisotopes, fluorophores, chemiluminophores, enzymes, colloidal particles, and fluorescent microparticles, as well as antigens, antibodies, haptens, avidin/streptavidin, biotin, haptens, or enzyme cofactors/substrates, enzymes).
  • labels e.g., radioisotopes, fluorophores, chemiluminophores, enzymes, colloidal particles, and fluorescent microparticles, as well as antigens, antibodies, haptens, avidin/streptavidin, biotin, haptens, or enzyme cofactors/substrates, enzymes).
  • Southern and Northern blotting is used to detect specific DNA or RNA sequences, respectively.
  • DNA or RNA extracted from a sample is fragmented, electrophoretically separated on a matrix gel, and transferred to a membrane filter.
  • the filter bound DNA or RNA is subject to hybridization with a labeled probe complementary to the sequence of interest. Hybridized probe bound to the filter is detected.
  • a variant of the procedure is the reverse Northern blot, in which the substrate nucleic acid that is affixed to the membrane is a collection of isolated DNA fragments and the probe is RNA extracted from a tissue and labeled.
  • ncRNAs may also be detected using in vivo imaging techniques, including but not limited to: radionuclide imaging; positron emission tomography (PET); computerized axial tomography, X-ray or magnetic resonance imaging method, fluorescence detection, and chemiluminescent detection.
  • in vivo imaging techniques are used to visualize the presence of or expression of cancer markers in an animal (e.g., a human or non-human mammal).
  • cancer marker mRNA or protein is labeled using a labeled antibody specific for the cancer marker.
  • a specifically bound and labeled antibody can be detected in an individual using an in vivo imaging method, including, but not limited to, radionuclide imaging, positron emission tomography, computerized axial tomography, X-ray or magnetic resonance imaging method, fluorescence detection, and chemiluminescent detection.
  • an in vivo imaging method including, but not limited to, radionuclide imaging, positron emission tomography, computerized axial tomography, X-ray or magnetic resonance imaging method, fluorescence detection, and chemiluminescent detection.
  • the in vivo imaging methods of embodiments of the present invention are useful in the identification of cancers that express ncRNAs (e.g., prostate cancer). In vivo imaging is used to visualize the presence or level of expression of a ncRNA. Such techniques allow for diagnosis without the use of an unpleasant biopsy.
  • the in vivo imaging methods of embodiments of the present invention can further be used to detect metastatic cancers in other parts of the body.
  • reagents e.g., antibodies
  • specific for the cancer markers of the present invention are fluorescently labeled.
  • the labeled antibodies are introduced into a subject (e.g., orally or parenterally). Fluorescently labeled antibodies are detected using any suitable method (e.g., using the apparatus described in U.S. Pat. No. 6,198,107, herein incorporated by reference).
  • antibodies are radioactively labeled.
  • the use of antibodies for in vivo diagnosis is well known in the art. Sumerdon et al., (Nucl. Med. Biol 17:247-254 [1990] have described an optimized antibody-chelator for the radioimmunoscintographic imaging of tumors using Indium-111 as the label. Griffin et al., (J Clin One 9:631-640 [1991]) have described the use of this agent in detecting tumors in patients suspected of having recurrent colorectal cancer. The use of similar agents with paramagnetic ions as labels for magnetic resonance imaging is known in the art (Lauffer, Magnetic Resonance in Medicine 22:339-342 [1991]).
  • Radioactive labels such as Indium-111, Technetium-99m, or Iodine-131 can be used for planar scans or single photon emission computed tomography (SPECT).
  • Positron emitting labels such as Fluorine-19 can also be used for positron emission tomography (PET).
  • PET positron emission tomography
  • paramagnetic ions such as Gadolinium (III) or Manganese (II) can be used.
  • Radioactive metals with half-lives ranging from 1 hour to 3.5 days are available for conjugation to antibodies, such as scandium-47 (3.5 days) gallium-67 (2.8 days), gallium-68 (68 minutes), technetiium-99m (6 hours), and indium-111 (3.2 days), of which gallium-67, technetium-99m, and indium-111 are preferable for gamma camera imaging, gallium-68 is preferable for positron emission tomography.
  • a useful method of labeling antibodies with such radiometals is by means of a bifunctional chelating agent, such as diethylenetriaminepentaacetic acid (DTPA), as described, for example, by Khaw et al. (Science 209:295 [1980]) for In-111 and Tc-99m, and by Scheinberg et al. (Science 215:1511 [1982]).
  • DTPA diethylenetriaminepentaacetic acid
  • Other chelating agents may also be used, but the 1-(p-carboxymethoxybenzyl)EDTA and the carboxycarbonic anhydride of DTPA are advantageous because their use permits conjugation without affecting the antibody's immunoreactivity substantially.
  • Another method for coupling DPTA to proteins is by use of the cyclic anhydride of DTPA, as described by Hnatowich et al. (Int. J. Appl. Radiat. Isot. 33:327 [1982]) for labeling of albumin with In-111, but which can be adapted for labeling of antibodies.
  • a suitable method of labeling antibodies with Tc-99m which does not use chelation with DPTA is the pretinning method of Crockford et al., (U.S. Pat. No. 4,323,546, herein incorporated by reference).
  • a method of labeling immunoglobulins with Tc-99m is that described by Wong et al. (Int. J. Appl. Radiat. Isot., 29:251 [1978]) for plasma protein, and recently applied successfully by Wong et al. (J. Nucl. Med., 23:229 [1981]) for labeling antibodies.
  • radiometals conjugated to the specific antibody it is likewise desirable to introduce as high a proportion of the radiolabel as possible into the antibody molecule without destroying its immunospecificity.
  • a further improvement may be achieved by effecting radiolabeling in the presence of the ncRNA, to insure that the antigen binding site on the antibody will be protected. The antigen is separated after labeling.
  • in vivo biophotonic imaging (Xenogen, Almeda, Calif.) is utilized for in vivo imaging.
  • This real-time in vivo imaging utilizes luciferase.
  • the luciferase gene is incorporated into cells, microorganisms, and animals (e.g., as a fusion protein with a cancer marker of the present invention). When active, it leads to a reaction that emits light.
  • a CCD camera and software is used to capture the image and analyze it.
  • a computer-based analysis program is used to translate the raw data generated by the detection assay (e.g., the presence, absence, or amount of a given marker or markers) into data of predictive value for a clinician.
  • the clinician can access the predictive data using any suitable means.
  • the present invention provides the further benefit that the clinician, who is not likely to be trained in genetics or molecular biology, need not understand the raw data.
  • the data is presented directly to the clinician in its most useful form. The clinician is then able to immediately utilize the information in order to optimize the care of the subject.
  • the present invention contemplates any method capable of receiving, processing, and transmitting the information to and from laboratories conducting the assays, information providers, medical personnel, and subjects.
  • a sample e.g., a biopsy or a serum or urine sample
  • a profiling service e.g., clinical lab at a medical facility, genomic profiling business, etc.
  • any part of the world e.g., in a country different than the country where the subject resides or where the information is ultimately used
  • the subject may visit a medical center to have the sample obtained and sent to the profiling center, or subjects may collect the sample themselves (e.g., a urine sample) and directly send it to a profiling center.
  • the sample comprises previously determined biological information
  • the information may be directly sent to the profiling service by the subject (e.g., an information card containing the information may be scanned by a computer and the data transmitted to a computer of the profiling center using an electronic communication systems).
  • the profiling service Once received by the profiling service, the sample is processed and a profile is produced (i.e., expression data), specific for the diagnostic or prognostic information desired for the subject.
  • the profile data is then prepared in a format suitable for interpretation by one or more medical personnel (e.g., a treating clinician, physician assistant, nurse, or pharmacist).
  • the prepared format may represent a diagnosis or risk assessment (e.g., presence or absence of a ncRNA) for the subject, along with recommendations for particular treatment options.
  • the data may be displayed to the medical personnel by any suitable method.
  • the profiling service generates a report that can be printed for the medical personnel (e.g., at the point of care) or displayed to the medical personnel on a computer monitor.
  • the information is first analyzed at the point of care or at a regional facility.
  • the raw data is then sent to a central processing facility for further analysis and/or to convert the raw data to information useful for medical personnel or patient.
  • the central processing facility provides the advantage of privacy (all data is stored in a central facility with uniform security protocols), speed, and uniformity of data analysis.
  • the central processing facility can then control the fate of the data following treatment of the subject. For example, using an electronic communication system, the central facility can provide data to the medical personnel, the subject, or researchers.
  • the subject is able to directly access the data using the electronic communication system.
  • the subject may chose further intervention or counseling based on the results.
  • the data is used for research use.
  • the data may be used to further optimize the inclusion or elimination of markers as useful indicators of a particular condition or stage of disease or as a companion diagnostic to determine a treatment course of action.
  • compositions for use in the diagnostic methods described herein include, but are not limited to, probes, amplification oligonucleotides, and the like.
  • the probe and antibody compositions of the present invention may also be provided in the form of an array.
  • compositions and kits may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more probes.
  • the probes may hybridize to 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more target molecules.
  • the target molecules may be a ncRNA, RNA, DNA, cDNA, mRNA, a portion or fragment thereof or a combination thereof. In some instances, at least a portion of the target molecules are ncRNAs.
  • the probes may hybridize to 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more ncRNAs disclosed herein.
  • the probes comprise a target specific sequence.
  • the target specific sequence may be complementary to at least a portion of the target molecule.
  • the target specific sequence may be at least about 50% or more, 55% or more, 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, or 100% complementary to at least a portion of the target molecule.
  • the target specific sequence may be at least about 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 16 or more, 17 or more, 18 or more, 19 or more, 20 or more nucleotides in length. In some instances, the target specific sequence is between about 8 to about 20 nucleotides, 10 to about 18 nucleotides, or 12 to about 16 nucleotides in length.
  • compositions and kits may comprise a plurality of probes, wherein the two or more probes of the plurality of probes comprise identical target specific sequences.
  • compositions and kits may comprise a plurality of probes, wherein the two or more probes of the plurality of probes comprise different target specific sequences.
  • the probes may further comprise a unique sequence.
  • the unique sequence is noncomplementary to the ncRNA.
  • the unique sequence may comprise a label, barcode, or unique identifier.
  • the unique sequence may comprise a random sequence, nonrandom sequence, or a combination thereof.
  • the unique sequence may be at least about 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 16 or more, 17 or more, 18 or more, 19 or more, 20 or more, 22 or more, 24 or more, 26 or more, 28 or more, 30 or more nucleotides in length.
  • the unique sequence is between about 8 to about 20 nucleotides, 10 to about 18 nucleotides, or 12 to about 16 nucleotides in length.
  • the unique sequence may allow differentiation of two or more target molecules.
  • the two or more target molecules may have identical sequences.
  • the unique sequence may allow quantification of a target molecule.
  • the two or more target molecules may have different sequences.
  • the unique sequence may allow detection of the target molecules.
  • the compositions and kits may comprise a plurality of probes for quantifying one or more target molecules.
  • the compositions and kits may comprise a plurality of probes for detecting one or more target molecules.
  • the unique sequence may allow differentiation of two or more samples.
  • the compositions and kits may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more probe sets for differentiating two or more samples from one or more subjects.
  • the two or more samples may be from two or more different subjects.
  • the compositions and kits comprise a first set of probes comprising a first unique sequence that is specific for a first subject and a second set of probes comprising a second unique sequence that is specific for a second subject.
  • the compositions and kits may further comprise one or more sets of probes with one or more unique sequences to differentiate one or more additional subjects.
  • compositions and kits may comprise 2 or more probe sets for differentiating from 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more samples from 1 or more subjects.
  • compositions and kits may comprise 2 or more probe sets for differentiating 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more samples from one or more cells, tissues, organs, bodily fluid, or a combination thereof.
  • compositions and kits may comprise 2 or more probe sets for differentiating samples from 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more subjects.
  • the two or more samples may be from two or more different timepoints from the same subject or different subjects.
  • the compositions and kits comprise a first set of probes comprising a first unique sequence that is specific for a first subject and a second set of probes comprising a second unique sequence that is specific for a second subject.
  • the compositions and kits may comprise 2 or more probe sets for differentiating samples from 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more timepoints.
  • the timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more hours.
  • the timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more days.
  • the timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more weeks.
  • the timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more months.
  • the timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more years.
  • the timepoints may be before diagnosis, after diagnosis, before treatment, during treatment, after treatment, before metastasis, after metastatis, before remission, during remission, or a combination thereof.
  • compositions and kits may comprise a first probe comprising a first target-specific sequence and a first unique sequence and a second probe comprising a second target-specific sequence and a second unique sequence, wherein the first target specific sequence and the second target specific sequence are identical and the first unique sequence and the second unique sequence are different.
  • the compositions and kits may comprise a first probe comprising a first target-specific sequence and a first unique sequence and a second probe comprising a second target-specific sequence and a second unique sequence, wherein the first target specific sequence and the second target specific sequence are different and the first unique sequence and the second unique sequence are different.
  • compositions and kits may comprise a first probe comprising a first target-specific sequence and a first unique sequence and a second probe comprising a second target-specific sequence and a second unique sequence, wherein the first target specific sequence and the second target specific sequence are identical and the first unique sequence and the second unique sequence are identical.
  • the compositions and kits may comprise a first probe comprising a first target-specific sequence and a first unique sequence and a second probe comprising a second target-specific sequence and a second unique sequence, wherein the first target specific sequence and the second target specific sequence are different and the first unique sequence and the second unique sequence are identical.
  • the probes may further comprise a universal sequence.
  • the universal sequence may comprise a primer binding site.
  • the universal sequence may enable detection of the target sequence.
  • the universal sequence may enable amplification of the target sequence.
  • the universal sequence may enable transcription or reverse transcription of the target sequence.
  • the universal sequence may enable sequencing of the target sequence.
  • the probe and antibody compositions of the present invention may also be provided on a solid support.
  • the solid support may comprise one or more beads, plates, solid surfaces, wells, chips, or a combination thereof.
  • the beads may be magnetic, antibody coated, protein A crosslinked, protein G crosslinked, streptavidin coated, oligonucleotide conjugated, silica coated, or a combination thereof.
  • beads include, but are not limited to, Ampure beads, AMPure XP beads, streptavidin beads, agarose beads, magnetic beads, Dynabeads®, MACS® microbeads, antibody conjugated beads (e.g., anti-immunoglobulin microbead), protein A conjugated beads, protein G conjugated beads, protein A/G conjugated beads, protein L conjugated beads, oligo-dT conjugated beads, silica beads, silica-like beads, anti-biotin microbead, anti-fluorochrome microbead, and BcMagTM Carboxy-Terminated Magnetic Beads.
  • compositions and kits may comprise primers and primer pairs capable of amplifying target molecules, or fragments or subsequences or complements thereof.
  • the nucleotide sequences of the target molecules may be provided in computer-readable media for in silico applications and as a basis for the design of appropriate primers for amplification of one or more target molecules.
  • Primers based on the nucleotide sequences of target molecules can be designed for use in amplification of the target molecules.
  • a pair of primers can be used.
  • the exact composition of the primer sequences is not critical to the invention, but for most applications the primers may hybridize to specific sequences of the target molecules or the universal sequence of the probe under stringent conditions, particularly under conditions of high stringency, as known in the art.
  • the pairs of primers are usually chosen so as to generate an amplification product of at least about 15 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 125 or more, 150 or more, 175 or more, 200 or more, 250 or more, 300 or more, 350 or more, 400 or more, 450 or more, 500 or more, 600 or more, 700 or more, 800 or more, 900 or more, or 1000 or more nucleotides.
  • Algorithms for the selection of primer sequences are generally known, and are available in commercial software packages. These primers may be used in standard quantitative or qualitative PCR-based assays to assess transcript expression levels of target molecules. Alternatively, these primers may be used in combination with probes, such as molecular beacons in amplifications using real-time PCR.
  • the primer may comprise nucleotide sequences at the 5′ and/or 3′ termini that are not derived from the target molecule.
  • Nucleotide sequences which are not derived from the nucleotide sequence of the target molecule may provide additional functionality to the primer. For example, they may provide a restriction enzyme recognition sequence or a “tag” that facilitates detection, isolation, purification or immobilization onto a solid support.
  • the additional nucleotides may provide a self-complementary sequence that allows the primer to adopt a hairpin configuration. Such configurations may be necessary for certain primers, for example, molecular beacon and Scorpion primers, which can be used in solution hybridization techniques.
  • the probes or primers can incorporate moieties useful in detection, isolation, purification, or immobilization, if desired.
  • moieties are well-known in the art (see, for example, Ausubel et al., (1997 & updates) Current Protocols in Molecular Biology , Wiley & Sons, New York) and are chosen such that the ability of the probe to hybridize with its target molecule is not affected.
  • Suitable moieties are detectable labels, such as radioisotopes, fluorophores, chemiluminophores, enzymes, colloidal particles, and fluorescent microparticles, as well as antigens, antibodies, haptens, avidin/streptavidin, biotin, haptens, enzyme cofactors/substrates, enzymes, and the like.
  • a label can optionally be attached to or incorporated into a probe or primer to allow detection and/or quantitation of a target polynucleotide representing the target molecule of interest.
  • the target polynucleotide may be the expressed target molecule RNA itself, a cDNA copy thereof, or an amplification product derived therefrom, and may be the positive or negative strand, so long as it can be specifically detected in the assay being used.
  • an antibody may be labeled.
  • labels used for detecting different target molecules may be distinguishable.
  • the label can be attached directly (e.g., via covalent linkage) or indirectly, e.g., via a bridging molecule or series of molecules (e.g., a molecule or complex that can bind to an assay component, or via members of a binding pair that can be incorporated into assay components, e.g. biotin-avidin or streptavidin).
  • a bridging molecule or series of molecules e.g., a molecule or complex that can bind to an assay component, or via members of a binding pair that can be incorporated into assay components, e.g. biotin-avidin or streptavidin.
  • Many labels are commercially available in activated forms which can readily be used for such conjugation (for example through amine acylation), or labels may be attached through known or determinable conjugation schemes, many of which are known in the art.
  • Labels useful in the invention described herein include any substance which can be detected when bound to or incorporated into the target molecule. Any effective detection method can be used, including optical, spectroscopic, electrical, piezoelectrical, magnetic, Raman scattering, surface plasmon resonance, colorimetric, calorimetric, etc.
  • a label is typically selected from a chromophore, a lumiphore, a fluorophore, one member of a quenching system, a chromogen, a hapten, an antigen, a magnetic particle, a material exhibiting nonlinear optics, a semiconductor nanocrystal, a metal nanoparticle, an enzyme, an antibody or binding portion or equivalent thereof, an aptamer, and one member of a binding pair, and combinations thereof.
  • Quenching schemes may be used, wherein a quencher and a fluorophore as members of a quenching pair may be used on a probe, such that a change in optical parameters occurs upon binding to the target introduce or quench the signal from the fluorophore.
  • a target polynucleotide may comprise a biotin-binding species, and an optically detectable label may be conjugated to biotin and then bound to the labeled target polynucleotide.
  • a polynucleotide sensor may comprise an immunological species such as an antibody or fragment, and a secondary antibody containing an optically detectable label may be added.
  • Chromophores useful in the methods described herein include any substance which can absorb energy and emit light.
  • a plurality of different signaling chromophores can be used with detectably different emission spectra.
  • the chromophore can be a lumophore or a fluorophore.
  • Typical fluorophores include fluorescent dyes, semiconductor nanocrystals, lanthanide chelates, polynucleotide-specific dyes and green fluorescent protein.
  • Coding schemes may optionally be used, comprising encoded particles and/or encoded tags associated with different polynucleotides of the invention.
  • a variety of different coding schemes are known in the art, including fluorophores, including SCNCs, deposited metals, and RF tags.
  • Polynucleotides from the described target molecules may be employed as probes for detecting target molecules expression, for ligation amplification schemes, or may be used as primers for amplification schemes of all or a portion of a target molecules. When amplified, either strand produced by amplification may be provided in purified and/or isolated form.
  • compositions and kits comprise a biomarker library.
  • the biomarker library may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more target molecules.
  • the target molecules may be a ncRNA, RNA, DNA, cDNA, mRNA, a portion or fragment thereof or a combination thereof.
  • the biomarker library may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more ncRNAs disclosed herein.
  • the biomarker library may comprise one or more PCATs, SChLAP-1, M41, ENST-75, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, any one of SEQ ID NOs 1-9, or a combination thereof.
  • a kit for analyzing a cancer comprising (a) a probe set comprising a plurality of probes comprising target specific sequences complementary to one or more target molecules, wherein the one or more target molecules comprise one or more ncRNAs; and (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the one or more target molecules in a sample.
  • the target molecules may comprise one or more PCATs, SChLAP-1, M41, ENST-75, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, any one of SEQ ID NOs 1-9, or a combination thereof.
  • a kit for analyzing a cancer comprising (a) a probe set comprising a plurality of probes comprising target specific sequences complementary to one or more target molecules of a biomarker library; and (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the one or more target molecules in a sample.
  • Control samples and/or nucleic acids may optionally be provided in the kit.
  • Control samples may include tissue and/or nucleic acids obtained from or representative of tumor samples from a healthy subject, as well as tissue and/or nucleic acids obtained from or representative of tumor samples from subjects diagnosed with a cancer.
  • kit Instructions for using the kit to perform one or more methods of the invention can be provided, and can be provided in any fixed medium.
  • the instructions may be located inside or outside a container or housing, and/or may be printed on the interior or exterior of any surface thereof.
  • a kit may be in multiplex form for concurrently detecting and/or quantitating one or more different target polynucleotides representing the expressed target molecules.
  • the devices can comprise means for characterizing the expression level of a target molecule of the invention, for example components for performing one or more methods of nucleic acid extraction, amplification, and/or detection.
  • Such components may include one or more of an amplification chamber (for example a thermal cycler), a plate reader, a spectrophotometer, capillary electrophoresis apparatus, a chip reader, and or robotic sample handling components. These components ultimately can obtain data that reflects the expression level of the target molecules used in the assay being employed.
  • the devices may include an excitation and/or a detection means. Any instrument that provides a wavelength that can excite a species of interest and is shorter than the emission wavelength(s) to be detected can be used for excitation. Commercially available devices can provide suitable excitation wavelengths as well as suitable detection component.
  • Exemplary excitation sources include a broadband UV light source such as a deuterium lamp with an appropriate filter, the output of a white light source such as a xenon lamp or a deuterium lamp after passing through a monochromator to extract out the desired wavelength(s), a continuous wave (cw) gas laser, a solid state diode laser, or any of the pulsed lasers.
  • Emitted light can be detected through any suitable device or technique; many suitable approaches are known in the art.
  • a fluorimeter or spectrophotometer may be used to detect whether the test sample emits light of a wavelength characteristic of a label used in an assay.
  • the devices typically comprise a means for identifying a given sample, and of linking the results obtained to that sample.
  • Such means can include manual labels, barcodes, and other indicators which can be linked to a sample vessel, and/or may optionally be included in the sample itself, for example where an encoded particle is added to the sample.
  • the results may be linked to the sample, for example in a computer memory that contains a sample designation and a record of expression levels obtained from the sample. Linkage of the results to the sample can also include a linkage to a particular sample receptacle in the device, which is also linked to the sample identity.
  • the devices also comprise a means for correlating the expression levels of the target molecules being studied with a prognosis of disease outcome.
  • Such means may comprise one or more of a variety of correlative techniques, including lookup tables, algorithms, multivariate models, and linear or nonlinear combinations of expression models or algorithms.
  • the expression levels may be converted to one or more likelihood scores, reflecting a likelihood that the patient providing the sample may exhibit a particular disease outcome.
  • the models and/or algorithms can be provided in machine readable format and can optionally further designate a treatment modality for a patient or class of patients.
  • the device also comprises output means for outputting the disease status, prognosis and/or a treatment modality.
  • output means can take any form which transmits the results to a patient and/or a healthcare provider, and may include a monitor, a printed format, or both.
  • the device may use a computer system for performing one or more of the steps provided.
  • the methods disclosed herein may also comprise the transmission of data/information.
  • data/information derived from the detection and/or quantification of the target may be transmitted to another device and/or instrument.
  • the information obtained from an algorithm may also be transmitted to another device and/or instrument.
  • Transmission of the data/information may comprise the transfer of data/information from a first source to a second source.
  • the first and second sources may be in the same approximate location (e.g., within the same room, building, block, campus). Alternatively, first and second sources may be in multiple locations (e.g., multiple cities, states, countries, continents, etc).
  • Transmission of the data/information may comprise digital transmission or analog transmission.
  • Digital transmission may comprise the physical transfer of data (a digital bit stream) over a point-to-point or point-to-multipoint communication channel. Examples of such channels are copper wires, optical fibres, wireless communication channels, and storage media.
  • the data may be represented as an electromagnetic signal, such as an electrical voltage, radiowave, microwave, or infrared signal.
  • Analog transmission may comprise the transfer of a continuously varying analog signal.
  • the messages can either be represented by a sequence of pulses by means of a line code (baseband transmission), or by a limited set of continuously varying wave forms (passband transmission), using a digital modulation method.
  • the passband modulation and corresponding demodulation also known as detection
  • modem equipment According to the most common definition of digital signal, both baseband and passband signals representing bit-streams are considered as digital transmission, while an alternative definition only considers the baseband signal as digital, and passband transmission of digital data as a form of digital-to-analog conversion.
  • Samples for use with the compositions and kits and in the methods of the present invention comprise nucleic acids suitable for providing RNA expression information.
  • the biological sample from which the expressed RNA is obtained and analyzed for target molecule expression can be any material suspected of comprising cancer tissue or cells.
  • the sample can be a biological sample used directly in a method of the invention.
  • the sample can be a sample prepared from a biological sample.
  • the sample or portion of the sample comprising or suspected of comprising cancer tissue or cells can be any source of biological material, including cells, tissue, secretions, or fluid, including bodily fluids.
  • the source of the sample include an aspirate, a needle biopsy, a cytology pellet, a bulk tissue preparation or a section thereof obtained for example by surgery or autopsy, lymph fluid, blood, plasma, serum, tumors, and organs.
  • the source of the sample can be urine, bile, excrement, sweat, tears, vaginal fluids, spinal fluid, and stool.
  • the sources of the sample are secretions.
  • the secretions are exosomes.
  • the samples may be archival samples, having a known and documented medical outcome, or may be samples from current patients whose ultimate medical outcome is not yet known.
  • the sample may be dissected prior to molecular analysis.
  • the sample may be prepared via macrodissection of a bulk tumor specimen or portion thereof, or may be treated via microdissection, for example via Laser Capture Microdissection (LCM).
  • LCD Laser Capture Microdissection
  • the sample may initially be provided in a variety of states, as fresh tissue, fresh frozen tissue, fine needle aspirates, and may be fixed or unfixed. Frequently, medical laboratories routinely prepare medical samples in a fixed state, which facilitates tissue storage.
  • fixatives can be used to fix tissue to stabilize the morphology of cells, and may be used alone or in combination with other agents. Exemplary fixatives include crosslinking agents, alcohols, acetone, Bouin's solution, Zenker solution, Hely solution, osmic acid solution and Carnoy solution.
  • Crosslinking fixatives can comprise any agent suitable for forming two or more covalent bonds, for example, an aldehyde.
  • Sources of aldehydes typically used for fixation include formaldehyde, paraformaldehyde, glutaraldehyde or formalin.
  • the crosslinking agent comprises formaldehyde, which may be included in its native form or in the form of paraformaldehyde or formalin.
  • One or more alcohols may be used to fix tissue, alone or in combination with other fixatives.
  • exemplary alcohols used for fixation include methanol, ethanol and isopropanol.
  • Formalin fixation is frequently used in medical laboratories.
  • Formalin comprises both an alcohol, typically methanol, and formaldehyde, both of which can act to fix a biological sample.
  • the biological sample may optionally be embedded in an embedding medium.
  • embedding media used in histology including paraffin, Tissue-Tek® V.I.P.TM, Paramat, Paramat Extra, Paraplast, Paraplast X-tra, Paraplast Plus, Peel Away Paraffin Embedding Wax, Polyester Wax, Carbowax Polyethylene Glycol, PolyfinTM, Tissue Freezing Medium TFMFM, Cryo-GefTM, and OCT Compound (Electron Microscopy Sciences, Hatfield, Pa.).
  • the embedding material may be removed via any suitable techniques, as known in the art.
  • the embedding material may be removed by extraction with organic solvent(s), for example xylenes.
  • Kits are commercially available for removing embedding media from tissues. Samples or sections thereof may be subjected to further processing steps as needed, for example serial hydration or dehydration steps.
  • the sample is a fixed, wax-embedded biological sample.
  • samples from medical laboratories are provided as fixed, wax-embedded samples, most commonly as formalin-fixed, paraffin embedded (FFPE) tissues.
  • FFPE formalin-fixed, paraffin embedded
  • the target polynucleotide that is ultimately assayed can be prepared synthetically (in the case of control sequences), but typically is purified from the biological source and subjected to one or more preparative steps.
  • the RNA may be purified to remove or diminish one or more undesired components from the biological sample or to concentrate it. Conversely, where the RNA is too concentrated for the particular assay, it may be diluted.
  • the present invention provides drug screening assays (e.g., to screen for anticancer drugs).
  • the screening methods of the present invention utilize ncRNAs.
  • the present invention provides methods of screening for compounds that alter the expression or activity of ncRNAs.
  • the compounds may increase the expression or activity of the ncRNAs.
  • the compounds may decrease the expression or activity of the ncRNAs.
  • the compounds or agents may interfere with transcription, by interacting, for example, with the promoter region.
  • the compounds or agents may interfere with mRNA (e.g., by RNA interference, antisense technologies, etc.).
  • the compounds or agents may interfere with pathways that are upstream or downstream of the biological activity of ncRNAs.
  • candidate compounds are antisense or interfering RNA agents (e.g., oligonucleotides) directed against ncRNAs.
  • candidate compounds are antibodies or small molecules that specifically bind to a ncRNA regulator.
  • the candidate compounds are expression products that inhibit the biological function of the ncRNAs.
  • candidate compounds are evaluated for their ability to alter ncRNAs expression by contacting a compound with a cell expressing a ncRNA and then assaying for the effect of the candidate compounds on expression.
  • the effect of candidate compounds on expression of ncRNAs is assayed for by detecting the level ncRNA expressed by the cell.
  • mRNA expression can be detected by any suitable method.
  • the methods, compositions, and kits disclosed herein may be used for the diagnosis, prognosis, and/or monitoring the status or outcome of a cancer in a subject.
  • the diagnosing, predicting, and/or monitoring the status or outcome of a cancer comprises determining the malignancy or malignant potential of the cancer or tumor.
  • the diagnosing, predicting, and/or monitoring the status or outcome of a cancer comprises determining the stage of the cancer.
  • the diagnosing, predicting, and/or monitoring the status or outcome of a cancer can comprise determining the tumor grade.
  • the diagnosing, predicting, and/or monitoring the status or outcome of a cancer comprises assessing the risk of developing a cancer.
  • the diagnosing, predicting, and/or monitoring the status or outcome of a cancer includes assessing the risk of cancer recurrence. In some embodiments, diagnosing, predicting, and/or monitoring the status or outcome of a cancer may comprise determining the efficacy of treatment.
  • diagnosing, predicting, and/or monitoring the status or outcome of a cancer may comprise determining a therapeutic regimen. Determining a therapeutic regimen may comprise administering an anti-cancer therapeutic. Alternatively, determining the treatment for the cancer may comprise modifying a therapeutic regimen. Modifying a therapeutic regimen may comprise increasing, decreasing, or terminating a therapeutic regimen.
  • the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 50%. In other instances, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 60%. The methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 65%. Alternatively, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 70%.
  • the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 75%. In other instances, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 80%. The methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 85%. Alternatively, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 90%. The methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 95%.
  • the invention also encompasses any of the methods disclosed herein where the sensitivity is at least about 45%. In some embodiments, the sensitivity is at least about 50%. In some embodiments, the sensitivity is at least about 55%. In some embodiments, the sensitivity is at least about 60%. In some embodiments, the sensitivity is at least about 65%. In some embodiments, the sensitivity is at least about 70%. In some embodiments, the sensitivity is at least about 75%. In some embodiments, the sensitivity is at least about 80%. In some embodiments, the sensitivity is at least about 85%. In some embodiments, the sensitivity is at least about 90%. In some embodiments, the sensitivity is at least about 95%.
  • the invention also encompasses any of the methods disclosed herein where the expression level determines the status or outcome of a cancer in the subject with at least about 45% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 50% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 55% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 60% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 65% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 70% specificity.
  • the expression level determines the status or outcome of a cancer in the subject with at least about 75% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 80% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 85% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 90% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 95% specificity.
  • a cancer is characterized by the uncontrolled growth of abnormal cells anywhere in a body.
  • the abnormal cells may be termed cancer cells, malignant cells, or tumor cells.
  • Many cancers and the abnormal cells that compose the cancer tissue are further identified by the name of the tissue that the abnormal cells originated from (for example, breast cancer, lung cancer, colon cancer, prostate cancer, pancreatic cancer, thyroid cancer). Cancer is not confined to humans; animals and other living organisms can get cancer.
  • the cancer may be malignant.
  • the cancer may be benign.
  • the cancer may be a recurrent and/or refractory cancer. Most cancers can be classified as a carcinoma, sarcoma, leukemia, lymphoma, myeloma, or a central nervous system cancer.
  • the cancer may be a sarcoma.
  • Sarcomas are cancers of the bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue.
  • Sarcomas include, but are not limited to, bone cancer, fibrosarcoma, chondrosarcoma, Ewing's sarcoma, malignant hemangioendothelioma, malignant schwannoma, bilateral vestibular schwannoma, osteosarcoma, soft tissue sarcomas (e.g.
  • alveolar soft part sarcoma alveolar soft part sarcoma, angiosarcoma, cystosarcoma phylloides, dermatofibrosarcoma, desmoid tumor, epithelioid sarcoma, extraskeletal osteosarcoma, fibrosarcoma, hemangiopericytoma, hemangiosarcoma, Kaposi's sarcoma, leiomyosarcoma, liposarcoma, lymphangiosarcoma, lymphosarcoma, malignant fibrous histiocytoma, neurofibrosarcoma, rhabdomyosarcoma, and synovial sarcoma).
  • the cancer may be a carcinoma.
  • Carcinomas are cancers that begin in the epithelial cells, which are cells that cover the surface of the body, produce hormones, and make up glands.
  • carcinomas include breast cancer, pancreatic cancer, lung cancer, colon cancer, colorectal cancer, rectal cancer, kidney cancer, bladder cancer, stomach cancer, prostate cancer, liver cancer, ovarian cancer, brain cancer, vaginal cancer, vulvar cancer, uterine cancer, oral cancer, penic cancer, testicular cancer, esophageal cancer, skin cancer, cancer of the fallopian tubes, head and neck cancer, gastrointestinal stromal cancer, adenocarcinoma, cutaneous or intraocular melanoma, cancer of the anal region, cancer of the small intestine, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, cancer of the urethra, cancer of the renal pelvis, cancer of the ureter, cancer of the
  • the cancer is a skin cancer, such as a basal cell carcinoma, squamous, melanoma, nonmelanoma, or actinic (solar) keratosis.
  • the cancer is a prostate cancer.
  • the cancer may be a thyroid cancer.
  • the cancer can be a pancreatic cancer.
  • the cancer is a bladder cancer.
  • the cancer is a lung cancer.
  • Lung cancer can start in the airways that branch off the trachea to supply the lungs (bronchi) or the small air sacs of the lung (the alveoli).
  • Lung cancers include non-small cell lung carcinoma (NSCLC), small cell lung carcinoma, and mesotheliomia.
  • NSCLC non-small cell lung carcinoma
  • Examples of NSCLC include squamous cell carcinoma, adenocarcinoma, and large cell carcinoma.
  • the mesothelioma may be a cancerous tumor of the lining of the lung and chest cavity (pleura) or lining of the abdomen (peritoneum). The mesothelioma may be due to asbestos exposure.
  • the cancer may be a brain cancer, such as a glioblastoma.
  • the cancer may be a central nervous system (CNS) tumor.
  • CNS tumors may be classified as gliomas or nongliomas.
  • the glioma may be malignant glioma, high grade glioma, diffuse intrinsic pontine glioma. Examples of gliomas include astrocytomas, oligodendrogliomas (or mixtures of oligodendroglioma and astocytoma elements), and ependymomas.
  • Astrocytomas include, but are not limited to, low-grade astrocytomas, anaplastic astrocytomas, glioblastoma multiforme, pilocytic astrocytoma, pleomorphic xanthoastrocytoma, and subependymal giant cell astrocytoma.
  • Oligodendrogliomas include low-grade oligodendrogliomas (or oligoastrocytomas) and anaplastic oligodendriogliomas.
  • Nongliomas include meningiomas, pituitary adenomas, primary CNS lymphomas, and medulloblastomas. In some instances, the cancer is a meningioma.
  • the cancer may be leukemia.
  • the leukemia may be an acute lymphocytic leukemia, acute myelocytic leukemia, chronic lymphocytic leukemia, or chronic myelocytic leukemia. Additional types of leukemias include hairy cell leukemia, chronic myelomonocytic leukemia, and juvenile myelomonocytic-leukemia.
  • the cancer is a lymphoma.
  • Lymphomas are cancers of the lymphocytes and may develop from either B or T lymphocytes.
  • the two major types of lymphoma are Hodgkin's lymphoma, previously known as Hodgkin's disease, and non-Hodgkin's lymphoma.
  • Hodgkin's lymphoma is marked by the presence of the Reed-Sternberg cell.
  • Non-Hodgkin's lymphomas are all lymphomas which are not Hodgkin's lymphoma.
  • Non-Hodgkin lymphomas may be indolent lymphomas and aggressive lymphomas.
  • Non-Hodgkin's lymphomas include, but are not limited to, diffuse large B cell lymphoma, follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, mantle cell lymphoma, Burkitt's lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), extranodal marginal zone B cell lymphoma, intravascular large B cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • MALT mucosa-associated lymphatic tissue lymphoma
  • MALT mucosa-associated lymphatic tissue lymphoma
  • small cell lymphocytic lymphoma mantle cell lymphoma
  • Burkitt's lymphoma mediastinal large B cell
  • Diagnosing, predicting, or monitoring a status or outcome of a cancer may comprise determining the stage of the cancer.
  • the stage of a cancer is a description (usually numbers I to IV with IV having more progression) of the extent the cancer has spread.
  • the stage often takes into account the size of a tumor, how deeply it has penetrated, whether it has invaded adjacent organs, how many lymph nodes it has metastasized to (if any), and whether it has spread to distant organs.
  • Staging of cancer can be used as a predictor of survival, and cancer treatment may be determined by staging. Determining the stage of the cancer may occur before, during, or after treatment. The stage of the cancer may also be determined at the time of diagnosis.
  • Cancer staging can be divided into a clinical stage and a pathologic stage.
  • Cancer staging may comprise the TNM classification.
  • TNM Classification of Malignant Tumours is a cancer staging system that describes the extent of cancer in a patient's body. T may describe the size of the tumor and whether it has invaded nearby tissue, N may describe regional lymph nodes that are involved, and M may describe distant metastasis (spread of cancer from one body part to another).
  • TNM Tumor, Node, Metastasis
  • clinical stage and pathologic stage are denoted by a small “c” or “p” before the stage (e.g., cT3N1M0 or pT2N0).
  • Clinical stage may be based on all of the available information obtained before a surgery to remove the tumor. Thus, it may include information about the tumor obtained by physical examination, radiologic examination, and endoscopy.
  • Pathologic stage can add additional information gained by examination of the tumor microscopically by a pathologist.
  • Pathologic staging can allow direct examination of the tumor and its spread, contrasted with clinical staging which may be limited by the fact that the information is obtained by making indirect observations at a tumor which is still in the body.
  • the TNM staging system can be used for most forms of cancer.
  • staging may comprise Ann Arbor staging.
  • Ann Arbor staging is the staging system for lymphomas, both in Hodgkin's lymphoma (previously called Hodgkin's disease) and Non-Hodgkin lymphoma (abbreviated NHL).
  • the stage may depend on both the place where the malignant tissue is located (as located with biopsy, CT scanning and increasingly positron emission tomography) and on systemic symptoms due to the lymphoma (“B symptoms”: night sweats, weight loss of >10% or fevers).
  • B symptoms night sweats, weight loss of >10% or fevers
  • the principal stage may be determined by location of the tumor.
  • Stage I may indicate that the cancer is located in a single region, usually one lymph node and the surrounding area. Stage I often may not have outward symptoms.
  • Stage II can indicate that the cancer is located in two separate regions, an affected lymph node or organ and a second affected area, and that both affected areas are confined to one side of the diaphragm—that is, both are above the diaphragm, or both are below the diaphragm.
  • Stage III often indicates that the cancer has spread to both sides of the diaphragm, including one organ or area near the lymph nodes or the spleen.
  • Stage IV may indicate diffuse or disseminated involvement of one or more extralymphatic organs, including any involvement of the liver, bone marrow, or nodular involvement of the lungs.
  • Modifiers may also be appended to some stages.
  • a or B may indicate the absence of constitutional (B-type) symptoms is denoted by adding an “A” to the stage; the presence is denoted by adding a “B” to the stage.
  • E can be used if the disease is “extranodal” (not in the lymph nodes) or has spread from lymph nodes to adjacent tissue.
  • X is often used if the largest deposit is >10 cm large (“bulky disease”), or whether the mediastinum is wider than 1 ⁇ 3 of the chest on a chest X-ray.
  • S may be used if the disease has spread to the spleen.
  • CS may denote that the clinical stage as obtained by doctor's examinations and tests.
  • PS may denote that the pathological stage as obtained by exploratory laparotomy (surgery performed through an abdominal incision) with splenectomy (surgical removal of the spleen).
  • Diagnosing, predicting, or monitoring a status or outcome of a cancer may comprise treating a cancer or preventing a cancer progression.
  • diagnosing, predicting, or monitoring a status or outcome of a cancer may comprise identifying or predicting responders to an anti-cancer therapy.
  • diagnosing, predicting, or monitoring may comprise determining a therapeutic regimen. Determining a therapeutic regimen may comprise administering an anti-cancer therapy. Alternatively, determining a therapeutic regimen may comprise modifying, recommending, continuing or discontinuing an anti-cancer regimen.
  • the expression patterns can be used to designate one or more treatment modalities (e.g., therapeutic regimens, anti-cancer regimen).
  • An anti-cancer regimen may comprise one or more anti-cancer therapies. Examples of anti-cancer therapies include surgery, chemotherapy, radiation therapy, immunotherapy/biological therapy, photodynamic therapy.
  • Surgical oncology uses surgical methods to diagnose, stage, and treat cancer, and to relieve certain cancer-related symptoms.
  • Surgery may be used to remove the tumor (e.g., excisions, resections, debulking surgery), reconstruct a part of the body (e.g., restorative surgery), and/or to relieve symptoms such as pain (e.g., palliative surgery).
  • Surgery may also include cryosurgery.
  • Cryosurgery also called cryotherapy
  • Cryosurgery may use extreme cold produced by liquid nitrogen (or argon gas) to destroy abnormal tissue.
  • Cryosurgery can be used to treat external tumors, such as those on the skin.
  • liquid nitrogen can be applied directly to the cancer cells with a cotton swab or spraying device.
  • Cryosurgery may also be used to treat tumors inside the body (internal tumors and tumors in the bone).
  • liquid nitrogen or argon gas may be circulated through a hollow instrument called a cryoprobe, which is placed in contact with the tumor.
  • An ultrasound or MRI may be used to guide the cryoprobe and monitor the freezing of the cells, thus limiting damage to nearby healthy tissue.
  • a ball of ice crystals may form around the probe, freezing nearby cells.
  • more than one probe is used to deliver the liquid nitrogen to various parts of the tumor. The probes may be put into the tumor during surgery or through the skin (percutaneously). After cryosurgery, the frozen tissue thaws and may be naturally absorbed by the body (for internal tumors), or may dissolve and form a scab (for external tumors).
  • Chemotherapeutic agents may also be used for the treatment of cancer.
  • examples of chemotherapeutic agents include alkylating agents, anti-metabolites, plant alkaloids and terpenoids, vinca alkaloids, podophyllotoxin, taxanes, topoisomerase inhibitors, and cytotoxic antibiotics.
  • Cisplatin, carboplatin, and oxaliplatin are examples of alkylating agents.
  • Other alkylating agents include mechlorethamine, cyclophosphamide, chlorambucil, ifosfamide.
  • Alkylating agents may impair cell function by forming covalent bonds with the amino, carboxyl, sulfhydryl, and phosphate groups in biologically important molecules.
  • alkylating agents may chemically modify a cell's DNA.
  • Anti-metabolites are another example of chemotherapeutic agents. Anti-metabolites may masquerade as purines or pyrimidines and may prevent purines and pyrimidines from becoming incorporated in to DNA during the “S” phase (of the cell cycle), thereby stopping normal development and division. Antimetabolites may also affect RNA synthesis. Examples of metabolites include azathioprine and mercaptopurine.
  • Alkaloids may be derived from plants and block cell division may also be used for the treatment of cancer. Alkyloids may prevent microtubule function. Examples of alkaloids are vinca alkaloids and taxanes. Vinca alkaloids may bind to specific sites on tubulin and inhibit the assembly of tubulin into microtubules (M phase of the cell cycle). The vinca alkaloids may be derived from the Madagascar periwinkle, Catharanthus roseus (formerly known as Vinca rosea ). Examples of vinca alkaloids include, but are not limited to, vincristine, vinblastine, vinorelbine, or vindesine. Taxanes are diterpenes produced by the plants of the genus Taxus (yews).
  • Taxanes may be derived from natural sources or synthesized artificially. Taxanes include paclitaxel (Taxol) and docetaxel (Taxotere). Taxanes may disrupt microtubule function. Microtubules are essential to cell division, and taxanes may stabilize GDP-bound tubulin in the microtubule, thereby inhibiting the process of cell division. Thus, in essence, taxanes may be mitotic inhibitors. Taxanes may also be radiosensitizing and often contain numerous chiral centers.
  • chemotherapeutic agents include podophyllotoxin.
  • Podophyllotoxin is a plant-derived compound that may help with digestion and may be used to produce cytostatic drugs such as etoposide and teniposide. They may prevent the cell from entering the G1 phase (the start of DNA replication) and the replication of DNA (the S phase).
  • Topoisomerases are essential enzymes that maintain the topology of DNA. Inhibition of type I or type II topoisomerases may interfere with both transcription and replication of DNA by upsetting proper DNA supercoiling. Some chemotherapeutic agents may inhibit topoisomerases.
  • some type I topoisomerase inhibitors include camptothecins: irinotecan and topotecan. Examples of type II inhibitors include amsacrine, etoposide, etoposide phosphate, and teniposide.
  • Cytotoxic antibiotics are a group of antibiotics that are used for the treatment of cancer because they may interfere with DNA replication and/or protein synthesis. Cytotoxic antiobiotics include, but are not limited to, actinomycin, anthracyclines, doxorubicin, daunorubicin, valrubicin, idarubicin, epirubicin, bleomycin, plicamycin, and mitomycin.
  • the anti-cancer treatment may comprise radiation therapy.
  • Radiation can come from a machine outside the body (external-beam radiation therapy) or from radioactive material placed in the body near cancer cells (internal radiation therapy, more commonly called brachytherapy).
  • Systemic radiation therapy uses a radioactive substance, given by mouth or into a vein that travels in the blood to tissues throughout the body.
  • External-beam radiation therapy may be delivered in the form of photon beams (either x-rays or gamma rays).
  • a photon is the basic unit of light and other forms of electromagnetic radiation.
  • An example of external-beam radiation therapy is called 3-dimensional conformal radiation therapy (3D-CRT).
  • 3D-CRT may use computer software and advanced treatment machines to deliver radiation to very precisely shaped target areas.
  • Many other methods of external-beam radiation therapy are currently being tested and used in cancer treatment. These methods include, but are not limited to, intensity-modulated radiation therapy (IMRT), image-guided radiation therapy (IGRT), Stereotactic radiosurgery (SRS), Stereotactic body radiation therapy (SBRT), and proton therapy.
  • IMRT intensity-modulated radiation therapy
  • IGRT image-guided radiation therapy
  • SRS Stereotactic radiosurgery
  • SBRT Stereotactic body radiation therapy
  • IMRT Intensity-modulated radiation therapy
  • collimators can be stationary or can move during treatment, allowing the intensity of the radiation beams to change during treatment sessions.
  • This kind of dose modulation allows different areas of a tumor or nearby tissues to receive different doses of radiation.
  • IMRT is planned in reverse (called inverse treatment planning). In inverse treatment planning, the radiation doses to different areas of the tumor and surrounding tissue are planned in advance, and then a high-powered computer program calculates the required number of beams and angles of the radiation treatment.
  • IMRT In contrast, during traditional (forward) treatment planning, the number and angles of the radiation beams are chosen in advance and computers calculate how much dose may be delivered from each of the planned beams.
  • the goal of IMRT is to increase the radiation dose to the areas that need it and reduce radiation exposure to specific sensitive areas of surrounding normal tissue.
  • IGRT image-guided radiation therapy
  • CT computed tomography
  • MRI magnetic resonance imaging
  • PET magnetic resonance imaging
  • CT computed tomography
  • MRI magnetic resonance imaging
  • PET magnetic resonance imaging
  • Imaging scans may be processed by computers to identify changes in a tumor's size and location due to treatment and to allow the position of the patient or the planned radiation dose to be adjusted during treatment as needed.
  • Repeated imaging can increase the accuracy of radiation treatment and may allow reductions in the planned volume of tissue to be treated, thereby decreasing the total radiation dose to normal tissue.
  • Tomotherapy is a type of image-guided IMRT.
  • a tomotherapy machine is a hybrid between a CT imaging scanner and an external-beam radiation therapy machine.
  • the part of the tomotherapy machine that delivers radiation for both imaging and treatment can rotate completely around the patient in the same manner as a normal CT scanner.
  • Tomotherapy machines can capture CT images of the patient's tumor immediately before treatment sessions, to allow for very precise tumor targeting and sparing of normal tissue.
  • Stereotactic radiosurgery can deliver one or more high doses of radiation to a small tumor.
  • SRS uses extremely accurate image-guided tumor targeting and patient positioning. Therefore, a high dose of radiation can be given without excess damage to normal tissue.
  • SRS can be used to treat small tumors with well-defined edges. It is most commonly used in the treatment of brain or spinal tumors and brain metastases from other cancer types. For the treatment of some brain metastases, patients may receive radiation therapy to the entire brain (called whole-brain radiation therapy) in addition to SRS.
  • SRS requires the use of a head frame or other device to immobilize the patient during treatment to ensure that the high dose of radiation is delivered accurately.
  • SBRT Stereotactic body radiation therapy
  • SBRT delivers radiation therapy in fewer sessions, using smaller radiation fields and higher doses than 3D-CRT in most cases.
  • SBRT may treat tumors that lie outside the brain and spinal cord. Because these tumors are more likely to move with the normal motion of the body, and therefore cannot be targeted as accurately as tumors within the brain or spine, SBRT is usually given in more than one dose.
  • SBRT can be used to treat small, isolated tumors, including cancers in the lung and liver.
  • SBRT systems may be known by their brand names, such as the CyberKnife®.
  • Protons are a type of charged particle. Proton beams differ from photon beams mainly in the way they deposit energy in living tissue. Whereas photons deposit energy in small packets all along their path through tissue, protons deposit much of their energy at the end of their path (called the Bragg peak) and deposit less energy along the way. Use of protons may reduce the exposure of normal tissue to radiation, possibly allowing the delivery of higher doses of radiation to a tumor.
  • Other charged particle beams such as electron beams may be used to irradiate superficial tumors, such as skin cancer or tumors near the surface of the body, but they cannot travel very far through tissue.
  • brachytherapy Internal radiation therapy
  • radiation sources radiation sources
  • brachytherapy techniques are used in cancer treatment.
  • Interstitial brachytherapy may use a radiation source placed within tumor tissue, such as within a prostate tumor.
  • Intracavitary brachytherapy may use a source placed within a surgical cavity or a body cavity, such as the chest cavity, near a tumor.
  • Episcleral brachytherapy which may be used to treat melanoma inside the eye, may use a source that is attached to the eye.
  • radioactive isotopes can be sealed in tiny pellets or “seeds.” These seeds may be placed in patients using delivery devices, such as needles, catheters, or some other type of carrier. As the isotopes decay naturally, they give off radiation that may damage nearby cancer cells.
  • Brachytherapy may be able to deliver higher doses of radiation to some cancers than external-beam radiation therapy while causing less damage to normal tissue.
  • Brachytherapy can be given as a low-dose-rate or a high-dose-rate treatment.
  • low-dose-rate treatment cancer cells receive continuous low-dose radiation from the source over a period of several days.
  • high-dose-rate treatment a robotic machine attached to delivery tubes placed inside the body may guide one or more radioactive sources into or near a tumor, and then removes the sources at the end of each treatment session.
  • High-dose-rate treatment can be given in one or more treatment sessions.
  • An example of a high-dose-rate treatment is the MammoSite® system.
  • Bracytherapy may be used to treat patients with breast cancer who have undergone breast-conserving surgery.
  • brachytherapy sources can be temporary or permanent.
  • the sources may be surgically sealed within the body and left there, even after all of the radiation has been given off. In some instances, the remaining material (in which the radioactive isotopes were sealed) does not cause any discomfort or harm to the patient.
  • Permanent brachytherapy is a type of low-dose-rate brachytherapy.
  • tubes (catheters) or other carriers are used to deliver the radiation sources, and both the carriers and the radiation sources are removed after treatment.
  • Temporary brachytherapy can be either low-dose-rate or high-dose-rate treatment.
  • Brachytherapy may be used alone or in addition to external-beam radiation therapy to provide a “boost” of radiation to a tumor while sparing surrounding normal tissue.
  • Radioactive iodine 131I
  • a monoclonal antibody may help target the radioactive substance to the right place. The antibody joined to the radioactive substance travels through the blood, locating and killing tumor cells.
  • the drug ibritumomab tiuxetan may be used for the treatment of certain types of B-cell non-Hodgkin lymphoma (NHL).
  • the antibody part of this drug recognizes and binds to a protein found on the surface of B lymphocytes.
  • the combination drug regimen of tositumomab and iodine I 131 tositumomab (Bexxar®) may be used for the treatment of certain types of cancer, such as NHL.
  • nonradioactive tositumomab antibodies may be given to patients first, followed by treatment with tositumomab antibodies that have 131I attached.
  • Tositumomab may recognize and bind to the same protein on B lymphocytes as ibritumomab.
  • the nonradioactive form of the antibody may help protect normal B lymphocytes from being damaged by radiation from 131I.
  • Some systemic radiation therapy drugs relieve pain from cancer that has spread to the bone (bone metastases). This is a type of palliative radiation therapy.
  • the radioactive drugs samarium-153-lexidronam (Quadramet®) and strontium-89 chloride (Metastron®) are examples of radiopharmaceuticals may be used to treat pain from bone metastases.
  • Biological therapy (sometimes called immunotherapy, biotherapy, or biological response modifier (BRM) therapy) uses the body's immune system, either directly or indirectly, to fight cancer or to lessen the side effects that may be caused by some cancer treatments.
  • Biological therapies include interferons, interleukins, colony-stimulating factors, monoclonal antibodies, vaccines, gene therapy, and nonspecific immunomodulating agents.
  • Interferons are types of cytokines that occur naturally in the body. Interferon alpha, interferon beta, and interferon gamma are examples of interferons that may be used in cancer treatment.
  • interleukins are cytokines that occur naturally in the body and can be made in the laboratory. Many interleukins have been identified for the treatment of cancer. For example, interleukin-2 (IL-2 or aldesleukin), interleukin 7, and interleukin 12 have may be used as an anti-cancer treatment. IL-2 may stimulate the growth and activity of many immune cells, such as lymphocytes, that can destroy cancer cells. Interleukins may be used to treat a number of cancers, including leukemia, lymphoma, and brain, colorectal, ovarian, breast, kidney and prostate cancers.
  • Colony-stimulating factors may also be used for the treatment of cancer.
  • CSFs include, but are not limited to, G-CSF (filgrastim) and GM-CSF (sargramostim).
  • CSFs may promote the division of bone marrow stem cells and their development into white blood cells, platelets, and red blood cells. Bone marrow is critical to the body's immune system because it is the source of all blood cells.
  • CSFs may be combined with other anti-cancer therapies, such as chemotherapy.
  • CSFs may be used to treat a large variety of cancers, including lymphoma, leukemia, multiple myeloma, melanoma, and cancers of the brain, lung, esophagus, breast, uterus, ovary, prostate, kidney, colon, and rectum.
  • MOABs monoclonal antibodies
  • MOABs monoclonal antibodies
  • human cancer cells may be injected into mice.
  • the mouse immune system can make antibodies against these cancer cells.
  • the mouse plasma cells that produce antibodies may be isolated and fused with laboratory-grown cells to create “hybrid” cells called hybridomas.
  • Hybridomas can indefinitely produce large quantities of these pure antibodies, or MOABs.
  • MOABs may be used in cancer treatment in a number of ways. For instance, MOABs that react with specific types of cancer may enhance a patient's immune response to the cancer. MOABs can be programmed to act against cell growth factors, thus interfering with the growth of cancer cells.
  • MOABs may be linked to other anti-cancer therapies such as chemotherapeutics, radioisotopes (radioactive substances), other biological therapies, or other toxins. When the antibodies latch onto cancer cells, they deliver these anti-cancer therapies directly to the tumor, helping to destroy it. MOABs carrying radioisotopes may also prove useful in diagnosing certain cancers, such as colorectal, ovarian, and prostate.
  • Rituxan® (rituximab) and Herceptin® (trastuzumab) are examples of MOABs that may be used as a biological therapy.
  • Rituxan may be used for the treatment of non-Hodgkin lymphoma.
  • Herceptin can be used to treat metastatic breast cancer in patients with tumors that produce excess amounts of a protein called HER2.
  • MOABs may be used to treat lymphoma, leukemia, melanoma, and cancers of the brain, breast, lung, kidney, colon, rectum, ovary, prostate, and other areas.
  • Cancer vaccines are another form of biological therapy. Cancer vaccines may be designed to encourage the patient's immune system to recognize cancer cells. Cancer vaccines may be designed to treat existing cancers (therapeutic vaccines) or to prevent the development of cancer (prophylactic vaccines). Therapeutic vaccines may be injected in a person after cancer is diagnosed. These vaccines may stop the growth of existing tumors, prevent cancer from recurring, or eliminate cancer cells not killed by prior treatments. Cancer vaccines given when the tumor is small may be able to eradicate the cancer. On the other hand, prophylactic vaccines are given to healthy individuals before cancer develops. These vaccines are designed to stimulate the immune system to attack viruses that can cause cancer. By targeting these cancer-causing viruses, development of certain cancers may be prevented.
  • cervarix and gardasil are vaccines to treat human papilloma virus and may prevent cervical cancer.
  • Therapeutic vaccines may be used to treat melanoma, lymphoma, leukemia, and cancers of the brain, breast, lung, kidney, ovary, prostate, pancreas, colon, and rectum. Cancer vaccines can be used in combination with other anti-cancer therapies.
  • Gene therapy is another example of a biological therapy.
  • Gene therapy may involve introducing genetic material into a person's cells to fight disease.
  • Gene therapy methods may improve a patient's immune response to cancer.
  • a gene may be inserted into an immune cell to enhance its ability to recognize and attack cancer cells.
  • cancer cells may be injected with genes that cause the cancer cells to produce cytokines and stimulate the immune system.
  • biological therapy includes nonspecific immunomodulating agents.
  • Nonspecific immunomodulating agents are substances that stimulate or indirectly augment the immune system. Often, these agents target key immune system cells and may cause secondary responses such as increased production of cytokines and immunoglobulins.
  • Two nonspecific immunomodulating agents used in cancer treatment are bacillus Calmette-Guerin (BCG) and levamisole.
  • BCG may be used in the treatment of superficial bladder cancer following surgery. BCG may work by stimulating an inflammatory, and possibly an immune, response. A solution of BCG may be instilled in the bladder.
  • Levamisole is sometimes used along with fluorouracil (5-FU) chemotherapy in the treatment of stage III (Dukes' C) colon cancer following surgery. Levamisole may act to restore depressed immune function.
  • Photodynamic therapy is an anti-cancer treatment that may use a drug, called a photosensitizer or photosensitizing agent, and a particular type of light.
  • a photosensitizer or photosensitizing agent When photosensitizers are exposed to a specific wavelength of light, they may produce a form of oxygen that kills nearby cells.
  • a photosensitizer may be activated by light of a specific wavelength. This wavelength determines how far the light can travel into the body. Thus, photosensitizers and wavelengths of light may be used to treat different areas of the body with PDT.
  • a photosensitizing agent may be injected into the bloodstream.
  • the agent may be absorbed by cells all over the body but may stay in cancer cells longer than it does in normal cells. Approximately 24 to 72 hours after injection, when most of the agent has left normal cells but remains in cancer cells, the tumor can be exposed to light.
  • the photosensitizer in the tumor can absorb the light and produces an active form of oxygen that destroys nearby cancer cells.
  • PDT may shrink or destroy tumors in two other ways. The photosensitizer can damage blood vessels in the tumor, thereby preventing the cancer from receiving necessary nutrients. PDT may also activate the immune system to attack the tumor cells.
  • the light used for PDT can come from a laser or other sources.
  • Laser light can be directed through fiber optic cables (thin fibers that transmit light) to deliver light to areas inside the body.
  • a fiber optic cable can be inserted through an endoscope (a thin, lighted tube used to look at tissues inside the body) into the lungs or esophagus to treat cancer in these organs.
  • Other light sources include light-emitting diodes (LEDs), which may be used for surface tumors, such as skin cancer.
  • PDT is usually performed as an outpatient procedure. PDT may also be repeated and may be used with other therapies, such as surgery, radiation, or chemotherapy.
  • Extracorporeal photopheresis is a type of PDT in which a machine may be used to collect the patient's blood cells.
  • the patient's blood cells may be treated outside the body with a photosensitizing agent, exposed to light, and then returned to the patient.
  • ECP may be used to help lessen the severity of skin symptoms of cutaneous T-cell lymphoma that has not responded to other therapies.
  • ECP may be used to treat other blood cancers, and may also help reduce rejection after transplants.
  • photosensitizing agent such as porfimer sodium or Photofrin®
  • Porfimer sodium may relieve symptoms of esophageal cancer when the cancer obstructs the esophagus or when the cancer cannot be satisfactorily treated with laser therapy alone.
  • Porfimer sodium may be used to treat non-small cell lung cancer in patients for whom the usual treatments are not appropriate, and to relieve symptoms in patients with non-small cell lung cancer that obstructs the airways.
  • Porfimer sodium may also be used for the treatment of precancerous lesions in patients with Barrett esophagus, a condition that can lead to esophageal cancer.
  • Laser therapy may use high-intensity light to treat cancer and other illnesses.
  • Lasers can be used to shrink or destroy tumors or precancerous growths.
  • Lasers are most commonly used to treat superficial cancers (cancers on the surface of the body or the lining of internal organs) such as basal cell skin cancer and the very early stages of some cancers, such as cervical, penile, vaginal, vulvar, and non-small cell lung cancer.
  • Lasers may also be used to relieve certain symptoms of cancer, such as bleeding or obstruction.
  • lasers can be used to shrink or destroy a tumor that is blocking a patient's trachea (windpipe) or esophagus.
  • Lasers also can be used to remove colon polyps or tumors that are blocking the colon or stomach.
  • Laser therapy is often given through a flexible endoscope (a thin, lighted tube used to look at tissues inside the body).
  • the endoscope is fitted with optical fibers (thin fibers that transmit light). It is inserted through an opening in the body, such as the mouth, nose, anus, or vagina. Laser light is then precisely aimed to cut or destroy a tumor.
  • LITT Laser-induced interstitial thermotherapy
  • interstitial laser photocoagulation also uses lasers to treat some cancers.
  • LITT is similar to a cancer treatment called hyperthermia, which uses heat to shrink tumors by damaging or killing cancer cells.
  • hyperthermia a cancer treatment
  • an optical fiber is inserted into a tumor. Laser light at the tip of the fiber raises the temperature of the tumor cells and damages or destroys them. LITT is sometimes used to shrink tumors in the liver.
  • Laser therapy can be used alone, but most often it is combined with other treatments, such as surgery, chemotherapy, or radiation therapy.
  • lasers can seal nerve endings to reduce pain after surgery and seal lymph vessels to reduce swelling and limit the spread of tumor cells.
  • Lasers used to treat cancer may include carbon dioxide (CO2) lasers, argon lasers, and neodymium:yttrium-aluminum-garnet (Nd:YAG) lasers. Each of these can shrink or destroy tumors and can be used with endoscopes. CO2 and argon lasers can cut the skin's surface without going into deeper layers. Thus, they can be used to remove superficial cancers, such as skin cancer. In contrast, the Nd:YAG laser is more commonly applied through an endoscope to treat internal organs, such as the uterus, esophagus, and colon. Nd:YAG laser light can also travel through optical fibers into specific areas of the body during LITT. Argon lasers are often used to activate the drugs used in PDT.
  • CO2 and argon lasers can cut the skin's surface without going into deeper layers. Thus, they can be used to remove superficial cancers, such as skin cancer.
  • the Nd:YAG laser is more commonly applied through an endoscope to treat internal organs
  • Unannotated transcripts were nominated based upon their absence in the UCSC, RefSeq, ENSEMBL, ENCODE, and Vega databases. Differential expression was determined using the Significance Analysis of Microarrays (SAM) algorithm (Tusher et al., Proc Natl Acad Sci USA 98 (9), 5116 (2001)) on log 2 mean expression in benign, cancer, and metastatic samples. Cancer outlier profile analysis (COPA) was performed as previously described (Tomlins et al., Science 310 (5748), 644 (2005)) with slight modifications. PCR experiments were performed according to standard protocols, and RACE was performed with the GeneRacer Kit (Invitrogen) according to manufacturer's instructions.
  • SAM Significance Analysis of Microarrays
  • COPA Cancer outlier profile analysis
  • ChIP-seq data was obtained from previously published data (Yu et al., Cancer Cell 17 (5), 443).
  • siRNA knockdown was performed with custom siRNA oligos (Dharmacon) with Oligofectamine (Invitrogen).
  • Transmembrane invasion assays were performed with Matrigel (BD Biosciences) and cell proliferation assays were performed by cell count with a Coulter counter.
  • Urine analyses were performed as previously described (Laxman et al., Cancer Res 68 (3), 645 (2008)) with minor modifications.
  • the benign immortalized prostate cell line RWPE as well as PC3, Du145, LNCaP, VCaP, 22Rv1, CWR22, C4-2B, NCI-660, MDA PCa 2b, WPMY-1, and LAPC-4 prostate cell lines were obtained from the American Type Culture Collection (Manassas, Va.). Benign non-immortalized prostate epithelial cells (PrEC) and prostate smooth muscle cells (PrSMC) were obtained from Lonza (Basel, Switzerland). Cell lines were maintained using standard media and conditions. For androgen treatment experiments, LNCaP and VCaP cells were grown in androgen depleted media lacking phenol red and supplemented with 10% charcoal-stripped serum and 1% penicillin-streptomycin.
  • LNCaP CDS 1, 2, and 3 are androgen-independent subclones derived from extended cell culture in androgendepleted media.
  • VCaP and WPMY-1 cells were grown in DMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) with 1% penicillin-streptomycin.
  • FBS fetal bovine serum
  • NCI-H660 cells were grown in RPMI 1640 supplemented with 0.005 mg/ml insulin, 0.01 mg/ml transferring, 30 nM sodium selenite, 10 nM hydrocortisone, 10 nM beta-estradiol, 5% FBS and an extra 2 mM of L-glutamine (for a final concentration of 4 mM).
  • MDA PCa 2b cells were grown in F-12K medium (Invitrogen) supplemented with 20% FBS, 25 ng/ml cholera toxin, 10 ng/ml EGF, 0.005 mM phosphoethanolamine, 100 pg/ml hydrocortisone, 45 nM selenious acid, and 0.005 mg/ml insulin.
  • LAPC-4 cells were grown in Iscove's media (Invitrogen) supplemented with 10% FBS and 1 nM R1881.
  • C4-2B cells were grown in 80% DMEM supplemented with 20% F12, 5% FBS, 3 g/L NaCo 3 , 5 ⁇ g/ml insulin, 13.6 pg/ml triiodothyonine, 5 ⁇ g/ml transferrin, 0.25 ⁇ g/ml biotin, and 25 ⁇ g/ml adenine.
  • PrEC cells were grown in PrEGM supplemented with 2 ml BPE, 0.5 ml hydrocortisone, 0.5 ml EGF, 0.5 ml epinephrine, 0.5 ml transferring, 0.5 ml insulin, 0.5 ml retinoic acid, and 0.5 ml triiodothyronine, as part of the PrEGM BulletKit (Lonza).
  • PrSMC cells were grown in SmGM-2 media supplemented with 2 ml BPE, 0.5 ml hydrocortisone, 0.5 ml EGF, 0.5 ml epinephrine, 0.5 ml transferring, 0.5 ml insulin, 0.5 ml retinoic acid, and 0.5 ml triiodothyronine, as part of the SmGM-2 BulletKit (Lonza).
  • RNA integrity was measured using an Agilent 2100 Bioanalyzer, and only samples with a RIN score >7.0 were advanced for library generation.
  • RNA was poly-A+ selected using the OligodT beads provided by Ilumina and fragmented with the Ambion Fragmentation Reagents kit (Ambion, Austin, Tex.).
  • cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina PCR adaptors were performed according to Illumina's protocol.
  • Libraries were then size-selected for 250-300 bp cDNA fragments on a 3.5% agarose gel and PCR-amplified using Phusion DNA polymerase (Finnzymes) for 15-18 PCR cycles. PCR products were then purified on a 2% agarose gel and gel-extracted. Library quality was credentialed by assaying each library on an Agilent 2100 Bioanalyzer of product size and concentration. Libraries were sequenced as 36-45mers on an Illumina Genome Analyzer I or Genome Analyzer II flowcell according to Illumina's protocol. All single read samples were sequenced on a Genome Analyzer I, and all paired-end samples were sequenced on a Genome Analyzer II.
  • Quantitative Real-time PCR was performed using Power SYBR Green Mastermix (Applied Biosystems, Foster City, Calif.) on an Applied Biosystems 7900HT Real-Time PCR System. All oligonucleotide primers were obtained from Integrated DNA Technologies (Coralville, Iowa). The housekeeping gene, GAPDH, was used as a loading control. Fold changes were calculated relative to GAPDH and normalized to the median value of the benign samples.
  • RT-PCR Reverse-transcription PCR
  • PCR products were resolved on a 2% agarose gel. PCR products were either sequenced directly (if only a single product was observed) or appropriate gel products were extracted using a Gel Extraction kit (Qiagen) and cloned into per4-TOPO vectors (Invitrogen). PCR products were bidirectionally sequenced at the University of Michigan Sequencing Core using either gene-specific primers or M13 forward and reverse primers for cloned PCR products. All oligonucleotide primers were obtained from Integrated DNA Technologies (Coralville, Iowa).
  • RACE 5′ and 3′ RACE was performed using the GeneRacer RLM-RACE kit (Invitrogen) according to the manufacturer's instructions.
  • RACE PCR products were obtained using Platinum Taq High Fidelity polymerase (Invitrogen), the supplied GeneRacer primers, and appropriate gene-specific primers.
  • RACEPCR products were separated on a 2% agarose gels. Gel products were extracted with a Gel Extraction kit (Qiagen), cloned into per4-TOPO vectors (Invitrogen), and sequenced bidirectionally using M13 forward and reverse primers at the University of Michigan Sequencing Core. At least three colonies were sequenced for every gel product that was purified.
  • RNA 2 ⁇ g total RNA was selected for polyA+ RNA using Sera-Mag oligo(dT) beads (Thermo Scientific), and paired-end next-generation sequencing libraries were prepared as previously described (Maher et al., supra) using Illumina-supplied universal adaptor oligos and PCR primers (Illumina). Samples were sequenced in a single lane on an Illumina Genome Analyzer II flowcell using previously described protocols (Maher et al., supra). 36-45 mer paired-end reads were according to the protocol provided by Illumina.
  • Cells were plated in 100 mM plates at a desired concentration and transfected with 20 ⁇ M experimental siRNA oligos or non-targeting controls twice, at 12 hours and 36 hours post-plating. Knockdowns were performed with Oligofectamine and Optimem. Knockdown efficiency was determined by qPCR. 72 hours post-transfection, cells were trypsinized, counted with a Coulter counter, and diluted to 1 million cells/mL. For proliferation assays, 200,000 cells were plated in 24-well plates and grown in regular media. 48 and 96 hours post-plating, cells were harvested and counted using a Coulter counter.
  • Matrigel was diluted 1:4 in serum-free media and 100 ⁇ L of the diluted Matrigel was applied to a Boyden chamber transmembrane insert and allowed to settle overnight at 37° C. 200,000 cells suspended in serum-free media were applied per insert and 500 ⁇ L of serum-containing media was placed in the bottom of the Boyden (fetal bovine serum functioning as a chemoattractant). Cells were allowed to invade for 48 hours, at which time inserts were removed and noninvading cells and Matrigel were gently removed with a cotton swab. Invading cells were stained with crystal violet for 15 minutes and air-dried.
  • Boyden fetal bovine serum functioning as a chemoattractant
  • the inserts were treated with 200 ⁇ l of 10% acetic acid and the absorbance at 560 nm was measured using a spectrophotometer.
  • WST-1 assays 20,000 cells were plated into 96-well plates and grown in 100 ⁇ L of serum-containing media. 48 and 96 hours post-plating, cells were measured for viability by adding 10 ⁇ L of WST-1 reagent to the cell media, incubating for 2 hours at 37° C. and measuring the absorbance at 450 nM using a spectrophotomer.
  • Urine samples were collected from 120 patients with informed consent following a digital rectal exam before either needle biopsy or radical prostatectomy at the University of Michigan with Institutional Review Board approval as described previously (Laxman et al., Cancer Res 68 (3), 645 (2008)). Isolation of RNA from urine and TransPlex whole transcriptome amplification were performed as described previously (Laxman et al., Neoplasia 8 (10), 885 (2006)). qPCR on urine samples was performed for KLK3 (PSA), TMPRSS2-ERG, GAPDH, PCA3, PCAT-1 and PCAT-14 using Power SYBR Mastermix (Applied Biosystems) as described above. Raw Ct values were extracted and normalized in the following manner.
  • samples with GAPDH Ct values >25 or KLK3 Ct values >30 were removed from analysis to ensure sufficient prostate cell collection, leaving 10 8 samples for analysis.
  • the GAPDH and KLK3 raw Ct values were average for each sample.
  • ⁇ Ct analysis was performed by measuring each value against the average of CtGAPDH and CtKLK3, and ⁇ Ct values were normalized to the median ⁇ Ct of the benign samples. Fold change was then calculated at 2 ⁇ Ct.
  • Samples were considered to be prostate cancer if histopathological analysis observed cancer or if the TMPRSS2-ERG transcript achieved a Ct value ⁇ 37. Benign samples were defined as samples with normal histology and TMPRSS2-ERG transcript Ct values >37.
  • TopHat aligns reads to the human genome using Bowtie (Langmead et al., Genome Biol 10, R25 (2009)) to determine a set of “coverage islands” that may represent putative exons. TopHat uses these exons as well as the presence of GT-AG genomic splicing motifs to build a second set of reference sequences spanning exon-exon junctions.
  • the unmapped reads from the initial genome alignment step are then remapped against this splice junction reference to discover all the junction-spanning reads in the sample.
  • TopHat outputs the reads that successfully map to either the genome or the splice junction reference in SAM format for further analysis.
  • a maximum intron size of 500 kb corresponding to over 99.98% of RefSeq (Wheeler et al. Nucleic Acids Res 28, 10-4 (2000)) introns was used.
  • the insert size was determined using an Agilent 2100 Bioanalyzer prior to data analysis, and it was found that this insert size agreed closely with software predictions. An insert size standard deviation of 20 bases was chosen in order to match the most common band size cut from gels during library preparation.
  • Cufflinks Aligned reads from TopHat were assembled into sample-specific transcriptomes with Cufflinks version 0.8.2 (Mar. 26, 2010) (Trapnell et al., Nat Biotechnol 28, 511-5). Cufflinks assembles exonic and splice-junction reads into transcripts using their alignment coordinates. To limit false positive assemblies a maximum intronic length of 300 kb, corresponding to the 99.93% percentile of known introns was used. After assembling transcripts, Cufflinks computes isoform-level abundances by finding a parsimonious allocation of reads to the transcripts within a locus. Transcripts with abundance less than 15% of the major transcript in the locus, and minor isoforms with abundance less than 5% of the major isoform were filtered. Default settings were used for the remaining parameters.
  • the Cufflinks assembly stage yielded a set of transcript annotations for each of the sequenced libraries.
  • the transcripts were partitioned by chromosome and the Cuffcompare utility provided by Cufflinks was used to merge the transcripts into a combined set of annotations.
  • the Cuffcompare program performs a union of all transcripts by merging transcripts that share all introns and exons. The 5′ and 3′ exons of transcripts were allowed to vary by up to 100 nt during the comparison process.
  • Cuffcompare reported a total of 8.25 million distinct transcripts. Manual inspection of these transcripts in known protein coding gene regions indicated that most of the transcripts were likely to be poor quality reconstructions of overlapping larger transcripts. Also, many of the transcripts were unspliced and had a total length smaller than the size selected fragment length of approximately ⁇ 250 nt. Furthermore, many of these transcripts were only present in a single sample. A statistical classifier to predict transcripts over background signal was designed to identify highly recurrent transcripts that may be altered in prostate cancer. AceView (Gold-Mieg et al. Genome Biol 7 Suppl 1, S12 1-14 (2006)) were used.
  • the statistical classifier predicted a total 2.88 million (34.9%) transcript fragments as “expressed” transcripts.
  • a program was developed to extend and merge intron-redundant transcripts to produce a minimum set of transcripts that describes the assemblies produced by Cufflinks.
  • the merging step produced a total of 123,554 independent transcripts. Tanscript abundance levels were re-computed for these revised transcripts in Reads per Kilobase per Million (RPKM) units. These expression levels were used for the remainder of the study.
  • RPKM Kilobase per Million
  • Transcripts that lacked a completely unambiguous genomic DNA stretch of at least 40 nt were also removed. Genomic uniqueness was measured using the Rosetta uniqueness track downloaded from the UCSC genome browser website. Transcripts that were not present in at least 5% of the cohort (>5 samples) at more than 5.0 RPKM were retained.
  • transcripts were observed that were interrupted by poorly mappable genomic regions. Additionally, for low abundance genes fragmentation due to the lack of splice junction or paired-end read evidence needed to connect nearby fragments were observed.
  • the difference in the Pearson correlation between expression of randomly chosen exons on the same transcript versus expression of spatially proximal exons on different transcripts was measured and it was found that in the cohort, a Pearson correlation >0.8 had a positive predictive value (PPV) of >95% for distinct exons to be part of the same transcript.
  • PPV positive predictive value
  • transcripts produced by the bioinformatics pipeline were classified by comparison with a comprehensive list of “annotated” transcripts from UCSC, RefSeq, ENCODE, Vega, and Ensembl.
  • transcripts corresponding to processed pseudogenes were separated. This was done to circumvent a known source of bias in the TopHat read aligner.
  • TopHat maps reads to genomic DNA in its first step, predisposing exon-exon junction reads to align to their spliced retroposed pseudogene homologues.
  • transcripts with >1 bp of overlap with at least one annotated gene on the correct strand were designated “annotated”, and the remainder were deemed “unannotated”.
  • Transcripts with no overlap with protein coding genes were subdivided into intronic, intergenic, or partially intronic antisense categories based on their relative genomic locations.
  • transcripts into “repeat” and “non-repeat” transcripts the genomic DNA corresponding to the transcript exons was extracted and the fraction of repeat-masked nucleotides in each sequence were calculated.
  • RepMask 3.2.7 UCSC Genome Browser track was used. It was observed that transcripts enriched with repetitive DNA tended to be poorly conserved and lacked ChIP-seq marks of active chromatin ( FIG. 12 ). Transcripts containing >25% repetitive DNA ( FIG. 11 ) were separated for the purposes of the ChIP-seq and conservation analyses discussed below.
  • the SiPhy package (Garber et al. Bioinformatics 25, i54-62 (2009)) was used to estimate the locate rate of variation (w) of all non-repetitive transcript exons across 29 placental mammals. The program was run as described on the SiPhy website.
  • H3K4me3-H3K36me3 chromatin signature used to identify lincRNAs was determined from the peak coordinates by associating each H3K4me3 peak with the closest H3K36me3-enriched region up to a maximum of 10 kb away.
  • the enhancer signature was determined by subtracting the set of overlapping H3K4me3 peaks from the entire set of H3K4me1 peaks.
  • a modified COPA analysis was performed on the 81 tissue samples in the cohort. RPKM expression values were used and shifted by 1.0 in order to avoid division by zero.
  • the COPA analysis had the following steps (MacDonald & Ghosh, Bioinformatics 22, 2950-1 (2006); Tomlins et al. Science 310, 644-8 (2005)): 1) gene expression values were median centered, using the median expression value for the gene across the all samples in the cohort. This sets the gene's median to zero. 2) The median absolute deviation (MAD) was calculated for each gene, and then each gene expression value was scaled by its MAD. 3) The 80, 85, 90, 98 percentiles of the transformed expression values were calculated for each gene and the average of those four values was taken.
  • genes were rank ordered according to this “average percentile”, which generated a list of outliers genes arranged by importance. 4) Finally, genes showing an outlier profile in the benign samples were discarded.
  • Six novel transcripts ranked as both outliers and differentially-expressed genes in the analyses. These six were manually classified either as differentially-expressed or outlier status based on what each individual's distribution across samples indicated.
  • each exon was padded by ⁇ 0 bp, 50 bp, 100 bp, or 500 bp of additional genomic sequence before intersecting the exons with repeat elements in the RepeatMasker 3.2.7 database. It was observed that padding by more than 50 bp did not improve enrichment results and padded exons by ⁇ 50 bp in subsequent analyses and tests. Finally, the Shapiro-Wilk test for normality was performed and it was verified that the number of matches to highly abundant repetitive element types was approximately normally distributed.
  • RNA-Seq Transcriptome sequencing
  • transcriptome was compared to the UCSC, Ensembl, Refseq, Vega, and ENCODE gene databases to identify and categorize transcripts. While the majority of the transcripts (77.3%) corresponded to annotated protein coding genes (72.1%) and noncoding RNAs (5.2%), a significant percentage (19.8%) lacked any overlap and were designated “unannotated” ( FIG. 1 a ). These included partially intronic antisense (2.44%), totally intronic (12.1%), and intergenic transcripts (5.25%).
  • non-repeat transcripts showed strong enrichment for histone marks of active transcription at their putative transcriptional start sites (TSSs), repeat-associated transcripts showed virtually no enrichment ( FIG. 12 ), and for the remaining ChIP-Seq analyses non-repeat transcripts only were considered.
  • TSSs putative transcriptional start sites
  • FIG. 12 ChIP-Seq analyses non-repeat transcripts only were considered.
  • strong enrichment for histone modifications characterizing TSSs and active transcription including H3K4me2, H3K4me3, Acetyl-H3 and RNA Polymerase II ( FIG. 1 d - g ) but not H3K4me1 was observed, which characterizes enhancer regions ( FIGS. 13 and 14 ).
  • Intergenic ncRNAs performed much better in these analyses than intronic ncRNAs ( FIG.
  • ncRNAs represented 7.4% of differentially-expressed genes, including the ncRNA PCA334, which resides within an intron of the PRUNE2 gene and ranked #4 overall (12.2 fold change; adj. p ⁇ 2 ⁇ 10-4, Wilcoxon rank sum test, Benjamini-Hochberg correction) ( FIG. 8 ). Finally, 9.8% of differentially-expressed genes corresponded to unannotated ncRNAs, including 3.2% within gene introns and 6.6% in intergenic regions, indicating that these species contribute significantly to the complexity of the prostate cancer transcriptome.
  • RNA-Seq library generation Methods for RNA-Seq library generation.
  • PCAT-14 but not PCAT-109 or PCAT-43, also showed differential expression when tested on a panel of matched tumor-normal samples, indicating that this transcript, which is comprised of an endogenous retrovirus in the HERV-K family (Bannert and Kurth, Proc Natl Acad Sci USA 101 Suppl 2, 14572 (2004)), can be used as a somatic marker for prostate cancer ( FIG. 19 ).
  • 5′ and 3′ rapid amplification of cDNA ends (RACE) at this locus revealed the presence of individual viral protein open reading frames (ORFs) and a transcript splicing together individual ORF 5′ untranslated region (UTR) sequences ( FIG. 20 ).
  • ncRNA resided in the chromosome 8q24 gene desert nearby to the c-Myc oncogene.
  • This ncRNA termed PCAT-1, is located on the edge of the prostate cancer susceptibility region 240-43 ( FIG. 4 a ) and is about 0.5 Mb away from c-Myc.
  • This transcript is supported by clear peaks in H3K4me3, Acetyl-H3, and RNA polymerase II ChIP-Seq data ( FIG. 4 b ).
  • the exon-exon junction in cell lines was validated by RT-PCR and Sanger sequencing of the junction ( FIG. 4 c ), and 5 ′ and 3′ RACE was performed to elucidate transcript structure ( FIG.
  • PCAT-1 is a mariner family transposase (Oosumi et al., Nature 378 (6558), 672 (1995); Robertson et al., Nat Genet. 12 (4), 360 (1996)) interrupted by an Alu retrotransposon and regulated by a viral long terminal repeat (LTR) promoter region ( FIG. 4 d and FIG. 21 ).
  • LTR long terminal repeat
  • PCAT-1 expression is specific to prostate tissue, with striking upregulation in prostate cancers and metastases compared to benign prostate tissue ( FIG. 4 e ).
  • PCAT-1 ranks as the second best overall prostate cancer biomarker, just behind AMACR (Table 3), indicating that this transcript is a powerful discriminator of this disease.
  • RNA interference was performed in VCaP cells using custom siRNAs targeting PCAT-1 sequences and no change in the cell proliferation or invasion upon PCAT-1 knockdown was observed ( FIG. 22 )
  • RNA-Seq platforms enable discovery and quantification of specific transposable elements expressed in cancer. As described above, it was observed that >50% of unannotated exons in the assembly overlap with at least one repetitive element ( FIG. 11 ). Since these elements pose mappability challenges when performing transcriptome assembly with unique reads, these loci typically appear as “mountain ranges” of expression, with uniquely mappable regions forming peaks of expression separated by unmappable “ravines” ( FIGS. 23 and 24 ). PCR and Sanger sequencing experiments were performed to confirm that these transposable elements of low mappability are expressed as part of these loci ( FIGS. 23 and 24 ).
  • SChLAP1 Second Chromosome Locus Associated with Prostate-1
  • FIG. 34 shows detection of prostate cancer RNAs in patient urine samples using qPCR. All RNA species were detectable in urine.
  • FIG. 35 shows that multiplexing urine SChLAP-1 measurements with serum PSA improves prostate cancer risk stratification. Individually, SChLAP-1 is a predictor for prostate cancers with intermediate or high clinical risk of aggressiveness. Multiplexing this measurement with serum PSA improves upon serum PSA's ability to predict for more aggressive disease.
  • FIG. 29 demonstrates that PCAT-1 expression sensitizes prostate cancer cells to treatment with PARP-1 inhibitors.
  • FIG. 30 demonstrates that PCAT-1 expression sensitizes prostate cells to radiation treatment.
  • FIG. 31 demonstrates that unannotated intergeic transcripts in SChLAP-1 differentiate prostate cancer and benign samples.
  • FIG. 32 demonstrates that SChLAP-1 is required for prostate cancer cell invasion and proliferation. Prostate cell lines, but not non-prostate cells, showed a reduction in invasion by Boyden chamber assays. EZH2 and non-targeting siRNAs served as positive and negative controls, respectively. Deletion analysis of SChLAP-1 was performed.
  • FIG. 33 shows that a region essential for its function was identified.
  • FIG. 36 Analysis of the lung cancer transcriptome ( FIG. 36 ) was performed. 38 lung cell lines were analyzed by RNA-Seq and then lncRNA transcripts were reconstructed. Unannotated transcripts accounted for 27% of all transcripts. Novel transcripts well more highly expressed than annotated ncRNAs but not protein-coding transcripts. An outlier analyses of 13 unannotated transcripts shows novel lncRNAs in subtypes of lung cancer cell lines.
  • FIG. 37 shows discovery of M41 and ENST-75 ncRNAs in lung cancer.
  • FIG. 38 shows that lncRNAs are drivers and biomarkers in lung cancer.
  • FIG. 39 shows identification of cancer-associated lncRNAs in breast and pancreatic cancer.
  • RNA-Seq data Three novel breast cancer lncRNAs were nominated from RNA-Seq data (TU0011194, TU0019356, and TU0024146. All show outlier expression patterns in breast cancer samples but not benign samples.
  • Three novel pancreatic cancer lncRNAs were nominated from RNA-Seq data (TU0009141, TU0062051, and TU0021861). All show outlier expression patterns in pancreatic cancer samples but not benign samples.
  • TU_0078322_0 chr12 32280254-32260805 4.52 6.82 ncRNA UPREG.
  • TU_0101270_0 chr21 41853044-41875166 9.82 6.79 PROTEIN UPREG.
  • TU_0027326_0 chrX 26874726-17077384 3.31 6.79 PROTEIN UPREG.
  • TU_0092114_0 chr11 60223535-60239968 7.48 6.65 PROTEIN UPREG.
  • TU_0044448_0 chr13 51509122-51537893 4.77 6.59 PROTEIN UPREG.
  • TU_0080728_0 chr12 120142512-120219979 3.26 6.13 PROTEIN UPREG.
  • TU_0123088_0 chr2 238164428-238165452 4.22 6.12
  • PROTEIN UPREG TU_0101111_0 chr21: 36989329-37045253 4.04 6.04
  • PROTEIN UPREG TU_0090152_0 chr11: 4965638-4969515 8.38 5.99
  • TU_0045026_0 chr13 94680907-94668260 3.68 5.97 ncRNA UPREG.
  • TU_0101274_0 chr21 41869930-41870631 8.95 5.88 PROTEIN UPREG.
  • TU_0046239_0 chr4 1181913-1189142 4.28 5.87 NOVEL UPREG.
  • TU_0101308_0 chr21 42605257-42608791 4.97 5.83 PROTEIN UPREG.
  • TU_0084137_0 chr5 13981150-13997615 3.91 5.80
  • TU_0084127_0 chr9 13882635-13892514 4.95
  • TU_0101119_0 chr22 37034016-37045253 3.56
  • TU_0054919_0 chr16 88188842-88191143 3.48
  • TU_0126563_0 chr2 172658361-172662549 27.56 5.88 PROTEIN UPREG.
  • TU_0044977_0 chr13 94524392-94621526 3.64 5.64 PROTEIN UPREG.
  • TU_0052614_0 chr16 20542057-20818514 8.85 5.63 NOVEL UPREG.
  • TU_00 _0 chr5 15839476-15955226 7.46 5.61
  • TU_0060406_0 chr1 28134091-28158290 3.03
  • TU_0060407_0 chr1 28155047-28175469 2.41 5.60 ncRNA UPREG.
  • TU_0100252_0 chr9 96357168-96369978 5.00 5.58 PROTEIN UPREG.
  • TU_0034719_0 chr14 73490756-73555773 2.51 5.57 PROTEIN UPREG.
  • TU_0070457_0 chr20 2258975-2269890 6.49 5.56 NOVEL UPREG.
  • TU_0114240_0 chr2 1534883-1538193 5.25 5.54
  • TU_0087676_0 chr5 138643394-138648458 2.75 5.50 PROTEIN UPREG.
  • TU_0084138_0 chr5 13976388-13981285 4.03 5.48 ncRNA UPREG.
  • TU_0046237_0 chr4 1162036-1195588 4.29 5.47 ncRNA UPREG.
  • TU_0060421_0 chr1 38157480-28158290 3.12 5.44 PROTEIN UPREG.
  • TU_0061436_0 chr1 37954250-37957136 2.66 5.41
  • TU_0044894_0 chr13 94476096-94752898 2.85 5.38 PROTEIN UPREG.
  • TU_0043059_0 chr13 94638351-94639152 2.93 5.28 ncRNA UPREG.
  • TU_0075807_0 chr10 101676895-101680649 2.61 5.27
  • TU_0078255_0 chr12 12150992-32421799 3.02 5.26
  • TU_0103019_0 chr9 87826642-87905011 2.77 5.22
  • TU_0046244_0 chr4 1185645-1216291 3.51 5.21 PROTEIN UPREG.
  • TU_0075664_0 chr10 98752046-98935267 4.15 5.20 PROTEIN UPREG.
  • TU_0090949_0 chr11 24475021-25059245 3.50 5.19 NOVEL UPREG.
  • TU_0099864_0 chr8 128094589-128103681 3.56 5.17
  • TU_0030278_0 chr8 106690714-106735138 3.52 5.16
  • TU_0090128_0 chr11 4654012-4675667 5.26 5.15 PROTEIN UPREG.
  • TU_0049368_0 chr4 106772318-106772770 3.40 5.03 PROTEIN UPREG.
  • TU_0115204_0 chr2 27175274-27195587 2.37 4.99
  • TU_0115205_0 chr2 27163593-27178264 2.49 4.98
  • TU_0062443_0 chr1 46418568-46424753 1.95 4.96
  • TU_0072027_0 chr20 35064872-36007156 3.91 4.95 ncRNA UPREG.
  • TU_0086706_0 chr5 116818427-116835522 2.91 4.92 PROTEIN UPREG.
  • TU_0084136_0 chr5 13972327-13976415 3.37 4.91
  • TU_0042761_0 chr13 23200813-23363662 3.54 4.90
  • TU_0114168_0 chr15 99658271-99847175 2.25 4.89 ncRNA UPREG.
  • TU_0018764_0 chr17 71650143-71652049 6.28 4.86 PROTEIN UPREG.
  • TU_0085832_0 chr5 76150810-78167655 3.54 4.86 NOVEL UPREG.
  • TU_0030142_0 chr11 4748677-4760103 12.08 4.86 PROTEIN UPREG.
  • TU_0103018_0 chr9 87745936-87851451 2.41 4.83 NOVEL UPREG.
  • TU_0096472_0 chr11 133844590-133862924 6.85 4.82 PROTEIN UPREG.
  • TU_0023229_0 chrX 70349443-70377690 2.34 4.81 NOVEL UPREG.
  • TU_0084305_0 chr5 15836315-15947088 5.37 4.78 PROTEIN UPREG.
  • TU_0024934_0 chr19 54352845-54407356 1.88 4.77 NOVEL UPREG.
  • TU_0095473_0 chr11 133844590-133852395 6.96 4.76 ncRNA UPREG.
  • TU_0003239_0 chr7 7362390-7537552 3.00 4.73 PROTEIN UPREG.
  • TU_0000022_0 chr6 1567540-2190842 2.14 4.72 PROTEIN UPREG.
  • TU_0085193_0 chr3 145122471-145183544 2.72 4.72 PROTEIN UPREG.
  • TU_0061439_0 chr1 37954250-37971671 2.46 4.71 ncRNA UPREG.
  • TU_0096470_0 chr11 133841573-133880753 6.44 4.70 PROTEIN UPREG.
  • TU_0046219_0 chr4 993725-995190 3.50 4.69 NOVEL UPREG.
  • TU_0078788_0 chr12 32393283-32405731 2.47 4.67 PROTEIN UPREG.
  • TU_0101115_0 chr21 37000839-37005920 3.31 4.67 NOVEL UPREG.
  • TU_0099884_0 chr8 128301493-128307578 2.65 4.56
  • TU_0008459_0 chr7 23885581-23708358 1.70 4.54
  • PROTEIN UPREG TU_0042767_0 chr13: 23186656-23204319 4.82 4.64 PROTEIN UPREG.
  • TU_0061430_0 chr1 37930752-37957012 2.30 4.64 PROTEIN UPREG.
  • TU_0079451_0 chr12 52696814-52736068 3.77 4.64 PROTEIN UPREG.
  • TU_0069545_0 chr2 226711356-226712534 2.36 4.63 PROTEIN UPREG.
  • TU_0045837_0 chr1 113151233-118151444 3.73 4.61 PROTEIN UPREG.
  • TU_0101138_0 chr21 18994126-37804810 3.54 4.61 PROTEIN UPREG.
  • TU_0049362_0 chr4 106693102106771686 3.06 4.58 PROTEIN UPREG.
  • TU_0055044_0 chr16 88589437-88613428 2.23 4.55 PROTEIN UPREG.
  • TU_0038605_0 chr3 52689830-52704551 1.54 4.55 ncRNA UPREG.
  • TU_0062653_0 chr1 51756544-51799759 2.52 4.54 PROTEIN UPREG.
  • TU_0080359_0 chr12 63512292-65558861 1.87 4.53 PROTEIN UPREG.
  • TU_0012481_0 chr7 111155336-111217889 2.04
  • TU_0076356_0 chr10 116970327-116995963 10.34
  • TU_0099892_0 chr8 128817416-128822629 2.33 4.51 ncRNA UPREG.
  • TU_0060484_0 chr1 38766931-28707187 2.53 4.51 PROTEIN UPREG.
  • TU_0046732_0 chr4 1147069-1175181 2.75 4.50 PROTEIN UPREG.
  • TU_0107858_0 chr22 40664589-40573116 2.27 4.50 PROTEIN UPREG.
  • TU_0042794_0 chr13 23228583-25228659 3.47 4.49
  • TU_0057850_0 chr1 1523259-1525323 2.80 4.48
  • TU_0023156_0 chr1 40109515-40127909 2.56 4.48 PROTEIN UPREG.
  • TU_0102821_0 chr9 78263916-78312152 2.98 4.48 PROTEIN UPREG.
  • TU_0081653_0 chr12 108638297-108780791 2.90 4.47 PROTEIN UPREG.
  • TU_0049370_0 chr4 106776991-106847637 2.15 4.47 PROTEIN UPREG.
  • TU_0047672_0 chr4 41807710-41840313 2.51 4.47 PROTEIN UPREG.
  • TU_0114959_0 chr2 24865850-24869912 1.68 4.46 PROTEIN UPREG.
  • TU_0037043_0 chr3 13332730-13436812 1.77 4.46 PROTEIN UPREG.
  • TU_0087443_0 chr5 135257637-135247034 4.09 4.46 PROTEIN UPREG.
  • TU_0086635_0 chr5 114489075-114543906 2.02 4.43 PROTEIN UPREG.
  • TU_0107859_0 chr22 40664589-40665721 2.38 4.42 NOVEL UPREG.
  • TU_0067165_0 chr3 160797907-160845987 1.81 4.40 PROTEIN UPREG.
  • TU_0020146_0 chr10 3728970-3737293 2.53 4.39 PROTEIN UPREG.
  • TU_0107642_0 chr22 39046992-39047479 1.69 4.38 PROTEIN UPREG.
  • TU_0016185_0 chr17 31415814-31422953 3.69 4.38 NOVEL UPREG.
  • TU_0104717_0 chr9 130697833-130698832 2.79 4.36 PROTEIN UPREG.
  • TU_0052105_0 chr16 4785874-4786488 2.99 4.36 PROTEIN UPREG.
  • TU_0058663_0 chr1 21795295-21850855 1.99 4.35 PROTEIN UPREG.
  • TU_0108056_0 chr22 43527112-46638770 1.74 4.34 PROTEIN UPREG.
  • TU_0098781_0 chr11 67151991-67154057 2.48 4.33 PROTEIN UPREG.
  • TU_0085924_0 chr5 126233852-126241807 2.89 4.32 PROTEIN UPREG.
  • TU_0048191_0 chr4 72423780-72424347 2.93 4.32 PROTEIN UPREG.
  • TU_0034727_0 chr14 73508223-73508442 2.29 4.32 PROTEIN UPREG.
  • TU_0096297_0 chr11 128342286-128353900 1.84 4.31 PROTEIN UPREG.
  • TU_0007829_0 chr2 3625233-4275129 4.39 4.30 PROTEIN UPREG.
  • TU_0115216_0 chr2 27179274-27177799 2.02 4.27 PROTEIN UPREG.
  • TU_0018409_0 chr17 66013419-65059811 2.02 4.26 PROTEIN UPREG.
  • TU_0090847_0 chr8 126511614-126519830 2.75 4.25 PROTEIN UPREG.
  • TU_0035182_0 chr14 81062781-81063412 2.22 4.25 PROTEIN UPREG.
  • TU_0040936_0 chr3 155391785-155458298 2.10 4.26 PROTEIN UPREG.
  • TU_0027558_0 chrX 23595491-23614435 1.66 4.25 PROTEIN UPREG.
  • TU_0076460_0 chr10 121248954-121292235 1.68 4.24 PROTEIN UPREG.
  • TU_0067170_0 chr1 160826739-1608726994 2.10 4.23 PROTEIN UPREG.
  • TU_0303050_0 chr9 89409881-89512477 2.30 4.23 PROTEIN UPREG.
  • TU_0090960_0 chr11 25059388-25060757 3.85 4.23 PROTEIN UPREG.
  • TU_0072165_0 chr20 40142077-40204030 4.69 4.22 PROTEIN UPREG.
  • TU_0044687_0 chr13 74756644-74954891 2.04 4.21 ncRNA UPREG.
  • TU_0096477_0 chr11 133479414-133850753 4.43 4.21 PROTEIN UPREG.
  • TU_0093947_0 chr11 68208575-68215218 1.41 4.20 PROTEIN UPREG.
  • TU_0103253_0 chr9 96405246-96442373 1.69 4.20 PROTEIN UPREG.
  • TU_0091863_0 chr11 57008498-57039966 2.69 4.20 PROTEIN UPREG.
  • TU_0106199_0 chr22 18300042-15014411 3.94 4.20 NOVEL UPREG.
  • TU_0090140_0 chr11 4748163-4759145 6.33 4.20 PROTEIN UPREG.
  • TU_0103051_0 chr9 89302442-89405899 2.37 4.19 NOVEL UPREG.
  • TU_0078290_0 chr12 32594534-32410838 3.20 4.19 PROTEIN UPREG.
  • TU_0029336_0 chrX 70869659-70712461 1.70 4.18 PROTEIN UPREG.
  • TU_0092155_0 chr11 60871597-60886554 1.80 4.18 PROTEIN UPREG.
  • TU_0095597_0 chr11 114549577-114880335 1.75 4.18 PROTEIN UPREG.
  • TU_0079770_0 chr12 55040665-55042824 4.25 4.16 PROTEIN UPREG.
  • TU_0000263_0 chr6 4060929-4080831 1.56 4.16 NOVEL UPREG.
  • TU_0040394_0 chr3 133418532-133441282 3.46 4.16 PROTEIN UPREG.
  • TU_0066594_0 chr1 15424543-154257368 1.40 4.15 PROTEIN UPREG.
  • TU_0099852_0 chr8 126515081-126519830 2.81 4.15 PROTEIN UPREG.
  • TU_0100363_0 chr8 144891741-144899588 2.24 4.14 PROTEIN UPREG.
  • TU_0095461_0 chr11 133751095-133757235 2.10 4.13 ncRNA UPREG.
  • TU_0044488_0 chr13 51641093-51641310 2.76 4.13 PROTEIN UPREG.
  • TU_0048990_0 chr4 95592056-95804933 2.30 4.13 NOVEL UPREG.
  • TU_0078293_0 chr12 12396393-32414822 2.90 4.13 PROTEIN UPREG.
  • TU_0046202_0 chr4 991841-1010686 2.57 4.12 PROTEIN UPREG.
  • TU_0091866_0 chr11 57008498-57010253 2.54 4.12 PROTEIN UPREG.
  • TU_0011133_0 chr7 94378726-94759741 1.77 4.12 PROTEIN UPREG.
  • TU_0122941_0 chr2 234410713-234427931 3.28 4.12 PROTEIN UPREG.
  • TU_0084131_0 chr5 13929880-13953380 2.62 4.12 NOVEL UPREG.
  • TU_0084142_0 chr5 14017046-14021379 3.59 4.11 PROTEIN UPREG.
  • TU_0087955_0 chr5 140931545-140931565 2.00 4.10 PROTEIN UPREG.
  • TU_0085953_0 chr5 79410392-79410389 3.35 4.10
  • TU_0022288_0 chr19 18357973-18360121 2.75 4.09 PROTEIN UPREG.
  • TU_0085951_0 chr5 79366959-79414885 3.01 4.09 PROTEIN UPREG.
  • TU_0060849_0 chr1 32572021-32574435 1.81 4.09 PROTEIN UPREG.
  • TU_0087441_0 chr5 134934290-134942617 2.74 4.09 PROTEIN UPREG.
  • TU_0042725_0 chr13 23148223-23200551 4.96 4.09 PROTEIN UPREG.
  • TU_0039018_0 chr3 66510505-66634168 1.68 4.08 PROTEIN UPREG.
  • TU_0022290_0 chr19 18357973-18359195 2.64 4.07 PROTEIN UPREG.
  • TU_0100684_0 chr8 146190487-146191030 1.89 4.06 PROTEIN UPREG.
  • TU_0042974_0 chr13 26148671-2614967 2.81 4.06 NOVEL UPREG.
  • TU_0084308_0 chr5 15938753-15949124 4.08 4.06 NOVEL UPREG.
  • TU_0082746_0 chr12 120197102-120197416 4.97 4.06 PROTEIN UPREG.
  • TU_0014355_0 chr17 2650561-2887730 1.92 4.05 PROTEIN UPREG.
  • TU_0114110_0 chr15 99250537-99274351 2.01 4.05 PROTEIN UPREG.
  • TU_0096341_0 chr11 129534843-129585464 1.54 4.04 PROTEIN UPREG.
  • TU_0052083_0 chr16 4784094-4805339 2.71 4.04 NOVEL UPREG.
  • TU_0078296_0 chr12 32394534-32405549 2.92 4.04 PROTEIN UPREG.
  • TU_0084126_0 chr5 13892443-13903812 3.64 4.03 NOVEL UPREG.
  • TU_0047312_0 chr4 39217669-39222163 3.83 4.02 PROTEIN UPREG.
  • TU_0008287_0 chr7 8119340-8268973 1.65 4.02 PROTEIN UPREG.
  • TU_0018937_0 chr17 73714011-73714967 1.61 4.01 PROTEIN UPREG.
  • TU_0048995_0 chr4 95805027-95808417 2.47 4.00 PROTEIN UPREG.
  • TU_0038694_0 chr3 53810226-53855769 2.03 3.99 ncRNA UPREG.
  • TU_0046233_0 chr4 1202157-1232168 2.45 3.99 PROTEIN UPREG.
  • TU_0019018_0 chr17 75372094-75381243 2.25 3.98 PROTEIN UPREG.
  • TU_0042326_0 chr 199123974-199125319 1.77 3.98 PROTEIN UPREG.
  • TU_0099893_0 chr8 128817416-128819105 2.23 3.98 PROTEIN UPREG.
  • TU_0012491_0 chr7 111304238-111362856 1.91 3.98 PROTEIN UPREG.
  • TU_0112385_0 chr15 70816880-70864494 1.71 3.97 PROTEIN UPREG.
  • TU_0042964_0 chr4 57020861-57038533 1.74 3.97 PROTEIN UPREG.
  • TU_0052565_0 chr1 19862784-19409995 1.98 3.96 NOVEL UPREG.
  • TU_0042717_0 chr13 25149908-23200198 4.95 3.96 PROTEIN UPREG.
  • TU_0017374_0 chr17 43300055-43404182 1.53 3.96 PROTEIN UPREG.
  • TU_0071058_0 chr20 20318209-20549154 2.02 3.96 PROTEIN UPREG.
  • TU_0105741_0 chrY 6971017-6998339 2.20 3.95 PROTEIN UPREG.
  • TU_0018995_0 chr17 74491566-74517485 1.64 3.94
  • TU_0103055_0 chr9 89512509-8 513285 1.92 3.93
  • TU_0041139_0 chr3 171237964-171285906 1.91 3.93 PROTEIN UPREG.
  • TU_0042325_0 chr3 199124975-199143480 1.74 3.93 PROTEIN UPREG.
  • TU_0020688_0 chr19 8180054-8237335 1.80 3.93 PROTEIN UPREG.
  • TU_0118314_0 chr2 90086923-99100654 1.78 3.92 PROTEIN UPREG.
  • TU_0017875_0 chr17 54652767-54706896 2.33 3.92 PROTEIN UPREG.
  • TU_0037277_0 chr3 24134438-24511318 1.75 3.92 PROTEIN UPREG.
  • TU_004759 _0 chr4 40445539-40457235 1.90 3.91 PROTEIN UPREG.
  • TU_0114108_0 chr15 99235494-99274389 2.00 3.91 ncRNA UPREG.
  • TU_0024530_0 chr19 50889160-50909766 1.72 3.91 PROTEIN UPREG.
  • TU_0008957_0 chr7 88308886-38325338 2.62 3.91 PROTEIN UPREG.
  • TU_0043122_0 chr13 28983555-28989371 1.73 3.90 PROTEIN UPREG.
  • TU_0076644_0 chr10 127398227-127398596 2.06 3.90 PROTEIN UPREG.
  • TU_0045423_0 chr13 10055877-100125079 2.02 3.89 PROTEIN UPREG.
  • TU_0045495_0 chr13 107720446-107737194 2.08 3.88 PROTEIN UPREG.
  • TU_0088857_0 chr5 172259171-172275517 1.69 3.87 NOVEL UPREG.
  • TU_0044453_0 chr13 51505777-51524522 2.95 3.86 NOVEL UPREG.
  • TU_0047380_0 chr4 39217641-39222163 3.43 3.86 PROTEIN UPREG.
  • TU_0100838_0 chr21 30508275-30510244 2.43 3.86 NOVEL UPREG.
  • TU_0100275_0 chr8 144520506-144537551 2.11 3.85 PROTEIN UPREG.
  • TU_0057466_0 chr18 72853744-72866791 1.58 3.84 PROTEIN UPREG.
  • TU_0040010_0 chr3 126331839-126412928 2.16 3.84 PROTEIN UPREG.
  • TU_0042800_0 chr13 23360816-23370548 2.73 3.84 PROTEIN UPREG.
  • TU_0112501_0 chr2 74065748-74174193 1.71 3.83 PROTEIN UPREG.
  • TU_0053389_0 chr1 45673980-45701001 2.66 3.83 PROTEIN UPREG.
  • TU_0087944_0 chr11 140874777-140978925 1.47 3.83 PROTEIN UPREG.
  • TU_0017393_0 chr17 43389397-43390800 1.90 3.82 PROTEIN UPREG.
  • TU_0008919_0 chr7 38257158-38271020 1.93 3.82 PROTEIN UPREG.
  • TU_0088393_0 chr14 50259793-50367616 1.51 3.82 PROTEIN UPREG.
  • TU_0049911_0 chr4 139304784-139382952 2.48 3.82 PROTEIN UPREG.
  • TU_0024366_0 chr19 50100808-50104487 1.88 3.82 PROTEIN UPREG.
  • TU_0070109_0 chr1 243979271-244159914 1.56 3.81 PROTEIN UPREG.
  • TU_0120975_0 chr2 182104651-182107832 1.89 3.80 NOVEL UPREG.
  • PROTEIN UPREG TU_0103689_0 chr9: 111019219-111122750 1.75 3.80 PROTEIN UPREG.
  • TU_0096460_0 chr11 133734857-133786962 2.09 3.79 PROTEIN UPREG.
  • TU_0071115_0 chr20 24934888-24986948 1.48 3.79 PROTEIN UPREG.
  • TU_0093788_0 chr11 67153661-67153870 2.48 3.79 PROTEIN UPREG.
  • TU_0112336_0 chr15 70880765-70838345 1.83 3.78 PROTEIN UPREG.
  • TU_0086664_0 chr1 154481433-154485049 2.29 3.78 PROTEIN UPREG.
  • TU_0018812_0 chr17 72119376-72151549 3.38 3.78 PROTEIN UPREG.
  • TU_0110225_0 chr15 48510091-48912722 3.60 3.78 ncRNA UPREG.
  • TU_0054545_0 chr16 79431010-79431652 10.28 3.78 PROTEIN UPREG.
  • TU_0107643_0 chr22 39072496-39093168 1.36 3.78 PROTEIN UPREG.
  • TU_0112004_0 chr18 67644390-67650387 3.56 3.76 PROTEIN UPREG.
  • TU_0043118_0 chr13 28981555-29067829 1.76 3.76 NOVEL UPREG.
  • TU_0112003_0 chr15 67645590-67775246 3.12 3.76 NOVEL UPREG.
  • TU_0060448_0 chr1 28438629-28450150 2.23 3.75 PROTEIN UPREG.
  • TU_0122972_0 chr2 236068012-236482693 1.69 3.75 NOVEL UPREG.
  • TU_0106545_0 chr22 22218478-22219162 3.99 3.74 PROTEIN UPREG.
  • TU_0087288_0 chr5 133755241-133766074 1.85 3.74 ncRNA UPREG.
  • TU_0025312_0 chr19 57059515-57145170 1.89 3.74 PROTEIN UPREG.
  • TU_0079679_0 chr12 54760142-54783545 1.58 3.73 PROTEIN UPREG.
  • TU_0074564_0 chr10 64241786-64246112 2.62 3.73 PROTEIN UPREG.
  • TU_0106189_0 chr22 18235213-18328816 1.82 3.73 PROTEIN UPREG.
  • TU_0078994_0 chr12 49412412-49428706 1.41 3.72 ncRNA UPREG.
  • TU_0003229_0 chr6 41598975-41621874 2.05 3.72 PROTEIN UPREG.
  • TU_0040937_0 chr3 155439710-155458293 1.96 3.72 PROTEIN UPREG.
  • TU_0040093_0 chr5 128880751-128874336 1.87 3.72 NOVEL UPREG.
  • TU_0106542_0 chr22 22213315-22220505 3.77 3.71 PROTEIN UPREG.
  • TU_0019375_0 chr17 77608812-77816980 1.63 3.71 PROTEIN UPREG.
  • TU_0042568_0 chr15 20264762-20334986 1.85 3.71 PROTEIN UPREG.
  • TU_0103386_0 chr9 99895734-99118148 1.89 3.71 PROTEIN UPREG.
  • TU_0030004_0 chrX 100534013-100534540 1.84 3.71 NOVEL UPREG.
  • TU_0089906_0 chr11 1042845-1045785 2.94 3.71 NOVEL UPREG.
  • TU_0089014_0 chr9 176014905-176015351 2.01 3.71 ncRNA UPREG.
  • TU_0056173_0 chr18 22525074-22557627 3.31 3.70 PROTEIN UPREG.
  • TU_0052880_0 chr16 28393117-28411069 1.48 3.70 PROTEIN UPREG.
  • TU_0100355_0 chr8 144884230-144910177 2.00 3.69 PROTEIN UPREG.
  • TU_0096216_0 chr11 125271293-125271517 2.08 3.69 PROTEIN UPREG.
  • TU_0092161_0 chr11 60884289-60892364 1.99 3.68
  • TU_0086926_0 chr5 126241958-126394149 2.27 3.68 NOVEL UPREG.
  • TU_0088230_0 chr5 148864170-148864752 1.94 3.68 ncRNA UPREG.
  • TU_0099940_0 chr8 129855546-129182684 1.61 3.68 PROTEIN UPREG.
  • TU_0089017_0 chr5 176222085-176240501 10.21 3.67 PROTEIN UPREG.
  • TU_0078586_0 chr12 46643629-46648944 1.47 3.67 PROTEIN UPREG.
  • TU_0053467_0 chr16 51028455-51138080 2.19 3.67 PROTEIN UPREG.
  • TU_0089452_0 chr5 179258704-179258997 1.62 3.67 PROTEIN UPREG.
  • TU_0076329_0 chr10 115501382-115531028 2.60 3.67 PROTEIN UPREG.
  • TU_0047688_0 chr4 42105164-42354144 1.68 3.67 PROTEIN UPREG.
  • TU_0059142_0 chr1 16203274-16206548 12.41 3.67 PROTEIN UPREG.
  • TU_0116906_0 chr2 63155968-53138462 2.81 3.66 PROTEIN UPREG.
  • TU_0000154_0 chr6 3063923-3099152 1.53 3.66 PROTEIN UPREG.
  • TU_0088782_0 chr5 170625426-170659598 1.78 3.66 NOVEL UPREG.
  • TU_0089905_0 chr11 1042845-1045785 2.77 3.66 PROTEIN UPREG.
  • TU_0101704_0 chr9 3265495-3516005 2.33 3.64 ncRNA UPREG.
  • TU_0044897_0 chr15 94746498-94760688 2.17 3.64 PROTEIN UPREG.
  • TU_0071059_0 chr20 20549245-20641260 2.39 3.64 ncRNA UPREG.
  • TU_0046268_0 chr4 1199698-1211108 1.93 3.63 PROTEIN UPREG.
  • TU_0100378_0 chr8 144899799-144900640 2.00 3.62 NOVEL UPREG.
  • TU_0112025_0 chr15 67780574-67782345 3.42 3.62 PROTEIN UPREG.
  • TU_0106031_0 chr22 16336630-16412806 2.01 3.62 PROTEIN UPREG.
  • TU_0050785_0 chr4 174895560-174453821 2.38 3.61 PROTEIN UPREG.
  • TU_0058834_0 chr1 11768665-11783670 1.50 3.61 PROTEIN UPREG.
  • TU_0039496_0 chr3 106753939-106754201 1.99 3.61 ncRNA UPREG.
  • TU_0098397_0 chr8 69379259-69406175 2.73 3.61 PROTEIN UPREG.
  • TU_0017847_0 chr17 54188675-54413808 2.82 3.61 PROTEIN UPREG.
  • TU_0108299_0 chr22 49267227-49270226 2.03 3.60 PROTEIN UPREG.
  • TU_0076846_0 chr10 135042714-155056676 2.27 3.59 PROTEIN UPREG.
  • TU_0096351_0 chr11 129611827-129689996 1.61 3.59 PROTEIN UPREG.
  • TU_0019298_0 chr17 77242472-77300154 1.51 3.59 PROTEIN UPREG.
  • TU_0057465_0 chr18 72830973-729737 9 1.55 3.59 PROTEIN UPREG.
  • TU_0013475_0 chr2 148137800-148212387 1.74 3.59 PROTEIN UPREG.
  • TU_00 1426_0 chr6 28688044-28662198 2.58 3.59 NOVEL UPREG.
  • TU_0089137_0 chr5 176814485-176815986 1.93 3.57 PROTEIN UPREG.
  • TU_0098700_0 chr8 87 06988-82333612 1.76 3.57 PROTEIN UPREG.
  • TU_0093785_0 chr11 67186209-67198838 3.74 3.57 NOVEL UPREG.
  • TU_0067222_0 chr1 164063363-194147501 1.63 3.57 PROTEIN UPREG.
  • TU_0052172_0 chr16 8799176-8790379 1.61 3.57 PROTEIN UPREG.
  • TU_0008350_0 chr7 16852301-16712672 1.45 3.57 PROTEIN UPREG.
  • TU_0035610_0 chr14 935 0687-93582188 2.08 3.56 PROTEIN UPREG.
  • TU_0000168_0 chr6 3100128-3102765 2.10 3.56 PROTEIN UPREG.
  • TU_0019649_0 chr3 115180992-115164502 1.72 3.56 PROTEIN UPREG.
  • TU_0052843_0 chr16 27143818-27187907 1.42 3.56 NOVEL UPREG.
  • TU_00 499_0 chr7 24236191-24236455 5.44 3.54 PROTEIN UPREG.
  • TU_0100172_0 chr8 142471307-142511866 1.79 3.54 NOVEL UPREG.
  • TU_0085543_0 chr5 110311813-110312092 1.53 3.53 PROTEIN UPREG.
  • TU_0072450_0 chr20 44161989 -44747359 1.83 3.53 NOVEL UPREG.
  • TU_0094972_0 chr15 94755980-94759735 2.15 3.53 PROTEIN UPREG.
  • TU_0093950_0 chr11 6 21474 -68215218 1.49 3.53 PROTEIN UPREG.
  • TU_0006239_0 chr6 13864933 -133671427 2.22 3.53 PROTEIN UPREG.
  • TU_0063894_0 chr1 150944684-150070988 1.54 3.52 PROTEIN UPREG.
  • TU_0078675_0 chr12 47602047-47602939 1.58 3.52 PROTEIN UPREG.
  • TU_0052150_0 chr16 8799176-65-64674 1.42 3.52 NOVEL UPREG.
  • TU_0112011_0 chr15 67762926-67783593 2.66 3.52 PROTEIN UPREG.
  • TU_0041581_0 chr3 185450132-185459240 1.77 3.52 PROTEIN UPREG.
  • TU_0017269_0 chr17 42127174-421 9979 1.59 3.52 PROTEIN UPREG.
  • TU_010138_0 chr6 94055563-94056963 1.61 3.52 PROTEIN UPREG.
  • TU_0078683_0 chr12 47503989-47604485 1.69 3.52 PROTEIN UPREG.
  • TU_0099209_0 chr11 6453771-6453210 1.44 3.51 ncRNA UPREG.
  • TU_004519 _0 chr15 97851959-97852689 1.98 3.51 PROTEIN UPREG.
  • TU_0050499_0 chr4 159862572-156862939 1.82 3.51 PROTEIN UPREG.
  • TU_0052554_0 chr16 10329285-19424714 1.78 3.51 PROTEIN UPREG.
  • TU_0085663_0 chr5 70918890-75990273 2.39 3.51 PROTEIN UPREG.
  • TU_0101238_0 chr21 41610496-41851888 1.89 3.50
  • TU_0098659_0 chr8 82355436-82355877 4.15 3.49
  • TU_0100271_0 chr8 144522379-144537551 1.33 3.49 PROTEIN UPREG.
  • TU_0013258_0 chr7 139750340-139773086 1.85 3.49 PROTEIN UPREG.
  • TU_0122559_0 chr2 224338108-224338327 2.32 3.49 PROTEIN UPREG.
  • TU_0062947_0 chr1 212567070-212567723 1.74 3.48 PROTEIN UPREG.
  • TU_0101300_0 chr21 42512421-42593934 1.60 3.48 PROTEIN UPREG.
  • TU_0105268_0 chr3 1382318731-138277254 1.49 3.47 PROTEIN UPREG.
  • TU_0080269_0 chr12 62524730-62664317 2.05 3.47 PROTEIN UPREG.
  • TU_0051992_0 chr6 31939105-31955076 1.56 3.47 PROTEIN UPREG.
  • TU_0018485_0 chr17 76458432-70490451 1.58 3.47 ncRNA UPREG.
  • TU_0050493_0 chr1 28705947-28706605 1.60 2.46 PROTEIN UPREG.
  • TU_0085975_0 chr5 79478814-79495113 1.91 3.46 PROTEIN UPREG.
  • TU_0018919_0 chr17 73678343-73714570 1.48 3.46 ncRNA UPREG.
  • TU_0054534_0 chr16 79404014-79431652 9.85 3.46 PROTEIN UPREG.
  • TU_0076107_0 chr10 104464315-104488075 1.67 3.45 ncRNA UPREG.
  • TU_0069658_0 chr1 229724782-229731269 1.75 3.45 NOVEL UPREG.
  • TU_0120387_0 chr2 170267824-170281385 2.10 3.45 PROTEIN UPREG.
  • TU_0013665_0 chr17 24073407-24077926 1.52 3.45 ncRNA UPREG.
  • TU_0070414_0 chr20 3254059-1303172 1.65 3.45 NOVEL UPREG.
  • TU_0012495_0 chr7 111373031-111411626 2.29 3.45 PROTEIN UPREG.
  • TU_0076659_0 chr10 177514501-127576128 1.31 3.45 PROTEIN UPREG.
  • TU_0088525_0 chr5 156525701-156755173 1.53 3.45 PROTEIN UPREG.
  • TU_0046096_0 chr4 759449-809939 2.01 3.44 ncRNA UPREG.
  • TU_0074332_0 chr10 43420869-43421283 1.52 3.44 PROTEIN UPREG.
  • TU_0082983_0 chr12 121778239-121779189 2.65 3.44 PROTEIN UPREG.
  • TU_0008361_0 chr2 16750923-16790805 1.58 3.44 PROTEIN UPREG.
  • TU_0081443_0 chr1 38032067-38039550 1.67 3.44 PROTEIN UPREG.
  • TU_0042715_0 chr13 25148223-23204319 3.68 3.43 ncRNA UPREG.
  • TU_0119128_0 chr2 118310197-118313068 1.62 3.43 PROTEIN UPREG.
  • TU_0112349_0 chr15 70834440-70835126 1.67 3.43 PROTEIN UPREG.
  • TU_0027543_0 chrX 21921233-21922374 2.48 3.43 PROTEIN UPREG.
  • TU_0082552_0 chr1 47889058-47552320 1.83 3.43 ncRNA UPREG.
  • TU_0080791_0 chr4 174322695-174323924 2.13 3.41 PROTEIN UPREG.
  • TU_0048346_0 chr4 77175264-77176185 2.48 3.41 NOVEL UPREG.
  • TU_0093068_0 chr11 64956618-64961189 2.13 3.41 PROTEIN UPREG.
  • TU_0033869_0 chr14 60248258-60250801 1.71 3.41 PROTEIN UPREG.
  • TU_0000031_0 chr6 2190031-2190908 2.44 3.41 PROTEIN UPREG.
  • TU_0082131_0 chr12 111152572-111152227 1.89 3.40 PROTEIN UPREG.
  • TU_0038169_0 chr3 49035494-49041923 1.35 3.40 NOVEL UPREG.
  • TU_0044898_0 chr13 94753009-94760688 2.11 3.40 PROTEIN UPREG.
  • TU_0089144_0 chrS 176814485-176815986 1.86 3.40 PROTEIN UPREG.
  • TU_0094504_0 chr11 74812477-74817273 2.40 3.40 PROTEIN UPREG.
  • TU_0035633_0 chr14 94304291-94305127 2.17 3.40 PROTEIN UPREG.
  • TU_0085819_0 chrS 75734806-76039614 1.64 3.40 PROTEIN UPREG.
  • TU_0061431_0 chr1 37961347-37973585 2.62 3.40 NOVEL UPREG.
  • TU_0078299_0 chr12 32290896-32292169 3.67 3.39 PROTEIN UPREG.
  • TU_0004059_0 chr6 52976578-53054598 1.65 3.39 PROTEIN UPREG.
  • TU_0098927_0 chr8 95722432-95788870 1.48 3.39 ncRNA UPREG.
  • TU_0013856_0 chr7 155957953-156090620 2.50 3.39 PROTEIN UPREG.
  • TU_0068377_0 chr1 201452418-201458956 1.84 3.39 NOVEL UPREG.
  • TU_0062957_0 chr1 54089897-54128073 1.43 3.39 PROTEIN UPREG.
  • TU_0099854_0 chr8 127633901-127639897 1.65 3.38 PROTEIN UPREG.
  • TU_0048743_0 chr4 87924751-87955166 1.47 3.38 PROTEIN UPREG.
  • TU_0086478_0 chr5 102510255-102521832 1.95 3.38 PROTEIN UPREG.
  • TU_0120565_0 chr2 172672776-172675279 4.31 3.38 PROTEIN UPREG.
  • TU_0122360_0 chr2 219554051-219557439 2.92 3.38 PROTEIN UPREG.
  • TU_0092154_0 chr11 60857271-60874474 1.44 3.37 PROTEIN UPREG.
  • TU_0015718_0 chr17 24095069-24100305 1.64 3.37 PROTEIN UPREG.
  • TU_0039284_0 chr3 95208686-95249573 2.23 3.37 PROTEIN UPREG.
  • TU_0082089_0 chr12 111082307-111187476 1.44 3.37 PROTEIN UPREG.
  • TU_0035148_0 chr14 81009021-81069951 1.64 3.37 PROTEIN UPREG.
  • TU_0054849_0 chr16 87403253-87406669 1.47 3.37 PROTEIN UPREG.
  • TU_0113376_0 chr15 87432650-87545107 2.13 3.36 PROTEIN UPREG.
  • TU_0019481_0 chr17 77998514-77999441 1.55 3.36 PROTEIN UPREG.
  • TU_0007004_0 chr6 158396021-158440190 1.47 3.36 PROTEIN UPREG.
  • TU_0092190_0 chr11 60876795-60877493 1.85 3.36 ncRNA UPREG.
  • TU_0001996_0 chr6 31941546-31959679 1.43 3.36 NOVEL UPREG.
  • TU_0066689_0 chr1 154509233-154510967 1.61 3.36 PROTEIN UPREG.
  • TU_0035151_0 chr14 81015445-81021875 2.00 3.35
  • TU_0092866_0 chr11 55975211-63975675 3.20 3.35 PROTEIN UPREG.
  • TU_0050482_0 chr4 156807332-156877628 1.69 3.35 PROTEIN UPREG.
  • TU_0087465_0 chr5 136431191-136431490 2.47 3.35 PROTEIN UPREG.
  • TU_0058703_0 chr1 10857547-10613394 0.66 ⁇ 3.37 NOVEL DOWNREG.
  • TU_0084922_0 chrS 44337219-44338127 0.51 ⁇ 3.37
  • TU_0067333_0 chr1 167362572-167539064 0.68 ⁇ 3.
  • TU_0031101_0 chrX 134247418-134254372 0.69 ⁇ 3.37 PROTEIN DOWNREG.
  • TU_0063762_0 chr1 87666944-87583813 0.66 ⁇ 3.38
  • PROTEIN DOWNREG. TU_0107584_0 chr22: 38075931-38123808 0.66 ⁇ 3.38
  • PROTEIN DOWNREG. TU_0102296_0 chr9: 34979701-34988409 0.57 ⁇ 3.38
  • TU_0038485_0 chr3 51981847-51958558 0.65 ⁇ 3.38
  • PROTEIN DOWNREG. TU_0062948_0 chr1: 53744574-53746867 0.48 ⁇ 3.38 PROTEIN DOWNREG.
  • TU_0030147_0 chrx 102727067-102729284 0.65 ⁇ 3.39 NOVEL DOWNREG.
  • TU_0030209_0 chrx 103250961-103253228 0.68 ⁇ 3.39 ncRNA DOWNREG.
  • TU_0068206_0 chr1 200132176-200134973 0.60 ⁇ 3.39 PROTEIN DOWNREG.
  • TU_0088194_0 chr2 200132176-200182322 0.59 ⁇ 3.40 PROTEIN DOWNREG.
  • TU_0049308_0 chr4 104220026-104220361 0.46 ⁇ 3.40 NOVEL DOWNREG.
  • TU_0068431_0 chr1 202350966-202363482 0.62 ⁇ 3.
  • TU_0073506_0 chr10 7630096-7723984 0.60 ⁇ 3.
  • TU_0012556_0 chr7 115934290-115935899 0.50 ⁇ 3.41 PROTEIN DOWNREG.
  • TU_0018647_0 chr17 71259157-71294839 0.74 ⁇ 3.41 NOVEL DOWNREG.
  • TU_0030577_0 chrX 118036531-118035860 0.43 ⁇ 3.41 PROTEIN DOWNREG.
  • TU_0089981_0 chr11 2248339-2247566 0.52 ⁇ 3.41 PROTEIN DOWNREG.
  • TU_0000858_0 chr6 19947236-19950403 0.56 ⁇ 3.41 PROTEIN DOWNREG.
  • TU_0002212_0 chr8 32224073-32229328 0.58 ⁇ 3.41 PROTEIN DOWNREG.
  • TU_0024749_0 chr10 52937559-52939100 0.58 ⁇ 3.41 PROTEIN DOWNREG.
  • TU_0102225_0 chr21 40161189-10181418 0.52 ⁇ 3.41 ncRNA DOWNREG.
  • TU_0100030_0 chrX 134893580-134659310 0.41 ⁇ 3.41 PROTEIN DOWNREG.
  • TU_0102256_0 chr9 34356684-34366854 0.56 ⁇ 3.41 PROTEIN DOWNREG.
  • TU_0039040_0 chr3 69107066-69108860 0.62 ⁇ 3.42 ncRAN DOWNREG.
  • TU_0115808_0 chr2 37722515-37725828 0.61 ⁇ 3.42 PROTEIN DOWNREG.
  • TU_0115807_0 chr2 37722515-37729828 0.61 ⁇ 3.42 NOVEL DOWNREG.
  • TU_0038811_0 chr8 57890130-58970834 0.43 ⁇ 3.43 PROTEIN DOWNREG.
  • TU_0065120_0 chr1 144274405-144279906 0.53 ⁇ 3.43 PROTEIN DOWNREG.
  • TU_0065093_0 chr1 144167535-144181746 0.72 ⁇ 3.43 PROTEIN DOWNREG.
  • TU_0066887_0 chr1 158352167-158370985 0.56 ⁇ 3.44 PROTEIN DOWNREG.
  • TU_0034681_0 chr14 75248251-73250867 0.61 ⁇ 3.44 PROTEIN DOWNREG.
  • TU_0064872_0 chr1 115373945-115394701 0.60 ⁇ 3.44 PROTEIN DOWNREG.
  • TU_0115146_0 chr2 26806070-26809827 0.49 ⁇ 3.44 PROTEIN DOWNREG.
  • TU_0102372_0 chr9 35672000-35681306 0.58 ⁇ 3.46 PROTEIN DOWNREG.
  • TU_0040491_0 chr3 134987802-134980829 0.35 ⁇ 3.46
  • TU_0063025_0 chr1 54832256-54849445 0.56 ⁇ 3.46
  • TU_0073672_0 chr12 65272841-55276238 0.78 ⁇ 3.47 NOVEL DOWNREG.
  • TU_0072214_0 chr20 42166331-42122501 0.45 ⁇ 3.47
  • TU_0069254_0 chr3 223745864-223750945 0.54 ⁇ 3.48
  • TU_0014474_0 chr17 4410320-4410814 0.34 ⁇ 3.48
  • TU_0082036_0 chr6 31975375-31977685 0.61 ⁇ 3.48 ncRNA DOWNREG.
  • TU_0115605_0 chr2 37722515-37727509 0.64 ⁇ 3.48 PROTEIN DOWNREG.
  • TU_0075679_0 chr10 96987317-970405910 0.65 ⁇ 3.48 PROTEIN DOWNREG.
  • TU_0108979_0 chr15 34659121-34889737 0.68 ⁇ 3.48 PRTEIN DOWNREG.
  • TU_0039868_0 chr3 123526763-123543198 0.51 ⁇ 3.48
  • TU_0032236_0 chr14 22839081-22833882 0.61 ⁇ 3.48
  • TU_0103902_0 chr9 115957988-116128421 0.59 ⁇ 3.49 PROTEIN DOWNREG.
  • TU_0064251_0 chr6 71589234-71069482 0.38 ⁇ 3.49 PROTEIN DOWNREG.
  • TU_0116344_0 chr2 27568254-27571682 0.64 ⁇ 3.49 NOVEL DOWNREG.
  • TU_0096307_0 chr11 7977293-7976927 0.69 ⁇ 3.49 NOVEL DOWNREG.
  • TU_0014009_0 chr2 158823186-158930217 0.48 ⁇ 3.50 PROTEIN DOWNREG.
  • TU_0111467_0 chr15 62817064-62854842 0.58 ⁇ 3.50 NOVEL DOWNREG.
  • TU_0058552_0 chr6 257103852-157120456 0.64 ⁇ 3.50 PROTEIN DOWNREG.
  • TU_0016616_0 chr17 36992068-37034423 0.44 ⁇ 3.50 PROTEIN DOWNREG.
  • TU_0083744_0 chr5 236838-297985 0.58 ⁇ 3.51 PROTEIN DOWNREG.
  • TU_0038899_0 chr3 58465926-58495812 0.58 ⁇ 3.51 PROTEIN DOWNREG.
  • TU_0018817_0 chr17 72185287-72184800 0.61 ⁇ 3.51 PROTEIN DOWNREG.
  • TU_0096362_0 chr11 129779777-129794214 0.56 ⁇ 3.51 ncRNA DOWNREG.
  • TU_0104765_0 chr9 131134480-131144297 0.53 ⁇ 3.51 PROTEIN DOWNREG.
  • TU_0047809_0 chr4 52581019-52582331 0.62 ⁇ 3.52 PROTEIN DOWNREG.
  • TU_0114638_0 chr2 11804195-11654972 0.68 ⁇ 3.52 PROTEIN DOWNREG.
  • TU_0110215_0 chr15 43246574-43254766 0.63 ⁇ 3.52
  • TU_0117024_0 chr2 66525747-66653430 0.61 ⁇ 3.52
  • TU_0109004_0 chr15 39178588-35180010 0.39 ⁇ 3.53 PROTEIN DOWNREG.
  • TU_0114005_0 chr15 97462760-97493368 0.56 ⁇ 3.53 PROTEIN DOWNREG.
  • TU_0079534_0 chr12 53260191-53268540 0.41 ⁇ 3.53 PROTEIN DOWNREG.
  • TU_0068435_0 chr1 202366748-202385528 0.62 ⁇ 3.53 PROTEIN DOWNREG.
  • TU_0014730_0 chr17 7034460-7061662 0.61 ⁇ 3.53 PROTEIN DOWNREG.
  • TU_0079355_0 chr12 51906987-51912605 0.54 ⁇ 3.54 PROTEIN DOWNREG.
  • TU_0107389_0 chr22 36670710-36671784 0.59 ⁇ 3.54 PROTEIN DOWNREG.
  • TU_0105434_0 chr9 138991774-138996018 0.54 ⁇ 3.54 ncRNA DOWNREG.
  • TU_0122441_0 chr2 220000172-220002664 0.38 ⁇ 3.54
  • TU_0114819_0 chr2 23779564-23785016 0.65 ⁇ 3.55 PROTEIN DOWNREG.
  • TU_0013666_0 chr7 150180552-150189309 0.34 ⁇ 3.55 PROTEIN DOWNREG.
  • TU_0036844_0 chr3 9930878-9933062 0.54 ⁇ 3.56
  • TU_0014467_0 chr17: 4407802-4410614 0.49 ⁇ 3.56 NOVEL DOWNREG.
  • TU_0061867_0 chr1 41618433-41621890 0.61 ⁇ 3.57 PROTEIN DOWNREG.
  • TU_0090901_0 chr11 20081238-20099725 0.60 ⁇ 3.57 PROTEIN DOWNREG.
  • TU_0089503_0 chr5 179949721-179951068 0.47 ⁇ 3.57 NOVEL DOWNREG.
  • TU_0052454_0 chr16 15702084-15702374 0.40 ⁇ 3.57 PROTEIN DOWNREG.
  • TU_0004248_0 chr6 70983350-71069482 0.52 ⁇ 3.57 PROTEIN DOWNREG.
  • TU_0111118_0 chr15 58426685-58428568 0.59 ⁇ 3.58
  • TU_0047256_0 chr4 38781223-38804733 0.63 ⁇ 3.58
  • TU_0092308_0 chr11 61385022-61325568 0.62 ⁇ 3.58 PROTEIN DOWNREG.
  • TU_0037381_0 chr3 33159367-33165995 0.70 ⁇ 3.59 PROTEIN DOWNREG.
  • TU_0088765_0 chr5 168737435-169749043 0.53 ⁇ 3.60
  • PROTEIN DOWNREG. TU_0039072_0 chr3: 70098064-70100160 0.63 ⁇ 3.60 NOVEL DOWNREG.
  • TU_0112059_0 chr15 69667695-69691724 0.41 ⁇ 3.60
  • TU_0030975_0 chrX 130235170-130235814 0.49 ⁇ 3.
  • TU_0038532_0 chr3 52258212-52287726 0.77 ⁇ 3.60 PROTEIN DOWNREG.
  • TU_0014418_0 chr17 3748115-3749717 0.39 ⁇ 3.60
  • PROTEIN DOWNREG. TU_0081986_0 chr6: 31791087-31793378 0.48 ⁇ 3.61
  • PROTEIN DOWNREG. TU_0111109_0 chr15: 53426655-58477514 0.86 ⁇ 3.61
  • PROTEIN DOWNREG. TU_0064151_0 chr1: 98933815-98937074 0.46 ⁇ 3.61
  • PROTEIN DOWNREG. TU_0111253_0 chr15: 81121812-61151157 0.63 ⁇ 3.61 PROTEIN DOWNREG.
  • TU_0058947_0 chr1 13782811-13817026 0.61 ⁇ 3.62 PROTEIN DOWNREG.
  • TU_0031484_0 chrX 151890690-151832673 0.59 ⁇ 3.62 PROTEIN DOWNREG.
  • TU_0076212_0 chr10 105781059-105835687 0.47 ⁇ 3.62 PROTEIN DOWNREG.
  • TU_0029358_0 chrX 71268703-71268507 0.66 ⁇ 3.63 PROTEIN DOWNREG.
  • TU_0065339_0 chr1 148457403-148475104 0.56 ⁇ 3.65 PROTEIN DOWNREG.
  • TU_0063769_0 chr1 87583567-87587259 0.58 ⁇ 3.65 NOVEL DOWNREG.
  • TU_0103872_0 chr9 115178483-115203441 0.59 ⁇ 3.63 PROTEIN DOWNREG.
  • TU_0050244_0 chr4 148585059-148685550 0.63 ⁇ 3.63 PROTEIN DOWNREG.
  • TU_0031913_0 chr14 20554755-20563715 0.64 ⁇ 3.63 PROTEIN DOWNREG.
  • TU_0065343_0 chr1 148501147-148501585 0.37 ⁇ 3.63 PROTEIN DOWNREG.
  • TU_0090542_0 chr11 8672475-8549482 0.64 ⁇ 3.64 PROTEIN DOWNREG.
  • TU_0038056_0 chr9 48563574-48623119 0.68 ⁇ 3.65 PROTEIN DOWNREG.
  • TU_0022088_0 chr10 168647988-16923718 0.55 ⁇ 3.65 ncRNA DOWNREG.
  • TU_0088408_0 chr12 129197899-129212499 0.58 ⁇ 3.85 PROTEIN DOWNREG.
  • TU_0046595_0 chr4 3264594-3411502 0.68 ⁇ 3.65 PROTEIN DOWNREG.
  • TU_0039476_0 chr8 108331106-108578694 0.58 ⁇ 3.66 PROTEIN DOWNREG.
  • TU_0091498_0 chr11 46834081-46889744 0.65 ⁇ 3.
  • TU_0098359_0 chr8 68585438-64499042 0.45 ⁇ 3.
  • TU_0046627_0 chr4 3795533-3740037 0.45 ⁇ 3.67 NOVEL DOWNREG.
  • TU_0103946_0 chr9 116821701-116822181 0.48 ⁇ 3.67 PROTEIN DOWNREG.
  • TU_0112386_0 chr15: 71818130-71820041 0.55 ⁇ 3.71 PROTEIN DOWNREG.
  • TU_0111315_0 chr15: 61676589-61681634 0.55 ⁇ 3.72 PROTEIN DOWNREG.
  • TU_0111311_0 chr15 61676589-61681634 0.55 ⁇ 3.72 PROTEIN DOWNREG.
  • TU_0023241_0 chr19 40856254-40861198 0.41 ⁇ 3.72 PROTEIN DOWNREG.
  • TU_0068139_0 chr8 199127296-199147465 0.42 ⁇ 3.72 ncRNA DOWNREG.
  • TU_0102684_0 chr9 70336502-70344481 0.56 ⁇ 3.73 PROTEIN DOWNREG.
  • TU_0068764_0 chr1 207854842-207892483 0.49 ⁇ 3.73 PROTEIN DOWNREG.
  • TU_0053636_0 chr18 55846971-55853340 0.58 ⁇ 3.74 PROTEIN DOWNREG.
  • TU_0084025_0 chr5 6501949-6545706 0.54 ⁇ 3.74 NOVEL DOWNREG.
  • TU_0032151_0 chr14 22508055-22508830 0.58 ⁇ 3.74 PROTEIN DOWNREG.
  • TU_0076124_0 chr10 104619299-104651033 0.60 ⁇ 3.75 PROTEIN DOWNREG.
  • TU_0063298_0 chr1 62474433-62474872 0.36 ⁇ 3.78
  • PROTEIN DOWNREG TU_0100861_0 chr21: 32604246-32608457 0.62 ⁇ 3.79
  • PROTEIN DOWNREG TU_0101015_0 chr21: 35010886-35012375 0.55 ⁇ 3.79
  • ncRNA DOWNREG TU_0081086_0 chrX: 133993992-133995935 0.73 ⁇ 3.79 PROTEIN DOWNREG.
  • TU_0068759_0 chr1 207669209-207672813 0.45 ⁇ 3.79 NOVEL DOWNREG.
  • TU_0069253_0 chr1 223741202-223745600 0.62 ⁇ 3.79 PROTEIN DOWNREG.
  • TU_0020150_0 chr19 3877291-3879097 0.52 ⁇ 3.79 ncRNA DOWNREG.
  • TU_0084059_0 chr5 9599140-9608833 0.50 ⁇ 3.80
  • TU_0016922_0 chr17 38430856-38435173 0.51 ⁇ 3.80
  • TU_0013053_0 chr7 134114695-134205949 0.58 ⁇ 3.81 PROTEIN DOWNREG.
  • TU_0016578_0 chr17 35883208-35884855 0.52 ⁇ 3.82 PROTEIN DOWNREG.
  • TU_0101224_0 chr21 40161189-40223184 0.50 ⁇ 3.82 PROTEIN DOWNREG.
  • TU_0064871_0 chr1 115391459-115433611 0.59 ⁇ 3.83
  • TU_0097462_0 chr8 37773618-37822041 0.55 ⁇ 3.85 PROTEIN DOWNREG.
  • TU_0066742_0 chr1 154860755-154862200 0.42 ⁇ 3.83 PROTEIN DOWNREG.
  • TU_0090638_0 chr11 14242208-14246823 0.55 ⁇ 3.83 PROTEIN DOWNREG.
  • TU_0046628_0 chr4 3735533-3740037 0.46 ⁇ 3.83 PROTEIN DOWNREG.
  • TU_0024608_0 chr19 51842692-51911641 0.53 ⁇ 3.83
  • TU_0080097_0 chr12 55301840-55307803 0.56 ⁇ 3.85 PROTEIN DOWNREG.
  • TU_0062615_0 chr1 48974664-48997227 0.51 ⁇ 3.85
  • PROTEIN DOWNREG. TU_0013669_0 chr7: 150272983-150305963 0.52 ⁇ 3.
  • PROTEIN DOWNREG. TU_0102682_0 chr9: 70197177-70337519 0.56 ⁇ 3.
  • PROTEIN DOWNREG. TU_0104855_0 chr9: 131689287-131691419 0.64 ⁇ 3.
  • TU_0116336_0 chr2 48677181-48685259 0.65 ⁇ 3.86 PROTEIN DOWNREG.
  • TU_0080098_0 chr12 56302807-56307767 0.56 ⁇ 3.88 PROTEIN DOWNREG.
  • TU_0034421_0 chr14 68410559-68412495 0.62 ⁇ 3.88
  • TU_0016601_0 chr17 36911114-36929728 0.39 ⁇ 3.88
  • TU_0079221_0 chr12 51194638-51200498 0.43 ⁇ 3.89
  • TU_0112752_0 chr15 76184009-76210733 0.55 ⁇ 3.90 PROTEIN DOWNREG.
  • TU_0028410_0 chrX 48910899-48929704 0.68 ⁇ 3.91 PROTEIN DOWNREG.
  • TU_0076488_0 chr10 123227854-123347940 0.55 ⁇ 3.92 NOVEL DOWNREG.
  • TU_0093208_0 chr11 65396933-65397655 0.45 ⁇ 3.92 PROTEIN DOWNREG.
  • TU_0064620_0 chr1 111962701-112059304 0.61 ⁇ 3.92 PROTEIN DOWNREG.
  • TU_0027357_0 chrX 17728093-17737982 0.57 ⁇ 3.94
  • PROTEIN DOWNREG TU_0071013_0 chr20: 19141491-19652034 0.55 ⁇ 3.95
  • PROTEIN DOWNREG TU_0060281_0 chr1: 27204050-27211524 0.48 ⁇ 3.95
  • PROTEIN DOWNREG TU_0096007_0 chr11: 119482708-119514087 0.45 ⁇ 3.95 PROTEIN DOWNREG.
  • TU_0058810_0 chr1 11631006-11637486 0.50 ⁇ 3.95 ncRNA DOWNREG.
  • TU_0102668_0 chr9 67902293-67904671 0.52 ⁇ 3.96 PROTEIN DOWNREG.
  • TU_0103226_0 chr9 93524079-93559558 0.55 ⁇ 3.96 PROTEIN DOWNREG.
  • TU_0098334_0 chr8 68508843-68581618 0.43 ⁇ 3.96 NOVEL DOWNREG.
  • TU_0018887_0 chr17 73068191-73068655 0.29 ⁇ 3.97 PROTEIN DOWNREG.
  • TU_0065854_0 chr1 149850009-149852298 0.46 ⁇ 3.98 PROTEIN DOWNREG.
  • TU_0073443_0 chr10 5556713-3558609 0.43 ⁇ 3.99 PROTEIN DOWNREG.
  • TU_0030581_0 chrX 118096546-118104692 0.38 ⁇ 3.99 PROTEIN DOWNREG.
  • TU_0019780_0 chr 120 -120 0.55 ⁇ 4.00 PROTEIN DOWNREG.
  • TU_0081660_0 chr12 108705678-108718771 0.50 ⁇ 4.00 PROTEIN DOWNREG.
  • TU_0046397_0 chr4 2932589-2050090 0.46 ⁇ 4.00 PROTEIN DOWNREG.
  • TU_0122440_0 chr2 219991398-219999705 0.53 ⁇ 4.01 PROTEIN DOWNREG.
  • TU_0011534_0 chr7 99085437-99096154 0.36 ⁇ 4.01 PROTEIN DOWNREG.
  • TU_0047205_0 chr4 37815997-37817290 0.59 ⁇ 4.02 PROTEIN DOWNREG.
  • TU_0017005_0 chr17 39308253-39337366 0.52 ⁇ 4.02 PROTEIN DOWNREG.
  • TU_0052436_0 chr16 15704459-15858435 0.54 ⁇ 4.03 PROTEIN DOWNREG.
  • TU_0102657_0 chr9 67902293-67908869 0.54 ⁇ 4.04 PROTEIN DOWNREG.
  • TU_0088729_0 chr8 43825496-43526789 0.55 ⁇ 4.04 PROTEIN DOWNREG.
  • TU_0071246_0 chr20 29913077-29921837 0.42 ⁇ 4.05 NOVEL DOWNREG.
  • TU_0050224_0 chr4 147115887-147190781 0.25 ⁇ 4.06 PROTEIN DOWNREG.
  • TU_0110166_0 chr15 48172154-43198892 0.49 ⁇ 4.07 PROTEIN DOWNREG.
  • TU_0030085_0 chrX 101782933-101800062 0.56 ⁇ 4.07 PROTEIN DOWNREG.
  • TU_0021042_0 chr19 10435466-10441506 0.61 ⁇ 4.08 PROTEIN DOWNREG.
  • TU_0097463_0 chr8 37812227-37826549 0.58 ⁇ 4.08 PROTEIN DOWNREG.
  • TU_0101682_0 chr9 734412-736069 0.67 ⁇ 4.08 PROTEIN DOWNREG.
  • TU_0030157_0 chrX 102750729-102751737 0.44 ⁇ 4.09 NOVEL DOWNREG.
  • TU_0031424_0 chrX 149482223-149433104 0.47 ⁇ 4.
  • 10 PROTEIN DOWNREG. TU_0065603_0 chr1: 149275738-149286201 0.42 ⁇ 4.
  • 10 PROTEIN DOWNREG. TU_0037859_0 chr3: 45240966-45242817 0.49 ⁇ 4.11 PROTEIN DOWNREG.
  • TU_0162271_0 chr9 34511045-34512853 0.50 ⁇ 4.11 PROTEIN DOWNREG.
  • TU_0035605_0 chr14 95254401-93273368 0.49 ⁇ 4.11 PROTEIN DOWNREG.
  • TU_0064621_0 chr1 112047963-1120 0.54 ⁇ 4.11 ncRNA DOWNREG.
  • TU_0031098_0 chrX 134057388-134058604 0.47 ⁇ 4.11 PROTEIN DOWNREG.
  • TU_0018799_0 chr17 72061371-72080938 0.61 ⁇ 4.11 PROTEIN DOWNREG.
  • TU_0011129_0 chr7 94135058-94136943 0.41 ⁇ 4.11 NOVEL DOWNREG.
  • TU_0036396_0 chr14 104617328-104619095 0.41 ⁇ 4.12 PROTEIN DOWNREG.
  • TU_0056255_0 chr5 92944260-92956054 0.57 ⁇ 4.12 ncRNA DOWNREG.
  • TU_0074501_0 chr10 60429298-60431031 0.42 ⁇ 4.12 PROTEIN DOWNREG.
  • TU_0073757_0 chr10 17672347-17899481 0.56 ⁇ 4.13
  • TU_0015457_0 chr17 195 1898-19287156 0.45 ⁇ 4.13 PROTEIN DOWNREG.
  • TU_0122402_0 chr2 219821926-219824741 0.61 ⁇ 4.13 PROTEIN DOWNREG.
  • TU_0116618_0 chr2 60932830-60633902 0.49 ⁇ 4.13 PROTEIN DOWNREG.
  • TU_0029963_0 chrX 100220537-100238065 0.51 ⁇ 4.
  • TU_0028949_0 chrK 64964077-64878513 0.61 ⁇ 4.
  • TU_0082443_0 chr5 154178336-164210363 0.57 ⁇ 4.16 PROTEIN DOWNREG.
  • TU_0107372_0 chr22 36668731-36871784 0.56 ⁇ 4.17 PROTEIN DOWNREG.
  • TU_0105435_0 chr9 138997874-138999099 0.37 ⁇ 4.19 PROTEIN DOWNREG.
  • TU_0015445_0 chr17 19415396-19422513 0.46 ⁇ 4.
  • TU_0013012_0 chr17 74597027-74930278 0.42 ⁇ 4.21
  • TU_0048538_0 chr4 21336928-81344460 0.41 ⁇ 4.22
  • TU_0000013_0 chr6 1287191-1259372 0.36 ⁇ 4.29 PROTEIN DOWNREG.
  • TU_0120707_0 chr2 17686568-176869190 0.45 ⁇ 4.31 PROTEIN DOWNREG.
  • TU_0016744_0 chr17 37790358-37809206 0.54 ⁇ 4.31 PROTEIN DOWNREG.
  • TU_0096964_0 chr8 22027917-22043914 0.47 ⁇ 4.35 PROTEIN DOWNREG.
  • TU_0030062_0 chrX 101267701-101269091 0.41 ⁇ 4.35 ncRNA DOWNREG.
  • TU_0120713_0 chr2 176930391-176969560 0.49 ⁇ 4.35 PROTEIN DOWNREG.
  • TU_0011537_0 chr7 99589728-99111736 0.39 ⁇ 4.39
  • TU_0107366_0 chr22 36038731-36673469 0.54 ⁇ 4.39 PROTEIN DOWNREG.
  • TU_0065341_0 chr1 148496851-148500610 0.35 ⁇ 4.39 PROTEIN DOWNREG.
  • TU_0013076_0 chr17 12510065-12612990 0.50 ⁇ 4.
  • TU_0087752_0 chr5 199206352-199211418 0.44 ⁇ 4.
  • TU_0062566_0 chr1 47037330-47057598 0.43 ⁇ 4.42 PROTEIN DOWNREG.
  • TU_0018825_0 chr17 2192513-2192794 0.47 ⁇ 4.43 PROTEIN DOWNREG.
  • TU_0002566_0 chr6 55797424-55798978 0.37 ⁇ 4.44 PROTEIN DOWNREG.
  • TU_0074074_0 chr10 29814868-29815135 0.26 ⁇ 4.44 PROTEIN DOWNREG.
  • TU_0082372_0 chr12 116130336-116130610 0.41 ⁇ 4.47 ncRNA DOWNREG.
  • TU_0102658_0 chr9 67902293-67908683 0.46 ⁇ 4.48
  • PROTEIN DOWNREG. TU_0024160_0 chr19: 48777171-48778386 0.51 ⁇ 4.49
  • PROTEIN DOWNREG. TU_0031081_0 chrX: 133993992-134013925 0.64 ⁇ 4.49
  • PROTEIN DOWNREG. TU_0015447_0 chr17: 19421649-19423000 0.46 ⁇ 4.50 PROTEIN DOWNREG.
  • TU_0016834_0 chr17 38072130-38072515 0.54 ⁇ 4.50 PROTEIN DOWNREG.
  • TU_0120709_0 chr2 176677352-176697902 0.49 ⁇ 4.50 PROTEIN DOWNREG.
  • TU_0041205_0 chr3 171619688-171634575 0.48 ⁇ 4.53
  • TU_0110178_0 chr15 43196270-43241274 0.43 ⁇ 4.54
  • TU_0084473_0 chr1 110000292-110079791 0.51 ⁇ 4.58 ncRNA DOWNREG.
  • TU_0120715_0 chr2 176692475-176697902 0.50 ⁇ 4.58 PROTEIN DOWNREG.
  • TU_0110180_0 chr15 43196205-43243358 0.43 ⁇ 4.63 PROTEIN DOWNREG.
  • TU_0024922_0 chr19 54255568-54259943 0.42 ⁇ 4.64 ncRNA DOWNREG.
  • TU_0119818_0 chr2 38109039-38116939 0.32 ⁇ 4.64 ncRNA DOWNREG.
  • TU_0067289_0 chr1 166307141-166318970 0.48 ⁇ 4.69 NOVEL DOWNREG.
  • TU_0095765_0 chr11 117640504-117642734 0.36 ⁇ 4.69 PROTEIN DOWNREG.
  • TU_0058445_0 chr1 9017797-9040122 0.33 ⁇ 4.70 PROTEIN DOWNREG.
  • TU_0047068_0 chr4 23402764-23403824 0.41 ⁇ 4.72 PROTEIN DOWNREG.
  • TU_0018882_0 chr17 38260060-38263683 0.51 ⁇ 4.82 NOVEL DOWNREG.
  • TU_0110177_0 chr15 43196768-43245735 0.47 ⁇ 4.86 PROTEIN DOWNREG.
  • Table 8 shows the number of cancer-associated lncRNAs nominated for four major cancer types. The number validated is indicated in the column on the right. This table reflects ongoing efforts.
  • SChLAP-1 or control expressing cell lines were generated by cloning SChLAP-1 or control into the pLenti6 vector (Invitrogen). Stably-transfected RWPE, HME and MCF7 cells were selected using blasticidin (Invitrogen).
  • Stably-transfected RWPE, HME and MCF7 cells were selected using blasticidin (Invitrogen).
  • LNCAP and 22Rv1 cells with stable knockdown of SChLAP-1 cells were transfected with SChLAP-1 or non-targeting shRNA lentiviral constructs for 48 hours. GFP+ cells were drug-selected using puromycin.
  • RNA isolation and cDNA synthesis was performed according standard protocols. Quantitative PCR was performed using Power SYBR Green Mastermix (Applied Biosystems, Foster City, Calif.), using GAPDH and HMBS as housekeeping control genes. The relative quantity of the target gene was completed for each sample using the ⁇ Ct method.
  • Intracardiac injection model 5 ⁇ 10 5 cells were introduced to CB-17 severe combine immunodeficient mice (CB-17 SCID) at 6 weeks of age. Beginning one week post injection, bioluminescent imaging of mice was performed weekly using a CCD IVIS system with a 50-mm lens (Xenogen Corp.) and the results were analyzed using LivingImage software (Xenogen).
  • RIP assays were performed using a Millipore EZ-Magna RIP RNA-Binding Protein Immunoprecipitation kit (Millipore, #17-701) according to the manufacturer's instructions.
  • FFPE Formalin-fixed paraffin embedded
  • RNA-Seq has been used to profile >100 prostate cell lines and tissues, including both localized and metastatic prostate cancers (Prensner, et al. Nat Biotechnol 29, 742-749, (2011)). Given that only a fraction of prostate cancers present with aggressive clinical features (Cooperberg et al., J Clin Oncol 23, 8146-8151 (2005)), cancer outlier profile analysis (COPA; Tomlins et al., Tomlins, S. A. et al.
  • siRNA knockdowns of this gene was performed using two independent siRNAs as well as siRNA to EZH2, which is essential for cancer cell invasion (Kleer, et al. Proc Natl Acad Sci USA 100, 11606-11611, (2003); Varambally, S. et al. Nature 419, 624-629, (2002)) as a positive control.
  • knockdown of SChLAP-1 dramatically impaired cell invasion in vitro at a level comparable to EZH2 ( FIG. 41 a ).
  • SChLAP-1 knockdown also impaired cell proliferation in prostate cells but not nonprostate cells.
  • deletion constructs tiling every 250 bp were overexpressed in RWPE cells.
  • Deletion of a single 250 bp region (bp 1001-1250 for SChLAP-1 isoform #1) shared by all three major isoforms abrogated SChLAP-1 mediated invasion in RWPE ( FIG. 41 c ).
  • RNAfold22 of the SChLAP-1 RNA structure indicated the presence of a RNA hairpin in this region that is lost specifically in deletion construct #5 ( FIG. 41 d ), implicating this secondary structure in the function of the molecule.
  • SWI/SNF complex operates as a large, multi-protein system that utilizes ATPase enzymatic activity to physically move nucleosomes and, in doing so, regulates gene transcription (Roberts, C. W. & Orkin, S. H. Nat Rev Cancer 4, 133-142, (2004)).
  • SWI/SNF complex members are the target of recurrent, inactivating mutations in cancer, including ARID1A (Wiegand, K. C. et al. N Engl J Med 363, 1532-1543, (2010); Jones, S. et al. Science 330, 228-231 (2010)), PBRM1 (Varela, I. et al.
  • BRM also known as SMARCA2
  • BRG1 also known as SMARCA4
  • SNF5 also known as SMARCB1
  • Knockdown of BRM, BRG1, and SNF5 in two prostate cell lines, 22Rv1 and LNCaP, followed by expression microarray profiling generated highly overlapping sets of up- and down-regulated genes, demonstrating that these factors have broad commonalities in their function in prostate cells.
  • Knockdown of BRM, BRG1 and SNF5 also increased the invasiveness and proliferation rate of 22Rv1 cells, consistent with the role of SWI/SNF in tumor suppression.
  • Comparison of genes commonly regulated by knockdown of all SWI/SNF proteins (BRM, BRG1, and SNF5) to genes regulated by SChLAP1 demonstrated an antagonistic relationship where SChLAP1 knockdown affected the same genes as SWI/SNF but in the opposing direction ( FIG. 42 b ).
  • SChLAP-1-SWI/SNF interactions were tested by evaluating SChLAP-1-SNF5 binding in the RWPE-SChLAP-1 overexpression model, including overexpression of SChLAP-1 deletion construct #5, which failed to induce cell invasion ( FIG. 41 c ).
  • Overexpression of both SChLAP-1 isoform #1 and isoform #2 robustly bound to SNF5, whereas deletion construct 5 (which lacks bps 1001-1250 in SChLAP-1 isoform #1) failed to bind SNF5 ( FIG. 42 e ).
  • AK093002 and LOC145837 two lncRNAs upregulated in subsets of prostate cancer that are endogenously expressed in RWPE were measured.
  • Control RIP experiments for SNRNP70 demonstrated uniformly strong binding of this protein to U1 in all RWPE cell lines evaluated.
  • SChLAP-1 regulates SWI/SNF complex activity by directly binding to SWI/SNF proteins through an interaction dependent on base pairs 1001-1250 of the RNA.
  • EZH2 a known metastasis gene
  • PCA3 a lncRNA biomarker over-expressed in prostate cancer and used in prostate cancer diagnosis (de Kok, J. B. et al. Cancer Res 62, 2695-2698 (2002); Tomlins, S. A. et al.
  • SChLAP-1 was highly similar to EZH2, the positive control, which is widely associated with aggressive, lethal prostate cancer, whereas PCA3 and AMACR, two biomarkers not associated with disease progression, strongly associated with Cancer vs. Normal concepts but not concepts associated with aggressive disease.
  • Kaplan-Meier analysis of publicly-available datasets for biochemical recurrence (Glinsky et al., J Clin Invest 113, 913-923, (2004)) and overall survival (Setlur, S. R. et al. J Natl Cancer Inst 100, 815-825, (2008)) similarly showed significant associations (log rank test, p ⁇ 0.01) between the SChLAP-1 signature and more rapid disease recurrence and decreased survival probability.
  • Affymetrix exon microarrays which harbor probes mapping to SChLAP-1 exons was used to profile its expression in a prospectively-designed study of 235 high-risk prostate cancer patients who underwent radical prostatectomy between 2000-2006 at the Mayo Clinic (Buerki, C. et al. ASCO Annual Meeting, Abstract #4565 (2012). Nakagawa, T. et al. PLoS One 3, e2318, (2008)).
  • Unsupervised clustering was used to define patients into low and high SChLAP-1 expression groups and the prognostic utility of SChLAP-1 was evaluated with three clinical endpoints: biochemical recurrence (BCR), clinical progression to systemic disease (CP), and prostate cancer-specific mortality (PCSM).
  • BCR biochemical recurrence
  • CP clinical progression to systemic disease
  • PCSM prostate cancer-specific mortality
  • SChLAP-1 expression is an independent predictor of prostate cancer aggressiveness with highly significant hazard ratios for predicting BCR, CP, and PCSM (HR or 3.045, 0.563, and 4.339, respectively, p ⁇ 0.01) which were comparable to other clinical factors such as Gleason score and advanced clinical stage.
  • receiver-operator curves demonstrated the discriminative ability of SChLAP-1 expression in the Mayo Clinic dataset with area-under-the-curve (AUC) values of 0.63, 0.65, and 0.74 for the 5-year prediction of BCR, CP, and PCSM, which were either equivalent to, or slightly higher than, the AUC values for Gleason score (0.59, 0.65, and 0.71, respectively).
  • SChLAP-1 expression either out-performs, or is comparable to, standard clinical parameters such as clinical stage, lymph node invasion, pre-operative serum PSA, surgical margin status (SMS) and Gleason score for the prediction of CP, PCSM, and BCR.
  • SMS surgical margin status
  • Gleason score for the prediction of CP, PCSM, and BCR.
  • the particularly strong prognostic value of SChLAP-1 expression for CP and PCSM is important, as it is known that patients who develop BCR do not necessarily progress further to lethal or clinically significant recurrent disease: that is, many patients who experience BCR nevertheless die with prostate cancer but not from it (Simmons et al., Eur Urol 51, 1175-1184, (2007); Boorjian, S. A. et al.
  • this example describes a lineage-specific lncRNA that is highly expressed in 15-30% of prostate cancers but not other tissue or cancer types.
  • the sensitivity ranges from 20-35% and the specificity ranges from 94-100%.
  • SChLAP-1 is highly expressed in a subset of cancers and is thus a highly specific marker for those cancers.
  • SChLAP-1 directly binds a core subunit in the SWI/SNF complex, leading to reversion of SWI/SNF mediated gene expression ( FIG. 44 f ).
  • SChLAP-1 coordinates prostate cancer cell invasion in vitro and metastatic spread in vivo, and in patient tissue samples SChLAP-1 expression characterizes a metastatic-like gene expression profile associated with high-grade localized prostate cancers and poor clinical outcomes. It was further demonstrated that patients with high SChLAP-1 expression are at markedly increased risk for developing metastatic and lethal prostate cancer.
  • Table 9 shows genes correlated with SChLAP-1.

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Abstract

The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to ncRNAs as diagnostic markers and clinical targets for prostate, lung, breast and pancreatic cancer.

Description

    CROSS REFERENCE TO RELATED APPLICATIONS
  • This application is a continuation-in-part of U.S. application Ser. No. 13/299,000 filed Nov. 17, 2011, which claims priority to U.S. Provisional Application No. 61/415,490, filed Nov. 19, 2010, each of which are herein incorporated by referenced in its entirety.
    • STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
  • This invention was made with government support under CA111275 awarded by the National Institutes of Health and @81XWH-08-1-0031 and @81XWH-11-1-0520 awarded by the U.S. Army Medical Research and Materiel Command. The government has certain rights in the invention.
    • FIELD OF THE INVENTION
  • The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to ncRNAs as diagnostic markers and clinical targets for prostate, lung, breast and pancreatic cancer.
    • BACKGROUND OF THE INVENTION
  • A central aim in cancer research is to identify altered genes that are causally implicated in oncogenesis. Several types of somatic mutations have been identified including base substitutions, insertions, deletions, translocations, and chromosomal gains and losses, all of which result in altered activity of an oncogene or tumor suppressor gene. First hypothesized in the early 1900's, there is now compelling evidence for a causal role for chromosomal rearrangements in cancer (Rowley, Nat Rev Cancer 1: 245 (2001)). Recurrent chromosomal aberrations were thought to be primarily characteristic of leukemias, lymphomas, and sarcomas. Epithelial tumors (carcinomas), which are much more common and contribute to a relatively large fraction of the morbidity and mortality associated with human cancer, comprise less than 1% of the known, disease-specific chromosomal rearrangements (Mitelman, Mutat Res 462: 247 (2000)). While hematological malignancies are often characterized by balanced, disease-specific chromosomal rearrangements, most solid tumors have a plethora of non-specific chromosomal aberrations. It is thought that the karyotypic complexity of solid tumors is due to secondary alterations acquired through cancer evolution or progression.
  • Two primary mechanisms of chromosomal rearrangements have been described. In one mechanism, promoter/enhancer elements of one gene are rearranged adjacent to a proto-oncogene, thus causing altered expression of an oncogenic protein. This type of translocation is exemplified by the apposition of immunoglobulin (IG) and T-cell receptor (TCR) genes to MYC leading to activation of this oncogene in B- and T-cell malignancies, respectively (Rabbitts, Nature 372: 143 (1994)). In the second mechanism, rearrangement results in the fusion of two genes, which produces a fusion protein that may have a new function or altered activity. The prototypic example of this translocation is the BCR-ABL gene fusion in chronic myelogenous leukemia (CML) (Rowley, Nature 243: 290 (1973); de Klein et al., Nature 300: 765 (1982)). Importantly, this finding led to the rational development of imatinib mesylate (Gleevec), which successfully targets the BCR-ABL kinase (Deininger et al., Blood 105: 2640 (2005)). Thus, diagnostic methods that specifically identify epithelial tumors are needed.
    • SUMMARY OF THE INVENTION
  • The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to ncRNAs as diagnostic markers and clinical targets for cancer (e.g., prostate, lung, breast and pancreatic cancer).
  • Embodiments of the present invention provide compositions, kits, and methods useful in the detection and screening of a cancer. Experiments conducted during the course of development of embodiments of the present invention identified upreguation of one or more non-coding RNAs in cancer. Some embodiments of the present invention provide compositions and methods for detecting expression levels of such ncRNAs. Identification of ncRNAs finds use in screening, diagnostic and research uses.
  • For example, in some embodiments, the present invention provides a method of screening for the presence of a cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of one or more non-coding RNAs (ncRNA); and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of a cancer in the subject. In some embodiments, the cancer is a prostate cancer. In some instances, the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample. The control sample may comprise one or more normal cells. In some instances, the normal cells are normal prostate cells. In other instances, the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point. Alternatively, the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level. In some embodiments, the ncRNAs are described by SEQ ID NOs: 1-9. In some embodiments, the non-coding RNAs comprise one or more PCAT transcripts. In some embodiments, the non-coding RNAs are selected from the group comprising PCAT1, PCAT14, PCAT43 and PCAT 109. In some embodiments, the sample is tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions or prostate cells. In some instances, detecting the level of expression of the ncRNA comprises one or more in vitro assays. In some embodiments, the detection is carried out utilizing a sequencing technique, a nucleic acid hybridization technique, a nucleic acid amplification technique, or an immunoassay. However, the invention is not limited to the technique employed. In some embodiments, the nucleic acid amplification technique is polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification or nucleic acid sequence based amplification. In some embodiments, the prostate cancer is localized prostate cancer or metastatic prostate cancer. In some embodiments, the reagent is a pair of amplification oligonucleotides or an oligonucleotide probe.
  • Additional embodiments provide a method of screening for the presence of a cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of two or more (e.g., 10 or more, 25 or more, 50 or more, 100 or more or all 121) non-coding RNAs (ncRNA); and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of cancer in the subject. In some embodiments, the cancer is a prostate cancer. In some instances, the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample. The control sample may comprise one or more normal cells. In some instances, the normal cells are normal prostate cells. In other instances, the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point. Alternatively, the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level. In some embodiments, at least one of the two or more ncRNAs are selected from a group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, and PCAT121. In some embodiments, the two or more ncRNAs are selected from the group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, and PCAT121. In some instances, detecting the level of expression of the ncRNA comprises one or more in vitro assays.
  • Further embodiments of the present invention provide an array, comprising reagents for detecting the level of expression of two or more (e.g., 10 or more, 25 or more, 50 or more, 100 or more or all 121) non-coding RNAs (ncRNA) selected from, for example, PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, or PCAT121. In some embodiments, the reagent is a pair of amplification oligonucleotides or an oligonucleotide probe.
  • In some embodiments, the present invention provides a method for screening for the presence of a cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of one or more non-coding RNAs; and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of cancer in the subject. In some instances, the cancer is a lung cancer. In some instances, the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample. The control sample may comprise one or more normal cells. In some instances, the normal cells are normal lung cells. In other instances, the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point. Alternatively, the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level. In some instances, the one or more non-coding RNAs are selected from the group comprising M41 and ENST-75. In some instances, detecting the level of expression of the ncRNA comprises one or more in vitro assays.
  • In some embodiments, the present invention provides a method for screening for the presence of a cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of one or more non-coding RNAs; and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of cancer in the subject. In some instances, the cancer is a breast cancer. In some instances, the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample. The control sample may comprise one or more normal cells. In some instances, the normal cells are normal breast cells. In other instances, the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point. Alternatively, the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level. In some instances, the one or more ncRNAs are selected from the group comprising TU0011194, TU0019356 and TU0024146. In some instances, detecting the level of expression of the ncRNA comprises one or more in vitro assays.
  • In some embodiments, the present invention provides a method for screening for the presence of cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the level of expression of one or more non-coding RNAs; and detecting the level of expression of the ncRNA in the sample, wherein an increased level of expression of the ncRNA in the sample is indicative of cancer in the subject. In some instances, the cancer is a pancreatic cancer. In some instances, the increased level of expression of the ncRNA in the sample is relative to the level of ncRNA in a control sample. The control sample may comprise one or more normal cells. In some instances, the normal cells are normal pancreatic cells. In other instances, the increased level of expression of the ncRNA in the sample is relative to the level of expression of the ncRNA in a sample from a prior time point. Alternatively, the increased level of expression of the ncRNA in the sample is relative to a pre-established threshold level. In some instances, the one or more ncRNAs are selected from the group comprising TU0011194, TU0019356 and TU0024146. In some instances, detecting the level of expression of the ncRNA comprises one or more in vitro assays.
  • In still further embodiments, the present invention provides a method of screening for the presence of a cancer in a subject, comprising (a) contacting a biological sample from a subject with a gene expression detection assay, wherein the gene expression detection assay comprises a gene expression informative reagent for identification of the level of expression of SChLAP-1; (b) detecting the level of expression of SChLAP-1 in the sample; and (c) diagnosing cancer in the subject when an increased level of expression of SChLAP-1 in the sample is detected. In some instances, the cancer is a prostate cancer. In some instances, the increased level of expression of SChLAP-1 in the sample is relative to the level of SChLAP-1 in a control sample. The control sample may comprise one or more normal cells. In some instances, the normal cells are normal prostate cells. In other instances, the increased level of expression of SChLAP-1 in the sample is relative to the level of expression of SChLAP-1 in a sample from a prior time point. Alternatively, the increased level of expression of SChLAP-1 in the sample is relative to a pre-established threshold level. In some instances, detecting the level of expression of SChLAP-1 comprises one or more in vitro assays. In some instances, the gene expression detection assay further comprises a gene expression informative reagent for identification of the level of expression of one or more ncRNAs.
  • In additional embodiments, the present invention provides a method of identifying subjects at risk of cancer metastatis, comprising (a) contacting a biological sample from a subject with a gene expression detection assay, wherein the gene expression detection assay comprises a gene expression informative reagent for identification of the level of expression of SChLAP-1; (b) detecting the level of expression of SChLAP-1 in the sample using an in vitro assay; and (c)
  • identifying subjects at risk of cancer metastasis when an increased level of expression of SChLAP-1 in the sample is detected. In some embodiments, the subject is at increased risk of lethal prostate cancer when an increased level of expression of SChLAP-1 in the sample is detected. In some instances, the cancer is a prostate cancer. In some instances, the increased level of expression of SChLAP-1 in the sample is relative to the level of SChLAP-1 in a control sample. The control sample may comprise one or more normal cells. In some instances, the normal cells are normal prostate cells. In other instances, the increased level of expression of SChLAP-1 in the sample is relative to the level of expression of SChLAP-1 in a sample from a prior time point. Alternatively, the increased level of expression of SChLAP-1 in the sample is relative to a pre-established threshold level. In some instances, detecting the level of expression of SChLAP-1 comprises one or more in vitro assays. In some instances, the gene expression detection assay further comprises a gene expression informative reagent for identification of the level of expression of one or more ncRNAs.
  • Disclosed herein may be methods, systems, compositions and kits for analyzing, diagnosing, prognosing, monitoring, and/or treating a cancer. Such systems may comprise (a) a probe set may comprise a plurality of probes, wherein the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; and (b) a computer model or algorithm for analyzing an expression level and/or expression profile of a target molecule hybridized to the probe in a sample from a subject suffering from a cancer. The PCAT may be selected from the group may comprise PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, and PCAT121.
  • The system may further comprise an electronic memory for capturing and storing an expression profile.
  • The system may further comprise a computer-processing device, optionally connected to a computer network.
  • The system may further comprise a software module executed by the computer-processing device to analyze an expression profile.
  • The system may further comprise a software module executed by the computer-processing device to compare the expression profile to a standard or control.
  • The system may further comprise a software module executed by the computer-processing device to determine the expression level of the target.
  • The system may further comprise a machine to isolate the target molecule or the probe from the sample.
  • The system may further comprise a machine to sequence the target molecule or the probe.
  • The system may further comprise a machine to amplify the target molecule or the probe.
  • The system may further comprise a label that specifically binds to the target molecule the probe, or a combination thereof.
  • The system may further comprise a software module executed by the computer-processing device to transmit an analysis of the expression profile to the subject or a medical professional treating the subject.
  • The system may further comprise a software module executed by the computer-processing device to transmit a diagnosis or prognosis to the subject or a medical professional treating the subject.
  • Further disclosed herein are kits comprising (a) a probe set may comprise a plurality of probes, wherein the plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; and (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the target molecules in a sample.
  • The kit may further comprise a computer model or algorithm for correlating the expression level or expression profile with disease state or outcome.
  • The kit may further comprise a computer model or algorithm for designating a treatment modality for the subject.
  • The kit may further comprise a computer model or algorithm for normalizing expression level or expression profile of the target molecules.
  • The kit may further comprise a computer model or algorithm may comprise a robust multichip average (RMA), probe logarithmic intensity error estimation (PLIER), non-linear fit (NLFIT) quantile-based, nonlinear normalization, or a combination thereof.
  • Methods for analyzing a cancer in a subject in need thereof may comprise (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile comprises one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; and (b) comparing the expression profile from the sample to an expression profile of a control or standard.
  • Disclosed herein may be methods, systems, compositions and kits for diagnosing a cancer. Such methods for diagnosing cancer in a subject in need thereof may comprise (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile may comprise one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; (b) comparing the expression profile from the sample to an expression profile of a control or standard; and (c) diagnosing a cancer in the subject if the expression profile of the sample (i) deviates from the control or standard from a healthy subject or population of healthy subjects, or (ii) matches the control or standard from a subject or population of subjects who have or have had the cancer.
  • Disclosed herein may be methods, systems, compositions and kits for predicting susceptibility to developing cancer. Such methods for predicting whether a subject may be susceptible to developing a cancer may comprise (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile may comprise one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; (b) comparing the expression profile from the sample to an expression profile of a control or standard; and (c) predicting the susceptibility of the subject for developing a cancer based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • Disclosed herein may be methods, systems, compositions and kits for predicting response to a treatment regimen for cancer. Such methods for predicting a subject's response to a treatment regimen for a cancer may comprise: (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile may comprise one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; (b) comparing the expression profile from the sample to an expression profile of a control or standard; and (c) predicting the subject's response to a treatment regimen based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • Disclosed herein may be methods, systems, compositions and kits for treating or determining a treatment regimen for cancer. Such methods treating or determining a treatment regimen for cancer may comprise: (a) obtaining an expression profile from a sample obtained from the subject, wherein the expression profile may comprise one or more target molecules selected from PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; (b) comparing the expression profile from the sample to an expression profile of a control or standard; and (c) treating or determining a treatment regimen for cancer based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • The method may further comprise a software module executed by a computer-processing device to compare the expression profiles.
  • The method may further comprise providing diagnostic or prognostic information to the subject about the cancer based on the comparison.
  • The method may further comprise diagnosing the subject with a cancer if the expression profile of the sample (a) deviates from the control or standard from a healthy subject or population of healthy subjects, or (b) matches the control or standard from a subject or population of subjects who have or have had the cancer.
  • The method may further comprise predicting the susceptibility of the subject for developing a cancer based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (b) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • The method may further comprise prescribing a treatment regimen based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (b) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • The method may further comprise altering a treatment regimen prescribed or administered to the subject based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (b) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • The method may further comprise predicting the subject's response to a treatment regimen based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy subject or population of healthy subjects, or (b) the similarity of the expression profiles of the sample and a control or standard derived from a subject or population of subjects who have or have had the cancer.
  • The method may further comprise using a machine to isolate the one or more target molecules, one or more probes, or one or more probe hybridized target molecules from the sample.
  • The method may further comprise contacting the sample with a label that specifically binds to the target molecule, the probe, or a combination thereof.
  • The method may further comprise contacting the sample with a label that specifically binds to one or more target molecules.
  • The method may further comprise amplifying at least a portion of the target molecule, the probe, or any combination thereof.
  • The method may further comprise sequencing at least a portion of the target molecule, the probe, or any combination thereof.
  • Further disclosed herein is a probe set for assessing a cancer status of a subject may comprise a plurality of probes, wherein the probes in the probe set may be capable of detecting an expression level of one or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9, wherein The expression level of the one or more target molecules may determine the cancer status of the subject with at least 40% accuracy.
  • The methods, systems, compositions and kits may comprise a plurality of probes. The plurality of probes may comprise a sequence that hybridizes to at least a portion of two or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9. The plurality of probes may comprise a sequence that hybridizes to at least a portion of three or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9. The plurality of probes may comprise a sequence that hybridizes to at least a portion of four or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9. The plurality of probes may comprise a sequence that hybridizes to at least a portion of five or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9. The plurality of probes may comprise a sequence that hybridizes to at least a portion of ten or more target molecules selected from the group may comprise PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9.
  • The plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise and SEQ ID NOs: 1-9. The plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise PCAT1, PCAT14, PCAT43 and PCAT 109. The plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules may comprise SChLAP-1. The plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, and PCAT121. The cancer may be a prostate cancer.
  • The plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise M41 and ENST-75. The cancer may be a lung cancer.
  • The plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise TU0011194, TU0019356 and TU0024146. The cancer may be a breast cancer.
  • The plurality of probes may comprise a sequence that hybridizes to at least a portion of one or more target molecules selected from the group may comprise TU0011194, TU0019356 and TU0024146. The cancer may be a pancreatic cancer.
  • The probes may be between about 15 nucleotides and about 500 nucleotides in length. The probes may be between about 15 nucleotides and about 450 nucleotides in length. The probes may be between about 15 nucleotides and about 400 nucleotides in length. The probes may be between about 15 nucleotides and about 350 nucleotides in length. The probes may be between about 15 nucleotides and about 300 nucleotides in length. The probes may be between about 15 nucleotides and about 250 nucleotides in length. The probes may be between about 15 nucleotides and about 200 nucleotides in length. The probes may be at least 15 nucleotides in length. The probes may be at least 25 nucleotides in length.
  • The cancer may be selected from the group may comprise prostate, lung, breast, and pancreatic cancer.
  • Assessing the cancer status may comprise assessing cancer recurrence risk. Assessing the cancer status may comprise determining a treatment modality. Assessing the cancer status may comprise determining the efficacy of treatment.
  • Obtaining an expression profile may comprise hybridizing one or more probes to the one or more target molecules to produce one or more probe hybridized target molecules.
  • The deviation may be the expression level of one or more targets from the sample may be greater than the expression level of one or more targets from a control or standard derived from a healthy subject or population of healthy subjects. The deviation may be the expression level of one or more targets from the sample may be at least about 30% greater than the expression level of one or more targets from a control or standard derived from a healthy subject or population of healthy subjects. The deviation may be the expression level of one or more targets from the sample may be less than the expression level of one or more targets from a control or standard derived from a healthy subject or population of healthy subjects. The deviation may be the expression level of one or more targets from the sample may be at least about 30% less than the expression level of one or more targets from a control or standard derived from a healthy subject or population of healthy subjects.
  • The expression level of the one or more target molecules may determine the cancer status of the subject with at least 50% accuracy. The expression level of the one or more target molecules may determine the cancer status of the subject with at least 60% accuracy. The expression level of the one or more target molecules may determine the cancer status of the subject with at least 65% accuracy. The expression level of the one or more target molecules may determine the cancer status of the subject with at least 70% accuracy. The expression level of the one or more target molecules may determine the cancer status of the subject with at least 75% accuracy. The expression level of the one or more target molecules may determine the cancer status of the subject with at least 80% accuracy.
  • The plurality of probes may determine the expression level of the one or more target molecules with at least about 50% specificity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 60% specificity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 65% specificity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 70% specificity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 75% specificity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 80% specificity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 85% specificity.
  • The plurality of probes may determine the expression level of the one or more target molecules with at least about 50% sensitivity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 60% sensitivity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 65% sensitivity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 70% sensitivity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 75% sensitivity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 80% sensitivity. The plurality of probes may determine the expression level of the one or more target molecules with at least about 85% sensitivity.
  • Additional embodiments are described herein.
    • DESCRIPTION OF THE FIGURES
  • FIG. 1 shows that prostate cancer transcriptome sequencing reveals dysregulation of exemplary transcripts identified herein. a. A global overview of transcription in prostate cancer. b. A line graph showing the cumulative fraction of genes that are expressed at a given RPKM level. c. Conservation analysis comparing unannotated transcripts to known genes and intronic controls shows a low but detectable degree of purifying selection among intergenic and intronic unannotated transcripts. d-g. Intersection plots displaying the fraction of unannotated transcripts enriched for H3K4me2 (d), H3K4me3 (e), Acetyl-H3 (f) or RNA polymerase II (g) at their transcriptional start site (TSS) using ChIP-Seq and RNA-Seq data for the VCaP prostate cancer cancer cell line. h. A heatmap representing differentially expressed transcripts, including novel unannotated transcripts, in prostate cancer.
  • FIG. 2 shows that unannotated intergenic transcripts differentiate prostate cancer and benign prostate samples. a. A histogram plotting the genomic distance between an unannotated ncRNA and the nearest protein-coding gene. b. A Circos plot displaying the location of annotated transcripts and unannotated transcripts on Chr15q. c. A heatmap of differentially expressed or outlier unannotated intergenic transcripts clusters benign samples, localized tumors, and metastatic cancers by unsupervised clustering analyses. d. Cancer outlier profile analysis (COPA) outlier analysis for the prostate cancer transcriptome reveals known outliers (SPINK1, ERG, and ETV1), as well as numerous unannotated transcripts.
  • FIG. 3 shows validation of tissue-specific prostate cancer-associated non-coding RNAs. a-c. Quantitative real-time PCR was performed on a panel of prostate and non-prostate samples to measure expression levels of three nominated non-coding RNAs (ncRNAs), PCAT-43, PCAT-109, and PCAT-14, upregulated in prostate cancer compared to normal prostate tissues. a. PCAT-43 is a 20 kb ncRNA located 40 kb upstream of PMEPA1 on chr20q13.31. b. PCAT-109, located in a large, 0.5 Mb gene desert region on chr2q31.3 displays widespread transcription in prostate tissues, particularly metastases. c. PCAT-14, a genomic region on chr22q11.23 encompassing a human endogenous retrovirus exhibits marked upregulation in prostate tumors but not metastases.
  • FIG. 4 shows that prostate cancer ncRNAs populate the Chr8q24 gene desert. a. A schematic of the chr8q24 region. b. Comprehensive analysis of the chr8q24 region by RNA-Seq and ChIP-Seq reveals numerous transcripts supported by histone modifications, such as Acetyl-H3 and H3K4me3, demarcating active chromatin. c. RT-PCR and Sanger sequencing validation of the PCAT-1 exon-exon junction. d. The genomic location of PCAT-1 determined by 5′ and 3′ RACE. Sequence analysis of PCAT-1 shows that it is a viral long terminal repeat (LTR) promoter splicing to a marniner family transposase that has been bisected by an Alu repeat. e. qPCR on a panel of prostate and non-prostate samples shows prostate-specific expression and upregulation in prostate cancers and metastases compared to benign prostate samples. f. Four matched tumor/normal pairs included in the analysis in e. demonstrate somatic upregulation of PCAT-1 in matched cancer samples.
  • FIG. 5 shows that ncRNAs serve as urine biomarkers for prostate cancer. a-c. Three ncRNAs displaying biomarker status in prostate cancer tissues were evaluated on a cohort of urine samples from 77 patients with prostate cancer and 31 controls with negative prostate biopsy results and absence of the TMPRSS2-ERG fusion transcript. PCA3 (a); PCAT-1 (b); and PCAT-14 (c). d. Scatter plots demonstrating distinct patient subsets scoring positively for PCA3, PCAT-1, or PCAT-14 expression. e. A heatmap displaying patients positive and negative for several different prostate cancer biomarkers in urine sediment samples. f. A table displaying the statistical significance of the ncRNA signature. g. A model for non-coding RNA (ncRNA) activation in prostate cancer.
  • FIG. 6 shows Ab initio assembly of the prostate cancer transcriptome. (a) Reads were mapped with TopHat and assembled into library-specific transcriptomes by Cufflinks. (b) Transcripts corresponding to processed pseudogenes were isolated, and the remaining transcripts were categorized based on overlap with an aggregated set of known gene annotations.
  • FIG. 7 shows classification tree results for Chromosome 1. The recursive regression and partitioning trees (rpart) machine learning algorithm was used to predict expressed transcripts versus background signal.
  • FIG. 8 shows transcript assembly of known genes. ab initio transcript assembly on prostate transcriptome sequencing data was used to reconstruct the known prostate transcriptome. a. SPINK1, a biomarker for prostate cancer. b. PRUNE2 with the PCA3 non-coding RNA within its intronic regions. c. NFKB1. d. COL9A2.
  • FIG. 9 shows analysis of EST support for exemplary transcripts. ESTs from the UCSC database table “Human ESTs” were used to evaluate the amount of overlap between ESTs and novel transcripts. a. A line graph showing the fraction of genes whose transcripts are supported by a particular fraction of ESTs. b. A table displaying the number of ESTs supporting each class of transcripts
  • FIG. 10 shows analysis of coding potential of unannotated transcripts. DNA sequences for each transcript were extracted and searched for open reading frames (ORFs) using the txCdsPredict program from the UCSC source tool set.
  • FIG. 11 shows repetitive content of novel transcripts. The percentage of repetitive sequences was assessed in all transcripts by calculating the percentage of repeatmasked nucleotides in each sequence.
  • FIG. 12 shows distinct ChIP-Seq signatures for repeat-associated and nonrepeat novel ncRNAs. Unannotated transcripts were divided into two groups, repeat-associated and non-repeat, and intersected with ChIP-Seq data for Acetyl-H3 and H3K4me3, two histone modifications strongly associated with transcriptional start sites (TSS), in two prostate cancer cell lines. a. Acetyl-H3 in LNCaP cells. b. H3K4me3 in LNCaP cells. c. Acetyl-H3 in VCaP cells. d. H3K4me3 in VCaP cells.
  • FIG. 13 shows overlap of unannotated transcripts with ChIP-Seq data in VCaP cells. Previously published ChIP-Seq data for VCaP prostate cancer cells were intersected with unannotated prostate cancer transcripts and annotated control genes. a. H3K4me1 b. H3K36me3.
  • FIG. 14 shows overlap of unannotated transcripts with ChIP-Seq data in LNCaP cells. ChIP-Seq data for LNCaP prostate cancer cells were intersected with unannotated transcripts and annotated control genes. ncRNAs were divided into intergenic and intronic. a. H3K4me1 b. H3K4me2 c. H3K4me3 d. Acetyl-H3 e. H3K36me3 f. RNA polymerase II.
  • FIG. 15 shows validation of a novel transcript on chromosome 15. a. Coverage maps showing the average expression levels (RPKM) across the benign, localized tumor, and metastatic samples shows upregulation of a novel transcript downstream of TLE3. b. Several predicted isoforms of this transcript were nominated which retained common exons 1 and 2. c. The exon-exon boundary between exons 1 and 2, as well as an internal portion of exon 3, was validated by RT-PCR in prostate cell line models. d. Sanger sequencing of the RT-PCR product confirmed the junction of exon 1 and exon 2.
  • FIG. 16 shows clustering of prostate cancer with outliers. Transcripts with outlier profile scores in the top 10% were clustered using hierarchical trees.
  • FIG. 17 shows validation of novel transcripts in prostate cell lines. 11/14 unannotated transcripts selected for validation by RT-PCR and qPCR were confirmed in cell line models. a. RT-PCR gels showing expected bands for the 11 transcripts that validated. b. Representative qPCR results using primers selected from a. The primers used in b are indicated by a red asterisk in a.
  • FIG. 18 shows that PCAT-14 is upregulated by androgen signaling. VCaP and LNCaP cells were treated 5 nM R1881 or vehicle (ethanol) control.
  • FIG. 19 shows that PCAT-14 is upregulated in matched tumor tissues. Four matched tumor-normal patient tissue samples were assayed for PCAT-14 expression by qPCR.
  • FIG. 20 shows analysis of PCAT-14 transcript structure. a. Representative 5′RACE results using a 3′ primer confirms the presence of the sense transcript PCAT-14. Predicted novel transcripts are displayed above the RACE results. b. DNA sequence analysis of PCAT-14 indicates expected splice donor sites, splice acceptor sites, and a polyadenylation site.
  • FIG. 21 shows analysis of PCAT-1 transcript structure. 5′ and 3′ RACE experiments showed a ncRNA transcript containing two exons.
  • FIG. 22 shows that knockdown of PCAT-1 does not affect invasion or proliferation of VCaP cells. VCaP cells were transfected with custom-made siRNAs targeting PCAT-1 or non-targeting controls. a. Knockdown efficiency for four siRNA oligos individually and pooled. b.-d. siRNAs 2-4 were tested for functional effect due to their higher efficiency of knockdown. b. A cell proliferation assay performed with a Coulter counter shows no significant difference in cell proliferation following knockdown of PCAT-1. c. A WST-1 assay indicates no change in VCaP cell viability following PCAT-1 knockdown. d. A transmembrane invasion assay shows no change in VCaP cell invasiveness following PCAT-1 knockdown.
  • FIG. 23 shows transcription of two Alu elements in a CACNA1D intron. a. Coverage maps representing average expression in RPKM in benign samples, localized tumors, and prostate metastases. b. RPKM expression values for the CACNA1D Alu transcript across the prostate transcriptome sequencing cohort. c. RT-PCR validation of the Alu transcript in cell line models. d. Sanger sequencing confirmation of RT-PCR fragments verifies the presence of AluSp transcript sequence. e. Raw sequencing data of a portion of the AluSp sequence.
  • FIG. 24 shows transcription of numerous repeat elements at the SChLAP1 locus. a. Coverage maps representing repeat elements transcribed at the chr2q31.3 locus. b. RPKM expression expression values for the LINE-1 repeat region on chr2q31.3 across the prostate transcriptome sequencing cohort. c. RTPCR validation of the LINE-1 repetitive element in cell line models. A 402 bp fragment was amplified. d. Sanger sequencing of the PCR fragment confirms identity of the LINE-1 amplicon.
  • FIG. 25 shows a heatmap of repeats clusters prostate cancer samples. Unannotated transcripts that contained repeat elements were used to cluster prostate cancer samples in an unsupervised manner.
  • FIG. 26 shows that the SChLAP1 locus spans >500 kb. Visualization of transcriptome sequencing data in the UCSC genome browser indicates that a large, almost 1 Mb section of chromosome 2 is highly activated in cancer, contributing to many individual transcripts regulated in a coordinated fashion.
  • FIG. 27 shows that the SChLAP1 locus is associated with ETS positive tumors. a. Expression of the SChLAP1 locus was assayed by qPCR as display in FIG. 3 b on a cohort of 14 benign prostate tissues, 47 localized prostate tumors and 10 metastatic prostate cancers. b. Quantification of the SChLAP1 association with ETS status using the threshold indicated by the blue dotted line in a.
  • FIG. 28 shows the sequence of PCAT-1 and PCAT-14.
  • FIG. 29 shows that PCAT-1 expression sensitizes prostate cancer cells to treatment with PARP-1 inhibitors. (a-d) treatment with the PARP 1 inhibitor olaparib, (e-h) treatment with the PARP1 inhibitor ABT-888. Stable PCAT-1 knockdown in LNCAP prostate cells reduces sensitivity to olaparib (a) and ABT-888 (e). Stable overexpression in Du145 prostate cancer and RWPE benign prostate cells increases sensitivity to olaparib (b,c) and ABT-888 (f,g). Overexpression of PCAT-1 in MCF7 breast cancer cells does not recapitulate this effect (d,h).
  • FIG. 30 shows that PCAT-1 expression sensitizes prostate cancer cells to radiation treatment. (a) Stable PCAT-1 knockdown in LNCAP prostate cells reduces sensitivity to radiation. (b,c) Stable overexpression in Du145 prostate cancer and RWPE benign prostate cells increases sensitivity to radiation. (d). Overexpression of PCAT-1 in MCF7 breast cancer cells does not recapitulate this effect.
  • FIG. 31 shows that unannotated intergenic transcripts differentiate prostate cancer and benign samples. (a) The genomic location and exon structure of SChLAP-1. SChLAP-1 is located on chromosome 2 in a previously unannotated region. (b) The isoform structure of SChLAP-1. (c) Cell fractionation into nuclear and cytoplasmic fractions demonstrates that SChLAP-1 is predominantly nuclear in its localization. (d) Expression of SChLAP-1 in a cohort of prostate cancer and benign tissues indicates that SChLAP-1 is a prostate cancer outlier associated with cancers.
  • FIG. 32 shows that SChLAP-1 is required for prostate cancer cell invasion and proliferation. (a) Prostate and non-prostate cancer cell lines were treated with SChLAP-1 siRNAs. (b and c) As in (a), prostate and non-prostate cell lines were assayed for cell proliferation following SChLAP-1 knockdown. (d) The three most abundant isoforms of SChLAP-1 were cloned and overexpressed in RWPE benign immortalized prostate cells at levels similar to LNCaP cancer cells. (e) RWPE cells overexpressing SChLAP-1 isoforms show an increased ability to invade through Matrigel in Boyden chamber assays.
  • FIG. 33 shows that deletion analysis of SChLAP-1 identifies a region essential for its function. (a) RWPE cells overexpressing SChLAP-1 deletion constructs or full-length isoform #1 were generated as shown in the schematic of the constructs. (b) RWPE cells overexpressing SChLAP-1 deletion constructs demonstrated an impaired ability to invade through Matrigel, while the other deletion constructs showed no reduction in their ability to induce RWPE cell invasion compared to the wild type SChLAP-1.
  • FIG. 34 shows detection of prostate cancer RNAs in patient urine samples. (a-e). (a) PCA3 (b) PCAT-14 (c) PCAT-1 (d) SChLAP-1 (e) PDLIM5
  • FIG. 35 shows multiplexing urine SChLAP-1 measurements with serum PSA improves prostate cancer risk stratification.
  • FIG. 36 shows analysis of the lung cancer transcriptome. (a) 38 lung cell lines were analyzed by RNA-Seq and then lncRNA transcripts were reconstructed. (b) Expression levels of transcripts observed in lung cell lines. (c) An outlier analyses of 13 unannotated transcripts shows the presence of novel lncRNAs in subtypes of lung cancer cell lines.
  • FIG. 37 shows discovery of M41 and ENST-75 in lung cancer. (a) The genomic location of M41, which resides in an intron of DSCAM. M41 is poorly conserved across species. (b) qPCR of M41 demonstrates outlier expression in 15-20% of lung adenocarcinomas as well as high expression in breast cells. (c) The genomic location of ENST-75, which demonstrates high conservation across species. (d) qPCR of ENST-75 shows up-regulation in lung cancer but not breast or prostate cancers. High expression is observed in normal testis.
  • FIG. 38 shows lncRNAs are drivers and biomarkers in lung cancer. (a) Knockdown of ENST-75 in H1299 cells with independent siRNAs achieving >70% knockdown. (b) Knockdown of ENST-75 in H1299 cells impairs cell proliferation. Error bars represent s.e.m. (c) ENST-75 expression in lung adenocarcinomas stratifies patient overall survival. (d) Serum detection levels of ENST-75 in normal and lung cancer patients. (e) Average ENST-75 expression in lung cancer patient sera compared to normal patient sera. Error bars represent s.e.m.
  • FIG. 39 shows nomination of cancer-associated lncRNAs in breast and pancreatic cancer. (a-c) (a) TU0011194 (b) TU0019356 (c) TU0024146 (d-f) Three novel pancreatic cancer lncRNAs nominated from RNA-Seq data. All show outlier expression patterns in pancreatic cancer samples but not benign samples. (d) TU0009141 (e) TU0062051 (f) TU0021861.
  • FIG. 40 shows discovery of SChLAP-1 as a prostate cancer lncRNA. (a) Cancer outlier profile analysis (COPA) for intergenic lncRNAs in prostate cancer nominates two transcripts, PCAT-109 and PCAT-114, as prominent outliers. (b) A comparison of lncRNA outliers nominated by COPA, including their location, frequency in clinical samples, their expression in tissues and cell lines, and whether they occur in metastatic prostate samples. (c) A representation of the SChLAP-1 gene and its annotations in current databases. SChLAP-1 may consist of up to seven exons on Chr2q31.3. (d) A schematic summarizing the observed SChLAP-1 isoforms. (e) qPCR for SChLAP-1 on a panel of benign prostate (n=33), localized prostate cancer (n=82), and metastatic prostate cancer (n=33) samples. (f) SChLAP-1 expression is predominantly nuclear.
  • FIG. 41 shows that SChLAP-1 coordinates prostate cancer cell invasion. (a) siRNA knockdown of SChLAP-1 in vitro. (b) Overexpression of SChLAP-1 in RWPE cells. (c) Deletion analysis of SChLAP-1. (d) RNA structural analysis of SChLAP-1. (e) Tumor seeding with SChLAP-1 knockdown in vivo. (f) The number of gross metastatic sites observed by luciferase signal in 22Rv1 shSChLAP-1 cells or shNT controls. (g) Example luciferase bioluminescence images from 22Rv1 shNT, shSChLAP-1 #1, and shSChLAP-1 #2 mice five weeks following intracardiac injection.
  • FIG. 42 shows that SChLAP-1 antagonizes SWI/SNF complex function. (a) Gene set enrichment analysis (GSEA) of LNCaP and 22Rv1 cells treated with SChLAP-1 siRNAs. (b) Heatmap results for SChLAP-1 or SWI/SNF knockdown in LNCaP and 22Rv1 cells. (c) GSEA analysis of SChLAP-1 and SWI/SNF knockdowns. (d) RNA immunoprecipitation (RIP) of SNF5 and AR demonstrates SChLAP-1 binding to SNF5 in 22Rv1 and LNCaP cells. (e) RIP analysis of SNF5 in RWPE cells overexpressing LacZ, SChLAP-1 isoform #1, SChLAP-1 isoform #2, or SChLAP-1 deletion construct 5.
  • FIG. 43 shows that SChLAP-1 expression characterizes aggressive prostate cancer. (a) Network representation of Oncomine concepts analysis of genes positively and negatively correlated with SChLAP-1 expression levels in localized prostate cancers profiled by RNA-Seq. (b) Heatmap representation of comparisons between co-expression gene signatures and molecular concepts. (c-e) Kaplan-Meier analyses of prostate cancer outcomes in the Mayo Clinic cohort. (c), clinical progression to systemic disease (d), and prostate cancer-specific mortality (e). (f) A model of SChLAP-1 activity in prostate cancer.
  • FIG. 44 shows that chromosome 2 region contains prostate cancer-associated transcripts.
  • FIG. 45 shows the structure and sequence of SChLAP1.
  • FIG. 46 shows expression of SChLAP-1 across cancers.
    •  DEFINITIONS
  • To facilitate an understanding of the present invention, a number of terms and phrases are defined below:
  • As used herein, the terms “detect”, “detecting” or “detection” may describe either the general act of discovering or discerning or the specific observation of a composition. Detecting a composition may comprise determining the presence or absence of a composition. Detecting may comprise quantifying a composition. For example, detecting comprises determining the expression level of a composition. The composition may comprise a nucleic acid molecule. For example, the composition may comprise at least a portion of the ncRNAs disclosed herein. Alternatively, or additionally, the composition may be a detectably labeled composition.
  • As used herein, the term “subject” refers to any organisms that are screened using the diagnostic methods described herein. Such organisms preferably include, but are not limited to, mammals (e.g., murines, simians, equines, bovines, porcines, canines, felines, and the like), and most preferably includes humans. Alternatively, the organism is an avian, amphibian, reptile or fish.
  • The term “diagnosed,” as used herein, refers to the recognition of a disease by its signs and symptoms, or genetic analysis, pathological analysis, histological analysis, and the like.
  • A “subject suspected of having cancer” encompasses an individual who has received an initial diagnosis (e.g., a CT scan showing a mass or increased PSA level) but for whom the stage of cancer or presence or absence of ncRNAs indicative of cancer is not known. The term further includes people who once had cancer (e.g., an individual in remission). In some embodiments, “subjects” are control subjects that are suspected of having cancer or diagnosed with cancer.
  • As used herein, the term “characterizing cancer in a subject” refers to the identification of one or more properties of a cancer sample in a subject, including but not limited to, the presence of benign, pre-cancerous or cancerous tissue, the stage of the cancer, and the subject's prognosis. Cancers may be characterized by the identification of the expression of one or more cancer marker genes, including but not limited to, the ncRNAs disclosed herein.
  • As used herein, the term “characterizing prostate tissue in a subject” refers to the identification of one or more properties of a prostate tissue sample (e.g., including but not limited to, the presence of cancerous tissue, the presence or absence of ncRNAs, the presence of pre-cancerous tissue that is likely to become cancerous, and the presence of cancerous tissue that is likely to metastasize). In some embodiments, tissues are characterized by the identification of the expression of one or more cancer marker genes, including but not limited to, the cancer markers disclosed herein.
  • As used herein, the term “stage of cancer” refers to a qualitative or quantitative assessment of the level of advancement of a cancer. Criteria used to determine the stage of a cancer include, but are not limited to, the size of the tumor and the extent of metastases (e.g., localized or distant).
  • As used herein, the term “nucleic acid molecule” refers to any nucleic acid containing molecule, including but not limited to, DNA or RNA. The nucleic acid molecule may comprise one or more nucleotides. The term encompasses sequences that include any of the known base analogs of DNA and RNA including, but not limited to, 4-acetylcytosine, 8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine, 5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarbonylmethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, N-uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and 2,6-diaminopurine.
  • The term “gene” refers to a nucleic acid (e.g., DNA) sequence that comprises coding sequences necessary for the production of a polypeptide, precursor, or RNA (e.g., rRNA, tRNA). The polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or functional properties (e.g., enzymatic activity, ligand binding, signal transduction, immunogenicity, etc.) of the full-length or fragments are retained. The term also encompasses the coding region of a structural gene and the sequences located adjacent to the coding region on both the 5′ and 3′ ends for a distance of about 1 kb or more on either end such that the gene corresponds to the length of the full-length mRNA. Sequences located 5′ of the coding region and present on the mRNA are referred to as 5′ non-translated sequences. Sequences located 3′ or downstream of the coding region and present on the mRNA are referred to as 3′ non-translated sequences. The term “gene” encompasses both cDNA and genomic forms of a gene. A genomic form or clone of a gene contains the coding region interrupted with non-coding sequences termed “introns” or “intervening regions” or “intervening sequences.” Introns are segments of a gene that are transcribed into nuclear RNA (hnRNA); introns may contain regulatory elements such as enhancers. Introns are removed or “spliced out” from the nuclear or primary transcript; introns therefore are absent in the messenger RNA (mRNA) transcript. The mRNA functions during translation to specify the sequence or order of amino acids in a nascent polypeptide.
  • As used herein, the term “oligonucleotide,” refers to a short length of single-stranded polynucleotide chain. Oligonucleotides are typically less than 200 residues long (e.g., between 15 and 100), however, as used herein, the term is also intended to encompass longer polynucleotide chains. Oligonucleotides are often referred to by their length. For example a 24 residue oligonucleotide is referred to as a “24-mer”. Oligonucleotides can form secondary and tertiary structures by self-hybridizing or by hybridizing to other polynucleotides. Such structures can include, but are not limited to, duplexes, hairpins, cruciforms, bends, and triplexes.
  • As used herein, the terms “complementary” or “complementarity” are used in reference to polynucleotides (i.e., a sequence of nucleotides) related by the base-pairing rules. For example, the sequence “5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.” Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, as well as detection methods that depend upon binding between nucleic acids.
  • The term “homology” refers to a degree of complementarity. There may be partial homology or complete homology (i.e., identity). A partially complementary sequence is a nucleic acid molecule that at least partially inhibits a completely complementary nucleic acid molecule from hybridizing to a target nucleic acid is “substantially homologous.” The inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or Northern blot, solution hybridization and the like) under conditions of low stringency. A substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous nucleic acid molecule to a target under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction. The absence of non-specific binding may be tested by the use of a second target that is substantially non-complementary (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second non-complementary target.
  • As used herein, the term “hybridization” is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is impacted by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, the Tm of the formed hybrid, and the G:C ratio within the nucleic acids. A single molecule that contains pairing of complementary nucleic acids within its structure is said to be “self-hybridized.”
  • As used herein the term “stringency” is used in reference to the conditions of temperature, ionic strength, and the presence of other compounds such as organic solvents, under which nucleic acid hybridizations are conducted. Under “low stringency conditions” a nucleic acid sequence of interest will hybridize to its exact complement, sequences with single base mismatches, closely related sequences (e.g., sequences with 90% or greater homology), and sequences having only partial homology (e.g., sequences with 50-90% homology). Under ‘medium stringency conditions,” a nucleic acid sequence of interest will hybridize only to its exact complement, sequences with single base mismatches, and closely relation sequences (e.g., 90% or greater homology). Under “high stringency conditions,” a nucleic acid sequence of interest will hybridize only to its exact complement, and (depending on conditions such a temperature) sequences with single base mismatches. In other words, under conditions of high stringency the temperature can be raised so as to exclude hybridization to sequences with single base mismatches.
  • The term “isolated” when used in relation to a nucleic acid, as in “an isolated oligonucleotide” or “isolated polynucleotide” refers to a nucleic acid sequence that is identified and separated from at least one component or contaminant with which it is ordinarily associated in its natural source. Isolated nucleic acid is such present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids as nucleic acids such as DNA and RNA found in the state they exist in nature. For example, a given DNA sequence (e.g., a gene) is found on the host cell chromosome in proximity to neighboring genes; RNA sequences, such as a specific mRNA sequence encoding a specific protein, are found in the cell as a mixture with numerous other mRNAs that encode a multitude of proteins. However, isolated nucleic acid encoding a given protein includes, by way of example, such nucleic acid in cells ordinarily expressing the given protein where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature. The isolated nucleic acid, oligonucleotide, or polynucleotide may be present in single-stranded or double-stranded form. When an isolated nucleic acid, oligonucleotide or polynucleotide is to be utilized to express a protein, the oligonucleotide or polynucleotide will contain at a minimum the sense or coding strand (i.e., the oligonucleotide or polynucleotide may be single-stranded), but may contain both the sense and anti-sense strands (i.e., the oligonucleotide or polynucleotide may be double-stranded).
  • As used herein, the term “purified” or “to purify” refers to the removal of components (e.g., contaminants) from a sample. For example, antibodies are purified by removal of contaminating non-immunoglobulin proteins; they are also purified by the removal of immunoglobulin that does not bind to the target molecule. The removal of non-immunoglobulin proteins and/or the removal of immunoglobulins that do not bind to the target molecule results in an increase in the percent of target-reactive immunoglobulins in the sample. In another example, recombinant polypeptides are expressed in bacterial host cells and the polypeptides are purified by the removal of host cell proteins; the percent of recombinant polypeptides is thereby increased in the sample.
  • As used herein, the term “sample” is used in its broadest sense. In one sense, it is meant to include a specimen or culture obtained from any source, as well as biological and environmental samples. Biological samples may be obtained from animals (including humans) and encompass fluids, solids, tissues, and gases. Biological samples include blood products, such as plasma, serum and the like. Such examples are not however to be construed as limiting the sample types applicable to the present invention.
    • DETAILED DESCRIPTION OF THE INVENTION
  • The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to ncRNAs as diagnostic markers and clinical targets for cancer. ncRNAs may be used as diagnostic markers and clinical targets for prostate, lung, breast and pancreatic cancer.
  • Experiments conducted during the development of embodiments of the present invention utilized RNA-Seq analyses of tissue samples and ab initio transcriptome assembly to predict the complete polyA+ transcriptome of prostate cancer. 6,144 novel ncRNAs found in prostate cancer were identified, including 121 ncRNAs that associated with disease progression (FIGS. 1, 2, 16 and 25). These data demonstrate the global utility of RNA-Seq in defining functionally-important elements of the genome.
  • The present invention is not limited to a particular mechanism. Indeed, an understanding of the mechanism is not necessary to practice the present invention. Nonetheless, although the biological role of these RNAs, especially the differentially-expressed ones, is not yet known, these results indicate a model in which specific intergenic loci are activated in prostate cancer, enabling the transcription of numerous disease-specific and tissue-specific ncRNAs (FIG. 5 g). Clinically, these ncRNA signatures are suitable for urine-based assays to detect and diagnose prostate cancer in a non-invasive manner (See e.g., Example 1). It is further contemplated that specific ncRNA signatures occur universally in all disease states and applying these methodologies to other diseases reveals clinically important biomarkers, particularly for diseases that currently lack good protein biomarkers.
  • While traditional approaches have focused on the annotated reference genome, data generated during the course of development of embodiments of the present invention implicate large swaths of unannotated genomic loci in prostate cancer progression and prostate-specific expression. One example of this is the SChLAP1 locus, which represents a >500 kb stretch of coordinately regulated expression, and the chr8q24 locus, which contains a prostate specific region with the prostate cancer biomarker PCAT-1. The fact that the SChLAP 1 locus is almost exclusively expressed in prostate cancers harboring an ETS gene fusion further confirms the capacity of ncRNAs to identify patient disease subtypes. In addition, these analyses reveal novel cancer-specific drivers of tumorigenesis. For example, the long ncRNA HOTAIR is known to direct cancer-promoting roles for EZH2 in breast cancer (Gupta et al., Nature 464 (7291), 1071 (2010)), while in the PC3 prostate cancer cell line a similar role has been proposed for the ANRIL ncRNA (Yap et al., Mol Cell 38 (5), 662 (2010)).
    • I. Diagnostic and Screening Methods
  • As described herein, embodiments of the present invention provide diagnostic and screening methods that utilize the detection of one or more ncRNAs. Exemplary ncRNAs include, but are not limited to, PCAT-1, PCAT-14, PCAT-43 and PCAT-109; SChLAP-1; and SEQ ID NOs: 1-9. Exemplary, non-limiting methods are described herein.
  • Any patient sample suspected of containing the ncRNAs may be tested according to methods of embodiments of the present invention. By way of non-limiting examples, the sample may be tissue (e.g., a biopsy sample, a prostate biopsy sample or a tissue sample obtained by prostatectomy), blood, urine, semen, prostatic secretions or a fraction thereof (e.g., plasma, serum, urine supernatant, urine cell pellet, cells or prostate cells). A urine sample may be collected immediately following an attentive digital rectal examination (DRE), which causes prostate cells from the prostate gland to shed into the urinary tract.
  • In some embodiments, the patient sample is subjected to preliminary processing designed to isolate or enrich the sample for the ncRNAs or cells that contain the ncRNAs. A variety of techniques known to those of ordinary skill in the art may be used for this purpose, including but not limited to: centrifugation; immunocapture; cell lysis; nucleic acid amplification; and, nucleic acid target capture (See, e.g., EP Pat. No. 1 409 727, herein incorporated by reference in its entirety).
  • The ncRNAs may be detected along with other markers in a multiplex or panel format. Markers may be selected for their predictive value alone or in combination with the gene fusions. Exemplary prostate cancer markers include, but are not limited to: AMACR/P504S (U.S. Pat. No. 6,262,245); PCA3 (U.S. Pat. No. 7,008,765); PCGEM1 (U.S. Pat. No. 6,828,429); prostein/P501S, P503S, P504S, P509S, P510S, prostase/P703P, P710P (U.S. Publication No. 20030185830); RAS/KRAS (Bos, Cancer Res. 49:4682-89 (1989); Kranenburg, Biochimica et Biophysica Acta 1756:81-82 (2005)); and, those disclosed in U.S. Pat. Nos. 5,854,206 and 6,034,218, 7,229,774, each of which is herein incorporated by reference in its entirety. Markers for other cancers, diseases, infections, and metabolic conditions are also contemplated for inclusion in a multiplex or panel format.
  • In some embodiments, multiplex or array formats are utilized to detect multiple markers in combination. For example, in some embodiments, the level of expression of one or more, 2 or more, 3 or more, 4 or more, 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more or all 121) non-coding RNAs (ncRNAs) is utilized in the research, screening, diagnostic and prognositic compositions and methods described herein. The one or more ncRNAs may be selected from the group comprising SChLAP-1, PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, and PCAT121.
  • i. DNA and RNA Detection
  • The ncRNAs of the present invention are detected using a variety of nucleic acid techniques known to those of ordinary skill in the art, including but not limited to: nucleic acid sequencing; nucleic acid hybridization; and, nucleic acid amplification.
  • The methods, compositions and kits may comprise one or more ncRNAs. The methods, compositions and kits may comprise 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more, 40 or more, 45 or more, 50 or more, 55 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more, 130 or more, 140 or more, 150 or more ncRNAs.
  • The one or more ncRNAs may be selected from the group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, PCAT121, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9. The one or more ncRNAs of the present invention may comprise one or more prostate cancer-associated ncRNA transcripts (PCATs). The one or more PCATs may be selected from the group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, and PCAT121. The one or more ncRNAs may comprise PCAT1, PCAT14, PCAT43, PCAT 109, or a combination thereof.
  • Alternatively, or additionally, the ncRNAs of the present invention may comprise SChLAP-1. The ncRNAs may comprise M41, ENST-75, or a combination thereof. The ncRNAs may comprise TU0011194, TU0019356, TU0024146, or a combination thereof. The ncRNAs may comprise TU0009141, TU0062051, TU0021861 or a combination thereof. The ncRNAs may comprise any one of SEQ ID NOs: 1-9 or a combination thereof.
  • 1. Sequencing
  • Illustrative non-limiting examples of nucleic acid sequencing techniques include, but are not limited to, chain terminator (Sanger) sequencing and dye terminator sequencing. Those of ordinary skill in the art will recognize that because RNA is less stable in the cell and more prone to nuclease attack experimentally RNA is usually reverse transcribed to DNA before sequencing.
  • Chain terminator sequencing uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. Extension is initiated at a specific site on the template DNA by using a short radioactive, or other labeled, oligonucleotide primer complementary to the template at that region. The oligonucleotide primer is extended using a DNA polymerase, standard four deoxynucleotide bases, and a low concentration of one chain terminating nucleotide, most commonly a di-deoxynucleotide. This reaction is repeated in four separate tubes with each of the bases taking turns as the di-deoxynucleotide. Limited incorporation of the chain terminating nucleotide by the DNA polymerase results in a series of related DNA fragments that are terminated only at positions where that particular di-deoxynucleotide is used. For each reaction tube, the fragments are size-separated by electrophoresis in a slab polyacrylamide gel or a capillary tube filled with a viscous polymer. The sequence is determined by reading which lane produces a visualized mark from the labeled primer as you scan from the top of the gel to the bottom.
  • Dye terminator sequencing alternatively labels the terminators. Complete sequencing can be performed in a single reaction by labeling each of the di-deoxynucleotide chain-terminators with a separate fluorescent dye, which fluoresces at a different wavelength.
  • A variety of nucleic acid sequencing methods are contemplated for use in the methods of the present disclosure including, for example, chain terminator (Sanger) sequencing, dye terminator sequencing, and high-throughput sequencing methods. Many of these sequencing methods are well known in the art. See, e.g., Sanger et al., Proc. Natl. Acad. Sci. USA 74:5463-5467 (1997); Maxam et al., Proc. Natl. Acad. Sci. USA 74:560-564 (1977); Drmanac, et al., Nat. Biotechnol. 16:54-58 (1998); Kato, Int. J. Clin. Exp. Med. 2:193-202 (2009); Ronaghi et al., Anal. Biochem. 242:84-89 (1996); Margulies et al., Nature 437:376-380 (2005); Ruparel et al., Proc. Natl. Acad. Sci. USA 102:5932-5937 (2005), and Harris et al., Science 320:106-109 (2008); Levene et al., Science 299:682-686 (2003); Korlach et al., Proc. Natl. Acad. Sci. USA 105:1176-1181 (2008); Branton et al., Nat. Biotechnol. 26(10):1146-53 (2008); Eid et al., Science 323:133-138 (2009); each of which is herein incorporated by reference in its entirety.
  • The methods disclosed herein can comprise transcriptome sequencing (e.g., RNA-Seq). Sequencing can comprise platforms such as the Illumina Genome Analyzer platform, ABI Solid Sequencing or Life Science's 454 Sequencing. Alternatively, sequencing comprises Helicos' Direct RNA Sequencing (DRS™) technology. The sequencing reactions may comprise capillary sequencing, next generation sequencing, Sanger sequencing, sequencing by synthesis, single molecule nanopore sequencing, sequencing by ligation, sequencing by hybridization, sequencing by nanopore current restriction, or a combination thereof. Sequencing by synthesis may comprise reversible terminator sequencing, processive single molecule sequencing, sequential nucleotide flow sequencing, or a combination thereof. Sequential nucleotide flow sequencing may comprise pyrosequencing, pH-mediated sequencing, semiconductor sequencing or a combination thereof. Conducting one or more sequencing reactions comprises whole genome sequencing or exome sequencing.
  • 2. Hybridization
  • Illustrative non-limiting examples of nucleic acid hybridization techniques include, but are not limited to, in situ hybridization (ISH), microarray, and Southern or Northern blot. In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA or RNA strand as a probe to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough, the entire tissue (whole mount ISH). DNA ISH can be used to determine the structure of chromosomes. RNA ISH is used to measure and localize mRNAs and other transcripts (e.g., ncRNAs) within tissue sections or whole mounts. Sample cells and tissues are usually treated to fix the target transcripts in place and to increase access of the probe. The probe hybridizes to the target sequence at elevated temperature, and then the excess probe is washed away. The probe that was labeled with either radio-, fluorescent- or antigen-labeled bases is localized and quantitated in the tissue using either autoradiography, fluorescence microscopy or immunohistochemistry, respectively. ISH can also use two or more probes, labeled with radioactivity or the other non-radioactive labels, to simultaneously detect two or more transcripts.
  • In some embodiments, ncRNAs are detected using fluorescence in situ hybridization (FISH). In some embodiments, FISH assays utilize bacterial artificial chromosomes (BACs). These have been used extensively in the human genome sequencing project (see Nature 409: 953-958 (2001)) and clones containing specific BACs are available through distributors that can be located through many sources, e.g., NCBI. Each BAC clone from the human genome has been given a reference name that unambiguously identifies it. These names can be used to find a corresponding GenBank sequence and to order copies of the clone from a distributor.
  • The present invention further provides a method of performing a FISH assay on the patient sample. The methods disclosed herein may comprise performing a FISH assay on one or more cells, tissues, organs, or fluids surrounding such cells, tissues and organs. In some instances, the methods disclosed herein further comprise performing a FISH assay on human prostate cells, human prostate tissue or on the fluid surrounding said human prostate cells or human prostate tissue. Alternatively, or additionally, the methods disclosed herein comprise performing a FISH assay on breast cells, lung cells, pancreatic cells, liver cells, breast tissue, lung tissue, pancreatic tissue, liver tissue, or on the fluid surrounding the cells or tissues. Specific protocols are well known in the art and can be readily adapted for the present invention. Guidance regarding methodology may be obtained from many references including: In situ Hybridization: Medical Applications (eds. G. R. Coulton and J. de Belleroche), Kluwer Academic Publishers, Boston (1992); In situ Hybridization: In Neurobiology; Advances in Methodology (eds. J. H. Eberwine, K. L. Valentino, and J. D. Barchas), Oxford University Press Inc., England (1994); In situ Hybridization: A Practical Approach (ed. D. G. Wilkinson), Oxford University Press Inc., England (1992)); Kuo, et al., Am. J. Hum. Genet. 49:112-119 (1991); Klinger, et al., Am. J. Hum. Genet. 51:55-65 (1992); and Ward, et al., Am. J. Hum. Genet. 52:854-865 (1993)). There are also kits that are commercially available and that provide protocols for performing FISH assays (available from e.g., Oncor, Inc., Gaithersburg, Md.). Patents providing guidance on methodology include U.S. Pat. Nos. 5,225,326; 5,545,524; 6,121,489 and 6,573,043. All of these references are hereby incorporated by reference in their entirety and may be used along with similar references in the art and with the information provided in the Examples section herein to establish procedural steps convenient for a particular laboratory.
  • The one or more ncRNAs may be detected by conducting one or more hybridization reactions. The one or more hybridization reactions may comprise one or more hybridization arrays, hybridization reactions, hybridization chain reactions, isothermal hybridization reactions, nucleic acid hybridization reactions, or a combination thereof. The one or more hybridization arrays may comprise hybridization array genotyping, hybridization array proportional sensing, DNA hybridization arrays, macroarrays, microarrays, high-density oligonucleotide arrays, genomic hybridization arrays, comparative hybridization arrays, or a combination thereof.
  • 3. Microarrays
  • Different kinds of biological assays are called microarrays including, but not limited to: DNA microarrays (e.g., cDNA microarrays and oligonucleotide microarrays); protein microarrays; tissue microarrays; transfection or cell microarrays; chemical compound microarrays; and, antibody microarrays. A DNA microarray, commonly known as gene chip, DNA chip, or biochip, is a collection of microscopic DNA spots attached to a solid surface (e.g., glass, plastic or silicon chip) forming an array for the purpose of expression profiling or monitoring expression levels for thousands of genes simultaneously. The affixed DNA segments are known as probes, thousands of which can be used in a single DNA microarray. Microarrays can be used to identify disease genes or transcripts (e.g., ncRNAs) by comparing gene expression in disease and normal cells. Microarrays can be fabricated using a variety of technologies, including but not limiting: printing with fine-pointed pins onto glass slides; photolithography using pre-made masks; photolithography using dynamic micromirror devices; ink-jet printing; or, electrochemistry on microelectrode arrays.
  • 3. Amplification
  • The methods disclosed herein may comprise conducting one or more amplification reactions. Nucleic acids (e.g., ncRNAs) may be amplified prior to or simultaneous with detection. Conducting one or more amplification reactions may comprise one or more PCR-based amplifications, non-PCR based amplifications, or a combination thereof. Illustrative non-limiting examples of nucleic acid amplification techniques include, but are not limited to, polymerase chain reaction (PCR), reverse transcription polymerase chain reaction (RT-PCR), nested PCR, linear amplification, multiple displacement amplification (MDA), real-time SDA, rolling circle amplification, circle-to-circle amplification transcription-mediated amplification (TMA), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence based amplification (NASBA). Those of ordinary skill in the art will recognize that certain amplification techniques (e.g., PCR) require that RNA be reversed transcribed to DNA prior to amplification (e.g., RT-PCR), whereas other amplification techniques directly amplify RNA (e.g., TMA and NASBA).
  • The polymerase chain reaction (U.S. Pat. Nos. 4,683,195, 4,683,202, 4,800,159 and 4,965,188, each of which is herein incorporated by reference in its entirety), commonly referred to as PCR, uses multiple cycles of denaturation, annealing of primer pairs to opposite strands, and primer extension to exponentially increase copy numbers of a target nucleic acid sequence. In a variation called RT-PCR, reverse transcriptase (RT) is used to make a complementary DNA (cDNA) from mRNA, and the cDNA is then amplified by PCR to produce multiple copies of DNA. For other various permutations of PCR see, e.g., U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159; Mullis et al., Meth. Enzymol. 155: 335 (1987); and, Murakawa et al., DNA 7: 287 (1988), each of which is herein incorporated by reference in its entirety.
  • Transcription mediated amplification (U.S. Pat. Nos. 5,480,784 and 5,399,491, each of which is herein incorporated by reference in its entirety), commonly referred to as TMA, synthesizes multiple copies of a target nucleic acid sequence autocatalytically under conditions of substantially constant temperature, ionic strength, and pH in which multiple RNA copies of the target sequence autocatalytically generate additional copies. See, e.g., U.S. Pat. Nos. 5,399,491 and 5,824,518, each of which is herein incorporated by reference in its entirety. In a variation described in U.S. Publ. No. 20060046265 (herein incorporated by reference in its entirety), TMA optionally incorporates the use of blocking moieties, terminating moieties, and other modifying moieties to improve TMA process sensitivity and accuracy.
  • The ligase chain reaction (Weiss, R., Science 254: 1292 (1991), herein incorporated by reference in its entirety), commonly referred to as LCR, uses two sets of complementary DNA oligonucleotides that hybridize to adjacent regions of the target nucleic acid. The DNA oligonucleotides are covalently linked by a DNA ligase in repeated cycles of thermal denaturation, hybridization and ligation to produce a detectable double-stranded ligated oligonucleotide product.
  • Strand displacement amplification (Walker, G. et al., Proc. Natl. Acad. Sci. USA 89: 392-396 (1992); U.S. Pat. Nos. 5,270,184 and 5,455,166, each of which is herein incorporated by reference in its entirety), commonly referred to as SDA, uses cycles of annealing pairs of primer sequences to opposite strands of a target sequence, primer extension in the presence of a dNTPαS to produce a duplex hemiphosphorothioated primer extension product, endonuclease-mediated nicking of a hemimodified restriction endonuclease recognition site, and polymerase-mediated primer extension from the 3′ end of the nick to displace an existing strand and produce a strand for the next round of primer annealing, nicking and strand displacement, resulting in geometric amplification of product. Thermophilic SDA (tSDA) uses thermophilic endonucleases and polymerases at higher temperatures in essentially the same method (EP Pat. No. 0 684 315).
  • Other amplification methods include, for example: nucleic acid sequence based amplification (U.S. Pat. No. 5,130,238, herein incorporated by reference in its entirety), commonly referred to as NASBA; one that uses an RNA replicase to amplify the probe molecule itself (Lizardi et al., BioTechnol. 6: 1197 (1988), herein incorporated by reference in its entirety), commonly referred to as Qβ replicase; a transcription based amplification method (Kwoh et al., Proc. Natl. Acad. Sci. USA 86:1173 (1989)); and, self-sustained sequence replication (Guatelli et al., Proc. Natl. Acad. Sci. USA 87: 1874 (1990), each of which is herein incorporated by reference in its entirety). For further discussion of known amplification methods see Persing, David H., “In Vitro Nucleic Acid Amplification Techniques” in Diagnostic Medical Microbiology: Principles and Applications (Persing et al., Eds.), pp. 51-87 (American Society for Microbiology, Washington, D.C. (1993)).
  • 4. Detection Methods
  • Non-amplified or amplified nucleic acids can be detected by any conventional means. For example, the ncRNAs can be detected by hybridization with a detectably labeled probe and measurement of the resulting hybrids. In another example, the ncRNAs can be detected by sequencing. Illustrative non-limiting examples of detection methods are described herein.
  • One illustrative detection method, the Hybridization Protection Assay (HPA) involves hybridizing a chemiluminescent oligonucleotide probe (e.g., an acridinium ester-labeled (AE) probe) to the target sequence, selectively hydrolyzing the chemiluminescent label present on unhybridized probe, and measuring the chemiluminescence produced from the remaining probe in a luminometer. See, e.g., U.S. Pat. No. 5,283,174 and Norman C. Nelson et al., Nonisotopic Probing, Blotting, and Sequencing, ch. 17 (Larry J. Kricka ed., 2d ed. 1995, each of which is herein incorporated by reference in its entirety).
  • Another illustrative detection method provides for quantitative evaluation of the amplification process in real-time. Evaluation of an amplification process in “real-time” involves determining the amount of amplicon in the reaction mixture either continuously or periodically during the amplification reaction, and using the determined values to calculate the amount of target sequence initially present in the sample. A variety of methods for determining the amount of initial target sequence present in a sample based on real-time amplification are well known in the art. These include methods disclosed in U.S. Pat. Nos. 6,303,305 and 6,541,205, each of which is herein incorporated by reference in its entirety. Another method for determining the quantity of target sequence initially present in a sample, but which is not based on a real-time amplification, is disclosed in U.S. Pat. No. 5,710,029, herein incorporated by reference in its entirety.
  • Amplification products may be detected in real-time through the use of various self-hybridizing probes, most of which have a stem-loop structure. Such self-hybridizing probes are labeled so that they emit differently detectable signals, depending on whether the probes are in a self-hybridized state or an altered state through hybridization to a target sequence. By way of non-limiting example, “molecular torches” are a type of self-hybridizing probe that includes distinct regions of self-complementarity (referred to as “the target binding domain” and “the target closing domain”) which are connected by a joining region (e.g., non-nucleotide linker) and which hybridize to each other under predetermined hybridization assay conditions. In a preferred embodiment, molecular torches contain single-stranded base regions in the target binding domain that are from 1 to about 20 bases in length and are accessible for hybridization to a target sequence present in an amplification reaction under strand displacement conditions. Under strand displacement conditions, hybridization of the two complementary regions, which may be fully or partially complementary, of the molecular torch is favored, except in the presence of the target sequence, which will bind to the single-stranded region present in the target binding domain and displace all or a portion of the target closing domain. The target binding domain and the target closing domain of a molecular torch include a detectable label or a pair of interacting labels (e.g., luminescent/quencher) positioned so that a different signal is produced when the molecular torch is self-hybridized than when the molecular torch is hybridized to the target sequence, thereby permitting detection of probe:target duplexes in a test sample in the presence of unhybridized molecular torches. Molecular torches and a variety of types of interacting label pairs are disclosed in U.S. Pat. No. 6,534,274, herein incorporated by reference in its entirety.
  • Another example of a detection probe having self-complementarity is a “molecular beacon.” Molecular beacons include nucleic acid molecules having a target complementary sequence, an affinity pair (or nucleic acid arms) holding the probe in a closed conformation in the absence of a target sequence present in an amplification reaction, and a label pair that interacts when the probe is in a closed conformation. Hybridization of the target sequence and the target complementary sequence separates the members of the affinity pair, thereby shifting the probe to an open conformation. The shift to the open conformation is detectable due to reduced interaction of the label pair, which may be, for example, a fluorophore and a quencher (e.g., DABCYL and EDANS). Molecular beacons are disclosed in U.S. Pat. Nos. 5,925,517 and 6,150,097, herein incorporated by reference in its entirety.
  • Other self-hybridizing probes are well known to those of ordinary skill in the art. By way of non-limiting example, probe binding pairs having interacting labels, such as those disclosed in U.S. Pat. No. 5,928,862 (herein incorporated by reference in its entirety) might be adapted for use in the present invention. Probe systems used to detect single nucleotide polymorphisms (SNPs) might also be utilized in the present invention. Additional detection systems include “molecular switches,” as disclosed in U.S. Publ. No. 20050042638, herein incorporated by reference in its entirety. Other probes, such as those comprising intercalating dyes and/or fluorochromes, are also useful for detection of amplification products in the present invention. See, e.g., U.S. Pat. No. 5,814,447 (herein incorporated by reference in its entirety). Additional detection methods may include microarrays and electrophoresis (e.g., gel electrophoresis). Detection methods can be quantitative or semi-quantitative. Detection methods may also comprise the use of one or more labels (e.g., radioisotopes, fluorophores, chemiluminophores, enzymes, colloidal particles, and fluorescent microparticles, as well as antigens, antibodies, haptens, avidin/streptavidin, biotin, haptens, or enzyme cofactors/substrates, enzymes).
  • Southern and Northern blotting is used to detect specific DNA or RNA sequences, respectively. DNA or RNA extracted from a sample is fragmented, electrophoretically separated on a matrix gel, and transferred to a membrane filter. The filter bound DNA or RNA is subject to hybridization with a labeled probe complementary to the sequence of interest. Hybridized probe bound to the filter is detected. A variant of the procedure is the reverse Northern blot, in which the substrate nucleic acid that is affixed to the membrane is a collection of isolated DNA fragments and the probe is RNA extracted from a tissue and labeled.
  • ii. In vivo Imaging
  • ncRNAs may also be detected using in vivo imaging techniques, including but not limited to: radionuclide imaging; positron emission tomography (PET); computerized axial tomography, X-ray or magnetic resonance imaging method, fluorescence detection, and chemiluminescent detection. In some embodiments, in vivo imaging techniques are used to visualize the presence of or expression of cancer markers in an animal (e.g., a human or non-human mammal). For example, in some embodiments, cancer marker mRNA or protein is labeled using a labeled antibody specific for the cancer marker. A specifically bound and labeled antibody can be detected in an individual using an in vivo imaging method, including, but not limited to, radionuclide imaging, positron emission tomography, computerized axial tomography, X-ray or magnetic resonance imaging method, fluorescence detection, and chemiluminescent detection. Methods for generating antibodies to the cancer markers of the present invention are described below.
  • The in vivo imaging methods of embodiments of the present invention are useful in the identification of cancers that express ncRNAs (e.g., prostate cancer). In vivo imaging is used to visualize the presence or level of expression of a ncRNA. Such techniques allow for diagnosis without the use of an unpleasant biopsy. The in vivo imaging methods of embodiments of the present invention can further be used to detect metastatic cancers in other parts of the body.
  • In some embodiments, reagents (e.g., antibodies) specific for the cancer markers of the present invention are fluorescently labeled. The labeled antibodies are introduced into a subject (e.g., orally or parenterally). Fluorescently labeled antibodies are detected using any suitable method (e.g., using the apparatus described in U.S. Pat. No. 6,198,107, herein incorporated by reference).
  • In other embodiments, antibodies are radioactively labeled. The use of antibodies for in vivo diagnosis is well known in the art. Sumerdon et al., (Nucl. Med. Biol 17:247-254 [1990] have described an optimized antibody-chelator for the radioimmunoscintographic imaging of tumors using Indium-111 as the label. Griffin et al., (J Clin One 9:631-640 [1991]) have described the use of this agent in detecting tumors in patients suspected of having recurrent colorectal cancer. The use of similar agents with paramagnetic ions as labels for magnetic resonance imaging is known in the art (Lauffer, Magnetic Resonance in Medicine 22:339-342 [1991]). The label used will depend on the imaging modality chosen. Radioactive labels such as Indium-111, Technetium-99m, or Iodine-131 can be used for planar scans or single photon emission computed tomography (SPECT). Positron emitting labels such as Fluorine-19 can also be used for positron emission tomography (PET). For MRI, paramagnetic ions such as Gadolinium (III) or Manganese (II) can be used.
  • Radioactive metals with half-lives ranging from 1 hour to 3.5 days are available for conjugation to antibodies, such as scandium-47 (3.5 days) gallium-67 (2.8 days), gallium-68 (68 minutes), technetiium-99m (6 hours), and indium-111 (3.2 days), of which gallium-67, technetium-99m, and indium-111 are preferable for gamma camera imaging, gallium-68 is preferable for positron emission tomography.
  • A useful method of labeling antibodies with such radiometals is by means of a bifunctional chelating agent, such as diethylenetriaminepentaacetic acid (DTPA), as described, for example, by Khaw et al. (Science 209:295 [1980]) for In-111 and Tc-99m, and by Scheinberg et al. (Science 215:1511 [1982]). Other chelating agents may also be used, but the 1-(p-carboxymethoxybenzyl)EDTA and the carboxycarbonic anhydride of DTPA are advantageous because their use permits conjugation without affecting the antibody's immunoreactivity substantially.
  • Another method for coupling DPTA to proteins is by use of the cyclic anhydride of DTPA, as described by Hnatowich et al. (Int. J. Appl. Radiat. Isot. 33:327 [1982]) for labeling of albumin with In-111, but which can be adapted for labeling of antibodies. A suitable method of labeling antibodies with Tc-99m which does not use chelation with DPTA is the pretinning method of Crockford et al., (U.S. Pat. No. 4,323,546, herein incorporated by reference).
  • A method of labeling immunoglobulins with Tc-99m is that described by Wong et al. (Int. J. Appl. Radiat. Isot., 29:251 [1978]) for plasma protein, and recently applied successfully by Wong et al. (J. Nucl. Med., 23:229 [1981]) for labeling antibodies.
  • In the case of the radiometals conjugated to the specific antibody, it is likewise desirable to introduce as high a proportion of the radiolabel as possible into the antibody molecule without destroying its immunospecificity. A further improvement may be achieved by effecting radiolabeling in the presence of the ncRNA, to insure that the antigen binding site on the antibody will be protected. The antigen is separated after labeling.
  • In still further embodiments, in vivo biophotonic imaging (Xenogen, Almeda, Calif.) is utilized for in vivo imaging. This real-time in vivo imaging utilizes luciferase. The luciferase gene is incorporated into cells, microorganisms, and animals (e.g., as a fusion protein with a cancer marker of the present invention). When active, it leads to a reaction that emits light. A CCD camera and software is used to capture the image and analyze it.
  • iii. Data Analysis
  • In some embodiments, a computer-based analysis program is used to translate the raw data generated by the detection assay (e.g., the presence, absence, or amount of a given marker or markers) into data of predictive value for a clinician. The clinician can access the predictive data using any suitable means. Thus, in some preferred embodiments, the present invention provides the further benefit that the clinician, who is not likely to be trained in genetics or molecular biology, need not understand the raw data. The data is presented directly to the clinician in its most useful form. The clinician is then able to immediately utilize the information in order to optimize the care of the subject.
  • The present invention contemplates any method capable of receiving, processing, and transmitting the information to and from laboratories conducting the assays, information providers, medical personnel, and subjects. For example, in some embodiments of the present invention, a sample (e.g., a biopsy or a serum or urine sample) is obtained from a subject and submitted to a profiling service (e.g., clinical lab at a medical facility, genomic profiling business, etc.), located in any part of the world (e.g., in a country different than the country where the subject resides or where the information is ultimately used) to generate raw data. Where the sample comprises a tissue or other biological sample, the subject may visit a medical center to have the sample obtained and sent to the profiling center, or subjects may collect the sample themselves (e.g., a urine sample) and directly send it to a profiling center. Where the sample comprises previously determined biological information, the information may be directly sent to the profiling service by the subject (e.g., an information card containing the information may be scanned by a computer and the data transmitted to a computer of the profiling center using an electronic communication systems). Once received by the profiling service, the sample is processed and a profile is produced (i.e., expression data), specific for the diagnostic or prognostic information desired for the subject.
  • The profile data is then prepared in a format suitable for interpretation by one or more medical personnel (e.g., a treating clinician, physician assistant, nurse, or pharmacist). For example, rather than providing raw expression data, the prepared format may represent a diagnosis or risk assessment (e.g., presence or absence of a ncRNA) for the subject, along with recommendations for particular treatment options. The data may be displayed to the medical personnel by any suitable method. For example, in some embodiments, the profiling service generates a report that can be printed for the medical personnel (e.g., at the point of care) or displayed to the medical personnel on a computer monitor.
  • In some embodiments, the information is first analyzed at the point of care or at a regional facility. The raw data is then sent to a central processing facility for further analysis and/or to convert the raw data to information useful for medical personnel or patient. The central processing facility provides the advantage of privacy (all data is stored in a central facility with uniform security protocols), speed, and uniformity of data analysis. The central processing facility can then control the fate of the data following treatment of the subject. For example, using an electronic communication system, the central facility can provide data to the medical personnel, the subject, or researchers.
  • In some embodiments, the subject is able to directly access the data using the electronic communication system. The subject may chose further intervention or counseling based on the results.
  • In some embodiments, the data is used for research use. For example, the data may be used to further optimize the inclusion or elimination of markers as useful indicators of a particular condition or stage of disease or as a companion diagnostic to determine a treatment course of action.
  • iv. Compositions & Kits
  • Compositions for use in the diagnostic methods described herein include, but are not limited to, probes, amplification oligonucleotides, and the like.
  • The probe and antibody compositions of the present invention may also be provided in the form of an array.
  • The compositions and kits may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more probes.
  • The probes may hybridize to 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more target molecules. The target molecules may be a ncRNA, RNA, DNA, cDNA, mRNA, a portion or fragment thereof or a combination thereof. In some instances, at least a portion of the target molecules are ncRNAs. The probes may hybridize to 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more ncRNAs disclosed herein.
  • Typically, the probes comprise a target specific sequence. The target specific sequence may be complementary to at least a portion of the target molecule. The target specific sequence may be at least about 50% or more, 55% or more, 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, or 100% complementary to at least a portion of the target molecule.
  • The target specific sequence may be at least about 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 16 or more, 17 or more, 18 or more, 19 or more, 20 or more nucleotides in length. In some instances, the target specific sequence is between about 8 to about 20 nucleotides, 10 to about 18 nucleotides, or 12 to about 16 nucleotides in length.
  • The compositions and kits may comprise a plurality of probes, wherein the two or more probes of the plurality of probes comprise identical target specific sequences. The compositions and kits may comprise a plurality of probes, wherein the two or more probes of the plurality of probes comprise different target specific sequences.
  • The probes may further comprise a unique sequence. The unique sequence is noncomplementary to the ncRNA. The unique sequence may comprise a label, barcode, or unique identifier. The unique sequence may comprise a random sequence, nonrandom sequence, or a combination thereof. The unique sequence may be at least about 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 16 or more, 17 or more, 18 or more, 19 or more, 20 or more, 22 or more, 24 or more, 26 or more, 28 or more, 30 or more nucleotides in length. In some instances, the unique sequence is between about 8 to about 20 nucleotides, 10 to about 18 nucleotides, or 12 to about 16 nucleotides in length.
  • The unique sequence may allow differentiation of two or more target molecules. The two or more target molecules may have identical sequences. Thus, the unique sequence may allow quantification of a target molecule. Alternatively, the two or more target molecules may have different sequences. Thus, the unique sequence may allow detection of the target molecules. The compositions and kits may comprise a plurality of probes for quantifying one or more target molecules. The compositions and kits may comprise a plurality of probes for detecting one or more target molecules.
  • The unique sequence may allow differentiation of two or more samples. The compositions and kits may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more probe sets for differentiating two or more samples from one or more subjects. The two or more samples may be from two or more different subjects. For example, the compositions and kits comprise a first set of probes comprising a first unique sequence that is specific for a first subject and a second set of probes comprising a second unique sequence that is specific for a second subject. The compositions and kits may further comprise one or more sets of probes with one or more unique sequences to differentiate one or more additional subjects.
  • The compositions and kits may comprise 2 or more probe sets for differentiating from 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more samples from 1 or more subjects.
  • The compositions and kits may comprise 2 or more probe sets for differentiating 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more samples from one or more cells, tissues, organs, bodily fluid, or a combination thereof.
  • The compositions and kits may comprise 2 or more probe sets for differentiating samples from 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more subjects.
  • Alternatively, or additionally, the two or more samples may be from two or more different timepoints from the same subject or different subjects. For example, the compositions and kits comprise a first set of probes comprising a first unique sequence that is specific for a first subject and a second set of probes comprising a second unique sequence that is specific for a second subject. The compositions and kits may comprise 2 or more probe sets for differentiating samples from 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more timepoints. The timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more hours. The timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more days. The timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more weeks. The timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more months. The timepoints may be every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or more years. The timepoints may be before diagnosis, after diagnosis, before treatment, during treatment, after treatment, before metastasis, after metastatis, before remission, during remission, or a combination thereof.
  • The compositions and kits may comprise a first probe comprising a first target-specific sequence and a first unique sequence and a second probe comprising a second target-specific sequence and a second unique sequence, wherein the first target specific sequence and the second target specific sequence are identical and the first unique sequence and the second unique sequence are different. The compositions and kits may comprise a first probe comprising a first target-specific sequence and a first unique sequence and a second probe comprising a second target-specific sequence and a second unique sequence, wherein the first target specific sequence and the second target specific sequence are different and the first unique sequence and the second unique sequence are different. The compositions and kits may comprise a first probe comprising a first target-specific sequence and a first unique sequence and a second probe comprising a second target-specific sequence and a second unique sequence, wherein the first target specific sequence and the second target specific sequence are identical and the first unique sequence and the second unique sequence are identical. The compositions and kits may comprise a first probe comprising a first target-specific sequence and a first unique sequence and a second probe comprising a second target-specific sequence and a second unique sequence, wherein the first target specific sequence and the second target specific sequence are different and the first unique sequence and the second unique sequence are identical.
  • The probes may further comprise a universal sequence. The universal sequence may comprise a primer binding site. The universal sequence may enable detection of the target sequence. The universal sequence may enable amplification of the target sequence. The universal sequence may enable transcription or reverse transcription of the target sequence. The universal sequence may enable sequencing of the target sequence.
  • The probe and antibody compositions of the present invention may also be provided on a solid support. The solid support may comprise one or more beads, plates, solid surfaces, wells, chips, or a combination thereof. The beads may be magnetic, antibody coated, protein A crosslinked, protein G crosslinked, streptavidin coated, oligonucleotide conjugated, silica coated, or a combination thereof. Examples of beads include, but are not limited to, Ampure beads, AMPure XP beads, streptavidin beads, agarose beads, magnetic beads, Dynabeads®, MACS® microbeads, antibody conjugated beads (e.g., anti-immunoglobulin microbead), protein A conjugated beads, protein G conjugated beads, protein A/G conjugated beads, protein L conjugated beads, oligo-dT conjugated beads, silica beads, silica-like beads, anti-biotin microbead, anti-fluorochrome microbead, and BcMag™ Carboxy-Terminated Magnetic Beads.
  • The compositions and kits may comprise primers and primer pairs capable of amplifying target molecules, or fragments or subsequences or complements thereof. The nucleotide sequences of the target molecules may be provided in computer-readable media for in silico applications and as a basis for the design of appropriate primers for amplification of one or more target molecules.
  • Primers based on the nucleotide sequences of target molecules can be designed for use in amplification of the target molecules. For use in amplification reactions such as PCR, a pair of primers can be used. The exact composition of the primer sequences is not critical to the invention, but for most applications the primers may hybridize to specific sequences of the target molecules or the universal sequence of the probe under stringent conditions, particularly under conditions of high stringency, as known in the art. The pairs of primers are usually chosen so as to generate an amplification product of at least about 15 or more, 20 or more, 30 or more, 40 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 125 or more, 150 or more, 175 or more, 200 or more, 250 or more, 300 or more, 350 or more, 400 or more, 450 or more, 500 or more, 600 or more, 700 or more, 800 or more, 900 or more, or 1000 or more nucleotides. Algorithms for the selection of primer sequences are generally known, and are available in commercial software packages. These primers may be used in standard quantitative or qualitative PCR-based assays to assess transcript expression levels of target molecules. Alternatively, these primers may be used in combination with probes, such as molecular beacons in amplifications using real-time PCR.
  • One skilled in the art also appreciates that the nucleotide sequence of the entire length of the primer does not need to be derived from the target sequence. Thus, for example, the primer may comprise nucleotide sequences at the 5′ and/or 3′ termini that are not derived from the target molecule. Nucleotide sequences which are not derived from the nucleotide sequence of the target molecule may provide additional functionality to the primer. For example, they may provide a restriction enzyme recognition sequence or a “tag” that facilitates detection, isolation, purification or immobilization onto a solid support. Alternatively, the additional nucleotides may provide a self-complementary sequence that allows the primer to adopt a hairpin configuration. Such configurations may be necessary for certain primers, for example, molecular beacon and Scorpion primers, which can be used in solution hybridization techniques.
  • The probes or primers can incorporate moieties useful in detection, isolation, purification, or immobilization, if desired. Such moieties are well-known in the art (see, for example, Ausubel et al., (1997 & updates) Current Protocols in Molecular Biology, Wiley & Sons, New York) and are chosen such that the ability of the probe to hybridize with its target molecule is not affected.
  • Examples of suitable moieties are detectable labels, such as radioisotopes, fluorophores, chemiluminophores, enzymes, colloidal particles, and fluorescent microparticles, as well as antigens, antibodies, haptens, avidin/streptavidin, biotin, haptens, enzyme cofactors/substrates, enzymes, and the like.
  • A label can optionally be attached to or incorporated into a probe or primer to allow detection and/or quantitation of a target polynucleotide representing the target molecule of interest. The target polynucleotide may be the expressed target molecule RNA itself, a cDNA copy thereof, or an amplification product derived therefrom, and may be the positive or negative strand, so long as it can be specifically detected in the assay being used. Similarly, an antibody may be labeled.
  • In certain multiplex formats, labels used for detecting different target molecules may be distinguishable. The label can be attached directly (e.g., via covalent linkage) or indirectly, e.g., via a bridging molecule or series of molecules (e.g., a molecule or complex that can bind to an assay component, or via members of a binding pair that can be incorporated into assay components, e.g. biotin-avidin or streptavidin). Many labels are commercially available in activated forms which can readily be used for such conjugation (for example through amine acylation), or labels may be attached through known or determinable conjugation schemes, many of which are known in the art.
  • Labels useful in the invention described herein include any substance which can be detected when bound to or incorporated into the target molecule. Any effective detection method can be used, including optical, spectroscopic, electrical, piezoelectrical, magnetic, Raman scattering, surface plasmon resonance, colorimetric, calorimetric, etc. A label is typically selected from a chromophore, a lumiphore, a fluorophore, one member of a quenching system, a chromogen, a hapten, an antigen, a magnetic particle, a material exhibiting nonlinear optics, a semiconductor nanocrystal, a metal nanoparticle, an enzyme, an antibody or binding portion or equivalent thereof, an aptamer, and one member of a binding pair, and combinations thereof. Quenching schemes may be used, wherein a quencher and a fluorophore as members of a quenching pair may be used on a probe, such that a change in optical parameters occurs upon binding to the target introduce or quench the signal from the fluorophore. One example of such a system is a molecular beacon. Suitable quencher/fluorophore systems are known in the art. The label may be bound through a variety of intermediate linkages. For example, a target polynucleotide may comprise a biotin-binding species, and an optically detectable label may be conjugated to biotin and then bound to the labeled target polynucleotide. Similarly, a polynucleotide sensor may comprise an immunological species such as an antibody or fragment, and a secondary antibody containing an optically detectable label may be added.
  • Chromophores useful in the methods described herein include any substance which can absorb energy and emit light. For multiplexed assays, a plurality of different signaling chromophores can be used with detectably different emission spectra. The chromophore can be a lumophore or a fluorophore. Typical fluorophores include fluorescent dyes, semiconductor nanocrystals, lanthanide chelates, polynucleotide-specific dyes and green fluorescent protein.
  • Coding schemes may optionally be used, comprising encoded particles and/or encoded tags associated with different polynucleotides of the invention. A variety of different coding schemes are known in the art, including fluorophores, including SCNCs, deposited metals, and RF tags.
  • Polynucleotides from the described target molecules may be employed as probes for detecting target molecules expression, for ligation amplification schemes, or may be used as primers for amplification schemes of all or a portion of a target molecules. When amplified, either strand produced by amplification may be provided in purified and/or isolated form.
  • In some instances, the compositions and kits comprise a biomarker library. The biomarker library may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more target molecules. The target molecules may be a ncRNA, RNA, DNA, cDNA, mRNA, a portion or fragment thereof or a combination thereof. In some instances, at least a portion of the target molecules are ncRNAs. The biomarker library may comprise 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 20 or more, 25 or more, 30 or more, 35 or more, 40 or more, 45 or more, 50 or more, 60 or more, 70 or more, 80 or more, 90 or more, 100 or more, 110 or more, 120 or more ncRNAs disclosed herein. The biomarker library may comprise one or more PCATs, SChLAP-1, M41, ENST-75, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, any one of SEQ ID NOs 1-9, or a combination thereof.
  • In some embodiments, is a kit for analyzing a cancer comprising (a) a probe set comprising a plurality of probes comprising target specific sequences complementary to one or more target molecules, wherein the one or more target molecules comprise one or more ncRNAs; and (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the one or more target molecules in a sample. The target molecules may comprise one or more PCATs, SChLAP-1, M41, ENST-75, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, any one of SEQ ID NOs 1-9, or a combination thereof.
  • In some embodiments, is a kit for analyzing a cancer comprising (a) a probe set comprising a plurality of probes comprising target specific sequences complementary to one or more target molecules of a biomarker library; and (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the one or more target molecules in a sample. Control samples and/or nucleic acids may optionally be provided in the kit. Control samples may include tissue and/or nucleic acids obtained from or representative of tumor samples from a healthy subject, as well as tissue and/or nucleic acids obtained from or representative of tumor samples from subjects diagnosed with a cancer.
  • Instructions for using the kit to perform one or more methods of the invention can be provided, and can be provided in any fixed medium. The instructions may be located inside or outside a container or housing, and/or may be printed on the interior or exterior of any surface thereof. A kit may be in multiplex form for concurrently detecting and/or quantitating one or more different target polynucleotides representing the expressed target molecules.
  • v. Devices
  • Devices useful for performing methods of the invention are also provided. The devices can comprise means for characterizing the expression level of a target molecule of the invention, for example components for performing one or more methods of nucleic acid extraction, amplification, and/or detection. Such components may include one or more of an amplification chamber (for example a thermal cycler), a plate reader, a spectrophotometer, capillary electrophoresis apparatus, a chip reader, and or robotic sample handling components. These components ultimately can obtain data that reflects the expression level of the target molecules used in the assay being employed.
  • The devices may include an excitation and/or a detection means. Any instrument that provides a wavelength that can excite a species of interest and is shorter than the emission wavelength(s) to be detected can be used for excitation. Commercially available devices can provide suitable excitation wavelengths as well as suitable detection component.
  • Exemplary excitation sources include a broadband UV light source such as a deuterium lamp with an appropriate filter, the output of a white light source such as a xenon lamp or a deuterium lamp after passing through a monochromator to extract out the desired wavelength(s), a continuous wave (cw) gas laser, a solid state diode laser, or any of the pulsed lasers. Emitted light can be detected through any suitable device or technique; many suitable approaches are known in the art. For example, a fluorimeter or spectrophotometer may be used to detect whether the test sample emits light of a wavelength characteristic of a label used in an assay.
  • The devices typically comprise a means for identifying a given sample, and of linking the results obtained to that sample. Such means can include manual labels, barcodes, and other indicators which can be linked to a sample vessel, and/or may optionally be included in the sample itself, for example where an encoded particle is added to the sample. The results may be linked to the sample, for example in a computer memory that contains a sample designation and a record of expression levels obtained from the sample. Linkage of the results to the sample can also include a linkage to a particular sample receptacle in the device, which is also linked to the sample identity.
  • The devices also comprise a means for correlating the expression levels of the target molecules being studied with a prognosis of disease outcome. Such means may comprise one or more of a variety of correlative techniques, including lookup tables, algorithms, multivariate models, and linear or nonlinear combinations of expression models or algorithms. The expression levels may be converted to one or more likelihood scores, reflecting a likelihood that the patient providing the sample may exhibit a particular disease outcome. The models and/or algorithms can be provided in machine readable format and can optionally further designate a treatment modality for a patient or class of patients.
  • The device also comprises output means for outputting the disease status, prognosis and/or a treatment modality. Such output means can take any form which transmits the results to a patient and/or a healthcare provider, and may include a monitor, a printed format, or both. The device may use a computer system for performing one or more of the steps provided.
  • The methods disclosed herein may also comprise the transmission of data/information. For example, data/information derived from the detection and/or quantification of the target may be transmitted to another device and/or instrument. In some instances, the information obtained from an algorithm may also be transmitted to another device and/or instrument. Transmission of the data/information may comprise the transfer of data/information from a first source to a second source. The first and second sources may be in the same approximate location (e.g., within the same room, building, block, campus). Alternatively, first and second sources may be in multiple locations (e.g., multiple cities, states, countries, continents, etc).
  • Transmission of the data/information may comprise digital transmission or analog transmission. Digital transmission may comprise the physical transfer of data (a digital bit stream) over a point-to-point or point-to-multipoint communication channel. Examples of such channels are copper wires, optical fibres, wireless communication channels, and storage media. The data may be represented as an electromagnetic signal, such as an electrical voltage, radiowave, microwave, or infrared signal.
  • Analog transmission may comprise the transfer of a continuously varying analog signal. The messages can either be represented by a sequence of pulses by means of a line code (baseband transmission), or by a limited set of continuously varying wave forms (passband transmission), using a digital modulation method. The passband modulation and corresponding demodulation (also known as detection) can be carried out by modem equipment. According to the most common definition of digital signal, both baseband and passband signals representing bit-streams are considered as digital transmission, while an alternative definition only considers the baseband signal as digital, and passband transmission of digital data as a form of digital-to-analog conversion.
  • vii. Samples
  • Samples for use with the compositions and kits and in the methods of the present invention comprise nucleic acids suitable for providing RNA expression information. In principle, the biological sample from which the expressed RNA is obtained and analyzed for target molecule expression can be any material suspected of comprising cancer tissue or cells. The sample can be a biological sample used directly in a method of the invention. Alternatively, the sample can be a sample prepared from a biological sample.
  • In one embodiment, the sample or portion of the sample comprising or suspected of comprising cancer tissue or cells can be any source of biological material, including cells, tissue, secretions, or fluid, including bodily fluids. Non-limiting examples of the source of the sample include an aspirate, a needle biopsy, a cytology pellet, a bulk tissue preparation or a section thereof obtained for example by surgery or autopsy, lymph fluid, blood, plasma, serum, tumors, and organs. Alternatively, or additionally, the source of the sample can be urine, bile, excrement, sweat, tears, vaginal fluids, spinal fluid, and stool. In some instances, the sources of the sample are secretions. In some instances, the secretions are exosomes.
  • The samples may be archival samples, having a known and documented medical outcome, or may be samples from current patients whose ultimate medical outcome is not yet known.
  • In some embodiments, the sample may be dissected prior to molecular analysis. The sample may be prepared via macrodissection of a bulk tumor specimen or portion thereof, or may be treated via microdissection, for example via Laser Capture Microdissection (LCM).
  • The sample may initially be provided in a variety of states, as fresh tissue, fresh frozen tissue, fine needle aspirates, and may be fixed or unfixed. Frequently, medical laboratories routinely prepare medical samples in a fixed state, which facilitates tissue storage. A variety of fixatives can be used to fix tissue to stabilize the morphology of cells, and may be used alone or in combination with other agents. Exemplary fixatives include crosslinking agents, alcohols, acetone, Bouin's solution, Zenker solution, Hely solution, osmic acid solution and Carnoy solution.
  • Crosslinking fixatives can comprise any agent suitable for forming two or more covalent bonds, for example, an aldehyde. Sources of aldehydes typically used for fixation include formaldehyde, paraformaldehyde, glutaraldehyde or formalin. Preferably, the crosslinking agent comprises formaldehyde, which may be included in its native form or in the form of paraformaldehyde or formalin. One of skill in the art would appreciate that for samples in which crosslinking fixatives have been used special preparatory steps may be necessary including for example heating steps and proteinase-k digestion.
  • One or more alcohols may be used to fix tissue, alone or in combination with other fixatives. Exemplary alcohols used for fixation include methanol, ethanol and isopropanol.
  • Formalin fixation is frequently used in medical laboratories. Formalin comprises both an alcohol, typically methanol, and formaldehyde, both of which can act to fix a biological sample.
  • Whether fixed or unfixed, the biological sample may optionally be embedded in an embedding medium. Exemplary embedding media used in histology including paraffin, Tissue-Tek® V.I.P.™, Paramat, Paramat Extra, Paraplast, Paraplast X-tra, Paraplast Plus, Peel Away Paraffin Embedding Wax, Polyester Wax, Carbowax Polyethylene Glycol, Polyfin™, Tissue Freezing Medium TFMFM, Cryo-Gef™, and OCT Compound (Electron Microscopy Sciences, Hatfield, Pa.). Prior to molecular analysis, the embedding material may be removed via any suitable techniques, as known in the art. For example, where the sample is embedded in wax, the embedding material may be removed by extraction with organic solvent(s), for example xylenes. Kits are commercially available for removing embedding media from tissues. Samples or sections thereof may be subjected to further processing steps as needed, for example serial hydration or dehydration steps.
  • In some embodiments, the sample is a fixed, wax-embedded biological sample. Frequently, samples from medical laboratories are provided as fixed, wax-embedded samples, most commonly as formalin-fixed, paraffin embedded (FFPE) tissues.
  • Whatever the source of the biological sample, the target polynucleotide that is ultimately assayed can be prepared synthetically (in the case of control sequences), but typically is purified from the biological source and subjected to one or more preparative steps. The RNA may be purified to remove or diminish one or more undesired components from the biological sample or to concentrate it. Conversely, where the RNA is too concentrated for the particular assay, it may be diluted.
    • II. Drug Screening Applications
  • In some embodiments, the present invention provides drug screening assays (e.g., to screen for anticancer drugs). The screening methods of the present invention utilize ncRNAs. For example, in some embodiments, the present invention provides methods of screening for compounds that alter the expression or activity of ncRNAs. The compounds may increase the expression or activity of the ncRNAs. The compounds may decrease the expression or activity of the ncRNAs. The compounds or agents may interfere with transcription, by interacting, for example, with the promoter region. The compounds or agents may interfere with mRNA (e.g., by RNA interference, antisense technologies, etc.). The compounds or agents may interfere with pathways that are upstream or downstream of the biological activity of ncRNAs. In some embodiments, candidate compounds are antisense or interfering RNA agents (e.g., oligonucleotides) directed against ncRNAs. In other embodiments, candidate compounds are antibodies or small molecules that specifically bind to a ncRNA regulator. Alternatively, or additionally, the candidate compounds are expression products that inhibit the biological function of the ncRNAs.
  • In one screening method, candidate compounds are evaluated for their ability to alter ncRNAs expression by contacting a compound with a cell expressing a ncRNA and then assaying for the effect of the candidate compounds on expression. In some embodiments, the effect of candidate compounds on expression of ncRNAs is assayed for by detecting the level ncRNA expressed by the cell. mRNA expression can be detected by any suitable method.
    • III. Diagnosis, Prognosis, and Monitoring
  • The methods, compositions, and kits disclosed herein may be used for the diagnosis, prognosis, and/or monitoring the status or outcome of a cancer in a subject. In some embodiments, the diagnosing, predicting, and/or monitoring the status or outcome of a cancer comprises determining the malignancy or malignant potential of the cancer or tumor. Alternatively, the diagnosing, predicting, and/or monitoring the status or outcome of a cancer comprises determining the stage of the cancer. The diagnosing, predicting, and/or monitoring the status or outcome of a cancer can comprise determining the tumor grade. Alternatively, the diagnosing, predicting, and/or monitoring the status or outcome of a cancer comprises assessing the risk of developing a cancer. In some embodiments, the diagnosing, predicting, and/or monitoring the status or outcome of a cancer includes assessing the risk of cancer recurrence. In some embodiments, diagnosing, predicting, and/or monitoring the status or outcome of a cancer may comprise determining the efficacy of treatment.
  • In some embodiments, diagnosing, predicting, and/or monitoring the status or outcome of a cancer may comprise determining a therapeutic regimen. Determining a therapeutic regimen may comprise administering an anti-cancer therapeutic. Alternatively, determining the treatment for the cancer may comprise modifying a therapeutic regimen. Modifying a therapeutic regimen may comprise increasing, decreasing, or terminating a therapeutic regimen.
  • In some instances, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 50%. In other instances, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 60%. The methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 65%. Alternatively, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 70%. In some instances, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 75%. In other instances, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 80%. The methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 85%. Alternatively, the methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 90%. The methods disclosed herein can diagnose, prognose, and/or monitor the status or outcome of a cancer in a subject with an accuracy of at least about 95%.
  • The invention also encompasses any of the methods disclosed herein where the sensitivity is at least about 45%. In some embodiments, the sensitivity is at least about 50%. In some embodiments, the sensitivity is at least about 55%. In some embodiments, the sensitivity is at least about 60%. In some embodiments, the sensitivity is at least about 65%. In some embodiments, the sensitivity is at least about 70%. In some embodiments, the sensitivity is at least about 75%. In some embodiments, the sensitivity is at least about 80%. In some embodiments, the sensitivity is at least about 85%. In some embodiments, the sensitivity is at least about 90%. In some embodiments, the sensitivity is at least about 95%.
  • The invention also encompasses any of the methods disclosed herein where the expression level determines the status or outcome of a cancer in the subject with at least about 45% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 50% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 55% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 60% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 65% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 70% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 75% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 80% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 85% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 90% specificity. In some embodiments, the expression level determines the status or outcome of a cancer in the subject with at least about 95% specificity.
  • Cancer
  • The systems, compositions and methods disclosed herein may be used to diagnosis, monitor and/or predict the status or outcome of a cancer. Generally, a cancer is characterized by the uncontrolled growth of abnormal cells anywhere in a body. The abnormal cells may be termed cancer cells, malignant cells, or tumor cells. Many cancers and the abnormal cells that compose the cancer tissue are further identified by the name of the tissue that the abnormal cells originated from (for example, breast cancer, lung cancer, colon cancer, prostate cancer, pancreatic cancer, thyroid cancer). Cancer is not confined to humans; animals and other living organisms can get cancer.
  • In some instances, the cancer may be malignant. Alternatively, the cancer may be benign. The cancer may be a recurrent and/or refractory cancer. Most cancers can be classified as a carcinoma, sarcoma, leukemia, lymphoma, myeloma, or a central nervous system cancer.
  • The cancer may be a sarcoma. Sarcomas are cancers of the bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. Sarcomas include, but are not limited to, bone cancer, fibrosarcoma, chondrosarcoma, Ewing's sarcoma, malignant hemangioendothelioma, malignant schwannoma, bilateral vestibular schwannoma, osteosarcoma, soft tissue sarcomas (e.g. alveolar soft part sarcoma, angiosarcoma, cystosarcoma phylloides, dermatofibrosarcoma, desmoid tumor, epithelioid sarcoma, extraskeletal osteosarcoma, fibrosarcoma, hemangiopericytoma, hemangiosarcoma, Kaposi's sarcoma, leiomyosarcoma, liposarcoma, lymphangiosarcoma, lymphosarcoma, malignant fibrous histiocytoma, neurofibrosarcoma, rhabdomyosarcoma, and synovial sarcoma).
  • Alternatively, the cancer may be a carcinoma. Carcinomas are cancers that begin in the epithelial cells, which are cells that cover the surface of the body, produce hormones, and make up glands. By way of non-limiting example, carcinomas include breast cancer, pancreatic cancer, lung cancer, colon cancer, colorectal cancer, rectal cancer, kidney cancer, bladder cancer, stomach cancer, prostate cancer, liver cancer, ovarian cancer, brain cancer, vaginal cancer, vulvar cancer, uterine cancer, oral cancer, penic cancer, testicular cancer, esophageal cancer, skin cancer, cancer of the fallopian tubes, head and neck cancer, gastrointestinal stromal cancer, adenocarcinoma, cutaneous or intraocular melanoma, cancer of the anal region, cancer of the small intestine, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, cancer of the urethra, cancer of the renal pelvis, cancer of the ureter, cancer of the endometrium, cancer of the cervix, cancer of the pituitary gland, neoplasms of the central nervous system (CNS), primary CNS lymphoma, brain stem glioma, and spinal axis tumors. In some instances, the cancer is a skin cancer, such as a basal cell carcinoma, squamous, melanoma, nonmelanoma, or actinic (solar) keratosis. Preferably, the cancer is a prostate cancer. Alternatively, the cancer may be a thyroid cancer. The cancer can be a pancreatic cancer. In some instances, the cancer is a bladder cancer.
  • In some instances, the cancer is a lung cancer. Lung cancer can start in the airways that branch off the trachea to supply the lungs (bronchi) or the small air sacs of the lung (the alveoli). Lung cancers include non-small cell lung carcinoma (NSCLC), small cell lung carcinoma, and mesotheliomia. Examples of NSCLC include squamous cell carcinoma, adenocarcinoma, and large cell carcinoma. The mesothelioma may be a cancerous tumor of the lining of the lung and chest cavity (pleura) or lining of the abdomen (peritoneum). The mesothelioma may be due to asbestos exposure. The cancer may be a brain cancer, such as a glioblastoma.
  • Alternatively, the cancer may be a central nervous system (CNS) tumor. CNS tumors may be classified as gliomas or nongliomas. The glioma may be malignant glioma, high grade glioma, diffuse intrinsic pontine glioma. Examples of gliomas include astrocytomas, oligodendrogliomas (or mixtures of oligodendroglioma and astocytoma elements), and ependymomas. Astrocytomas include, but are not limited to, low-grade astrocytomas, anaplastic astrocytomas, glioblastoma multiforme, pilocytic astrocytoma, pleomorphic xanthoastrocytoma, and subependymal giant cell astrocytoma. Oligodendrogliomas include low-grade oligodendrogliomas (or oligoastrocytomas) and anaplastic oligodendriogliomas. Nongliomas include meningiomas, pituitary adenomas, primary CNS lymphomas, and medulloblastomas. In some instances, the cancer is a meningioma.
  • The cancer may be leukemia. The leukemia may be an acute lymphocytic leukemia, acute myelocytic leukemia, chronic lymphocytic leukemia, or chronic myelocytic leukemia. Additional types of leukemias include hairy cell leukemia, chronic myelomonocytic leukemia, and juvenile myelomonocytic-leukemia.
  • In some instances, the cancer is a lymphoma. Lymphomas are cancers of the lymphocytes and may develop from either B or T lymphocytes. The two major types of lymphoma are Hodgkin's lymphoma, previously known as Hodgkin's disease, and non-Hodgkin's lymphoma. Hodgkin's lymphoma is marked by the presence of the Reed-Sternberg cell. Non-Hodgkin's lymphomas are all lymphomas which are not Hodgkin's lymphoma. Non-Hodgkin lymphomas may be indolent lymphomas and aggressive lymphomas. Non-Hodgkin's lymphomas include, but are not limited to, diffuse large B cell lymphoma, follicular lymphoma, mucosa-associated lymphatic tissue lymphoma (MALT), small cell lymphocytic lymphoma, mantle cell lymphoma, Burkitt's lymphoma, mediastinal large B cell lymphoma, Waldenström macroglobulinemia, nodal marginal zone B cell lymphoma (NMZL), splenic marginal zone lymphoma (SMZL), extranodal marginal zone B cell lymphoma, intravascular large B cell lymphoma, primary effusion lymphoma, and lymphomatoid granulomatosis.
  • Cancer Staging
  • Diagnosing, predicting, or monitoring a status or outcome of a cancer may comprise determining the stage of the cancer. Generally, the stage of a cancer is a description (usually numbers I to IV with IV having more progression) of the extent the cancer has spread. The stage often takes into account the size of a tumor, how deeply it has penetrated, whether it has invaded adjacent organs, how many lymph nodes it has metastasized to (if any), and whether it has spread to distant organs. Staging of cancer can be used as a predictor of survival, and cancer treatment may be determined by staging. Determining the stage of the cancer may occur before, during, or after treatment. The stage of the cancer may also be determined at the time of diagnosis.
  • Cancer staging can be divided into a clinical stage and a pathologic stage. Cancer staging may comprise the TNM classification. Generally, the TNM Classification of Malignant Tumours (TNM) is a cancer staging system that describes the extent of cancer in a patient's body. T may describe the size of the tumor and whether it has invaded nearby tissue, N may describe regional lymph nodes that are involved, and M may describe distant metastasis (spread of cancer from one body part to another). In the TNM (Tumor, Node, Metastasis) system, clinical stage and pathologic stage are denoted by a small “c” or “p” before the stage (e.g., cT3N1M0 or pT2N0).
  • Often, clinical stage and pathologic stage may differ. Clinical stage may be based on all of the available information obtained before a surgery to remove the tumor. Thus, it may include information about the tumor obtained by physical examination, radiologic examination, and endoscopy. Pathologic stage can add additional information gained by examination of the tumor microscopically by a pathologist. Pathologic staging can allow direct examination of the tumor and its spread, contrasted with clinical staging which may be limited by the fact that the information is obtained by making indirect observations at a tumor which is still in the body. The TNM staging system can be used for most forms of cancer.
  • Alternatively, staging may comprise Ann Arbor staging. Generally, Ann Arbor staging is the staging system for lymphomas, both in Hodgkin's lymphoma (previously called Hodgkin's disease) and Non-Hodgkin lymphoma (abbreviated NHL). The stage may depend on both the place where the malignant tissue is located (as located with biopsy, CT scanning and increasingly positron emission tomography) and on systemic symptoms due to the lymphoma (“B symptoms”: night sweats, weight loss of >10% or fevers). The principal stage may be determined by location of the tumor. Stage I may indicate that the cancer is located in a single region, usually one lymph node and the surrounding area. Stage I often may not have outward symptoms. Stage II can indicate that the cancer is located in two separate regions, an affected lymph node or organ and a second affected area, and that both affected areas are confined to one side of the diaphragm—that is, both are above the diaphragm, or both are below the diaphragm. Stage III often indicates that the cancer has spread to both sides of the diaphragm, including one organ or area near the lymph nodes or the spleen. Stage IV may indicate diffuse or disseminated involvement of one or more extralymphatic organs, including any involvement of the liver, bone marrow, or nodular involvement of the lungs.
  • Modifiers may also be appended to some stages. For example, the letters A, B, E, X, or S can be appended to some stages. Generally, A or B may indicate the absence of constitutional (B-type) symptoms is denoted by adding an “A” to the stage; the presence is denoted by adding a “B” to the stage. E can be used if the disease is “extranodal” (not in the lymph nodes) or has spread from lymph nodes to adjacent tissue. X is often used if the largest deposit is >10 cm large (“bulky disease”), or whether the mediastinum is wider than ⅓ of the chest on a chest X-ray. S may be used if the disease has spread to the spleen.
  • The nature of the staging may be expressed with CS or PS. CS may denote that the clinical stage as obtained by doctor's examinations and tests. PS may denote that the pathological stage as obtained by exploratory laparotomy (surgery performed through an abdominal incision) with splenectomy (surgical removal of the spleen).
  • Therapeutic Regimens
  • Diagnosing, predicting, or monitoring a status or outcome of a cancer may comprise treating a cancer or preventing a cancer progression. In addition, diagnosing, predicting, or monitoring a status or outcome of a cancer may comprise identifying or predicting responders to an anti-cancer therapy. In some instances, diagnosing, predicting, or monitoring may comprise determining a therapeutic regimen. Determining a therapeutic regimen may comprise administering an anti-cancer therapy. Alternatively, determining a therapeutic regimen may comprise modifying, recommending, continuing or discontinuing an anti-cancer regimen. In some instances, if the sample expression patterns are consistent with the expression pattern for a known disease or disease outcome, the expression patterns can be used to designate one or more treatment modalities (e.g., therapeutic regimens, anti-cancer regimen). An anti-cancer regimen may comprise one or more anti-cancer therapies. Examples of anti-cancer therapies include surgery, chemotherapy, radiation therapy, immunotherapy/biological therapy, photodynamic therapy.
  • Surgical oncology uses surgical methods to diagnose, stage, and treat cancer, and to relieve certain cancer-related symptoms. Surgery may be used to remove the tumor (e.g., excisions, resections, debulking surgery), reconstruct a part of the body (e.g., restorative surgery), and/or to relieve symptoms such as pain (e.g., palliative surgery). Surgery may also include cryosurgery. Cryosurgery (also called cryotherapy) may use extreme cold produced by liquid nitrogen (or argon gas) to destroy abnormal tissue. Cryosurgery can be used to treat external tumors, such as those on the skin. For external tumors, liquid nitrogen can be applied directly to the cancer cells with a cotton swab or spraying device. Cryosurgery may also be used to treat tumors inside the body (internal tumors and tumors in the bone). For internal tumors, liquid nitrogen or argon gas may be circulated through a hollow instrument called a cryoprobe, which is placed in contact with the tumor. An ultrasound or MRI may be used to guide the cryoprobe and monitor the freezing of the cells, thus limiting damage to nearby healthy tissue. A ball of ice crystals may form around the probe, freezing nearby cells. Sometimes more than one probe is used to deliver the liquid nitrogen to various parts of the tumor. The probes may be put into the tumor during surgery or through the skin (percutaneously). After cryosurgery, the frozen tissue thaws and may be naturally absorbed by the body (for internal tumors), or may dissolve and form a scab (for external tumors).
  • Chemotherapeutic agents may also be used for the treatment of cancer. Examples of chemotherapeutic agents include alkylating agents, anti-metabolites, plant alkaloids and terpenoids, vinca alkaloids, podophyllotoxin, taxanes, topoisomerase inhibitors, and cytotoxic antibiotics. Cisplatin, carboplatin, and oxaliplatin are examples of alkylating agents. Other alkylating agents include mechlorethamine, cyclophosphamide, chlorambucil, ifosfamide. Alkylating agents may impair cell function by forming covalent bonds with the amino, carboxyl, sulfhydryl, and phosphate groups in biologically important molecules. Alternatively, alkylating agents may chemically modify a cell's DNA.
  • Anti-metabolites are another example of chemotherapeutic agents. Anti-metabolites may masquerade as purines or pyrimidines and may prevent purines and pyrimidines from becoming incorporated in to DNA during the “S” phase (of the cell cycle), thereby stopping normal development and division. Antimetabolites may also affect RNA synthesis. Examples of metabolites include azathioprine and mercaptopurine.
  • Alkaloids may be derived from plants and block cell division may also be used for the treatment of cancer. Alkyloids may prevent microtubule function. Examples of alkaloids are vinca alkaloids and taxanes. Vinca alkaloids may bind to specific sites on tubulin and inhibit the assembly of tubulin into microtubules (M phase of the cell cycle). The vinca alkaloids may be derived from the Madagascar periwinkle, Catharanthus roseus (formerly known as Vinca rosea). Examples of vinca alkaloids include, but are not limited to, vincristine, vinblastine, vinorelbine, or vindesine. Taxanes are diterpenes produced by the plants of the genus Taxus (yews). Taxanes may be derived from natural sources or synthesized artificially. Taxanes include paclitaxel (Taxol) and docetaxel (Taxotere). Taxanes may disrupt microtubule function. Microtubules are essential to cell division, and taxanes may stabilize GDP-bound tubulin in the microtubule, thereby inhibiting the process of cell division. Thus, in essence, taxanes may be mitotic inhibitors. Taxanes may also be radiosensitizing and often contain numerous chiral centers.
  • Alternative chemotherapeutic agents include podophyllotoxin. Podophyllotoxin is a plant-derived compound that may help with digestion and may be used to produce cytostatic drugs such as etoposide and teniposide. They may prevent the cell from entering the G1 phase (the start of DNA replication) and the replication of DNA (the S phase).
  • Topoisomerases are essential enzymes that maintain the topology of DNA. Inhibition of type I or type II topoisomerases may interfere with both transcription and replication of DNA by upsetting proper DNA supercoiling. Some chemotherapeutic agents may inhibit topoisomerases. For example, some type I topoisomerase inhibitors include camptothecins: irinotecan and topotecan. Examples of type II inhibitors include amsacrine, etoposide, etoposide phosphate, and teniposide.
  • Another example of chemotherapeutic agents is cytotoxic antibiotics. Cytotoxic antibiotics are a group of antibiotics that are used for the treatment of cancer because they may interfere with DNA replication and/or protein synthesis. Cytotoxic antiobiotics include, but are not limited to, actinomycin, anthracyclines, doxorubicin, daunorubicin, valrubicin, idarubicin, epirubicin, bleomycin, plicamycin, and mitomycin.
  • In some instances, the anti-cancer treatment may comprise radiation therapy. Radiation can come from a machine outside the body (external-beam radiation therapy) or from radioactive material placed in the body near cancer cells (internal radiation therapy, more commonly called brachytherapy). Systemic radiation therapy uses a radioactive substance, given by mouth or into a vein that travels in the blood to tissues throughout the body.
  • External-beam radiation therapy may be delivered in the form of photon beams (either x-rays or gamma rays). A photon is the basic unit of light and other forms of electromagnetic radiation. An example of external-beam radiation therapy is called 3-dimensional conformal radiation therapy (3D-CRT). 3D-CRT may use computer software and advanced treatment machines to deliver radiation to very precisely shaped target areas. Many other methods of external-beam radiation therapy are currently being tested and used in cancer treatment. These methods include, but are not limited to, intensity-modulated radiation therapy (IMRT), image-guided radiation therapy (IGRT), Stereotactic radiosurgery (SRS), Stereotactic body radiation therapy (SBRT), and proton therapy.
  • Intensity-modulated radiation therapy (IMRT) is an example of external-beam radiation and may use hundreds of tiny radiation beam-shaping devices, called collimators, to deliver a single dose of radiation. The collimators can be stationary or can move during treatment, allowing the intensity of the radiation beams to change during treatment sessions. This kind of dose modulation allows different areas of a tumor or nearby tissues to receive different doses of radiation. IMRT is planned in reverse (called inverse treatment planning). In inverse treatment planning, the radiation doses to different areas of the tumor and surrounding tissue are planned in advance, and then a high-powered computer program calculates the required number of beams and angles of the radiation treatment. In contrast, during traditional (forward) treatment planning, the number and angles of the radiation beams are chosen in advance and computers calculate how much dose may be delivered from each of the planned beams. The goal of IMRT is to increase the radiation dose to the areas that need it and reduce radiation exposure to specific sensitive areas of surrounding normal tissue.
  • Another example of external-beam radiation is image-guided radiation therapy (IGRT). In IGRT, repeated imaging scans (CT, MRI, or PET) may be performed during treatment. These imaging scans may be processed by computers to identify changes in a tumor's size and location due to treatment and to allow the position of the patient or the planned radiation dose to be adjusted during treatment as needed. Repeated imaging can increase the accuracy of radiation treatment and may allow reductions in the planned volume of tissue to be treated, thereby decreasing the total radiation dose to normal tissue.
  • Tomotherapy is a type of image-guided IMRT. A tomotherapy machine is a hybrid between a CT imaging scanner and an external-beam radiation therapy machine. The part of the tomotherapy machine that delivers radiation for both imaging and treatment can rotate completely around the patient in the same manner as a normal CT scanner. Tomotherapy machines can capture CT images of the patient's tumor immediately before treatment sessions, to allow for very precise tumor targeting and sparing of normal tissue.
  • Stereotactic radiosurgery (SRS) can deliver one or more high doses of radiation to a small tumor. SRS uses extremely accurate image-guided tumor targeting and patient positioning. Therefore, a high dose of radiation can be given without excess damage to normal tissue. SRS can be used to treat small tumors with well-defined edges. It is most commonly used in the treatment of brain or spinal tumors and brain metastases from other cancer types. For the treatment of some brain metastases, patients may receive radiation therapy to the entire brain (called whole-brain radiation therapy) in addition to SRS. SRS requires the use of a head frame or other device to immobilize the patient during treatment to ensure that the high dose of radiation is delivered accurately.
  • Stereotactic body radiation therapy (SBRT) delivers radiation therapy in fewer sessions, using smaller radiation fields and higher doses than 3D-CRT in most cases. SBRT may treat tumors that lie outside the brain and spinal cord. Because these tumors are more likely to move with the normal motion of the body, and therefore cannot be targeted as accurately as tumors within the brain or spine, SBRT is usually given in more than one dose. SBRT can be used to treat small, isolated tumors, including cancers in the lung and liver. SBRT systems may be known by their brand names, such as the CyberKnife®.
  • In proton therapy, external-beam radiation therapy may be delivered by proton. Protons are a type of charged particle. Proton beams differ from photon beams mainly in the way they deposit energy in living tissue. Whereas photons deposit energy in small packets all along their path through tissue, protons deposit much of their energy at the end of their path (called the Bragg peak) and deposit less energy along the way. Use of protons may reduce the exposure of normal tissue to radiation, possibly allowing the delivery of higher doses of radiation to a tumor.
  • Other charged particle beams such as electron beams may be used to irradiate superficial tumors, such as skin cancer or tumors near the surface of the body, but they cannot travel very far through tissue.
  • Internal radiation therapy (brachytherapy) is radiation delivered from radiation sources (radioactive materials) placed inside or on the body. Several brachytherapy techniques are used in cancer treatment. Interstitial brachytherapy may use a radiation source placed within tumor tissue, such as within a prostate tumor. Intracavitary brachytherapy may use a source placed within a surgical cavity or a body cavity, such as the chest cavity, near a tumor. Episcleral brachytherapy, which may be used to treat melanoma inside the eye, may use a source that is attached to the eye. In brachytherapy, radioactive isotopes can be sealed in tiny pellets or “seeds.” These seeds may be placed in patients using delivery devices, such as needles, catheters, or some other type of carrier. As the isotopes decay naturally, they give off radiation that may damage nearby cancer cells. Brachytherapy may be able to deliver higher doses of radiation to some cancers than external-beam radiation therapy while causing less damage to normal tissue.
  • Brachytherapy can be given as a low-dose-rate or a high-dose-rate treatment. In low-dose-rate treatment, cancer cells receive continuous low-dose radiation from the source over a period of several days. In high-dose-rate treatment, a robotic machine attached to delivery tubes placed inside the body may guide one or more radioactive sources into or near a tumor, and then removes the sources at the end of each treatment session. High-dose-rate treatment can be given in one or more treatment sessions. An example of a high-dose-rate treatment is the MammoSite® system. Bracytherapy may be used to treat patients with breast cancer who have undergone breast-conserving surgery.
  • The placement of brachytherapy sources can be temporary or permanent. For permanent brachytherapy, the sources may be surgically sealed within the body and left there, even after all of the radiation has been given off. In some instances, the remaining material (in which the radioactive isotopes were sealed) does not cause any discomfort or harm to the patient. Permanent brachytherapy is a type of low-dose-rate brachytherapy. For temporary brachytherapy, tubes (catheters) or other carriers are used to deliver the radiation sources, and both the carriers and the radiation sources are removed after treatment. Temporary brachytherapy can be either low-dose-rate or high-dose-rate treatment. Brachytherapy may be used alone or in addition to external-beam radiation therapy to provide a “boost” of radiation to a tumor while sparing surrounding normal tissue.
  • In systemic radiation therapy, a patient may swallow or receive an injection of a radioactive substance, such as radioactive iodine or a radioactive substance bound to a monoclonal antibody. Radioactive iodine (131I) is a type of systemic radiation therapy commonly used to help treat cancer, such as thyroid cancer. Thyroid cells naturally take up radioactive iodine. For systemic radiation therapy for some other types of cancer, a monoclonal antibody may help target the radioactive substance to the right place. The antibody joined to the radioactive substance travels through the blood, locating and killing tumor cells. For example, the drug ibritumomab tiuxetan (Zevalin®) may be used for the treatment of certain types of B-cell non-Hodgkin lymphoma (NHL). The antibody part of this drug recognizes and binds to a protein found on the surface of B lymphocytes. The combination drug regimen of tositumomab and iodine I 131 tositumomab (Bexxar®) may be used for the treatment of certain types of cancer, such as NHL. In this regimen, nonradioactive tositumomab antibodies may be given to patients first, followed by treatment with tositumomab antibodies that have 131I attached. Tositumomab may recognize and bind to the same protein on B lymphocytes as ibritumomab. The nonradioactive form of the antibody may help protect normal B lymphocytes from being damaged by radiation from 131I.
  • Some systemic radiation therapy drugs relieve pain from cancer that has spread to the bone (bone metastases). This is a type of palliative radiation therapy. The radioactive drugs samarium-153-lexidronam (Quadramet®) and strontium-89 chloride (Metastron®) are examples of radiopharmaceuticals may be used to treat pain from bone metastases.
  • Biological therapy (sometimes called immunotherapy, biotherapy, or biological response modifier (BRM) therapy) uses the body's immune system, either directly or indirectly, to fight cancer or to lessen the side effects that may be caused by some cancer treatments. Biological therapies include interferons, interleukins, colony-stimulating factors, monoclonal antibodies, vaccines, gene therapy, and nonspecific immunomodulating agents.
  • Interferons (IFNs) are types of cytokines that occur naturally in the body. Interferon alpha, interferon beta, and interferon gamma are examples of interferons that may be used in cancer treatment.
  • Like interferons, interleukins (ILs) are cytokines that occur naturally in the body and can be made in the laboratory. Many interleukins have been identified for the treatment of cancer. For example, interleukin-2 (IL-2 or aldesleukin), interleukin 7, and interleukin 12 have may be used as an anti-cancer treatment. IL-2 may stimulate the growth and activity of many immune cells, such as lymphocytes, that can destroy cancer cells. Interleukins may be used to treat a number of cancers, including leukemia, lymphoma, and brain, colorectal, ovarian, breast, kidney and prostate cancers.
  • Colony-stimulating factors (CSFs) (sometimes called hematopoietic growth factors) may also be used for the treatment of cancer. Some examples of CSFs include, but are not limited to, G-CSF (filgrastim) and GM-CSF (sargramostim). CSFs may promote the division of bone marrow stem cells and their development into white blood cells, platelets, and red blood cells. Bone marrow is critical to the body's immune system because it is the source of all blood cells. Because anticancer drugs can damage the body's ability to make white blood cells, red blood cells, and platelets, stimulation of the immune system by CSFs may benefit patients undergoing other anti-cancer treatment, thus CSFs may be combined with other anti-cancer therapies, such as chemotherapy. CSFs may be used to treat a large variety of cancers, including lymphoma, leukemia, multiple myeloma, melanoma, and cancers of the brain, lung, esophagus, breast, uterus, ovary, prostate, kidney, colon, and rectum.
  • Another type of biological therapy includes monoclonal antibodies (MOABs or MoABs). These antibodies may be produced by a single type of cell and may be specific for a particular antigen. To create MOABs, human cancer cells may be injected into mice. In response, the mouse immune system can make antibodies against these cancer cells. The mouse plasma cells that produce antibodies may be isolated and fused with laboratory-grown cells to create “hybrid” cells called hybridomas. Hybridomas can indefinitely produce large quantities of these pure antibodies, or MOABs. MOABs may be used in cancer treatment in a number of ways. For instance, MOABs that react with specific types of cancer may enhance a patient's immune response to the cancer. MOABs can be programmed to act against cell growth factors, thus interfering with the growth of cancer cells.
  • MOABs may be linked to other anti-cancer therapies such as chemotherapeutics, radioisotopes (radioactive substances), other biological therapies, or other toxins. When the antibodies latch onto cancer cells, they deliver these anti-cancer therapies directly to the tumor, helping to destroy it. MOABs carrying radioisotopes may also prove useful in diagnosing certain cancers, such as colorectal, ovarian, and prostate.
  • Rituxan® (rituximab) and Herceptin® (trastuzumab) are examples of MOABs that may be used as a biological therapy. Rituxan may be used for the treatment of non-Hodgkin lymphoma. Herceptin can be used to treat metastatic breast cancer in patients with tumors that produce excess amounts of a protein called HER2. Alternatively, MOABs may be used to treat lymphoma, leukemia, melanoma, and cancers of the brain, breast, lung, kidney, colon, rectum, ovary, prostate, and other areas.
  • Cancer vaccines are another form of biological therapy. Cancer vaccines may be designed to encourage the patient's immune system to recognize cancer cells. Cancer vaccines may be designed to treat existing cancers (therapeutic vaccines) or to prevent the development of cancer (prophylactic vaccines). Therapeutic vaccines may be injected in a person after cancer is diagnosed. These vaccines may stop the growth of existing tumors, prevent cancer from recurring, or eliminate cancer cells not killed by prior treatments. Cancer vaccines given when the tumor is small may be able to eradicate the cancer. On the other hand, prophylactic vaccines are given to healthy individuals before cancer develops. These vaccines are designed to stimulate the immune system to attack viruses that can cause cancer. By targeting these cancer-causing viruses, development of certain cancers may be prevented. For example, cervarix and gardasil are vaccines to treat human papilloma virus and may prevent cervical cancer. Therapeutic vaccines may be used to treat melanoma, lymphoma, leukemia, and cancers of the brain, breast, lung, kidney, ovary, prostate, pancreas, colon, and rectum. Cancer vaccines can be used in combination with other anti-cancer therapies.
  • Gene therapy is another example of a biological therapy. Gene therapy may involve introducing genetic material into a person's cells to fight disease. Gene therapy methods may improve a patient's immune response to cancer. For example, a gene may be inserted into an immune cell to enhance its ability to recognize and attack cancer cells. In another approach, cancer cells may be injected with genes that cause the cancer cells to produce cytokines and stimulate the immune system.
  • In some instances, biological therapy includes nonspecific immunomodulating agents. Nonspecific immunomodulating agents are substances that stimulate or indirectly augment the immune system. Often, these agents target key immune system cells and may cause secondary responses such as increased production of cytokines and immunoglobulins. Two nonspecific immunomodulating agents used in cancer treatment are bacillus Calmette-Guerin (BCG) and levamisole. BCG may be used in the treatment of superficial bladder cancer following surgery. BCG may work by stimulating an inflammatory, and possibly an immune, response. A solution of BCG may be instilled in the bladder. Levamisole is sometimes used along with fluorouracil (5-FU) chemotherapy in the treatment of stage III (Dukes' C) colon cancer following surgery. Levamisole may act to restore depressed immune function.
  • Photodynamic therapy (PDT) is an anti-cancer treatment that may use a drug, called a photosensitizer or photosensitizing agent, and a particular type of light. When photosensitizers are exposed to a specific wavelength of light, they may produce a form of oxygen that kills nearby cells. A photosensitizer may be activated by light of a specific wavelength. This wavelength determines how far the light can travel into the body. Thus, photosensitizers and wavelengths of light may be used to treat different areas of the body with PDT.
  • In the first step of PDT for cancer treatment, a photosensitizing agent may be injected into the bloodstream. The agent may be absorbed by cells all over the body but may stay in cancer cells longer than it does in normal cells. Approximately 24 to 72 hours after injection, when most of the agent has left normal cells but remains in cancer cells, the tumor can be exposed to light. The photosensitizer in the tumor can absorb the light and produces an active form of oxygen that destroys nearby cancer cells. In addition to directly killing cancer cells, PDT may shrink or destroy tumors in two other ways. The photosensitizer can damage blood vessels in the tumor, thereby preventing the cancer from receiving necessary nutrients. PDT may also activate the immune system to attack the tumor cells.
  • The light used for PDT can come from a laser or other sources. Laser light can be directed through fiber optic cables (thin fibers that transmit light) to deliver light to areas inside the body. For example, a fiber optic cable can be inserted through an endoscope (a thin, lighted tube used to look at tissues inside the body) into the lungs or esophagus to treat cancer in these organs. Other light sources include light-emitting diodes (LEDs), which may be used for surface tumors, such as skin cancer. PDT is usually performed as an outpatient procedure. PDT may also be repeated and may be used with other therapies, such as surgery, radiation, or chemotherapy.
  • Extracorporeal photopheresis (ECP) is a type of PDT in which a machine may be used to collect the patient's blood cells. The patient's blood cells may be treated outside the body with a photosensitizing agent, exposed to light, and then returned to the patient. ECP may be used to help lessen the severity of skin symptoms of cutaneous T-cell lymphoma that has not responded to other therapies. ECP may be used to treat other blood cancers, and may also help reduce rejection after transplants.
  • Additionally, photosensitizing agent, such as porfimer sodium or Photofrin®, may be used in PDT to treat or relieve the symptoms of esophageal cancer and non-small cell lung cancer. Porfimer sodium may relieve symptoms of esophageal cancer when the cancer obstructs the esophagus or when the cancer cannot be satisfactorily treated with laser therapy alone. Porfimer sodium may be used to treat non-small cell lung cancer in patients for whom the usual treatments are not appropriate, and to relieve symptoms in patients with non-small cell lung cancer that obstructs the airways. Porfimer sodium may also be used for the treatment of precancerous lesions in patients with Barrett esophagus, a condition that can lead to esophageal cancer.
  • Laser therapy may use high-intensity light to treat cancer and other illnesses. Lasers can be used to shrink or destroy tumors or precancerous growths. Lasers are most commonly used to treat superficial cancers (cancers on the surface of the body or the lining of internal organs) such as basal cell skin cancer and the very early stages of some cancers, such as cervical, penile, vaginal, vulvar, and non-small cell lung cancer.
  • Lasers may also be used to relieve certain symptoms of cancer, such as bleeding or obstruction. For example, lasers can be used to shrink or destroy a tumor that is blocking a patient's trachea (windpipe) or esophagus. Lasers also can be used to remove colon polyps or tumors that are blocking the colon or stomach.
  • Laser therapy is often given through a flexible endoscope (a thin, lighted tube used to look at tissues inside the body). The endoscope is fitted with optical fibers (thin fibers that transmit light). It is inserted through an opening in the body, such as the mouth, nose, anus, or vagina. Laser light is then precisely aimed to cut or destroy a tumor.
  • Laser-induced interstitial thermotherapy (LITT), or interstitial laser photocoagulation, also uses lasers to treat some cancers. LITT is similar to a cancer treatment called hyperthermia, which uses heat to shrink tumors by damaging or killing cancer cells. During LITT, an optical fiber is inserted into a tumor. Laser light at the tip of the fiber raises the temperature of the tumor cells and damages or destroys them. LITT is sometimes used to shrink tumors in the liver.
  • Laser therapy can be used alone, but most often it is combined with other treatments, such as surgery, chemotherapy, or radiation therapy. In addition, lasers can seal nerve endings to reduce pain after surgery and seal lymph vessels to reduce swelling and limit the spread of tumor cells.
  • Lasers used to treat cancer may include carbon dioxide (CO2) lasers, argon lasers, and neodymium:yttrium-aluminum-garnet (Nd:YAG) lasers. Each of these can shrink or destroy tumors and can be used with endoscopes. CO2 and argon lasers can cut the skin's surface without going into deeper layers. Thus, they can be used to remove superficial cancers, such as skin cancer. In contrast, the Nd:YAG laser is more commonly applied through an endoscope to treat internal organs, such as the uterus, esophagus, and colon. Nd:YAG laser light can also travel through optical fibers into specific areas of the body during LITT. Argon lasers are often used to activate the drugs used in PDT.
    • EXPERIMENTAL
  • The following examples are provided in order to demonstrate and further illustrate certain preferred embodiments and aspects of the present invention and are not to be construed as limiting the scope thereof.
    • Example 1 A. Methods
  • Methods Summary
  • All prostate tissue samples were obtained from the University of Michigan Specialized Program Of Research Excellence (S.P.O.R.E.) using an IRB-approved informed consent protocol. Next generation sequencing and library preparation was performed as previously described (Maher et al., Proc Natl Acad Sci USA 106 (30), 12353 (2009)). Uniquely mapping sequencing reads were aligned with TopHat and sequencing data for all samples was merged. Ab initio transcriptome assembly was performed by aligning sequences with TopHat and using uniquely mapped read positions to build transcripts with Cufflinks. Informatics approaches were used to refine the assembly and predict expressed transcriptional units. Unannotated transcripts were nominated based upon their absence in the UCSC, RefSeq, ENSEMBL, ENCODE, and Vega databases. Differential expression was determined using the Significance Analysis of Microarrays (SAM) algorithm (Tusher et al., Proc Natl Acad Sci USA 98 (9), 5116 (2001)) on log 2 mean expression in benign, cancer, and metastatic samples. Cancer outlier profile analysis (COPA) was performed as previously described (Tomlins et al., Science 310 (5748), 644 (2005)) with slight modifications. PCR experiments were performed according to standard protocols, and RACE was performed with the GeneRacer Kit (Invitrogen) according to manufacturer's instructions. ChIP-seq data was obtained from previously published data (Yu et al., Cancer Cell 17 (5), 443). siRNA knockdown was performed with custom siRNA oligos (Dharmacon) with Oligofectamine (Invitrogen). Transmembrane invasion assays were performed with Matrigel (BD Biosciences) and cell proliferation assays were performed by cell count with a Coulter counter. Urine analyses were performed as previously described (Laxman et al., Cancer Res 68 (3), 645 (2008)) with minor modifications.
  • Cell Lines and Tissues
  • The benign immortalized prostate cell line RWPE as well as PC3, Du145, LNCaP, VCaP, 22Rv1, CWR22, C4-2B, NCI-660, MDA PCa 2b, WPMY-1, and LAPC-4 prostate cell lines were obtained from the American Type Culture Collection (Manassas, Va.). Benign non-immortalized prostate epithelial cells (PrEC) and prostate smooth muscle cells (PrSMC) were obtained from Lonza (Basel, Switzerland). Cell lines were maintained using standard media and conditions. For androgen treatment experiments, LNCaP and VCaP cells were grown in androgen depleted media lacking phenol red and supplemented with 10% charcoal-stripped serum and 1% penicillin-streptomycin. After 48 hours, cells were treated with 5 nM methyltrienolone (R1881, NEN Life Science Products) or an equivalent volume of ethanol. Cells were harvested for RNA at 6, 24, and 48 hours post-treatment. Prostate tissues were obtained from the radical prostatectomy series and Rapid Autopsy Program at the University of Michigan tissue core. These programs are part of the University of Michigan Prostate Cancer Specialized Program Of Research Excellence (S.P.O.R.E.). All tissue samples were collected with informed consent under an Institutional Review Board (IRB) approved protocol at the University of Michigan.
  • PC3, Du145, LNCaP, 22Rv1, and CRW22 cells were grown in RPMI 1640 (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. LNCaP CDS parent cells were grown in RPMI 1640 lacking phenol red (Invitrogen) supplemented with 10% charcoal-dextran stripped FBS (Invitrogen) and 1% penicillin-streptomycin. LNCaP CDS 1, 2, and 3 are androgen-independent subclones derived from extended cell culture in androgendepleted media. VCaP and WPMY-1 cells were grown in DMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) with 1% penicillin-streptomycin. NCI-H660 cells were grown in RPMI 1640 supplemented with 0.005 mg/ml insulin, 0.01 mg/ml transferring, 30 nM sodium selenite, 10 nM hydrocortisone, 10 nM beta-estradiol, 5% FBS and an extra 2 mM of L-glutamine (for a final concentration of 4 mM). MDA PCa 2b cells were grown in F-12K medium (Invitrogen) supplemented with 20% FBS, 25 ng/ml cholera toxin, 10 ng/ml EGF, 0.005 mM phosphoethanolamine, 100 pg/ml hydrocortisone, 45 nM selenious acid, and 0.005 mg/ml insulin. LAPC-4 cells were grown in Iscove's media (Invitrogen) supplemented with 10% FBS and 1 nM R1881. C4-2B cells were grown in 80% DMEM supplemented with 20% F12, 5% FBS, 3 g/L NaCo3, 5 μg/ml insulin, 13.6 pg/ml triiodothyonine, 5 μg/ml transferrin, 0.25 μg/ml biotin, and 25 μg/ml adenine. PrEC cells were grown in PrEGM supplemented with 2 ml BPE, 0.5 ml hydrocortisone, 0.5 ml EGF, 0.5 ml epinephrine, 0.5 ml transferring, 0.5 ml insulin, 0.5 ml retinoic acid, and 0.5 ml triiodothyronine, as part of the PrEGM BulletKit (Lonza). PrSMC cells were grown in SmGM-2 media supplemented with 2 ml BPE, 0.5 ml hydrocortisone, 0.5 ml EGF, 0.5 ml epinephrine, 0.5 ml transferring, 0.5 ml insulin, 0.5 ml retinoic acid, and 0.5 ml triiodothyronine, as part of the SmGM-2 BulletKit (Lonza).
  • RNA-Seq Library Preparation.
  • Next generation sequencing of RNA was performed on 21 prostate cell lines, 20 benign adjacent prostates, 47 localized tumors, and 14 metastatic tumors according to Illumina's protocol using 2 μg of RNA. RNA integrity was measured using an Agilent 2100 Bioanalyzer, and only samples with a RIN score >7.0 were advanced for library generation. RNA was poly-A+ selected using the OligodT beads provided by Ilumina and fragmented with the Ambion Fragmentation Reagents kit (Ambion, Austin, Tex.). cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina PCR adaptors (single read or paired-end where appropriate) were performed according to Illumina's protocol. Libraries were then size-selected for 250-300 bp cDNA fragments on a 3.5% agarose gel and PCR-amplified using Phusion DNA polymerase (Finnzymes) for 15-18 PCR cycles. PCR products were then purified on a 2% agarose gel and gel-extracted. Library quality was credentialed by assaying each library on an Agilent 2100 Bioanalyzer of product size and concentration. Libraries were sequenced as 36-45mers on an Illumina Genome Analyzer I or Genome Analyzer II flowcell according to Illumina's protocol. All single read samples were sequenced on a Genome Analyzer I, and all paired-end samples were sequenced on a Genome Analyzer II.
  • RNA Isolation and cDNA Synthesis
  • Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) with DNase I digestion according to the manufacturer's instructions. RNA integrity was verified on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, Calif.). cDNA was synthesized from total RNA using Superscript III (Invitrogen) and random primers (Invitrogen).
  • Quantitative Real-Time PCR
  • Quantitative Real-time PCR (qPCR) was performed using Power SYBR Green Mastermix (Applied Biosystems, Foster City, Calif.) on an Applied Biosystems 7900HT Real-Time PCR System. All oligonucleotide primers were obtained from Integrated DNA Technologies (Coralville, Iowa). The housekeeping gene, GAPDH, was used as a loading control. Fold changes were calculated relative to GAPDH and normalized to the median value of the benign samples.
  • Reverse-Transcription PCR
  • Reverse-transcription PCR (RT-PCR) was performed for primer pairs using Platinum Taq High Fidelity polymerase (Invitrogen). PCR products were resolved on a 2% agarose gel. PCR products were either sequenced directly (if only a single product was observed) or appropriate gel products were extracted using a Gel Extraction kit (Qiagen) and cloned into per4-TOPO vectors (Invitrogen). PCR products were bidirectionally sequenced at the University of Michigan Sequencing Core using either gene-specific primers or M13 forward and reverse primers for cloned PCR products. All oligonucleotide primers were obtained from Integrated DNA Technologies (Coralville, Iowa).
  • RNA-Ligase-Mediated Rapid Amplification of cDNA Ends (RACE)
  • 5′ and 3′ RACE was performed using the GeneRacer RLM-RACE kit (Invitrogen) according to the manufacturer's instructions. RACE PCR products were obtained using Platinum Taq High Fidelity polymerase (Invitrogen), the supplied GeneRacer primers, and appropriate gene-specific primers. RACEPCR products were separated on a 2% agarose gels. Gel products were extracted with a Gel Extraction kit (Qiagen), cloned into per4-TOPO vectors (Invitrogen), and sequenced bidirectionally using M13 forward and reverse primers at the University of Michigan Sequencing Core. At least three colonies were sequenced for every gel product that was purified.
  • Paired-End Next-Generation Sequencing of RNA
  • 2 μg total RNA was selected for polyA+ RNA using Sera-Mag oligo(dT) beads (Thermo Scientific), and paired-end next-generation sequencing libraries were prepared as previously described (Maher et al., supra) using Illumina-supplied universal adaptor oligos and PCR primers (Illumina). Samples were sequenced in a single lane on an Illumina Genome Analyzer II flowcell using previously described protocols (Maher et al., supra). 36-45 mer paired-end reads were according to the protocol provided by Illumina.
  • siRNA Knockdown Studies
  • Cells were plated in 100 mM plates at a desired concentration and transfected with 20 μM experimental siRNA oligos or non-targeting controls twice, at 12 hours and 36 hours post-plating. Knockdowns were performed with Oligofectamine and Optimem. Knockdown efficiency was determined by qPCR. 72 hours post-transfection, cells were trypsinized, counted with a Coulter counter, and diluted to 1 million cells/mL. For proliferation assays, 200,000 cells were plated in 24-well plates and grown in regular media. 48 and 96 hours post-plating, cells were harvested and counted using a Coulter counter. For invasion assays, Matrigel was diluted 1:4 in serum-free media and 100 μL of the diluted Matrigel was applied to a Boyden chamber transmembrane insert and allowed to settle overnight at 37° C. 200,000 cells suspended in serum-free media were applied per insert and 500 μL of serum-containing media was placed in the bottom of the Boyden (fetal bovine serum functioning as a chemoattractant). Cells were allowed to invade for 48 hours, at which time inserts were removed and noninvading cells and Matrigel were gently removed with a cotton swab. Invading cells were stained with crystal violet for 15 minutes and air-dried. For colorimetric assays, the inserts were treated with 200 μl of 10% acetic acid and the absorbance at 560 nm was measured using a spectrophotometer. For WST-1 assays, 20,000 cells were plated into 96-well plates and grown in 100 μL of serum-containing media. 48 and 96 hours post-plating, cells were measured for viability by adding 10 μL of WST-1 reagent to the cell media, incubating for 2 hours at 37° C. and measuring the absorbance at 450 nM using a spectrophotomer.
  • Urine qPCR
  • Urine samples were collected from 120 patients with informed consent following a digital rectal exam before either needle biopsy or radical prostatectomy at the University of Michigan with Institutional Review Board approval as described previously (Laxman et al., Cancer Res 68 (3), 645 (2008)). Isolation of RNA from urine and TransPlex whole transcriptome amplification were performed as described previously (Laxman et al., Neoplasia 8 (10), 885 (2006)). qPCR on urine samples was performed for KLK3 (PSA), TMPRSS2-ERG, GAPDH, PCA3, PCAT-1 and PCAT-14 using Power SYBR Mastermix (Applied Biosystems) as described above. Raw Ct values were extracted and normalized in the following manner. First, samples with GAPDH Ct values >25 or KLK3 Ct values >30 were removed from analysis to ensure sufficient prostate cell collection, leaving 108 samples for analysis. The GAPDH and KLK3 raw Ct values were average for each sample. ΔCt analysis was performed by measuring each value against the average of CtGAPDH and CtKLK3, and ΔCt values were normalized to the median ΔCt of the benign samples. Fold change was then calculated at 2−ΔCt. Samples were considered to be prostate cancer if histopathological analysis observed cancer or if the TMPRSS2-ERG transcript achieved a Ct value <37. Benign samples were defined as samples with normal histology and TMPRSS2-ERG transcript Ct values >37.
  • Statistical Analyses for Experimental Studies
  • All data are presented as means±s.e.m. All experimental assays were performed in duplicate or triplicate.
  • Bioinformatics Analyses
  • To achieve an ab initio prediction of the prostate cancer transcriptome existing publicly tools for mapping, assembly, and quantification of transcripts were supplemented with additional informatics filtering steps to enrich the results for the most robust transcript predictions (FIG. 6 a). Transcripts were then identified and classified by comparing them against gene annotation databases (FIG. 6 b). Details of the bioinformatics analyses are provided below.
  • Mapping Reads with TopHat
  • Reads were aligned using TopHat v1.0.13 (Feb. 5, 2010) (Trapnell et al., Bioinformatics 25, 1105-11 (2009)), a gapped aligner capable of discovering splice junctions ab initio. Briefly, TopHat aligns reads to the human genome using Bowtie (Langmead et al., Genome Biol 10, R25 (2009)) to determine a set of “coverage islands” that may represent putative exons. TopHat uses these exons as well as the presence of GT-AG genomic splicing motifs to build a second set of reference sequences spanning exon-exon junctions. The unmapped reads from the initial genome alignment step are then remapped against this splice junction reference to discover all the junction-spanning reads in the sample. TopHat outputs the reads that successfully map to either the genome or the splice junction reference in SAM format for further analysis. For this study a maximum intron size of 500 kb, corresponding to over 99.98% of RefSeq (Wheeler et al. Nucleic Acids Res 28, 10-4 (2000)) introns was used. For sequencing libraries the insert size was determined using an Agilent 2100 Bioanalyzer prior to data analysis, and it was found that this insert size agreed closely with software predictions. An insert size standard deviation of 20 bases was chosen in order to match the most common band size cut from gels during library preparation. In total, 1.723 billion fragments were generated from 201 lanes of sequencing on the Illumina Genome Analyzer and Illumina Genome Analyzer II. Reads were mapped to the human genome (hg18) downloaded from the UCSC genome browser website (Karolchik et al., Nucleic Acids Res 31, 51-4 (2003); Kent et al., Genome Res 12, 996-1006 (2002)). 1.418 billion unique alignments were obtained, including 114.4 million splice junctions for use in transcriptome assembly. Reads with multiple alignments with less than two mismatches were discarded.
  • Ab Initio Assembly and Quantification with Cufflinks
  • Aligned reads from TopHat were assembled into sample-specific transcriptomes with Cufflinks version 0.8.2 (Mar. 26, 2010) (Trapnell et al., Nat Biotechnol 28, 511-5). Cufflinks assembles exonic and splice-junction reads into transcripts using their alignment coordinates. To limit false positive assemblies a maximum intronic length of 300 kb, corresponding to the 99.93% percentile of known introns was used. After assembling transcripts, Cufflinks computes isoform-level abundances by finding a parsimonious allocation of reads to the transcripts within a locus. Transcripts with abundance less than 15% of the major transcript in the locus, and minor isoforms with abundance less than 5% of the major isoform were filtered. Default settings were used for the remaining parameters.
  • The Cufflinks assembly stage yielded a set of transcript annotations for each of the sequenced libraries. The transcripts were partitioned by chromosome and the Cuffcompare utility provided by Cufflinks was used to merge the transcripts into a combined set of annotations. The Cuffcompare program performs a union of all transcripts by merging transcripts that share all introns and exons. The 5′ and 3′ exons of transcripts were allowed to vary by up to 100 nt during the comparison process.
  • Distinguishing Transcripts from Background Signal
  • Cuffcompare reported a total of 8.25 million distinct transcripts. Manual inspection of these transcripts in known protein coding gene regions indicated that most of the transcripts were likely to be poor quality reconstructions of overlapping larger transcripts. Also, many of the transcripts were unspliced and had a total length smaller than the size selected fragment length of approximately ˜250 nt. Furthermore, many of these transcripts were only present in a single sample. A statistical classifier to predict transcripts over background signal was designed to identify highly recurrent transcripts that may be altered in prostate cancer. AceView (Thierry-Mieg et al. Genome Biol 7 Suppl 1, S12 1-14 (2006)) were used. For each transcript predicted by Cufflinks the following statistics were collected: length (bp), number of exons, recurrence (number of samples in which the transcript was predicted), 95th percentile of abundance (measured in Fragments per Kilobase per Million reads (FPKM)) across all samples, and uniqueness of genomic DNA harboring the transcript transcript (measured using the Rosetta uniqueness track from UCSC (Rhead et al. 2010. Nucleic Acids Res 38, D613-9). Using this information, recursive partitioning and regression trees in R (package rpart) were used to predict, for each transcript, whether its expression patterns and structural properties resembled those of annotated genes. Classification was performed independently for each chromosome in order to incorporate the effect of gene density variability on expression thresholds. Transcripts that were not classified as annotated genes were discarded, and the remainder were subjected to additional analysis and filtering steps. By examining the decision tree results it was observed that the 95th percentile of expression across all samples as well as the recurrence of each transcript were most frequently the best predictors of expressed versus background transcripts (FIG. 7).
  • Refinement of Transcript Fragments
  • The statistical classifier predicted a total 2.88 million (34.9%) transcript fragments as “expressed” transcripts. A program was developed to extend and merge intron-redundant transcripts to produce a minimum set of transcripts that describes the assemblies produced by Cufflinks. The merging step produced a total of 123,554 independent transcripts. Tanscript abundance levels were re-computed for these revised transcripts in Reads per Kilobase per Million (RPKM) units. These expression levels were used for the remainder of the study. Several additional filtering steps were used to isolate the most robust transcripts. First, transcripts with a total length less than 200 nt were discarded. Single exon transcripts with greater than 75% overlap to another longer transcript were also discarded. Transcripts that lacked a completely unambiguous genomic DNA stretch of at least 40 nt were also removed. Genomic uniqueness was measured using the Rosetta uniqueness track downloaded from the UCSC genome browser website. Transcripts that were not present in at least 5% of the cohort (>5 samples) at more than 5.0 RPKM were retained.
  • In certain instances transcripts were observed that were interrupted by poorly mappable genomic regions. Additionally, for low abundance genes fragmentation due to the lack of splice junction or paired-end read evidence needed to connect nearby fragments were observed. The difference in the Pearson correlation between expression of randomly chosen exons on the same transcript versus expression of spatially proximal exons on different transcripts was measured and it was found that in the cohort, a Pearson correlation >0.8 had a positive predictive value (PPV) of >95% for distinct exons to be part of the same transcript. Using this criteria, hierarchical agglomerative clustering to extend transcript fragments into larger transcriptional units was performed. Pairs of transcripts further than 100 kb apart, transcripts on opposite strands, and overlapping transcripts were not considered for clustering. Groups of correlated transcripts were merged, and introns <40 nt in length were removed.
  • Comparison with Gene Annotation Databases
  • The 44,534 transcripts produced by the bioinformatics pipeline were classified by comparison with a comprehensive list of “annotated” transcripts from UCSC, RefSeq, ENCODE, Vega, and Ensembl. First, transcripts corresponding to processed pseudogenes were separated. This was done to circumvent a known source of bias in the TopHat read aligner. TopHat maps reads to genomic DNA in its first step, predisposing exon-exon junction reads to align to their spliced retroposed pseudogene homologues. Next, transcripts with >1 bp of overlap with at least one annotated gene on the correct strand were designated “annotated”, and the remainder were deemed “unannotated”. Transcripts with no overlap with protein coding genes were subdivided into intronic, intergenic, or partially intronic antisense categories based on their relative genomic locations.
  • Informatics Filtering of Unspliced Pre-mRNA Isoforms
  • An increase in the percentage of intronic transcripts in the assembly relative to known intronic ncRNAs was observed. This led to the observation that in many cases unspliced pre mRNAs appear at sufficient levels to escape the filtering steps employed by Cufflinks during the assembly stage. Intronic and antisense transcripts that were correlated (Pearson correlation >0.5) to their overlapping protein coding genes were removed. This effectively removed transcripts within genes such as PCA3 and HPN that were obvious premRNA artifacts, while leaving truly novel intronic transcripts—such as those within FBXL7 and CDH13—intact. These steps produced a consensus set of 35,415 transcripts supporting long polyadenylated RNA molecules in human prostate tissues and cell lines. Per chromosome transcript counts closely mirrored known transcript databases (Table 2), indicating that the informatics procedures employed compensate well for gene density variability across chromosomes. Overall a similar number of transcripts as present in the either the RefSeq or UCSC databases (Wheeler et al. Nucleic Acids Res 28, 10-4 (2000)) were detected.
  • Coding Potential Analysis
  • To analyze coding potential, DNA sequences for each transcript were extracted and searched for open reading frames (ORFs) using the txCdsPredict program from the UCSC source tool set (Kent et al. Genome Res 12, 996-1006 (2002)). This program produces a score corresponding to the protein coding capacity of a given sequence, and scores >800 are ˜90% predictive of protein coding genes. This threshold was used to count transcripts with coding potential, and found only 5 of 6,641 unannotated genes with scores >800, compared with 1,669 of 25,414 protein coding transcripts. Additionally, it was observed that protein coding genes possess consistently longer ORFs than either unannotated or annotated ncRNA transcripts, indicating that the vast majority of the unannotated transcripts represent ncRNAs (FIG. 10).
  • Separation of Transcripts into Repetitive and Non-Repetitive Categories
  • To separate transcripts into “repeat” and “non-repeat” transcripts, the genomic DNA corresponding to the transcript exons was extracted and the fraction of repeat-masked nucleotides in each sequence were calculated. For the designation of repeat classes, RepMask 3.2.7 UCSC Genome Browser track (Kent, supra) was used. It was observed that transcripts enriched with repetitive DNA tended to be poorly conserved and lacked ChIP-seq marks of active chromatin (FIG. 12). Transcripts containing >25% repetitive DNA (FIG. 11) were separated for the purposes of the ChIP-seq and conservation analyses discussed below.
  • Conservation Analysis
  • The SiPhy package (Garber et al. Bioinformatics 25, i54-62 (2009)) was used to estimate the locate rate of variation (w) of all non-repetitive transcript exons across 29 placental mammals. The program was run as described on the SiPhy website.
  • ChIP-Seq Datasets
  • Published ChIP-Seq datasets for H3K4me1, H3K4me2, H3K4me3, Acetylated H3, Pan-H3, and H3K36me3 were used (Yu et al. Cancer Cell 17, 443-54). These data are publicly available through the NCBI Geo Omnibus (GEO GSM353632). The raw ChIP-Seq data was analyzed using MACS34 (H3K4me1, H3K4me2, H3K4me3, Acetylated H3, and Pan-H3) or SICER35 (H3K36me3) peak finder programs using default settings. These peak finders were used based upon their preferential suitability to detect different types of histone modifications (Pepke et al., Nat Methods 6, S22-32 (2009)). The H3K4me3-H3K36me3 chromatin signature used to identify lincRNAs was determined from the peak coordinates by associating each H3K4me3 peak with the closest H3K36me3-enriched region up to a maximum of 10 kb away. The enhancer signature (H3K4me1 but not H3K4me3) was determined by subtracting the set of overlapping H3K4me3 peaks from the entire set of H3K4me1 peaks. These analyses were performed with the bx-python libraries distributed as part of the Galaxy bioinformatics infrastructure.
  • Differential Expression Analysis
  • To predict differentially expressed transcripts a matrix of log-transformed, normalized RPKM expression values was prepared by using the base 2 logarithm after adding 0.1 to all RPKM values. The data were first centered by subtracting the median expression of the benign samples for each transcript. The Significance Analysis of Microarrays (SAM) method (Tusher et al., Proc Natl Acad Sci USA 98, 5116-21 (2001)) with 250 permutations of the Tusher et al. S0 selection method was used to predict differentially expressed genes. A delta value corresponding to the 90th percentile FDR desired for individual analyses was used. The MultiExperiment Viewer application (Chu et al., Genome Biol 9, R118 (2008)) was used to run SAM and generate heatmaps. It was confirmed that the results matched expected results through comparison with microarrays and known prostate cancer biomarkers.
  • Outlier Analysis
  • A modified COPA analysis was performed on the 81 tissue samples in the cohort. RPKM expression values were used and shifted by 1.0 in order to avoid division by zero. The COPA analysis had the following steps (MacDonald & Ghosh, Bioinformatics 22, 2950-1 (2006); Tomlins et al. Science 310, 644-8 (2005)): 1) gene expression values were median centered, using the median expression value for the gene across the all samples in the cohort. This sets the gene's median to zero. 2) The median absolute deviation (MAD) was calculated for each gene, and then each gene expression value was scaled by its MAD. 3) The 80, 85, 90, 98 percentiles of the transformed expression values were calculated for each gene and the average of those four values was taken. Then, genes were rank ordered according to this “average percentile”, which generated a list of outliers genes arranged by importance. 4) Finally, genes showing an outlier profile in the benign samples were discarded. Six novel transcripts ranked as both outliers and differentially-expressed genes in the analyses. These six were manually classified either as differentially-expressed or outlier status based on what each individual's distribution across samples indicated.
  • Repeat Enrichment Analysis
  • To assess the enrichment of repetitive elements in the assembly, 100 random permutations of the transcript positions on the same chromosome and strand were generated. To mirror the original constraints used to nominate transcripts it was ensured that permuted transcript positions contained a uniquely mappable stretch of genomic DNA at least 50 nt long. To account for the effects of mappability difficulties, each exon was padded by ±0 bp, 50 bp, 100 bp, or 500 bp of additional genomic sequence before intersecting the exons with repeat elements in the RepeatMasker 3.2.7 database. It was observed that padding by more than 50 bp did not improve enrichment results and padded exons by ±50 bp in subsequent analyses and tests. Finally, the Shapiro-Wilk test for normality was performed and it was verified that the number of matches to highly abundant repetitive element types was approximately normally distributed.
    • B. Results
  • Prostate Cancer Transcriptome Sequencing
  • Transcriptome sequencing (RNA-Seq) was performed on 21 prostate cell lines, 20 benign adjacent prostates (benign), 47 localized tumors (PCA), and 14 metastatic tumors (MET). A total of 201 RNA-Seq libraries from this cohort were sequenced yielding a total of 1.41 billion mapped reads, with a median 4.70 million mapped reads per sample (Table 1 for sample information).
  • To analyze these data a method for ab initio transcriptome assembly to reconstruct transcripts and transcript abundance levels was used (FIG. 6 and Table 2) (Trapnell et al., NatBiotechnol 28 (5), 511; Trapnell et al., Bioinformatics 25 (9), 1105 (2009)). Sample-specific transcriptomes were predicted and individual predication were merged into a consensus transcriptome and the most robust transcripts were retained (FIG. 7). The ab initio transcriptome assembly and subsequent refinement steps yielded 35,415 distinct transcriptional loci (see FIG. 8 for examples).
  • The assembled transcriptome was compared to the UCSC, Ensembl, Refseq, Vega, and ENCODE gene databases to identify and categorize transcripts. While the majority of the transcripts (77.3%) corresponded to annotated protein coding genes (72.1%) and noncoding RNAs (5.2%), a significant percentage (19.8%) lacked any overlap and were designated “unannotated” (FIG. 1 a). These included partially intronic antisense (2.44%), totally intronic (12.1%), and intergenic transcripts (5.25%). These results agree with previous data indicating that large fractions of the transcriptome represent unannotated transcription (Birney et al., Nature 447 (7146), 799 (2007); Carninci et al., Science 309 (5740), 1559 (2005) and that significant percentages of genes may harbor related antisense transcripts (He et al., Science 322 (5909), 1855 (2008); Yelin et al., Nat Biotechnol 21 (4), 379 (2003)). Due to the added complexity of characterizing antisense or partially intronic transcripts without strand-specific RNA-Seq libraries, studies focused on totally intronic and intergenic transcripts.
  • Characterization of Novel Transcripts
  • Global characterization of novel transcripts corroborated previous reports that they are relatively poorly conserved and more lowly expressed than protein coding genes (Guttman et al., Nat Biotechnol 28 (5), 503; Guttman et al., Nature 458 (7235), 223 (2009)). Expression levels of unannotated prostate cancer transcripts were consistently higher than randomly permuted controls, but lower than annotated ncRNAs or protein coding genes (FIG. 1 b). Unannotated transcripts also showed less overlap with known expressed sequence tags (ESTs) than protein-coding genes but more than randomly permuted controls (FIG. 5). Unannotated transcripts showed a clear but subtle increase in conservation over control genomic intervals (novel intergenic transcripts p=2.7×10−4±0.0002 for 0.4<ω<0.8; novel intronic transcripts p=2.6×10−5±0.0017 for 0<ω<0.4, FIG. 1 c). Only a small subset of novel intronic transcripts showed increased conservation (FIG. 1 c insert), but this conservation was quite profound. By contrast, a larger number of novel intergenic transcripts showed more mild increases in conservation. Finally, analysis of coding potential revealed that only 5 of 6,144 transcripts harbored a high quality open reading frame (ORF), indicating that the overwhelming majority of these transcripts represent ncRNAs (FIG. 10).
  • Next, published prostate cancer ChIP-Seq data for two prostate cell lines (Yu et al., Cancer Cell 17 (5), 443; VCaP and LNCaP was used in order to interrogate the overlap of unannotated transcripts with histone modifications supporting active transcription (H3K4me1, H3K4me2, H3K4me3, H3K36me3, Acetyl-H3 and RNA polymerase II, see Table 3). Because unannotated ncRNAs showed two clear subtypes, repeat-associated and non-repeats (FIG. 11 and discussed below), it was contemplated that these two subtypes may display distinct histone modifications as noted in previous research (Day et al., Genome Biol 11 (6), R69). Whereas non-repeat transcripts showed strong enrichment for histone marks of active transcription at their putative transcriptional start sites (TSSs), repeat-associated transcripts showed virtually no enrichment (FIG. 12), and for the remaining ChIP-Seq analyses non-repeat transcripts only were considered. In this set of unannotated transcripts, strong enrichment for histone modifications characterizing TSSs and active transcription, including H3K4me2, H3K4me3, Acetyl-H3 and RNA Polymerase II (FIG. 1 d-g) but not H3K4me1 was observed, which characterizes enhancer regions (FIGS. 13 and 14). Intergenic ncRNAs performed much better in these analyses than intronic ncRNAs (FIG. 1 d-g). To elucidate global changes in transcript abundance between prostate cancer and benign tissues, differential expression was performed analysis for all transcripts. 836 genes differentially-expressed between benign and PCA samples (FDR <0.01) were found, with protein-coding genes constituting 82.8% of all differentially-expressed genes (FIG. 1 h and Table 4). This category contained the most significant transcripts, including numerous known prostate cancer genes such as AMACR32 and Hepsin (Dhanasekaran et al., Nature 412 (6849), 822 (2001)). Annotated ncRNAs represented 7.4% of differentially-expressed genes, including the ncRNA PCA334, which resides within an intron of the PRUNE2 gene and ranked #4 overall (12.2 fold change; adj. p<2×10-4, Wilcoxon rank sum test, Benjamini-Hochberg correction) (FIG. 8). Finally, 9.8% of differentially-expressed genes corresponded to unannotated ncRNAs, including 3.2% within gene introns and 6.6% in intergenic regions, indicating that these species contribute significantly to the complexity of the prostate cancer transcriptome.
  • Dysregulation of Unannotated Non-Coding RNAs
  • Recent reports of functional long intervening non-coding RNAs (Dhanasekaran et al., Nature 412 (6849), 822 (2001); Gupta et al., Nature 464 (7291), 1071; Rinn et al., Cell 129 (7), 1311 (2007); Guttman et al., Nature 458 (7235), 223 (2009)) (lincRNAs) in intergenic regions led to an exploration of intergenic ncRNAs further. A total of 1859 unannotated intergenic RNAs were found throughout the human genome. The present invention is not limited to a particular mechanism. Indeed, an understanding of the mechanism is not necessary to practice the present invention. Nonetheless it is contemplated that this is an underestimate due to the inability to detect small RNAs eliminated by the ˜250 bp size selection performed during RNA-Seq library generation (Methods). Overall, novel intergenic RNAs resided closer to protein-coding genes than protein-coding genes do to each other (the median distance to the nearest protein-coding gene is 4292 kb for novel genes and 8559 kb for protein-coding genes, FIG. 2 a). For instance, if two protein-coding genes, Gene A and Gene B, are separated by the distance AB, then the furthest an unannotated ncRNA can be from both of them is 0.5*AB, which is exactly what was observed (4292/8559=0.501). Supporting this observation, 34.1% of unannotated transcripts are located ≧10 kb from the nearest protein-coding gene. As an example, the Chr15q arm was visualized using the Circos program. Eighty-nine novel intergenic transcripts were nominated across this chromosomal region, including several differentially-expressed loci centromeric to TLE3 (FIG. 2 b) which were validated by PCR in prostate cancer cell lines (FIG. 15). A focused analysis of the 1859 novel intergenic RNAs yielded 106 that were differentially expressed in localized tumors (FDR <0.05; FIG. 2 c). These Prostate Cancer Associated Transcripts (PCATs) were ranked according to their fold change in localized tumor versus benign tissue (Tables 5 and 6).
  • Similarly, performing a modified cancer outlier profile analysis (COPA) on the RNA-Seq dataset re-discovered numerous known prostate cancer outliers, such as ERG7, ETV17, SPINK135, and CRISP336,37, and nominated numerous unannotated ncRNAs as outliers (FIG. 2 d and Tables 6 and 7). Merging the results from the differential expression and COPA analyses resulted in a set of 121 unannotated transcripts that accurately discriminated benign, localized tumor, and metastatic prostate samples by unsupervised clustering (FIG. 2 c). These data provide evidence that PCATs serve as biomarkers for prostate cancer and novel prostate cancer subtypes. Clustering analyses using novel ncRNA outliers also provide disease subtypes (FIG. 16).
  • Confirmation and Tissue-Specificity of ncRNAs
  • Validation studies were performed on 14 unannotated expressed regions, including ones both included and not present in the list of differentially expressed transcripts. Reverse transcription PCR(RT-PCR) and quantitative real-time PCR (qPCR) experiments demonstrated a ˜78% (11/14) validation rate in predicted cell line models for both transcript identity and expression level (FIG. 17). Next, three transcripts (PCAT-109, PCAT-14, and PCAT-43) selectively upregulated in prostate cancer compared to normal prostate were examined. From the sequencing data, each genomic loci shows significantly increased expression in prostate cancer and metastases, except for PCAT-14, which appears absent in metastases (FIG. 3 a-c). PCAT-109 also ranks as the #5 best outlier in prostate cancer, just ahead of ERG (FIG. 2 d and Table 6). qPCR on a cohort of 14 benign prostates, 47 tumors, and 10 metastases confirmed expression of these transcripts (FIG. 3 a-c). All three appear to be prostate-specific, with no expression seen in breast or lung cancer cell lines or in 19 normal tissue types (Table 8). This tissue specificity was not necessarily due to regulation by androgen signaling, as only PCAT-14 expression was induced by treatment of androgen responsive VCaP and LNCaP cells with the synthetic androgen R1881, consistent with previous data from this genomic locus (FIG. 18) (Tomlins et al., Nature 448 (7153), 595 (2007); Stavenhagen et al., Cell 55 (2), 247 (1988)). PCAT-14, but not PCAT-109 or PCAT-43, also showed differential expression when tested on a panel of matched tumor-normal samples, indicating that this transcript, which is comprised of an endogenous retrovirus in the HERV-K family (Bannert and Kurth, Proc Natl Acad Sci USA 101 Suppl 2, 14572 (2004)), can be used as a somatic marker for prostate cancer (FIG. 19). 5′ and 3′ rapid amplification of cDNA ends (RACE) at this locus revealed the presence of individual viral protein open reading frames (ORFs) and a transcript splicing together individual ORF 5′ untranslated region (UTR) sequences (FIG. 20). It was observed that the top-ranked intergenic ncRNA resided in the chromosome 8q24 gene desert nearby to the c-Myc oncogene. This ncRNA, termed PCAT-1, is located on the edge of the prostate cancer susceptibility region 240-43 (FIG. 4 a) and is about 0.5 Mb away from c-Myc. This transcript is supported by clear peaks in H3K4me3, Acetyl-H3, and RNA polymerase II ChIP-Seq data (FIG. 4 b). The exon-exon junction in cell lines was validated by RT-PCR and Sanger sequencing of the junction (FIG. 4 c), and 5′ and 3′ RACE was performed to elucidate transcript structure (FIG. 4 d). By this analysis, PCAT-1 is a mariner family transposase (Oosumi et al., Nature 378 (6558), 672 (1995); Robertson et al., Nat Genet. 12 (4), 360 (1996)) interrupted by an Alu retrotransposon and regulated by a viral long terminal repeat (LTR) promoter region (FIG. 4 d and FIG. 21). By qPCR, PCAT-1 expression is specific to prostate tissue, with striking upregulation in prostate cancers and metastases compared to benign prostate tissue (FIG. 4 e). PCAT-1 ranks as the second best overall prostate cancer biomarker, just behind AMACR (Table 3), indicating that this transcript is a powerful discriminator of this disease. Matched tumor normal pairs similarly showed marked upregulation in the matched tumor samples (FIG. 4 f). RNA interference (RNAi) was performed in VCaP cells using custom siRNAs targeting PCAT-1 sequences and no change in the cell proliferation or invasion upon PCAT-1 knockdown was observed (FIG. 22)
  • Selective Re-Expression of Repetitive Elements in Cancer
  • The presence of repetitive elements in PCAT-1 led to an exploration of repetitive elements. Repetitive elements, such as Alu and LINE-1 retrotransposons, are broadly known to be degenerate in humans (Oosumi et al, supra; Robertson et al., supra; Cordaux et al., Nat Rev Genet. 10 (10), 691 (2009), with only ˜100 LINE-1 elements (out of 12˜500,000) showing possible retrotransposon activity (Brouha et al., Proc Natl Acad Sci U S A 100 (9), 5280 (2003)). While transcription of these elements is frequently repressed through DNA methylation and repressive chromatin modifications (Slotkin and Martienssen, Nat Rev Genet. 8 (4), 272 (2007)), in cancer widespread hypomethylation has been reported (Cho et al., J Pathol 211 (3), 269 (2007); Chalitchagorn et al., Oncogene 23 (54), 8841 (2004); Yegnasubramanian et al., Cancer Res 68 (21), 8954 (2008)). Moreover, recent evidence indicates that these elements have functional roles in both normal biology (Kunarso et al., Nat. Genet.) and cancer (Lin et al., Cell 139 (6), 1069 (2009)), even if their sequences have mutated away from their evolutionary ancestral sequence (Chow et al., Cell 141 (6), 956). To date, only RNA-Seq platforms enable discovery and quantification of specific transposable elements expressed in cancer. As described above, it was observed that >50% of unannotated exons in the assembly overlap with at least one repetitive element (FIG. 11). Since these elements pose mappability challenges when performing transcriptome assembly with unique reads, these loci typically appear as “mountain ranges” of expression, with uniquely mappable regions forming peaks of expression separated by unmappable “ravines” (FIGS. 23 and 24). PCR and Sanger sequencing experiments were performed to confirm that these transposable elements of low mappability are expressed as part of these loci (FIGS. 23 and 24). To probe this observation further, the exons from unannotated transcripts in the assembly, with the addition of the flanking 50, 100, or 500 bp of additional genomic sequence to the 5′ and 3′ end of the exons were generated, the overlap of these intervals with repetitive elements to randomly permuted genomic intervals of similar sizes was performed. A highly significant enrichment for repetitive elements in the dataset was observed (OR 2.82 (95% CI 2.68-2.97), p<10-100). Examination of the individual repetitive element classes revealed a specific enrichment for SINE elements, particularly Alus (p≦2×10-16, Tables 10 and 11). A subset of LINE-1 and Alu transposable elements demonstrate marked differential expression in a subset of prostate cancer tumors (FIG. 25). One locus on chromosome 2 (also highlighted in FIG. 3 b) is a 500+ kb region with numerous expressed transposable elements (FIG. 26). This locus, termed Second Chromosome Locus Associated with Prostate-1 (SChLAP1), harbors transcripts that perform extremely well in outlier analyses for prostate cancer (Tables 6 and 7). PCAT-109, discussed above, is one outlier transcript in this region. Moreover, the SChLAP1 locus is highly associated with patients positive for ETS gene fusions (p<0.0001, Fisher's exact test, FIG. 27), whereas this association was not observed with other expressed repeats. A direct regulatory role for ERG on this region was not identified using siRNA-mediated knockdown of ERG in the VCaP cell line. These data indicate that the dysregulation of repeats in cancer is highly specific, and that this phenomenon associates with only a subset of tumors and metastases. Thus, the broad hypomethylation of repeat elements observed in cancer (Cho et al., J Pathol 211 (3), 269 (2007); Chalitchagorn et al., Oncogene 23 (54), 8841 (2004); Yegnasubramanian et al., Cancer Res 68 (21), 8954 (2008)) does not account for the high specificity of repeat expression.
  • Non-Invasive Detection of ncRNAs in Urine
  • Taken together, these data show an abundance of novel ncRNA biomarkers for prostate cancer, many of which appear to have tissue specificity. 77 urine sediments obtained from patients with prostate cancer and 31 control patients without known disease were analyzed (Laxman et al., Cancer Res 68 (3), 645 (2008)). The control patients are defined as those lacking cancer histology upon prostate biopsy and lacking the TMPRSS2-ERG fusion transcript in urine sediment RNA (Laxman et al., supra). PCAT-1 and PCAT-14, as well as the known ncRNA biomarker PCA3, were selected for evaluation on this urine panel due to their biomarker status in patient tissue samples. qPCR analysis led to an observation of specificity in their ability to detect prostate cancer patients and not patients with normal prostates (FIG. 5 a-c). In several cases, patients with ETS-negative prostate cancer that were misclassified as “benign” are clearly evident (FIGS. 5 a and 5 c). Moreover, PCAT-14 appears to perform almost as well as PCA3 as a urine biomarker, nearly achieving statistical significance (p=0.055, Fisher's exact test) despite the small number of patients used for this panel. It was next evaluated whether these unannotated ncRNAs identified a redundant set of patients that would also be identified by other urine tests, such as PCA3 or TMPRSS2-ERG transcripts. Comparing PCAT-1 and PCAT-14 expression in urine samples to PCA3 or to each other revealed that these ncRNAs identified distinct patient sets, indicating that a patient's urine typically harbors PCAT-1 or PCAT-14 transcripts but not both (FIG. 5 d). Using the cut-offs displayed in FIG. 5 a-c, a binary heatmap comparing these three ncRNAs with patients' TMPRSS2-ERG status was generated (FIG. 5 e). The ncRNAs were able to detect additional ETS-negative patients with prostate cancer through this urine test, indicating that they have clinical utility as highly specific markers for prostate cancer using a multiplexed urine test. Combining PCAT-1, PCAT-14 and PCA3 into a single “non-coding RNA signature” generated a highly specific urine signature (p=0.0062, Fisher's exact test, FIG. 5 f) that identifies a number of prostate cancer patients that is broadly comparable to the TMPRSS2-ERG fusion (33% vs. 45%).
  • FIG. 34 shows detection of prostate cancer RNAs in patient urine samples using qPCR. All RNA species were detectable in urine. FIG. 35 shows that multiplexing urine SChLAP-1 measurements with serum PSA improves prostate cancer risk stratification. Individually, SChLAP-1 is a predictor for prostate cancers with intermediate or high clinical risk of aggressiveness. Multiplexing this measurement with serum PSA improves upon serum PSA's ability to predict for more aggressive disease.
    • Additional Characterization
  • Additional experiments were conducted related to PCAT-1 and SChLAP-1 region in prostate cancer. FIG. 29 demonstrates that PCAT-1 expression sensitizes prostate cancer cells to treatment with PARP-1 inhibitors. FIG. 30 demonstrates that PCAT-1 expression sensitizes prostate cells to radiation treatment.
  • FIG. 31 demonstrates that unannotated intergeic transcripts in SChLAP-1 differentiate prostate cancer and benign samples. FIG. 32 demonstrates that SChLAP-1 is required for prostate cancer cell invasion and proliferation. Prostate cell lines, but not non-prostate cells, showed a reduction in invasion by Boyden chamber assays. EZH2 and non-targeting siRNAs served as positive and negative controls, respectively. Deletion analysis of SChLAP-1 was performed. FIG. 33 shows that a region essential for its function was identified.
  • ncRNAs in Lung, Breast, and Pancreatic Cancers
  • Analysis of the lung cancer transcriptome (FIG. 36) was performed. 38 lung cell lines were analyzed by RNA-Seq and then lncRNA transcripts were reconstructed. Unannotated transcripts accounted for 27% of all transcripts. Novel transcripts well more highly expressed than annotated ncRNAs but not protein-coding transcripts. An outlier analyses of 13 unannotated transcripts shows novel lncRNAs in subtypes of lung cancer cell lines. FIG. 37 shows discovery of M41 and ENST-75 ncRNAs in lung cancer. FIG. 38 shows that lncRNAs are drivers and biomarkers in lung cancer. FIG. 39 shows identification of cancer-associated lncRNAs in breast and pancreatic cancer. Three novel breast cancer lncRNAs were nominated from RNA-Seq data (TU0011194, TU0019356, and TU0024146. All show outlier expression patterns in breast cancer samples but not benign samples. Three novel pancreatic cancer lncRNAs were nominated from RNA-Seq data (TU0009141, TU0062051, and TU0021861). All show outlier expression patterns in pancreatic cancer samples but not benign samples.
  • TABLE 1
    Sample Read Total Reads
    Library ID Sample Name Type Type Read Type Length (x2 for PE)
    cts_42898AAXX_2 PWP-1E RNA-Seq CellLine paired_end 40 7363040
    mctp_30022AAXX_5 prEC RNA-Seq Cell Line single_read 40 30784563
    mctp_209599AAXX_3 prEC RNA-Seq Cell Line single_read 30 3319065
    mctp_31472AAXX_1 prEC RNA-Seq Cell Line paired_end 40 7748627
    mctp_35351AAXX_2 prEC RNA-Seq Cell Line paired_end 40 5853455
    mctp_31471AAXX_2 P-SMC RNA-Seq Cell Line paired_end 40 3465529
    mctp_20E5CAAXX_5 RWPE RNA-Seq Cell Line single_read 36 5300135
    mctp_20E6CAAXX_7 RWPE RNA-Seq Cell Line single_read 36 5347764
    mctp_3085CAAXX_5 RWPE RNA-Seq Cell Line single_read 36 4778245
    mctp_20F05AAXX_6 RWPE RNA-Seq Cell Line single_read 36 4033615
    mctp_20F0BAAXX_7 RWPE RNA-Seq Cell Line single_read 36 5005497
    mctp_30F0BAAXX_5 RWPE RNA-Seq Cell Line single_read 36 4955662
    mctp_20F0GAAXX_7 RWPE RNA-Seq Cell Line single_read 36 4066435
    mctp_20FDGAAXX_8 RWPE RNA-Seq Cell Line single_read 36 4009235
    mctp_20F0GAAXX_5 RWPE RNA-Seq Cell Line single_read 35 4934467
    mctp_4250BAAXX_3 WPM1-2 RNA-Seq Cell Line paired_end 40 7593911
    mctp_20F58AAXX_1 22Fx1 RNA-Seq Cell Line single_read 34 5301733
    mctp_32401AAXX_6 22Rv1 RNA-Seq Cell Line paired_end 40 9314220
    mctp_42974AAXX_5 CA-HPV-20 RNA-Seq Cell Line paired_end 40 33854951
    mctp_42974AAXX_7 CWR32 RNA-Seq Cell Line paired_end 40 23852984
    mctp_3058DAAXX_2 VCaP RNA-Seq Cell Line single_read 55 3575900
    mctp_20CCAAXX_7 VCaP RNA-Seq Cell Line single_read 36 5372014
    mctp_20CCAAXX_6 VCaP RNA-Seq Cell Line single_read 30 5210393
    mctp_20CCAAAXX_6 VCaP RNA-Seq Cell Line single_read 38 5220542
    mctp_200CAAAXX_3 VCaP RNA-Seq Cell Line single_read 36 5405226
    mctp_200CAAAXX_2 VCaP RNA-Seq Cell Line single_read 36 5092526
    mctp_20CCAAAXX_2 VCaP RNA-Seq Cell Line single_read 36 4273325
    mctp_20E5CAAXX_1 VCaP RNA-Seq Cell Line single_read 36 4727524
    mctp_20CCAAAXX_9 VCaP RNA-Seq Cell Line single_read 36 5024204
    mctp_20766AAXX_1 VCaP RNA-Seq Cell Line single_read 36 4491727
    mctp_42874AAXX_4 NC-H560 RNA-Seq Cell Line paired_end 40 12322606
    mctp_20FDGAAXX_4 LNCaP RNA-Seq Cell Line single_read 36 5209503
    mctp_30F0GAAXX_2 LNCaP RNA-Seq Cell Line single_read 35 5015345
    mctp_20F0GAAXX_3 LNCaP RNA-Seq Cell Line single_read 35 5106724
    mctp_20F0GAAXX_2 LNCaP RNA-Seq Cell Line single_read 36 4990256
    mctp_2056CAAXX_2 LNCaP RNA-Seq Cell Line single_read 34 4593759
    mctp_2056CAAXX_3 LNCaP RNA-Seq Cell Line single_read 36 5432656
    mctp_2056CAAXX_4 LNCaP RNA-Seq Cell Line single_read 34 4553947
    mctp_42434UAAXX_6 LNCaP CDS2 RNA-Seq Cell Line paired_end 33 10714839
    mctp_42822UAAXX_7 LNCaP CDS3 RNA-Seq Cell Line paired_end 33 5613473
    mctp_42TASAAXX_7 DU-145 RNA-Seq Cell Line paired_end 38 13804352
    mctp_42TAAAAXX_6 DU-145 RNA-Seq Cell Line paired_end 38 15785849
    mctp_42TA8AAXX_5 DU-145 RNA-Seq Cell Line paired_end 33 14197743
    mctp_42TASAAXX_1 DU-145 RNA-Seq Cell Line paired_end 35 13152293
    mctp_42TAAAAXX_2 DU-145 RNA-Seq Cell Line paired_end 32 12583746
    mctp_42TA8AAXX_5 DU-145 RNA-Seq Cell Line paired_end 33 10944553
    mctp_42TBDAAXX_9 DU-145 RNA-Seq Cell Line paired_end 35 9229144
    mctp_42PFAAAXX_4 LNCaP CDS RNA-Seq Cell Line paired_end 35 12368574
    parent
    mctp_42FFAAAXX_5 LNCaP CDS2 RNA-Seq Cell Line paired_end 33 14489865
    mctp_20BC5AAXX_8 DU-145 RNA-Seq Cell Line single_read 36 5351486
    mctp_20F59AAXX_2 DU-145 RNA-Seq Cell Line single_read 34 5069245
    mctp_3063DAAXX_3 DU-145 RNA-Seq Cell Line single_read 45 3506532
    mctp_42FFAAXX_3 LAFC-4 RNA-Seq Cell Line paired_end 40 14725226
    mctp_3564YAAXX_1 pc3 RNA-Seq Cell Line paired_end 40 10267396
    mctp_20F69AAXX_3 pc3 RNA-Seq Cell Line single_read 33 5364050
    mctp_42554AAXX_2 C4-2B RNA-Seq Cell Line paired_end 40 12754909
    mctp_42974AAXX_6 MDA FCa 22 RNA-Seq Cell Line paired_end 40 13341323
    mctp_42602AAXX_4 WPE1-HB26 RNA-Seq Cell Line paired_end 40 10593810
    mctp_42548AAXX_4 PrBe10023 RNA-Seq Cell Line paired_end 40 15313195
    mctp_30WUZAAXX_5 PrBE20013 RNA-Seq Cell Line paired_end 35 1022744
    mctp_42813AAXX_0 PrBE20014 RNA-Seq Cell Line paired_end 50 11242542
    mctp_42PFAAAXX_2 PrBE20024 RNA-Seq Cell Line paired_end 33 5646551
    mctp_30WUZAAXX_6 PrBE20014 RNA-Seq Cell Line paired_end 35 3377105
    mctp_42CUAAXX_7 PrBE20015 RNA-Seq Cell Line paired_end 50 7595450
    mctp_41N14AAXX_1 PrBE20025 RNA-Seq Cell Line paired_end 32 14331227
    mctp_42543AAXX_2 PrBe10016 RNA-Seq Tissue paired_end 49 12122394
    mctp_42NY9AAXX_3 PrBe10016 RNA-Seq Tissue paired_end 30 11309596
    mctp_30WUZAAXX_7 PrBe10017 RNA-Seq Tissue paired_end 38 1059393
    mctp_420JFAAXX_5 PrBe10017 RNA-Seq Tissue paired_end 49 14245723
    mctp_43830AAXX_5 PrBe10018 RNA-Seq Tissue paired_end 35 16616393
    mctp_42NY4AAXX_6 PrBe10018 RNA-Seq Tissue paired_end 35 15877694
    mctp_42D3MAAXX_5 aN10_6 RNA-Seq Tissue paired_end 49 10102953
    mctp_3054YAAXX_2 aN11_1 RNA-Seq Tissue paired_end 49 9792955
    mctp_42P6UAAXX_1 aN11_1 RNA-Seq Tissue paired_end 49 14656035
    mctp_3040WAAXX_1 aN13_2 RNA-Seq Tissue paired_end 49 14755527
    mctp_42P6GAAXX_4 aN13_2 RNA-Seq Tissue paired_end 49 18107801
    mctp_3G54YAAXX_2 aN14_4 RNA-Seq Tissue paired_end 49 9252092
    mctp_42P6UAAXX_3 aN14_4 RNA-Seq Tissue paired_end 49 12317092
    mctp_30653AAXX_5 PrBe10002 RNA-Seq Tissue paired_end 49 10282226
    mctp_30CVWAAXX_6 PrBe10002 RNA-Seq Tissue single_read 49 4359340
    mctp_3GCYWAAXX_7 PrBe10003 RNA-Seq Tissue single_read 49 4724195
    mctp_42P6UAAXX_3 aN15_3 RNA-Seq Tissue paired_end 49 14035929
    mctp_3054YAAXX_3 aN15_3 RNA-Seq Tissue paired_end 49 6772663
    mctp_30CM2AAXX_6 aN23 RNA-Seq Tissue single_read 35 8359098
    mctp_30CM2AAXX_4 aN25 RNA-Seq Tissue single_read 35 5162304
    mctp_30CM2AAXX_5 aN25 RNA-Seq Tissue single_read 35 5867482
    mctp_30CM3AAXX_1 aN27 RNA-Seq Tissue single_read 35 4771651
    mctp_30CM2AAXX_2 aN27 RNA-Seq Tissue single_read 35 5643509
    mctp_30CM2AAXX_7 aN28 RNA-Seq Tissue single_read 35 5661552
    mctp_30CM2AAXX_8 aN29 RNA-Seq Tissue single_read 35 5201944
    mctp_ZCFCKAAXX_1 aN31 RNA-Seq Tissue single_read 36 4206554
    mctp_ZCFCKAAXX_2 aN31 RNA-Seq Tissue single_read 35 5624043
    mctp_ZCFCKAAXX_4 aN32 RNA-Seq Tissue single_read 36 4445596
    mctp_ZCFCKAAXX_3 aN32 RNA-Seq Tissue single_read 36 4352455
    mctp_ZCFCKAAXX_7 aN33 RNA-Seq Tissue single_read 35 5375947
    mctp_ZCFCKAAXX_8 aN33 RNA-Seq Tissue single_read 35 3974253
    mctp_42D3MAAXX_6 aT12_4 RNA-Seq Tissue paired_end 40 10323733
    mctp_42P6UAAXX_6 aT12_4 RNA-Seq Tissue paired_end 40 12591651
    mctp_2GACMAAXX_7 aT54 RNA-Seq Tissue single_read 35 4951150
    mctp_3050WAAXX_3 aT5_5 RNA-Seq Tissue paired_end 40 14290070
    mctp_20AGMAAXX_2 aT62 RNA-Seq Tissue single_read 35 5144018
    mctp_20G93AAXX_3 aT76 RNA-Seq Tissue single_read 39 4492543
    mctp_4203NAAXX_7 aT8_3 RNA-Seq Tissue paired_end 40 5949944
    mctp_42P6UAAXX_7 aT2_2 RNA-Seq Tissue paired_end 49 15165443
    mctp_2GACMAAXX_6 aT20 RNA-Seq Tissue single_read 35 4905934
    mctp_30Y5NAAXX_6 aT52 RNA-Seq Tissue paired_end 34 9555243
    mctp_20593AAXX_4 PrCa10001 RNA-Seq Tissue single_read 39 5073375
    mctp_30CVWAAXX_2 PrCa10002 RNA-Seq Tissue single_read 49 5579844
    mctp_20G95AAXX_7 PrCa10002 RNA-Seq Tissue single_read 30 5337734
    mctp_30CW7AAXX_4 PrCa10003 RNA-Seq Tissue single_read 49 7245008
    mctp_30CVWAAXX_5 PrCa10003 RNA-Seq Tissue single_read 40 2232676
    mctp_20G93AAXX_6 PrCa10003 RNA-Seq Tissue single_read 30 4209584
    mctp_20G93AAXX_2 PrCa10004 RNA-Seq Tissue single_read 30 4277613
    mctp_30CW2AAXX_2 PrCa10004 RNA-Seq Tissue single_read 49 2502651
    mctp_20G93AAXX_1 PrCa10006 RNA-Seq Tissue single_read 30 4897349
    mctp_30CW2AAXX_5 PrCa10006 RNA-Seq Tissue single_read 40 7780454
    mctp_30WU2AAXX_3 PrCa10013 RNA-Seq Tissue paired_end 39 7094073
    mctp_42FFAAAXX_3 PrCa10013 RNA-Seq Tissue paired_end 39 13129950
    mctp_42CJFAAXX_4 PrCa10013 RNA-Seq Tissue paired_end 40 11855634
    mctp_42603AAXX_5 PrCa10014 RNA-Seq Tissue paired_end 49 11559506
    mctp_42808AAXX_1 PrCa10014 RNA-Seq Tissue paired_end 40 4829325
    mctp_42CJ1AAXX_5 PrCa10014 RNA-Seq Tissue paired_end 40 15125424
    mctp_30WU2AAXX_1 PrCa10014 RNA-Seq Tissue paired_end 39 13032345
    mctp_42543AAXX_3 PrCa10015 RNA-Seq Tissue paired_end 49 14322429
    mctp_30WUJAAXX_4 PrCa10015 RNA-Seq Tissue paired_end 35 5051535
    mctp_42NY4AAXX_4 PrCa10016 RNA-Seq Tissue paired_end 38 11279130
    mctp_42843AAXX_6 PrCa10016 RNA-Seq Tissue paired_end 49 11883528
    mctp_42843AAXX_2 PrCa10017 RNA-Seq Tissue paired_end 40 7503235
    mctp_429FAAAXX_1 PrCa10017 RNA-Seq Tissue paired_end 38 13554764
    mctp_42NY4AAXX_5 PrCa10018 RNA-Seq Tissue paired_end 38 16107721
    mctp_42CJFAAXX_1 PrCa10018 RNA-Seq Tissue paired_end 40 12506692
    mctp_30V5NAAXX_4 PrCa10018 RNA-Seq Tissue paired_end 34 8565125
    mctp_42CUAAXX_9 PrCa10019 RNA-Seq Tissue paired_end 49 24204481
    mctp_42543AAXX_5 PrCa10021 RNA-Seq Tissue paired_end 49 24583654
    mctp_42CJFAAXX_5 PrCa10023 RNA-Seq Tissue paired_end 40 5473417
    mctp_42CUAAXX_6 PrCa10024 RNA-Seq Tissue paired_end 49 5249645
    mctp_42PF0AAXX_3 PrCa10024 RNA-Seq Tissue paired_end 30 6109134
    mctp_42C16AAXX_3 PrCa10028 RNA-Seq Tissue paired_end 40 3344365
    mctp_42T69AAXX_3 PrCa10030 RNA-Seq Tissue paired_end 38 37238720
    mctp_42T89AAXX_2 PrCa10031 RNA-Seq Tissue paired_end 38 27981940
    mctp_42T69AAXX_6 PrCa10032 RNA-Seq Tissue paired_end 30 36892304
    mctp_42T69AAXX_2 PrCa10033 RNA-Seq Tissue paired_end 38 20735050
    mctp_42T89AAXX_7 PrCa10034 RNA-Seq Tissue paired_end 38 26494766
    mctp_42P0UAAXX_5 aT1_3 RNA-Seq Tissue paired_end 40 54052093
    mctp_302XWAAXX_2 aT1_3 RNA-Seq Tissue paired_end 40 24017933
    mctp_42543AAXX_7 aT30 RNA-Seq Tissue paired_end 40 23023075
    mctp_50V5NAAXX_3 aT38 RNA-Seq Tissue paired_end 34 9143041
    mctp_42Y27AAXX_2 aT42 RNA-Seq Tissue paired_end 35 33907739
    mctp_30GJ0AAXX_5 aT41 RNA-Seq Tissue single_read 45 9446722
    mctp_42Y2TAAXX_3 aT45 RNA-Seq Tissue paired_end 30 36395435
    mctp_300JQAAXX_6 aT45 RNA-Seq Tissue single_read 45 9254922
    mctp_32503AAXX_7 aT53 RNA-Seq Tissue paired_end 40 52164543
    mctp_20F66AAXX_4 aT55 RNA-Seq Tissue single_read 36 4655382
    mctp_300WTAAXX_3 aT55 RNA-Seq Tissue single_read 40 7356627
    mctp_20F85AAXX_1 aT56 RNA-Seq Tissue single_read 36 4594327
    mctp_30U09AAXX_4 aT57 RNA-Seq Tissue paired_end 40 9490697
    mctp_420JFAAXX_0 aT59 RNA-Seq Tissue paired_end 36 4260293
    mctp_42500AAXX_3 aT62 RNA-Seq Tissue paired_end 40 20252280
    mctp_20F66AAXX_7 aT46 RNA-Seq Tissue single_read 40 5026217
    mctp_300W7AAXX_1 aT65 RNA-Seq Tissue single_read 40 5035624
    mctp_20F85AAXX_1 aT56 RNA-Seq Tissue single_read 36 5226270
    mctp_42P5UAAXX_0 aT6_1 RNA-Seq Tissue paired_end 40 936249
    mctp_420JFAAXX_7 aT6_1 RNA-Seq Tissue paired_end 36 9420907
    mctp_42FFAAAXX_4 aT6_1 RNA-Seq Tissue paired_end 40 23242928
    mctp_300W3AAXX_7 PrCa10007 RNA-Seq Tissue single_read 40 7909933
    mctp_4203NAAXX_1 PrCa10025 RNA-Seq Tissue paired_end 30 9614303
    mctp_4202NAAXX_1 PrCa10026 RNA-Seq Tissue paired_end 42 7901264
    mctp_4203NAAXX_3 PrCa10027 RNA-Seq Tissue paired_end 40 20305382
    mctp_42T89AAXX_4 PrCa10029 RNA-Seq Tissue paired_end 40 0674521
    mctp_42Y6WAAXX_6 PrCa10029 RNA-Seq Tissue paired_end 40 53229893
    mctp_3064YAAXX_4 ULM2927 RNA-Seq Tissue paired_end 30 9342506
    mctp_4283YAAXX_4 aT47 RNA-Seq Tissue paired_end 30 7506523
    mctp_2GF06AAXX_3 aM23 RNA-Seq Tissue single_read 40 4560303
    mctp_2GF66AAXX_4 aM23 RNA-Seq Tissue single_read 40 4923493
    mctp_20F69AAXX_4 aM23 RNA-Seq Tissue single_read 36 5374538
    mctp_20LV8AAXX_5 aM23 RNA-Seq Tissue single_read 36 3527555
    mctp_20LV8AAXX_7 aM23 RNA-Seq Tissue single_read 36 5542795
    mctp_20AGMAAXX_4 aM29 RNA-Seq Tissue single_read 30 4905232
    mctp_20FETAAXX_8 aM29 RNA-Seq Tissue single_read 30 5092373
    mctp_2074VAAXX_1 aM30 RNA-Seq Tissue single_read 35 5126432
    mctp_30CVMAAXX_4 aM38 RNA-Seq Tissue single_read 36 4759734
    mctp_30TVGAAXX_3 aM30 RNA-Seq Tissue paired_end 36 6778934
    mctp_43620AAXX_6 aM15 RNA-Seq Tissue paired_end 40 23925385
    mctp_3074VAAXX_3 aM15 RNA-Seq Tissue single_read 40 4744055
    mctp_3074VAAXX_5 aM37 RNA-Seq Tissue single_read 38 4309553
    mctp_305KAAAXX_2 aM41 RNA-Seq Tissue single_read 36 4480735
    mctp_20FETAAXX_6 aM41 RNA-Seq Tissue single_read 36 3372965
    mctp_2074VAXX_2 aM41 RNA-Seq Tissue single_read 36 5232746
    mctp_3064VAAXX_6 ULMB815239- RNA-Seq Tissue paired_end 36 9663726
    97
    mctp_3064VAAXX_5 ULMB2440-97 RNA-Seq Tissue paired_end 36 9232376
    mctp_20E2PAAXX_7 aM11 RNA-Seq Tissue single_read 40 3201585
    mctp_42CJFAAXX_6 aM20 RNA-Seq Tissue paired_end 40 9038499
    mctp_20EXPAAXX_5 aM35 RNA-Seq Tissue single_read 36 5587558
    mctp_30CW7AAXX_5 aM35 RNA-Seq Tissue single_read 40 9398611
    mctp_307VGAAXX_1 aM35 RNA-Seq Tissue paired_end 40 7749513
    mctp_205K4AAXX_2 aM35 RNA-Seq Tissue single_read 36 5697473
    mctp_20E7PAAXX_2 aM39 RNA-Seq Tissue single_read 36 3526549
    mctp_307YGAAXX_3 aM39 RNA-Seq Tissue paired_end 40 6279375
    mctp_20FETAAXX_7 aM39 RNA-Seq Tissue single_read 36 5354844
    mctp_20E2PAAXX_8 aM43 RNA-Seq Tissue single_read 36 5497785
    mctp_30CW7AAXX_7 aM83 RNA-Seq Tissue single_read 40 5459329
    TOTAL 1723713421
    TopHat
    Mapped TopHat splice % ETS
    Library ID Reads Reaction Reads Splice Diagnosis status
    cts_42898AAXX_2 8367325 1041179 13.04% Benign Negative
    mctp_30022AAXX_5 855130 107315 11.24% Benign Negative
    mctp_209599AAXX_3 871580 67613 7.76% Benign Negative
    mctp_31472AAXX_1 7443379 747751 10.05% Benign Negative
    mctp_35351AAXX_2 9562343 892320 9.33% Benign Negative
    mctp_31471AAXX_2 6515281 935503 50.54% Benign Negative
    mctp_20E5CAAXX_5 1693464 149395 8.02% Benign Negative
    mctp_20E6CAAXX_7 1710762 250130 8.79% Benign Negative
    mctp_3085CAAXX_5 1539225 135955 8.84% Benign Negative
    mctp_20F05AAXX_6 1365250 137416 8.78% Benign Negative
    mctp_20F0BAAXX_7 1523033 143125 8.83% Benign Negative
    mctp_30F0BAAXX_5 1507224 141350 5.50% Benign Negative
    mctp_20F0GAAXX_7 1566635 130224 8.01% Benign Negative
    mctp_20FDGAAXX_8 1550957 156049 8.77% Benign Negative
    mctp_20F0GAAXX_5 1580424 135674 8.77% Benign Negative
    mctp_4250BAAXX_3 8103303 1011039 12.40% Benign Negative
    mctp_20F58AAXX_1 2345205 109257 7.32% Localized Negative
    mctp_32401AAXX_6 9500616 1003132 11.07% Localized Negative
    mctp_42974AAXX_5 14751620 1750426 12.50% Localized Negative
    mctp_42974AAXX_7 14791325 1530790 20.35% Localized Negative
    mctp_3058DAAXX_2 1450656 167748 51.58% Metastatic ERG+
    mctp_20CCAAXX_7 981204 89640 9.14% Metastatic ERG+
    mctp_20CCAAXX_6 957549 26199 9.00% Metastatic ERG+
    mctp_20CCAAAXX_6 958823 52342 9.23% Metastatic ERG+
    mctp_200CAAAXX_3 988972 96075 9.11% Metastatic ERG+
    mctp_200CAAAXX_2 938272 15147 9.07% Metastatic ERG+
    mctp_20CCAAAXX_2 804085 72504 8.05 Metastatic ERG+
    mctp_20E5CAAXX_1 861856 75161 9.07% Metastatic ERG+
    mctp_20CCAAAXX_9 926254 25535 9.23% Metastatic ERG+
    mctp_20766AAXX_1 307597 73610 9.11% Metastatic ERG+
    mctp_42874AAXX_4 15104197 1377700 9.12% Metastatic ERG+
    mctp_20FDGAAXX_4 1430548 119573 9.35% Metastatic ETV1+
    mctp_30F0GAAXX_2 1402514 117293 5.36% Metastatic ETV1+
    mctp_20F0GAAXX_3 1426334 119462 5.37% Metastatic ETV1+
    mctp_20F0GAAXX_2 1395161 117850 2.43% Metastatic ETV1+
    mctp_2056CAAXX_2 1370920 112874 5.30% Metastatic ETV1+
    mctp_2056CAAXX_3 1520040 125277 5.96% Metastatic ETV1+
    mctp_2056CAAXX_4 1304247 112429 3.62% Metastatic ETV1+
    mctp_42434UAAXX_6 10272130 1057573 50.30% Metastatic Negative
    mctp_42822UAAXX_7 5336305 973617 10.56% Metastatic Negative
    mctp_42TASAAXX_7 13651384 1372507 10.04% Metastatic Negative
    mctp_42TAAAAXX_6 13915895 1320336 9.85% Metastatic Negative
    mctp_42TA8AAXX_5 14950079 1485334 9.93% Metastatic Negative
    mctp_42TASAAXX_1 13047548 1330224 20.17% Metastatic Negative
    mctp_42TAAAAXX_2 13715578 1324118 50.09% Metastatic Negative
    mctp_42TA8AAXX_5 6437207 653992 10.36% Metastatic Negative
    mctp_42TBDAAXX_9 20026773 1013721 20.11% Metastatic Negative
    mctp_42PFAAAXX_4 9518829 366543 20.15% Metastatic Negative
    mctp_42FFAAAXX_5 13995752 1611356 50.08% Metastatic Negative
    mctp_20BC5AAXX_8 3560642 135083 9.13% Metastatic Negative
    mctp_20F59AAXX_2 2717193 225574 9.25% Metastatic Negative
    mctp_3063DAAXX_3 4162580 498466 51.97% Metastatic Negative
    mctp_42FFAAXX_3 16711055 1790250 10.71% Metastatic Negative
    mctp_3564YAAXX_1 20291560 1185473 11.52% Metastatic Negative
    mctp_20F69AAXX_3 2547308 237597 8.33% Metastatic Negative
    mctp_42554AAXX_2 12823209 1391197 12.41% Metastatic Negative
    mctp_42974AAXX_6 12909546 1834544 10.96% Metastatic Negative
    mctp_42602AAXX_4 9930521 1240043 52.49% Metastatic Negative
    mctp_42548AAXX_4 13040537 1435670 7.95% Benign Negative
    mctp_30WUZAAXX_5 12263152 927593 7.56% Benign Negative
    mctp_42813AAXX_0 4036070 715451 7.92% Benign Negative
    mctp_42PFAAAXX_2 6359375 471353 7.33% Benign Negative
    mctp_30WUZAAXX_6 4553890 321695 7.55% Benign Negative
    mctp_42CUAAXX_7 7927754 632270 7.90% Benign Negative
    mctp_41N14AAXX_1 12577994 936438 7.27% Benign Negative
    mctp_42543AAXX_2 11750831 820750 6.98% Benign Negative
    mctp_42NY9AAXX_3 11367053 751959 6.53% Benign Negative
    mctp_30WUZAAXX_7 1256367 152020 7.05% Benign Negative
    mctp_420JFAAXX_5 14323797 1025161 7.13% Benign Negative
    mctp_43830AAXX_5 17052415 1465145 2.62% Benign Negative
    mctp_42NY4AAXX_6 16459392 1428434 2.52% Benign Negative
    mctp_42D3MAAXX_5 11943284 936291 7.85% Benign Negative
    mctp_3054YAAXX_2 10708089 944683 7.08% Benign Negative
    mctp_42P6UAAXX_1 10917492 323126 7.54% Benign Negative
    mctp_3040WAAXX_1 15547535 1174999 7.56% Benign Negative
    mctp_42P6GAAXX_4 16070565 1311984 7.57% Benign Negative
    mctp_3G54YAAXX_2 9526530 733492 7.70% Benign Negative
    mctp_42P6UAAXX_3 11960962 894323 7.47% Benign Negative
    mctp_30653AAXX_5 3430927 190504 5.47% Benign Negative
    mctp_30CVWAAXX_6 577145 39135 4.45% Benign Negative
    mctp_3GCYWAAXX_7 352030 17102 4.40% Benign Negative
    mctp_42P6UAAXX_3 10590995 926250 5.53% Benign Negative
    mctp_3054YAAXX_3 8101379 714429 8.02% Benign Negative
    mctp_30CM2AAXX_6 1993000 171398 5.72% Benign Negative
    mctp_30CM2AAXX_4 2131784 100935 4.53% Benign Negative
    mctp_30CM2AAXX_5 2632652 123735 4.70% Benign Negative
    mctp_30CM3AAXX_1 2356628 93265 5.02% Benign Negative
    mctp_30CM2AAXX_2 2093972 105544 4.95% Benign Negative
    mctp_30CM2AAXX_7 5555510 87547 5.63% Benign Negative
    mctp_30CM2AAXX_8 2472975 23463 5.87% Benign Negative
    mctp_ZCFCKAAXX_1 1642651 122140 7.44% Benign Negative
    mctp_ZCFCKAAXX_2 1504320 107996 7.18% Benign Negative
    mctp_ZCFCKAAXX_4 1355001 112140 6.33% Benign Negative
    mctp_ZCFCKAAXX_3 1835242 115276 6.31% Benign Negative
    mctp_ZCFCKAAXX_7 3024782 122564 6.05% Benign Negative
    mctp_ZCFCKAAXX_8 1597569 96704 6.09% Benign Negative
    mctp_42D3MAAXX_6 10700318 891273 8.34% Localized ERG+
    mctp_42P6UAAXX_6 12687328 1035842 8.16% Localized ERG+
    mctp_2GACMAAXX_7 2395363 153160 6.39% Localized ERG+
    mctp_3050WAAXX_3 15157510 1231918 5.13% Localized ERG+
    mctp_20AGMAAXX_2 2594526 146253 5.56% Localized ERG+
    mctp_20G93AAXX_3 3095390 77035 3.58% Localized ERG+
    mctp_4203NAAXX_7 10259470 745408 7.38% Localized ERG+
    mctp_42P6UAAXX_7 12753016 925564 7.25% Localized ERG+
    mctp_2GACMAAXX_6 2330259 169032 7.06% Localized ETV1+
    mctp_30Y5NAAXX_6 15235237 579321 5.19% Localized ETV1+
    mctp_20593AAXX_4 2003723 51777 4.03% Localized Negative
    mctp_30CVWAAXX_2 2573890 142307 9.04% Localized Negative
    mctp_20G95AAXX_7 2185509 134758 6.17% Localized Negative
    mctp_30CW7AAXX_4 3325450 300975 6.04% Localized Negative
    mctp_30CVWAAXX_5 996717 47048 4.72% Localized Negative
    mctp_20G93AAXX_6 1080531 80219 4.29% Localized Negative
    mctp_20G93AAXX_2 2429172 101279 4.17% Localized Negative
    mctp_30CW2AAXX_2 4537952 261552 6.03% Localized Negative
    mctp_20G93AAXX_1 2219403 36343 3.09% Localized Negative
    mctp_30CW2AAXX_5 3325903 211003 5.52% Localized Negative
    mctp_30WU2AAXX_3 5465055 698526 5.25% Localized Negative
    mctp_42FFAAAXX_3 14850387 1205327 5.12% Localized Negative
    mctp_42CJFAAXX_4 13599347 1193752 3.39% Localized Negative
    mctp_42603AAXX_5 11273990 925485 5.19% Localized Negative
    mctp_42808AAXX_1 7576252 705179 9.31% Localized Negative
    mctp_42CJ1AAXX_5 17200396 1126961 7.71% Localized Negative
    mctp_30WU2AAXX_1 15793364 1123174 7.11% Localized Negative
    mctp_42543AAXX_3 14744516 1043965 7.08% Localized Negative
    mctp_30WUJAAXX_4 10010115 575580 6.75% Localized Negative
    mctp_42NY4AAXX_4 13526717 954376 7.06% Localized Negative
    mctp_42843AAXX_6 13459171 1027559 7.53% Localized Negative
    mctp_42843AAXX_2 7555611 622237 8.24% Localized Negative
    mctp_429FAAAXX_1 11020052 352274 7.53% Localized Negative
    mctp_42NY4AAXX_5 12636010 1472952 7.90% Localized Negative
    mctp_42CJFAAXX_1 14935373 1361243 8.71% Localized Negative
    mctp_30V5NAAXX_4 10521893 649435 6.17% Localized Negative
    mctp_42CUAAXX_9 12315156 984253 7.23% Localized Negative
    mctp_42543AAXX_5 15470222 1147556 7.42% Localized Negative
    mctp_42CJFAAXX_5 15040535 939157 8.31% Localized Negative
    mctp_42CUAAXX_6 5541745 232904 7.81% Localized Negative
    mctp_42PF0AAXX_3 7501266 551558 7.21% Localized Negative
    mctp_42C16AAXX_3 6256993 516424 0.25% Localized Negative
    mctp_42T69AAXX_3 10212019 1265021 6.95% Localized Negative
    mctp_42T89AAXX_2 19792732 1358072 5.25% Localized Negative
    mctp_42T69AAXX_6 12313947 1420305 7.75% Localized Negative
    mctp_42T69AAXX_2 7140283 460789 6.45% Localized Negative
    mctp_42T89AAXX_7 18626453 1426932 7.51% Localized Negative
    mctp_42P0UAAXX_5 15523365 1059323 7.22% Localized Negative
    mctp_302XWAAXX_2 15424771 1520415 7.26% Localized Negative
    mctp_42543AAXX_7 14206815 1075647 7.57% Localized Negative
    mctp_50V5NAAXX_3 10357079 634126 5.84% Localized Negative
    mctp_42Y27AAXX_2 17336936 1111429 6.41% Localized Negative
    mctp_30GJ0AAXX_5 4597927 345891 7.52% Localized Negative
    mctp_42Y2TAAXX_3 13743230 814457 5.92% Localized Negative
    mctp_300JQAAXX_6 3910924 273181 5.97% Localized Negative
    mctp_32503AAXX_7 12040032 1053171 0.09% Localized Negative
    mctp_20F66AAXX_4 2002331 109234 5.40% Localized Negative
    mctp_300WTAAXX_3 3042283 359576 5.22% Localized Negative
    mctp_20F85AAXX_1 1955958 106306 5.50% Localized Negative
    mctp_30U09AAXX_4 3463761 608415 7.32% Localized Negative
    mctp_420JFAAXX_0 4703591 384743 5.22% Localized Negative
    mctp_42500AAXX_3 10445196 710220 5.08% Localized Negative
    mctp_20F66AAXX_7 2455283 153987 6.27% Localized Negative
    mctp_300W7AAXX_1 3791023 269411 7.08% Localized Negative
    mctp_20F85AAXX_1 2368556 149558 6.31% Localized Negative
    mctp_42P5UAAXX_0 496194 70695 7.80% Localized Negative
    mctp_420JFAAXX_7 2353536 524419 7.13% Localized Negative
    mctp_42FFAAAXX_4 9178356 610109 6.65% Localized Negative
    mctp_300W3AAXX_7 3244264 303730 8.36% Localized Negative
    mctp_4203NAAXX_1 9055904 903693 9.94% Localized Negative
    mctp_4202NAAXX_1 3539677 301237 8.39% Localized Negative
    mctp_4203NAAXX_3 19427244 1110543 9.72% Localized Negative
    mctp_42T89AAXX_4 9910831 724269 7.41% Localized Negative
    mctp_42Y6WAAXX_6 14063533 1050520 7.34% Localized Negative
    mctp_3064YAAXX_4 8623527 638903 7.41% Localized Negative
    mctp_4283YAAXX_4 3010760 354001 5.05% Localized Negative
    mctp_2GF06AAXX_3 3049530 118179 5.87% Metastatic ERG+
    mctp_2GF66AAXX_4 3187536 127972 5.85% Metastatic ERG+
    mctp_20F69AAXX_4 2203543 93339 4.51% Metastatic ERG+
    mctp_20LV8AAXX_5 2234538 79079 3.54% Metastatic ERG+
    mctp_20LV8AAXX_7 2250821 90013 3.55% Metastatic ERG+
    mctp_20AGMAAXX_4 2839767 75792 4.01% Metastatic ERG+
    mctp_20FETAAXX_8 1771721 73465 4.13% Metastatic ERG+
    mctp_2074VAAXX_1 2559946 350933 5.90% Metastatic ERG+
    mctp_30CVMAAXX_4 2207003 139731 6.11% Metastatic ERG+
    mctp_30TVGAAXX_3 3639592 300553 7.50% Metastatic ERG+
    mctp_43620AAXX_6 13684423 950874 5.14% Metastatic ERG+
    mctp_3074VAAXX_3 2097670 95100 4.50% Metastatic ERG+
    mctp_3074VAAXX_5 2941952 91631 4.72% Metastatic ETV1+
    mctp_305KAAAXX_2 1702029 74575 4.38% Metastatic ETV1+
    mctp_20FETAAXX_6 2031692 32655 4.63% Metastatic ETV1+
    mctp_2074VAXX_2 1184030 50720 4.06% Metastatic ETV1+
    mctp_3064VAAXX_6 10247077 1004315 9.80% Metastatic Negative
    mctp_3064VAAXX_5 10358541 951393 9.14% Metastatic Negative
    mctp_20E2PAAXX_7 2533757 108578 4.65% Metastatic Negative
    mctp_42CJFAAXX_6 8021509 572135 5.49% Metastatic Negative
    mctp_20EXPAAXX_5 2277395 104747 4.60% Metastatic Negative
    mctp_30CW7AAXX_5 3833469 193479 5.05% Metastatic Negative
    mctp_307VGAAXX_1 2430300 141723 5.03% Metastatic Negative
    mctp_205K4AAXX_2 2217807 236224 5.00% Metastatic Negative
    mctp_20E7PAAXX_2 2339252 113274 4.34% Metastatic Negative
    mctp_307YGAAXX_3 3352921 237294 5.42% Metastatic Negative
    mctp_20FETAAXX_7 2117551 103001 4.02% Metastatic Negative
    mctp_20E2PAAXX_8 2620052 71719 4.33% Metastatic Negative
    mctp_30CW7AAXX_7 8952621 260253 5.07% Metastatic Negative
    1417627939 114148345 0.07%
  • TABLE 2
    Merge
    intron- Join Filter
    Classification redundant Informatic transcript intronic UCSC
    Chromosome Cuffcompare tree filter transcripts filters fragments pre-mRNA Canonical Refseq
    chr1 759121 272072 12701 5030 4489 3652 2499 3334
    chr2 581574 206281 9353 3224 2856 2361 1579 2023
    chr3 518621 167071 5706 2917 2560 2053 1312 1816
    chr4 329950 103113 5160 2019 1731 1444 977 1238
    chr5 380613 126139 5833 2365 2067 1694 1104 1465
    chr6 396848 145607 7580 2590 2309 1874 1370 1667
    chr7 432152 134051 6432 2355 2132 1703 1326 1583
    chr8 308935 97724 4226 1729 1529 1243 848 1210
    chr9 359300 122626 4069 1937 1767 1402 1114 1272
    chr10 354625 103512 3509 1672 1508 1226 998 1382
    chr11 424606 165211 6909 2922 2640 2102 1566 2023
    chr12 425280 138650 6872 2653 2373 1858 1233 1668
    chr13 159649 68284 3616 1118 908 751 425 549
    chr14 261497 123741 4842 1806 1619 1308 855 1102
    chr15 291241 108058 5816 1884 1626 1321 1362 1127
    chr16 364747 124182 3968 2002 1835 1386 1093 1311
    chr17 473261 168469 5581 2780 2582 1950 1480 1907
    chr18 144300 49112 2504 785 682 539 377 459
    chr19 494738 189411 7209 3543 3239 2269 1668 2314
    chr20 217223 70308 3059 1243 1158 907 659 926
    chr21 113368 29728 939 495 436 354 306 427
    chr22 223385 73509 2401 1156 1068 798 633 771
    chrX 222743 94591 4997 1516 1349 1161 959 1841
    chrY 15190 4039 272 81 71 59 148 254
    Total 8253710 2885489 123554 49822 44534 35415 25921 33669
  • TABLE 3
    # Uniquely
    Peak mapped
    Antibody Antibody Finder reads (in # Peaks
    GEO ID File name Pubmed ID used vendor Used millions) Called
    GSM353631 VCaP_regular_medium_H3K4me1 20478527 ab8865 Abcam MACS 6.96 23116
    GSM353632 VCaP_regular_medium_H3K4me2 20478527 ab7756 Abcam MACS 5.97 74153
    GSM353620 VCaP_regular_medium_H3K4me3 20478527 ab8580 Abcam MACS 10.95 30043
    GSM353624 VCaP_regular_medium_H3K35me3 20478527 ab9050 Abcam SICER 9.91 29860
    GSM353629 VCaP_regular_medium_Ace_H3 20478527 06-599 Millipore MACS 4.76 41971
    GSM353622 VCaP_regular_medium_Pan_H3 20478527 ab1791 Abcam MACS 5.91 control
    GSM353623 VCaP_regular_medium_Polil 20478527 ab817 Abcam MACS 8.88 16041
    GSM353634 LNCaP_regular_medium_H3K4me1 20478527 ab8895 Abcam MACS 6.19 31109
    GSM353635 LNCaP_regular_medium_H3K4me2 20478527 ab7765 Abcam MACS 6.14 62061
    GSM353626 LNCaP_regular_medium_H3K4me3 20478527 ab8580 Abcam MACS 10.22 19638
    GSM353627 LNCaP_regular_medium_H3K36me3 20478527 ab9050 Abcam SICER 9.15 24932
    GSM353628 LNCaP_regular_medium_Ace_H3 20478527 06-599 Millipore MACS 4.75 33211
    GSM353617 LNCaP_Ethl_Polil 20478527 ab817 Abcam MACS 1.35  8232
    GSM353653 tissue_H3K4me3 20478527 ab8580 Abcam MACS 11.85 23750
  • TABLE 4
    Fold
    change SAM score
    Category Type Name Interval (Unlogged) ((r)/(s + s0))
    PROTEIN UPREG. TU_0084471_0 chr8: 33380738-34087770 12.75 7.71
    NOVEL UPREG. TU_0099865_0 chr8: 128087842-128095202 7.07 7.41
    PROTEIN UPREG. TU_0123088_0 chr2: 238147710-238169707 3.01 7.01
    ncRNA UPREG. TU_0102832_0 chr9: 78569118-78593537 12.23 6.93
    PROTEIN UPREG. TU_0078322_0 chr12: 32280254-32260805 4.52 6.82
    ncRNA UPREG. TU_0101270_0 chr21: 41853044-41875166 9.82 6.79
    PROTEIN UPREG. TU_0027326_0 chrX: 26874726-17077384 3.31 6.79
    PROTEIN UPREG. TU_0092114_0 chr11: 60223535-60239968 7.48 6.65
    PROTEIN UPREG. TU_0044448_0 chr13: 51509122-51537893 4.77 6.59
    PROTEIN UPREG. TU_0023159_0 chr19: 40224450-40249318 3.59 6.56
    PROTEIN UPREG. TU_0092116_0 chr11: 60238919-60239968 7.50 6.44
    PROTEIN UPREG. TU_0123090_0 chr2: 238164428-238165452 3.57 6.24
    ncRNA UPREG. TU_0046239_0 chr4: 1185645-1201937 5.19 6.22
    PROTEIN UPREG. TU_0122750_0 chr2: 231610299-231625861 4.56 6.14
    PROTEIN UPREG. TU_0080728_0 chr12: 120142512-120219979 3.26 6.13
    PROTEIN UPREG. TU_0123088_0 chr2: 238164428-238165452 4.22 6.12
    PROTEIN UPREG. TU_0101111_0 chr21: 36989329-37045253 4.04 6.04
    PROTEIN UPREG. TU_0090152_0 chr11: 4965638-4969515 8.38 5.99
    PROTEIN UPREG. TU_0101113_0 chr36994126-37045263 3.76 5.98
    PROTEIN UPREG. TU_0045026_0 chr13: 94680907-94668260 3.68 5.97
    ncRNA UPREG. TU_0101274_0 chr21: 41869930-41870631 8.95 5.88
    PROTEIN UPREG. TU_0046239_0 chr4: 1181913-1189142 4.28 5.87
    NOVEL UPREG. TU_0064603_0 chr16: 82380933-2394836 7.25 5.84
    PROTEIN UPREG. TU_0101308_0 chr21: 42605257-42608791 4.97 5.83
    PROTEIN UPREG. TU_0084137_0 chr5: 13981150-13997615 3.91 5.80
    PROTEIN UPREG. TU_0084127_0 chr9: 13882635-13892514 4.95 5.79
    PROTEIN UPREG. TU_0101119_0 chr22: 37034016-37045253 3.56 5.78
    PROTEIN UPREG. TU_0054919_0 chr16: 88188842-88191143 3.48 5.79
    PROTEIN UPREG. TU_0126563_0 chr2: 172658361-172662549 27.56 5.88
    PROTEIN UPREG. TU_0044977_0 chr13: 94524392-94621526 3.64 5.64
    PROTEIN UPREG. TU_0052614_0 chr16: 20542057-20818514 8.85 5.63
    NOVEL UPREG. TU_00
    Figure US20130267443A1-20131010-P00899
    _0    		 chr5: 15839476-15955226 7.46 5.61
    PROTEIN UPREG. TU_0060406_0 chr1: 28134091-28158290 3.03 5.61
    PROTEIN UPREG. TU_0060407_0 chr1: 28155047-28175469 2.41 5.60
    ncRNA UPREG. TU_0100252_0 chr9: 96357168-96369978 5.00 5.58
    PROTEIN UPREG. TU_0034719_0 chr14: 73490756-73555773 2.51 5.57
    PROTEIN UPREG. TU_0070457_0 chr20: 2258975-2269890 6.49 5.56
    NOVEL UPREG. TU_0114240_0 chr2: 1534883-1538193 5.25 5.54
    PROTEIN UPREG. TU_0087676_0 chr5: 138643394-138648458 2.75 5.50
    PROTEIN UPREG. TU_0084138_0 chr5: 13976388-13981285 4.03 5.48
    ncRNA UPREG. TU_0046237_0 chr4: 1162036-1195588 4.29 5.47
    ncRNA UPREG. TU_0060421_0 chr1: 38157480-28158290 3.12 5.44
    PROTEIN UPREG. TU_0061436_0 chr1: 37954250-37957136 2.66 5.41
    PROTEIN UPREG. TU_0044894_0 chr13: 94476096-94752898 2.85 5.38
    PROTEIN UPREG. TU_0034720_0 chr14: 73486603-73503474 2.20 5.38
    PROTEIN UPREG. TU_0090158_0 chr11: 4965009-4970186 7.37 5.34
    PROTEIN UPREG. TU_0061432_0 chr1: 37954250-37958879 2.65 5.31
    PROTEIN UPREG. TU_0090268_0 chr11: 6659768-6661138 1.76 5.30
    PROTEIN UPREG. TU_0034120_0 chr5: 13743434-13864884 3.59 5.29
    PROTEIN UPREG. TU_0043059_0 chr13: 94638351-94639152 2.93 5.28
    ncRNA UPREG. TU_0075807_0 chr10: 101676895-101680649 2.61 5.27
    PROTEIN UPREG. TU_0078255_0 chr12: 12150992-32421799 3.02 5.26
    PROTEIN UPREG. TU_0103019_0 chr9: 87826642-87905011 2.77 5.22
    PROTEIN UPREG. TU_0046244_0 chr4: 1185645-1216291 3.51 5.21
    PROTEIN UPREG. TU_0075664_0 chr10: 98752046-98935267 4.15 5.20
    PROTEIN UPREG. TU_0090949_0 chr11: 24475021-25059245 3.50 5.19
    NOVEL UPREG. TU_0099864_0 chr8: 128094589-128103681 3.56 5.17
    PROTEIN UPREG. TU_0030278_0 chr8: 106690714-106735138 3.52 5.16
    PROTEIN UPREG. TU_0090128_0 chr11: 4654012-4675667 5.26 5.15
    PROTEIN UPREG. TU_0017700_0 chr17: 51183394-51209728 2.05 5.13
    ncRNA UPREG. TU_0018760_0 chr17: 71645643-71652049 6.41 5.08
    PROTEIN UPREG. TU_0018765_0 chr17: 71652262-71747927 5.18 5.06
    ncRNA UPREG. TU_0114235_0 chr2: 1521347-1608388 4.22 5.04
    PROTEIN UPREG. TU_008
    Figure US20130267443A1-20131010-P00899
    2_0    		 chr5: 13964456-13969509 4.30 5.03
    NOVEL UPREG. TU_0049368_0 chr4: 106772318-106772770 3.40 5.03
    PROTEIN UPREG. TU_0115204_0 chr2: 27175274-27195587 2.37 4.99
    PROTEIN UPREG. TU_0115205_0 chr2: 27163593-27178264 2.49 4.98
    PROTEIN UPREG. TU_0062443_0 chr1: 46418568-46424753 1.95 4.96
    PROTEIN UPREG. TU_0072027_0 chr20: 35064872-36007156 3.91 4.95
    ncRNA UPREG. TU_0086706_0 chr5: 116818427-116835522 2.91 4.92
    PROTEIN UPREG. TU_0084136_0 chr5: 13972327-13976415 3.37 4.91
    PROTEIN UPREG. TU_0042761_0 chr13: 23200813-23363662 3.54 4.90
    PROTEIN UPREG. TU_0114168_0 chr15: 99658271-99847175 2.25 4.89
    ncRNA UPREG. TU_0018764_0 chr17: 71650143-71652049 6.28 4.86
    PROTEIN UPREG. TU_0085832_0 chr5: 76150810-78167655 3.54 4.86
    NOVEL UPREG. TU_0030142_0 chr11: 4748677-4760103 12.08 4.86
    PROTEIN UPREG. TU_0103018_0 chr9: 87745936-87851451 2.41 4.83
    NOVEL UPREG. TU_0096472_0 chr11: 133844590-133862924 6.85 4.82
    PROTEIN UPREG. TU_0023229_0 chrX: 70349443-70377690 2.34 4.81
    NOVEL UPREG. TU_0084305_0 chr5: 15836315-15947088 5.37 4.78
    PROTEIN UPREG. TU_0024934_0 chr19: 54352845-54407356 1.88 4.77
    NOVEL UPREG. TU_0095473_0 chr11: 133844590-133852395 6.96 4.76
    ncRNA UPREG. TU_0101131_0 chr21: 36994125-37041774 3.57 4.74
    PROTEIN UPREG. TU_0003239_0 chr7: 7362390-7537552 3.00 4.73
    PROTEIN UPREG. TU_0000022_0 chr6: 1567540-2190842 2.14 4.72
    PROTEIN UPREG. TU_0085193_0 chr3: 145122471-145183544 2.72 4.72
    PROTEIN UPREG. TU_0061439_0 chr1: 37954250-37971671 2.46 4.71
    ncRNA UPREG. TU_0096470_0 chr11: 133841573-133880753 6.44 4.70
    PROTEIN UPREG. TU_0046219_0 chr4: 993725-995190 3.50 4.69
    NOVEL UPREG. TU_0078788_0 chr12: 32393283-32405731 2.47 4.67
    PROTEIN UPREG. TU_0101115_0 chr21: 37000839-37005920 3.31 4.67
    NOVEL UPREG. TU_0099884_0 chr8: 128301493-128307578 2.65 4.56
    PROTEIN UPREG. TU_0008459_0 chr7: 23885581-23708358 1.70 4.54
    PROTEIN UPREG. TU_0042767_0 chr13: 23186656-23204319 4.82 4.64
    PROTEIN UPREG. TU_0061430_0 chr1: 37930752-37957012 2.30 4.64
    PROTEIN UPREG. TU_0079451_0 chr12: 52696814-52736068 3.77 4.64
    PROTEIN UPREG. TU_0069545_0 chr2: 226711356-226712534 2.36 4.63
    PROTEIN UPREG. TU_0045837_0 chr1: 113151233-118151444 3.73 4.61
    PROTEIN UPREG. TU_0101138_0 chr21: 18994126-37804810 3.54 4.61
    PROTEIN UPREG. TU_0049362_0 chr4: 106693102106771686 3.06 4.58
    PROTEIN UPREG. TU_0055044_0 chr16: 88589437-88613428 2.23 4.55
    PROTEIN UPREG. TU_0038605_0 chr3: 52689830-52704551 1.54 4.55
    ncRNA UPREG. TU_0062653_0 chr1: 51756544-51799759 2.52 4.54
    PROTEIN UPREG. TU_0080359_0 chr12: 63512292-65558861 1.87 4.53
    PROTEIN UPREG. TU_0012481_0 chr7: 111155336-111217889 2.04 4.52
    PROTEIN UPREG. TU_0076356_0 chr10: 116970327-116995963 10.34 4.52
    PROTEIN UPREG. TU_0099892_0 chr8: 128817416-128822629 2.33 4.51
    ncRNA UPREG. TU_0060484_0 chr1: 38766931-28707187 2.53 4.51
    PROTEIN UPREG. TU_0046732_0 chr4: 1147069-1175181 2.75 4.50
    PROTEIN UPREG. TU_0107858_0 chr22: 40664589-40573116 2.27 4.50
    PROTEIN UPREG. TU_0042794_0 chr13: 23228583-25228659 3.47 4.49
    PROTEIN UPREG. TU_0057850_0 chr1: 1523259-1525323 2.80 4.48
    PROTEIN UPREG. TU_0023156_0 chr1: 40109515-40127909 2.56 4.48
    PROTEIN UPREG. TU_0102821_0 chr9: 78263916-78312152 2.98 4.48
    PROTEIN UPREG. TU_0081653_0 chr12: 108638297-108780791 2.90 4.47
    PROTEIN UPREG. TU_0049370_0 chr4: 106776991-106847637 2.15 4.47
    PROTEIN UPREG. TU_0047672_0 chr4: 41807710-41840313 2.51 4.47
    PROTEIN UPREG. TU_0114959_0 chr2: 24865850-24869912 1.68 4.46
    PROTEIN UPREG. TU_0037043_0 chr3: 13332730-13436812 1.77 4.46
    PROTEIN UPREG. TU_0087443_0 chr5: 135257637-135247034 4.09 4.46
    PROTEIN UPREG. TU_0086635_0 chr5: 114489075-114543906 2.02 4.43
    PROTEIN UPREG. TU_0107859_0 chr22: 40664589-40665721 2.38 4.42
    NOVEL UPREG. TU_0106548_0 chr22: 22209111-22212855 6.49 4.42
    PROTEIN UPREG. TU_0067165_0 chr3: 160797907-160845987 1.81 4.40
    PROTEIN UPREG. TU_0020146_0 chr10: 3728970-3737293 2.53 4.39
    PROTEIN UPREG. TU_0107642_0 chr22: 39046992-39047479 1.69 4.38
    PROTEIN UPREG. TU_0016185_0 chr17: 31415814-31422953 3.69 4.38
    NOVEL UPREG. TU_0104717_0 chr9: 130697833-130698832 2.79 4.36
    PROTEIN UPREG. TU_0052105_0 chr16: 4785874-4786488 2.99 4.36
    PROTEIN UPREG. TU_0058663_0 chr1: 21795295-21850855 1.99 4.35
    PROTEIN UPREG. TU_0108056_0 chr22: 43527112-46638770 1.74 4.34
    PROTEIN UPREG. TU_0098781_0 chr11: 67151991-67154057 2.48 4.33
    PROTEIN UPREG. TU_0085924_0 chr5: 126233852-126241807 2.89 4.32
    PROTEIN UPREG. TU_0048191_0 chr4: 72423780-72424347 2.93 4.32
    PROTEIN UPREG. TU_0034727_0 chr14: 73508223-73508442 2.29 4.32
    PROTEIN UPREG. TU_0096297_0 chr11: 128342286-128353900 1.84 4.31
    PROTEIN UPREG. TU_0007829_0 chr2: 3625233-4275129 4.39 4.30
    PROTEIN UPREG. TU_0116252_0 chr2: 47449510-47467636 1.93 4.30
    PROTEIN UPREG. TU_0115216_0 chr2: 27179274-27177799 2.02 4.27
    PROTEIN UPREG. TU_0018409_0 chr17: 66013419-65059811 2.02 4.26
    PROTEIN UPREG. TU_0090847_0 chr8: 126511614-126519830 2.75 4.25
    PROTEIN UPREG. TU_0035182_0 chr14:81062781-81063412 2.22 4.25
    PROTEIN UPREG. TU_0040936_0 chr3: 155391785-155458298 2.10 4.26
    PROTEIN UPREG. TU_0027558_0 chrX: 23595491-23614435 1.66 4.25
    PROTEIN UPREG. TU_0076460_0 chr10: 121248954-121292235 1.68 4.24
    PROTEIN UPREG. TU_0067170_0 chr1: 160826739-1608726994 2.10 4.23
    PROTEIN UPREG. TU_0303050_0 chr9: 89409881-89512477 2.30 4.23
    PROTEIN UPREG. TU_0112868_0 chr19: 77590455-77402342 1.55 4.23
    PROTEIN UPREG. TU_0090960_0 chr11: 25059388-25060757 3.85 4.23
    PROTEIN UPREG. TU_0072165_0 chr20: 40142077-40204030 4.69 4.22
    PROTEIN UPREG. TU_0044687_0 chr13: 74756644-74954891 2.04 4.21
    ncRNA UPREG. TU_0096477_0 chr11: 133479414-133850753 4.43 4.21
    PROTEIN UPREG. TU_0093947_0 chr11: 68208575-68215218 1.41 4.20
    PROTEIN UPREG. TU_0103253_0 chr9: 96405246-96442373 1.69 4.20
    PROTEIN UPREG. TU_0091863_0 chr11: 57008498-57039966 2.69 4.20
    PROTEIN UPREG. TU_0106199_0 chr22: 18300042-15014411 3.94 4.20
    NOVEL UPREG. TU_0090140_0 chr11: 4748163-4759145 6.33 4.20
    PROTEIN UPREG. TU_0103051_0 chr9: 89302442-89405899 2.37 4.19
    NOVEL UPREG. TU_0078290_0 chr12: 32594534-32410838 3.20 4.19
    PROTEIN UPREG. TU_0029336_0 chrX: 70869659-70712461 1.70 4.18
    PROTEIN UPREG. TU_0092155_0 chr11: 60871597-60886554 1.80 4.18
    PROTEIN UPREG. TU_0095597_0 chr11: 114549577-114880335 1.75 4.18
    PROTEIN UPREG. TU_0082724_0 chr12: 120230545-120274615 1.42 4.17
    PROTEIN UPREG. TU_0079770_0 chr12: 55040665-55042824 4.25 4.16
    PROTEIN UPREG. TU_0000263_0 chr6: 4060929-4080831 1.56 4.16
    NOVEL UPREG. TU_0040394_0 chr3: 133418532-133441282 3.46 4.16
    PROTEIN UPREG. TU_0066594_0 chr1: 15424543-154257368 1.40 4.15
    PROTEIN UPREG. TU_0099852_0 chr8: 126515081-126519830 2.81 4.15
    PROTEIN UPREG. TU_0100363_0 chr8: 144891741-144899588 2.24 4.14
    PROTEIN UPREG. TU_0095461_0 chr11: 133751095-133757235 2.10 4.13
    ncRNA UPREG. TU_0044488_0 chr13: 51641093-51641310 2.76 4.13
    PROTEIN UPREG. TU_0048990_0 chr4: 95592056-95804933 2.30 4.13
    NOVEL UPREG. TU_0078293_0 chr12: 12396393-32414822 2.90 4.13
    PROTEIN UPREG. TU_0046202_0 chr4: 991841-1010686 2.57 4.12
    PROTEIN UPREG. TU_0091866_0 chr11: 57008498-57010253 2.54 4.12
    PROTEIN UPREG. TU_0011133_0 chr7: 94378726-94759741 1.77 4.12
    PROTEIN UPREG. TU_0122941_0 chr2: 234410713-234427931 3.28 4.12
    PROTEIN UPREG. TU_0084131_0 chr5: 13929880-13953380 2.62 4.12
    NOVEL UPREG. TU_0084142_0 chr5: 14017046-14021379 3.59 4.11
    PROTEIN UPREG. TU_0087955_0 chr5: 140931545-140931565 2.00 4.10
    PROTEIN UPREG. TU_0085953_0 chr5: 79410392-79410389 3.35 4.10
    PROTEIN UPREG. TU_0022288_0 chr19: 18357973-18360121 2.75 4.09
    PROTEIN UPREG. TU_0085951_0 chr5: 79366959-79414885 3.01 4.09
    PROTEIN UPREG. TU_0060849_0 chr1: 32572021-32574435 1.81 4.09
    PROTEIN UPREG. TU_0087441_0 chr5: 134934290-134942617 2.74 4.09
    PROTEIN UPREG. TU_0042725_0 chr13: 23148223-23200551 4.96 4.09
    PROTEIN UPREG. TU_0039018_0 chr3: 66510505-66634168 1.68 4.08
    PROTEIN UPREG. TU_0096299_0 chr11: 128340164-128347506 1.70 4.07
    PROTEIN UPREG. TU_0022290_0 chr19: 18357973-18359195 2.64 4.07
    PROTEIN UPREG. TU_0100684_0 chr8: 146190487-146191030 1.89 4.06
    PROTEIN UPREG. TU_0042974_0 chr13: 26148671-2614967 2.81 4.06
    NOVEL UPREG. TU_0084308_0 chr5: 15938753-15949124 4.08 4.06
    NOVEL UPREG. TU_0082746_0 chr12: 120197102-120197416 4.97 4.06
    PROTEIN UPREG. TU_0014355_0 chr17: 2650561-2887730 1.92 4.05
    PROTEIN UPREG. TU_0114110_0 chr15: 99250537-99274351 2.01 4.05
    PROTEIN UPREG. TU_0096341_0 chr11: 129534843-129585464 1.54 4.04
    PROTEIN UPREG. TU_0052083_0 chr16: 4784094-4805339 2.71 4.04
    NOVEL UPREG. TU_0078296_0 chr12: 32394534-32405549 2.92 4.04
    PROTEIN UPREG. TU_0084126_0 chr5: 13892443-13903812 3.64 4.03
    NOVEL UPREG. TU_0047312_0 chr4: 39217669-39222163 3.83 4.02
    PROTEIN UPREG. TU_0008287_0 chr7: 8119340-8268973 1.65 4.02
    PROTEIN UPREG. TU_0018937_0 chr17: 73714011-73714967 1.61 4.01
    PROTEIN UPREG. TU_0048995_0 chr4: 95805027-95808417 2.47 4.00
    PROTEIN UPREG. TU_0038694_0 chr3: 53810226-53855769 2.03 3.99
    ncRNA UPREG. TU_0046233_0 chr4: 1202157-1232168 2.45 3.99
    PROTEIN UPREG. TU_0019018_0 chr17: 75372094-75381243 2.25 3.98
    PROTEIN UPREG. TU_0042326_0 chr
    Figure US20130267443A1-20131010-P00899
    : 199123974-199125319    		 1.77 3.98
    PROTEIN UPREG. TU_0099893_0 chr8: 128817416-128819105 2.23 3.98
    PROTEIN UPREG. TU_0012491_0 chr7: 111304238-111362856 1.91 3.98
    PROTEIN UPREG. TU_0112385_0 chr15: 70816880-70864494 1.71 3.97
    PROTEIN UPREG. TU_0042964_0 chr4: 57020861-57038533 1.74 3.97
    PROTEIN UPREG. TU_0052565_0 chr1
    Figure US20130267443A1-20131010-P00899
    : 19862784-19409995    		 1.98 3.96
    NOVEL UPREG. TU_0042717_0 chr13: 25149908-23200198 4.95 3.96
    PROTEIN UPREG. TU_0017374_0 chr17: 43300055-43404182 1.53 3.96
    PROTEIN UPREG. TU_0071058_0 chr20: 20318209-20549154 2.02 3.96
    PROTEIN UPREG. TU_0105741_0 chrY: 6971017-6998339 2.20 3.95
    PROTEIN UPREG. TU_0018995_0 chr17: 74491566-74517485 1.64 3.94
    PROTEIN UPREG. TU_0103055_0 chr9: 89512509-8
    Figure US20130267443A1-20131010-P00899
    513285    		 1.92 3.93
    PROTEIN UPREG. TU_0041139_0 chr3: 171237964-171285906 1.91 3.93
    PROTEIN UPREG. TU_0042325_0 chr3: 199124975-199143480 1.74 3.93
    PROTEIN UPREG. TU_0020688_0 chr19: 8180054-8237335 1.80 3.93
    PROTEIN UPREG. TU_0118314_0 chr2: 90086923-99100654 1.78 3.92
    PROTEIN UPREG. TU_0017875_0 chr17: 54652767-54706896 2.33 3.92
    PROTEIN UPREG. TU_0037277_0 chr3: 24134438-24511318 1.75 3.92
    PROTEIN UPREG. TU_004759
    Figure US20130267443A1-20131010-P00899
    _0    		 chr4: 40445539-40457235 1.90 3.91
    PROTEIN UPREG. TU_0114108_0 chr15: 99235494-99274389 2.00 3.91
    ncRNA UPREG. TU_0024530_0 chr19: 50889160-50909766 1.72 3.91
    PROTEIN UPREG. TU_0008957_0 chr7: 88308886-38325338 2.62 3.91
    PROTEIN UPREG. TU_0043122_0 chr13: 28983555-28989371 1.73 3.90
    PROTEIN UPREG. TU_0076644_0 chr10: 127398227-127398596 2.06 3.90
    PROTEIN UPREG. TU_0045423_0 chr13: 10055877-100125079 2.02 3.89
    PROTEIN UPREG. TU_0045495_0 chr13: 107720446-107737194 2.08 3.88
    PROTEIN UPREG. TU_0076648_0 chr10-127412714-127442685 1.64 3.88
    NOVEL UPREG. TU_0088857_0 chr5: 172259171-172275517 1.69 3.87
    NOVEL UPREG. TU_0044453_0 chr13: 51505777-51524522 2.95 3.86
    NOVEL UPREG. TU_0047380_0 chr4: 39217641-39222163 3.43 3.86
    PROTEIN UPREG. TU_0100838_0 chr21: 30508275-30510244 2.43 3.86
    NOVEL UPREG. TU_0106544_0 chr22: 22210421-22220506 4.27 3.85
    ncRNA UPREG. TU_0100275_0 chr8: 144520506-144537551 2.11 3.85
    PROTEIN UPREG. TU_0057466_0 chr18: 72853744-72866791 1.58 3.84
    PROTEIN UPREG. TU_0040010_0 chr3: 126331839-126412928 2.16 3.84
    PROTEIN UPREG. TU_0042800_0 chr13: 23360816-23370548 2.73 3.84
    PROTEIN UPREG. TU_0112501_0 chr2: 74065748-74174193 1.71 3.83
    PROTEIN UPREG. TU_0053389_0 chr1
    Figure US20130267443A1-20131010-P00899
    : 45673980-45701001    		 2.66 3.83
    PROTEIN UPREG. TU_0087944_0 chr11: 140874777-140978925 1.47 3.83
    PROTEIN UPREG. TU_0017393_0 chr17: 43389397-43390800 1.90 3.82
    PROTEIN UPREG. TU_0008919_0 chr7: 38257158-38271020 1.93 3.82
    PROTEIN UPREG. TU_0088393_0 chr14: 50259793-50367616 1.51 3.82
    PROTEIN UPREG. TU_0049911_0 chr4: 139304784-139382952 2.48 3.82
    PROTEIN UPREG. TU_0024366_0 chr19: 50100808-50104487 1.88 3.82
    PROTEIN UPREG. TU_0070109_0 chr1: 243979271-244159914 1.56 3.81
    PROTEIN UPREG. TU_0120975_0 chr2: 182104651-182107832 1.89 3.80
    NOVEL UPREG. TU_0044933_0 chr18: 94765992-94760688 2.52 3.80
    PROTEIN UPREG. TU_0103689_0 chr9: 111019219-111122750 1.75 3.80
    PROTEIN UPREG. TU_0096460_0 chr11: 133734857-133786962 2.09 3.79
    PROTEIN UPREG. TU_0071115_0 chr20: 24934888-24986948 1.48 3.79
    PROTEIN UPREG. TU_0093788_0 chr11: 67153661-67153870 2.48 3.79
    PROTEIN UPREG. TU_0047591_0 chr4: 40457999-40508855 1.79 3.79
    PROTEIN UPREG. TU_0112336_0 chr15: 70880765-70838345 1.83 3.78
    PROTEIN UPREG. TU_0086664_0 chr1: 154481433-154485049 2.29 3.78
    PROTEIN UPREG. TU_0018812_0 chr17: 72119376-72151549 3.38 3.78
    PROTEIN UPREG. TU_0110225_0 chr15: 48510091-48912722 3.60 3.78
    ncRNA UPREG. TU_0054545_0 chr16: 79431010-79431652 10.28 3.78
    PROTEIN UPREG. TU_0107643_0 chr22: 39072496-39093168 1.36 3.78
    PROTEIN UPREG. TU_0025230_0 chr19: 55992773-56000199 1.86 3.78
    PROTEIN UPREG. TU_0012480_0 chr7: 111153704-111155311 1.81 3.77
    PROTEIN UPREG. TU_0070821_0 chr20: 8997167-9409281 1.64 3.77
    PROTEIN UPREG. TU_0103873_0 chr9: 115151636-115178183 1.52 3.77
    PROTEIN UPREG. TU_0018813_0 chr17: 72128611-72133119 3.56 3.76
    NOVEL UPREG. TU_0112004_0 chr18: 67644390-67650387 3.56 3.76
    PROTEIN UPREG. TU_0043118_0 chr13: 28981555-29067829 1.76 3.76
    NOVEL UPREG. TU_0112003_0 chr15: 67645590-67775246 3.12 3.76
    NOVEL UPREG. TU_0060448_0 chr1: 28438629-28450150 2.23 3.75
    PROTEIN UPREG. TU_0122972_0 chr2: 236068012-236482693 1.69 3.75
    NOVEL UPREG. TU_0106545_0 chr22: 22218478-22219162 3.99 3.74
    PROTEIN UPREG. TU_0087288_0 chr5: 133755241-133766074 1.85 3.74
    ncRNA UPREG. TU_0025312_0 chr19: 57059515-57145170 1.89 3.74
    PROTEIN UPREG. TU_0079679_0 chr12: 54760142-54783545 1.58 3.73
    PROTEIN UPREG. TU_0074564_0 chr10: 64241786-64246112 2.62 3.73
    PROTEIN UPREG. TU_0106189_0 chr22: 18235213-18328816 1.82 3.73
    PROTEIN UPREG. TU_0078994_0 chr12: 49412412-49428706 1.41 3.72
    ncRNA UPREG. TU_0003229_0 chr6: 41598975-41621874 2.05 3.72
    PROTEIN UPREG. TU_0040937_0 chr3: 155439710-155458293 1.96 3.72
    PROTEIN UPREG. TU_0040093_0 chr5: 128880751-128874336 1.87 3.72
    NOVEL UPREG. TU_0106542_0 chr22: 22213315-22220505 3.77 3.71
    PROTEIN UPREG. TU_0019375_0 chr17: 77608812-77816980 1.63 3.71
    PROTEIN UPREG. TU_0042568_0 chr15: 20264762-20334986 1.85 3.71
    PROTEIN UPREG. TU_0103386_0 chr9: 99895734-99118148 1.89 3.71
    PROTEIN UPREG. TU_0030004_0 chrX: 100534013-100534540 1.84 3.71
    NOVEL UPREG. TU_0089906_0 chr11: 1042845-1045785 2.94 3.71
    NOVEL UPREG. TU_0089014_0 chr9: 176014905-176015351 2.01 3.71
    ncRNA UPREG. TU_0056173_0 chr18: 22525074-22557627 3.31 3.70
    PROTEIN UPREG. TU_0052880_0 chr16: 28393117-28411069 1.48 3.70
    PROTEIN UPREG. TU_0100355_0 chr8: 144884230-144910177 2.00 3.69
    PROTEIN UPREG. TU_0096216_0 chr11: 125271293-125271517 2.08 3.69
    PROTEIN UPREG. TU_0092161_0 chr11: 60884289-60892364 1.99 3.68
    PROTEIN UPREG. TU_0086926_0 chr5: 126241958-126394149 2.27 3.68
    NOVEL UPREG. TU_0088230_0 chr5: 148864170-148864752 1.94 3.68
    ncRNA UPREG. TU_0099940_0 chr8: 129855546-129182684 1.61 3.68
    PROTEIN UPREG. TU_0089017_0 chr5: 176222085-176240501 10.21 3.67
    PROTEIN UPREG. TU_0078586_0 chr12: 46643629-46648944 1.47 3.67
    PROTEIN UPREG. TU_0053467_0 chr16: 51028455-51138080 2.19 3.67
    PROTEIN UPREG. TU_0089452_0 chr5: 179258704-179258997 1.62 3.67
    PROTEIN UPREG. TU_0076329_0 chr10: 115501382-115531028 2.60 3.67
    PROTEIN UPREG. TU_0047688_0 chr4: 42105164-42354144 1.68 3.67
    PROTEIN UPREG. TU_0059142_0 chr1: 16203274-16206548 12.41 3.67
    PROTEIN UPREG. TU_0116906_0 chr2: 63155968-53138462 2.81 3.66
    PROTEIN UPREG. TU_0000154_0 chr6: 3063923-3099152 1.53 3.66
    PROTEIN UPREG. TU_0088782_0 chr5: 170625426-170659598 1.78 3.66
    NOVEL UPREG. TU_0089905_0 chr11: 1042845-1045785 2.77 3.66
    PROTEIN UPREG. TU_0101704_0 chr9: 3265495-3516005 2.33 3.64
    ncRNA UPREG. TU_0044897_0 chr15: 94746498-94760688 2.17 3.64
    PROTEIN UPREG. TU_0071059_0 chr20: 20549245-20641260 2.39 3.64
    ncRNA UPREG. TU_0046268_0 chr4: 1199698-1211108 1.93 3.63
    PROTEIN UPREG. TU_0071601_0 chr20:32827590-32828002 1.75 3.62
    PROTEIN UPREG. TU_0100712_0 chr21: 15258179-15359100 2.14 3.62
    PROTEIN UPREG. TU_0092158_0 chr11: 60885030-60893249 1.45 3.62
    PROTEIN UPREG. TU_0091402_0 chr11: 46255779-46299542 1.71 3.62
    PROTEIN UPREG. TU_0039019_0 chr3: 66376322-66514060 1.50 3.62
    PROTEIN UPREG. TU_0100378_0 chr8: 144899799-144900640 2.00 3.62
    NOVEL UPREG. TU_0112025_0 chr15: 67780574-67782345 3.42 3.62
    PROTEIN UPREG. TU_0106031_0 chr22: 16336630-16412806 2.01 3.62
    PROTEIN UPREG. TU_0050785_0 chr4: 174895560-174453821 2.38 3.61
    PROTEIN UPREG. TU_0058834_0 chr1: 11768665-11783670 1.50 3.61
    PROTEIN UPREG. TU_0039496_0 chr3: 106753939-106754201 1.99 3.61
    ncRNA UPREG. TU_0098397_0 chr8: 69379259-69406175 2.73 3.61
    PROTEIN UPREG. TU_0017847_0 chr17: 54188675-54413808 2.82 3.61
    PROTEIN UPREG. TU_0108299_0 chr22: 49267227-49270226 2.03 3.60
    PROTEIN UPREG. TU_0076846_0 chr10: 135042714-155056676 2.27 3.59
    PROTEIN UPREG. TU_0096351_0 chr11: 129611827-129689996 1.61 3.59
    PROTEIN UPREG. TU_0019298_0 chr17: 77242472-77300154 1.51 3.59
    PROTEIN UPREG. TU_0057465_0 chr18: 72830973-729737
    Figure US20130267443A1-20131010-P00899
    9    		 1.55 3.59
    PROTEIN UPREG. TU_0013475_0 chr2: 148137800-148212387 1.74 3.59
    PROTEIN UPREG. TU_00
    Figure US20130267443A1-20131010-P00899
    1426_0    		 chr6: 28688044-28662198 2.58 3.59
    NOVEL UPREG. TU_01
    Figure US20130267443A1-20131010-P00899
    541_0    		 chr22: 22209111-22219162 4.02 3.58
    PROTEIN UPREG. TU_0071803_0 chr10: 19005564-19007053 1.94 3.58
    PROTEIN UPREG. TU_0010100_0 chr3: 129253916-129269610 1.39 3.58
    PROTEIN UPREG. TU_0001432_0 chr6: 28978594-28999755 1.33 3.58
    PROTEIN UPREG. TU_0076643_0 chr10: 127398227-127407663 1.73 3.57
    PROTEIN UPREG. TU_0089137_0 chr5: 176814485-176815986 1.93 3.57
    PROTEIN UPREG. TU_0098700_0 chr8: 87
    Figure US20130267443A1-20131010-P00899
    06988-82333612    		 1.76 3.57
    PROTEIN UPREG. TU_0093785_0 chr11: 67186209-67198838 3.74 3.57
    NOVEL UPREG. TU_0056163_0 chr18: 22477042-22477665 3.05 3.57
    PROTEIN UPREG. TU_0067222_0 chr1: 164063363-194147501 1.63 3.57
    PROTEIN UPREG. TU_0052172_0 chr16: 8799176-8790379 1.61 3.57
    PROTEIN UPREG. TU_0008350_0 chr7: 16852301-16712672 1.45 3.57
    PROTEIN UPREG. TU_0035610_0 chr14: 935
    Figure US20130267443A1-20131010-P00899
    0687-93582188    		 2.08 3.56
    PROTEIN UPREG. TU_0000168_0 chr6: 3100128-3102765 2.10 3.56
    PROTEIN UPREG. TU_0019649_0 chr3: 115180992-115164502 1.72 3.56
    PROTEIN UPREG. TU_0052843_0 chr16: 27143818-27187907 1.42 3.56
    NOVEL UPREG. TU_0024950_0 chr19: 54450100-54432968 2.11 3.55
    PROTEIN UPREG. TU_0008504_0 chr7: 24656812-24693891 1.99 3.55
    PROTEIN UPREG. TU_0061102_0 chr1: 35571678-35795597 1.44 3.55
    PROTEIN UPREG. TU_0032850_0 chr14: 36736878: 36788106 2.36 3.55
    ncRNA UPREG. TU_0045241_0 chr4: 1198292-1167180 2.53 3.55
    NOVEL UPREG. TU_00
    Figure US20130267443A1-20131010-P00899
    499_0    		 chr7: 24236191-24236455 5.44 3.54
    PROTEIN UPREG. TU_0100172_0 chr8: 142471307-142511866 1.79 3.54
    NOVEL UPREG. TU_0085543_0 chr5: 110311813-110312092 1.53 3.53
    PROTEIN UPREG. TU_0072450_0 chr20: 44161989
    Figure US20130267443A1-20131010-P00899
    -44747359    		 1.83 3.53
    NOVEL UPREG. TU_0094972_0 chr15: 94755980-94759735 2.15 3.53
    PROTEIN UPREG. TU_0093950_0 chr11: 6
    Figure US20130267443A1-20131010-P00899
    21474
    Figure US20130267443A1-20131010-P00899
    -68215218    		 1.49 3.53
    PROTEIN UPREG. TU_0006239_0 chr6: 13864933
    Figure US20130267443A1-20131010-P00899
    -133671427    		 2.22 3.53
    PROTEIN UPREG. TU_0063894_0 chr1: 150944684-150070988 1.54 3.52
    PROTEIN UPREG. TU_0078675_0 chr12: 47602047-47602939 1.58 3.52
    PROTEIN UPREG. TU_0052150_0 chr16: 8799176-65-64674 1.42 3.52
    NOVEL UPREG. TU_0112011_0 chr15: 67762926-67783593 2.66 3.52
    PROTEIN UPREG. TU_0041581_0 chr3: 185450132-185459240 1.77 3.52
    PROTEIN UPREG. TU_0017269_0 chr17: 42127174-421
    Figure US20130267443A1-20131010-P00899
    9979    		 1.59 3.52
    PROTEIN UPREG. TU_010138_0 chr6: 94055563-94056963 1.61 3.52
    PROTEIN UPREG. TU_0078683_0 chr12: 47503989-47604485 1.69 3.52
    PROTEIN UPREG. TU_0099209_0 chr11: 6453771-6453210 1.44 3.51
    ncRNA UPREG. TU_004519
    Figure US20130267443A1-20131010-P00899
    _0    		 chr15: 97851959-97852689 1.98 3.51
    PROTEIN UPREG. TU_0050499_0 chr4: 159862572-156862939 1.82 3.51
    PROTEIN UPREG. TU_0088025_0 chr5: 142130154-142254088 1.89 3.51
    PROTEIN UPREG. TU_0052554_0 chr16: 10329285-19424714 1.78 3.51
    PROTEIN UPREG. TU_0085663_0 chr5: 70918890-75990273 2.39 3.51
    PROTEIN UPREG. TU_0101238_0 chr21: 41610496-41851888 1.89 3.50
    PROTEIN UPREG. TU_0098659_0 chr8: 82355436-82355877 4.15 3.49
    PROTEIN UPREG. TU_0100271_0 chr8: 144522379-144537551 1.33 3.49
    PROTEIN UPREG. TU_0013258_0 chr7: 139750340-139773086 1.85 3.49
    PROTEIN UPREG. TU_0122559_0 chr2: 224338108-224338327 2.32 3.49
    PROTEIN UPREG. TU_0062947_0 chr1: 212567070-212567723 1.74 3.48
    PROTEIN UPREG. TU_0101300_0 chr21: 42512421-42593934 1.60 3.48
    PROTEIN UPREG. TU_0105268_0 chr3: 1382318731-138277254 1.49 3.47
    PROTEIN UPREG. TU_0080269_0 chr12: 62524730-62664317 2.05 3.47
    PROTEIN UPREG. TU_0051992_0 chr6: 31939105-31955076 1.56 3.47
    PROTEIN UPREG. TU_0018485_0 chr17: 76458432-70490451 1.58 3.47
    ncRNA UPREG. TU_0050493_0 chr1: 28705947-28706605 1.60 2.46
    PROTEIN UPREG. TU_0085975_0 chr5: 79478814-79495113 1.91 3.46
    PROTEIN UPREG. TU_0018919_0 chr17: 73678343-73714570 1.48 3.46
    ncRNA UPREG. TU_0054534_0 chr16: 79404014-79431652 9.85 3.46
    PROTEIN UPREG. TU_0076107_0 chr10: 104464315-104488075 1.67 3.45
    ncRNA UPREG. TU_0069658_0 chr1: 229724782-229731269 1.75 3.45
    NOVEL UPREG. TU_0120387_0 chr2: 170267824-170281385 2.10 3.45
    PROTEIN UPREG. TU_0013665_0 chr17: 24073407-24077926 1.52 3.45
    ncRNA UPREG. TU_0070414_0 chr20: 3254059-1303172 1.65 3.45
    NOVEL UPREG. TU_0072624_0 chr20: 47335522-47338977 1.65 3.45
    PROTEIN UPREG. TU_0012495_0 chr7: 111373031-111411626 2.29 3.45
    PROTEIN UPREG. TU_0076659_0 chr10: 177514501-127576128 1.31 3.45
    PROTEIN UPREG. TU_0088525_0 chr5: 156525701-156755173 1.53 3.45
    PROTEIN UPREG. TU_0046096_0 chr4: 759449-809939 2.01 3.44
    ncRNA UPREG. TU_0074332_0 chr10: 43420869-43421283 1.52 3.44
    PROTEIN UPREG. TU_0082983_0 chr12: 121778239-121779189 2.65 3.44
    PROTEIN UPREG. TU_0008361_0 chr2: 16750923-16790805 1.58 3.44
    PROTEIN UPREG. TU_0081443_0 chr1: 38032067-38039550 1.67 3.44
    PROTEIN UPREG. TU_0042715_0 chr13: 25148223-23204319 3.68 3.43
    ncRNA UPREG. TU_0119128_0 chr2: 118310197-118313068 1.62 3.43
    PROTEIN UPREG. TU_0112349_0 chr15: 70834440-70835126 1.67 3.43
    PROTEIN UPREG. TU_0027543_0 chrX: 21921233-21922374 2.48 3.43
    PROTEIN UPREG. TU_0082552_0 chr1: 47889058-47552320 1.83 3.43
    ncRNA UPREG. TU_0080791_0 chr4: 174322695-174323924 2.13 3.41
    PROTEIN UPREG. TU_0048346_0 chr4: 77175264-77176185 2.48 3.41
    NOVEL UPREG. TU_0093068_0 chr11: 64956618-64961189 2.13 3.41
    PROTEIN UPREG. TU_0033869_0 chr14: 60248258-60250801 1.71 3.41
    PROTEIN UPREG. TU_0000031_0 chr6: 2190031-2190908 2.44 3.41
    PROTEIN UPREG. TU_0082131_0 chr12: 111152572-111152227 1.89 3.40
    PROTEIN UPREG. TU_0038169_0 chr3: 49035494-49041923 1.35 3.40
    NOVEL UPREG. TU_0044898_0 chr13: 94753009-94760688 2.11 3.40
    PROTEIN UPREG. TU_0089144_0 chrS: 176814485-176815986 1.86 3.40
    PROTEIN UPREG. TU_0094504_0 chr11: 74812477-74817273 2.40 3.40
    PROTEIN UPREG. TU_0035633_0 chr14: 94304291-94305127 2.17 3.40
    PROTEIN UPREG. TU_0085819_0 chrS: 75734806-76039614 1.64 3.40
    PROTEIN UPREG. TU_0061431_0 chr1: 37961347-37973585 2.62 3.40
    NOVEL UPREG. TU_0078299_0 chr12: 32290896-32292169 3.67 3.39
    PROTEIN UPREG. TU_0004059_0 chr6: 52976578-53054598 1.65 3.39
    PROTEIN UPREG. TU_0098927_0 chr8: 95722432-95788870 1.48 3.39
    ncRNA UPREG. TU_0013856_0 chr7: 155957953-156090620 2.50 3.39
    PROTEIN UPREG. TU_0068377_0 chr1: 201452418-201458956 1.84 3.39
    NOVEL UPREG. TU_0101035_0 chr21: 35419563-36421930 1.84 3.39
    PROTEIN UPREG. TU_0062957_0 chr1: 54089897-54128073 1.43 3.39
    PROTEIN UPREG. TU_0099854_0 chr8: 127633901-127639897 1.65 3.38
    PROTEIN UPREG. TU_0048743_0 chr4: 87924751-87955166 1.47 3.38
    PROTEIN UPREG. TU_0086478_0 chr5: 102510255-102521832 1.95 3.38
    PROTEIN UPREG. TU_0120565_0 chr2: 172672776-172675279 4.31 3.38
    PROTEIN UPREG. TU_0122360_0 chr2: 219554051-219557439 2.92 3.38
    PROTEIN UPREG. TU_0092154_0 chr11: 60857271-60874474 1.44 3.37
    PROTEIN UPREG. TU_0015718_0 chr17: 24095069-24100305 1.64 3.37
    PROTEIN UPREG. TU_0039284_0 chr3: 95208686-95249573 2.23 3.37
    PROTEIN UPREG. TU_0082089_0 chr12: 111082307-111187476 1.44 3.37
    PROTEIN UPREG. TU_0035148_0 chr14: 81009021-81069951 1.64 3.37
    PROTEIN UPREG. TU_0054849_0 chr16: 87403253-87406669 1.47 3.37
    PROTEIN UPREG. TU_0113376_0 chr15: 87432650-87545107 2.13 3.36
    PROTEIN UPREG. TU_0019481_0 chr17: 77998514-77999441 1.55 3.36
    PROTEIN UPREG. TU_0007004_0 chr6: 158396021-158440190 1.47 3.36
    PROTEIN UPREG. TU_0092190_0 chr11: 60876795-60877493 1.85 3.36
    ncRNA UPREG. TU_0001996_0 chr6: 31941546-31959679 1.43 3.36
    NOVEL UPREG. TU_0066689_0 chr1: 154509233-154510967 1.61 3.36
    PROTEIN UPREG. TU_0035151_0 chr14: 81015445-81021875 2.00 3.35
    PROTEIN UPREG. TU_0092866_0 chr11: 55975211-63975675 3.20 3.35
    PROTEIN UPREG. TU_0050482_0 chr4: 156807332-156877628 1.69 3.35
    PROTEIN UPREG. TU_0022391_0 chr19: 19076718-19094443 1.60 3.35
    PROTEIN UPREG. TU_0048729_0 chr4: 87734463-87924734 1.74 3.35
    PROTEIN UPREG. TU_0103472_0 chr9: 100534124-100570357 1.61 3.35
    PROTEIN UPREG. TU_0087465_0 chr5: 136431191-136431490 2.47 3.35
    PROTEIN UPREG. TU_0058833_0 chr1: 11768665-11788581 1.45 3.34
    PROTEIN DOWNREG. TU_0009047_0 chr7: 41967123-41970103 0.65 −3.35
    PROTEIN DOWNREG. TU_0020039_0 chr19: 2948637-2980244 0.65 −3.36
    PROTEIN DOWNREG. TU_0024046_0 chr19: 47194316-47201741 0.53 −3.36
    PROTEIN DOWNREG. TU_0120035_0 chr: 154042114-154043553 0.49 −3.36
    PROTEIN DOWNREG. TU_0014542_0 chr17: 4790024-47790984 0.77 −3.36
    PROTEIN DOWNREG. TU_0058703_0 chr1: 10857547-10613394 0.66 −3.37
    NOVEL DOWNREG. TU_0084922_0 chrS: 44337219-44338127 0.51 −3.37
    PROTEIN DOWNREG. TU_0067333_0 chr1: 167362572-167539064 0.68 −3.37
    PROTEIN DOWNREG. TU_0030086_0 chrX: 101794939-101798995 0.64 −3.37
    PROTEIN DOWNREG. TU_0031101_0 chrX: 134247418-134254372 0.69 −3.37
    PROTEIN DOWNREG. TU_0063762_0 chr1: 87666944-87583813 0.66 −3.38
    PROTEIN DOWNREG. TU_0107584_0 chr22: 38075931-38123808 0.66 −3.38
    PROTEIN DOWNREG. TU_0102296_0 chr9: 34979701-34988409 0.57 −3.38
    PROTEIN DOWNREG. TU_0038485_0 chr3: 51981847-51958558 0.65 −3.38
    PROTEIN DOWNREG. TU_0062948_0 chr1: 53744574-53746867 0.48 −3.38
    PROTEIN DOWNREG. TU_0092656_0 chr11: 63282470-63288729 0.73 −3.38
    PROTEIN DOWNREG. TU_0035606_0 chr14: 95470258-93500717 0.58 −3.38
    PROTEIN DOWNREG. TU_0053588_0 chr18: 10470831-10478690 0.58 −3.38
    PROTEIN DOWNREG. TU_0056465_0 chr18: 41558112-41584622 0.49 −3.39
    PROTEIN DOWNREG. TU_0002739_0 chr6: 35321958-35328561 0.55 −3.39
    PROTEIN DOWNREG. TU_0030147_0 chrx: 102727067-102729284 0.65 −3.39
    NOVEL DOWNREG. TU_0030209_0 chrx: 103250961-103253228 0.68 −3.39
    ncRNA DOWNREG. TU_0068206_0 chr1: 200132176-200134973 0.60 −3.39
    PROTEIN DOWNREG. TU_0081627_0 chr12: 108186419-108190411 0.63 −3.40
    PROTEIN DOWNREG. TU_0088194_0 chr2: 200132176-200182322 0.59 −3.40
    PROTEIN DOWNREG. TU_0049308_0 chr4: 104220026-104220361 0.46 −3.40
    NOVEL DOWNREG. TU_0068431_0 chr1: 202350966-202363482 0.62 −3.40
    PROTEIN DOWNREG. TU_0073506_0 chr10: 7630096-7723984 0.60 −3.40
    PROTEIN DOWNREG. TU_0054695_0 chr16: 83411108-83499914 0.62 −3.40
    PROTEIN DOWNREG. TU_0012556_0 chr7: 115934290-115935899 0.50 −3.41
    PROTEIN DOWNREG. TU_0018647_0 chr17: 71259157-71294839 0.74 −3.41
    NOVEL DOWNREG. TU_0030577_0 chrX: 118036531-118035860 0.43 −3.41
    PROTEIN DOWNREG. TU_0089981_0 chr11: 2248339-2247566 0.52 −3.41
    PROTEIN DOWNREG. TU_0000858_0 chr6: 19947236-19950403 0.56 −3.41
    PROTEIN DOWNREG. TU_0002212_0 chr8: 32224073-32229328 0.58 −3.41
    PROTEIN DOWNREG. TU_0024749_0 chr10: 52937559-52939100 0.58 −3.41
    PROTEIN DOWNREG. TU_0102225_0 chr21: 40161189-10181418 0.52 −3.41
    ncRNA DOWNREG. TU_0100030_0 chrX: 134893580-134659310 0.41 −3.41
    PROTEIN DOWNREG. TU_0102256_0 chr9: 34356684-34366854 0.56 −3.41
    PROTEIN DOWNREG. TU_0039040_0 chr3: 69107066-69108860 0.62 −3.42
    ncRAN DOWNREG. TU_0115808_0 chr2: 37722515-37725828 0.61 −3.42
    PROTEIN DOWNREG. TU_0115807_0 chr2: 37722515-37729828 0.61 −3.42
    NOVEL DOWNREG. TU_0038811_0 chr8: 57890130-58970834 0.43 −3.43
    PROTEIN DOWNREG. TU_0107000_0 chr22: 29790122-29830660 0.60 −3.43
    PROTEIN DOWNREG. TU_0065120_0 chr1: 144274405-144279906 0.53 −3.43
    PROTEIN DOWNREG. TU_0065093_0 chr1: 144167535-144181746 0.72 −3.43
    PROTEIN DOWNREG. TU_0066887_0 chr1: 158352167-158370985 0.56 −3.44
    PROTEIN DOWNREG. TU_0034681_0 chr14: 75248251-73250867 0.61 −3.44
    PROTEIN DOWNREG. TU_0064872_0 chr1: 115373945-115394701 0.60 −3.44
    PROTEIN DOWNREG. TU_0115146_0 chr2: 26806070-26809827 0.49 −3.44
    PROTEIN DOWNREG. TU_0023552_0 chr19: 43433715-43439100 0.52 −3.44
    PROTEIN DOWNREG. TU_0013056_0 chr2: 134269121-134268574 0.41 −3.44
    PROTEIN DOWNREG. TU_0078015_0 chr12: 21809160-21817495 0.61 −3.45
    PROTEIN DOWNREG. TU_0010849_0 chr7: 84462824-84464278 0.41 −3.45
    PROTEIN DOWNREG. TU_0018278_0 chr17: 62235564-62237319 0.62 −3.45
    PROTEIN DOWNREG. TU_0106896_0 chr22: 28206216-28217370 0.46 −3.46
    PROTEIN DOWNREG. TU_0086308_0 chr6: 95168335-95184222 0.54 −3.46
    PROTEIN DOWNREG. TU_0053500_0 chr1: 19842799-19857540 0.66 −3.46
    PROTEIN DOWNREG. TU_0030156_0 chrX: 102740504-102752163 0.61 −3.46
    PROTEIN DOWNREG. TU_0053209_0 chr16: 30815439-60839057 0.45 −3.46
    PROTEIN DOWNREG. TU_0102372_0 chr9: 35672000-35681306 0.58 −3.46
    PROTEIN DOWNREG. TU_0040491_0 chr3: 134987802-134980829 0.35 −3.46
    PROTEIN DOWNREG. TU_0063025_0 chr1: 54832256-54849445 0.56 −3.46
    PROTEIN DOWNREG. TU_0016741_0 chr17: 37808007-37818100 0.61 −3.47
    PROTEIN DOWNREG. TU_0073672_0 chr12: 65272841-55276238 0.78 −3.47
    NOVEL DOWNREG. TU_0072214_0 chr20: 42166331-42122501 0.45 −3.47
    PROTEIN DOWNREG. TU_0069254_0 chr3: 223745864-223750945 0.54 −3.48
    PROTEIN DOWNREG. TU_0014474_0 chr17: 4410320-4410814 0.34 −3.48
    PROTEIN DOWNREG. TU_0082036_0 chr6: 31975375-31977685 0.61 −3.48
    ncRNA DOWNREG. TU_0115605_0 chr2: 37722515-37727509 0.64 −3.48
    PROTEIN DOWNREG. TU_0106457_0 chr22: 21742726-21732216 0.56 −3.48
    PROTEIN DOWNREG. TU_0100880_0 chr21: 32808766-62809639 0.62 −3.48
    PROTEIN DOWNREG. TU_0028060_0 chrX: 64873768-64873981 0.59 −3.48
    PROTEIN DOWNREG. TU_0183717_0 chr9: 112675354-112576369 0.59 −3.48
    PROTEIN DOWNREG. TU_0016732_0 chr17: 37807991-37828819 0.65 −3.48
    PROTEIN DOWNREG. TU_0075679_0 chr10: 96987317-970405910 0.65 −3.48
    PROTEIN DOWNREG. TU_0108979_0 chr15: 34659121-34889737 0.68 −3.48
    PRTEIN DOWNREG. TU_0039868_0 chr3: 123526763-123543198 0.51 −3.48
    PROTEIN DOWNREG. TU_0032236_0 chr14: 22839081-22833882 0.61 −3.48
    PROTEIN DOWNREG. TU_0103902_0 chr9: 115957988-116128421 0.59 −3.49
    PROTEIN DOWNREG. TU_0064251_0 chr6: 71589234-71069482 0.38 −3.49
    PROTEIN DOWNREG. TU_0116344_0 chr2: 27568254-27571682 0.64 −3.49
    NOVEL DOWNREG. TU_0096307_0 chr11: 7977293-7976927 0.69 −3.49
    NOVEL DOWNREG. TU_0020914_0 chr19: 9718612-9723799 0.47 −3.49
    PROTEIN DOWNREG. TU_0014009_0 chr2: 158823186-158930217 0.48 −3.50
    PROTEIN DOWNREG. TU_0111467_0 chr15: 62817064-62854842 0.58 −3.50
    NOVEL DOWNREG. TU_0058552_0 chr6: 257103852-157120456 0.64 −3.50
    PROTEIN DOWNREG. TU_0016616_0 chr17: 36992068-37034423 0.44 −3.50
    PROTEIN DOWNREG. TU_0109820_0 chr15: 41600571-41611159 0.56 −3.51
    PROTEIN DOWNREG. TU_0083744_0 chr5: 236838-297985 0.58 −3.51
    PROTEIN DOWNREG. TU_0038899_0 chr3: 58465926-58495812 0.58 −3.51
    PROTEIN DOWNREG. TU_0018817_0 chr17: 72185287-72184800 0.61 −3.51
    PROTEIN DOWNREG. TU_0096362_0 chr11: 129779777-129794214 0.56 −3.51
    ncRNA DOWNREG. TU_0104765_0 chr9: 131134480-131144297 0.53 −3.51
    PROTEIN DOWNREG. TU_0047809_0 chr4: 52581019-52582331 0.62 −3.52
    PROTEIN DOWNREG. TU_0114638_0 chr2: 11804195-11654972 0.68 −3.52
    PROTEIN DOWNREG. TU_0110215_0 chr15: 43246574-43254766 0.63 −3.52
    PROTEIN DOWNREG. TU_0117024_0 chr2: 66525747-66653430 0.61 −3.52
    PROTEIN DOWNREG. TU_0109004_0 chr15: 39178588-35180010 0.39 −3.53
    PROTEIN DOWNREG. TU_0114005_0 chr15: 97462760-97493368 0.56 −3.53
    PROTEIN DOWNREG. TU_0079534_0 chr12: 53260191-53268540 0.41 −3.53
    PROTEIN DOWNREG. TU_0068435_0 chr1: 202366748-202385528 0.62 −3.53
    PROTEIN DOWNREG. TU_0014730_0 chr17: 7034460-7061662 0.61 −3.53
    PROTEIN DOWNREG. TU_0111099_0 chr15: 57738640-57756015 0.70 −3.54
    PROTEIN DOWNREG. TU_0079355_0 chr12: 51906987-51912605 0.54 −3.54
    PROTEIN DOWNREG. TU_0107389_0 chr22: 36670710-36671784 0.59 −3.54
    PROTEIN DOWNREG. TU_0105434_0 chr9: 138991774-138996018 0.54 −3.54
    ncRNA DOWNREG. TU_0122441_0 chr2: 220000172-220002664 0.38 −3.54
    PROTEIN DOWNREG. TU_0074041_0 chr10: 29785041-30865975 0.84 −3.55
    PROTEIN DOWNREG. TU_0114819_0 chr2: 23779564-23785016 0.65 −3.55
    PROTEIN DOWNREG. TU_0013666_0 chr7: 150180552-150189309 0.34 −3.55
    PROTEIN DOWNREG. TU_0036844_0 chr3: 9930878-9933062 0.54 −3.56
    PROTEIN DOWNREG. TU_0014467_0 chr17: 4407802-4410614 0.49 −3.56
    NOVEL DOWNREG. TU_0086397_0 chr14: 104617328-104624500 0.45 −3.56
    PROTEIN DOWNREG. TU_0014721_0 chr17: 6882853-6884238 0.60 −3.57
    PROTEIN DOWNREG. TU_0061867_0 chr1: 41618433-41621890 0.61 −3.57
    PROTEIN DOWNREG. TU_0090901_0 chr11: 20081238-20099725 0.60 −3.57
    PROTEIN DOWNREG. TU_0089503_0 chr5: 179949721-179951068 0.47 −3.57
    NOVEL DOWNREG. TU_0112056_0 chr15: 69658838-69878469 0.46 −3.57
    NOVEL DOWNREG. TU_0052454_0 chr16: 15702084-15702374 0.40 −3.57
    PROTEIN DOWNREG. TU_0004248_0 chr6: 70983350-71069482 0.52 −3.57
    PROTEIN DOWNREG. TU_0111118_0 chr15: 58426685-58428568 0.59 −3.58
    PROTEIN DOWNREG. TU_0047256_0 chr4: 38781223-38804733 0.63 −3.58
    PROTEIN DOWNREG. TU_0092308_0 chr11: 61385022-61325568 0.62 −3.58
    PROTEIN DOWNREG. TU_0037381_0 chr3: 33159367-33165995 0.70 −3.59
    PROTEIN DOWNREG. TU_0088765_0 chr5: 168737435-169749043 0.53 −3.60
    PROTEIN DOWNREG. TU_0039072_0 chr3: 70098064-70100160 0.63 −3.60
    NOVEL DOWNREG. TU_0112059_0 chr15: 69667695-69691724 0.41 −3.60
    PROTEIN DOWNREG. TU_0030975_0 chrX: 130235170-130235814 0.49 −3.60
    PROTEIN DOWNREG. TU_0038532_0 chr3: 52258212-52287726 0.77 −3.60
    PROTEIN DOWNREG. TU_0014418_0 chr17: 3748115-3749717 0.39 −3.60
    PROTEIN DOWNREG. TU_0081986_0 chr6: 31791087-31793378 0.48 −3.61
    PROTEIN DOWNREG. TU_0111109_0 chr15: 53426655-58477514 0.86 −3.61
    PROTEIN DOWNREG. TU_0064151_0 chr1: 98933815-98937074 0.46 −3.61
    PROTEIN DOWNREG. TU_0111253_0 chr15: 81121812-61151157 0.63 −3.61
    PROTEIN DOWNREG. TU_0058947_0 chr1: 13782811-13817026 0.61 −3.62
    PROTEIN DOWNREG. TU_0031484_0 chrX: 151890690-151832673 0.59 −3.62
    PROTEIN DOWNREG. TU_0076212_0 chr10: 105781059-105835687 0.47 −3.62
    PROTEIN DOWNREG. TU_0062567_0 chr1: 47050692-47056967 0.47 −3.62
    NOVEL DOWNREG. TU_0020667_0 chr19: 7888598-7889980 0.41 −3.62
    PROTEIN DOWNREG. TU_0029358_0 chrX: 71268703-71268507 0.66 −3.63
    PROTEIN DOWNREG. TU_0065339_0 chr1: 148457403-148475104 0.56 −3.65
    PROTEIN DOWNREG. TU_0063769_0 chr1: 87583567-87587259 0.58 −3.65
    NOVEL DOWNREG. TU_0036395_0 chr14: 104617328-104623671 0.53 −3.63
    PROTEIN DOWNREG. TU_0103872_0 chr9: 115178483-115203441 0.59 −3.63
    PROTEIN DOWNREG. TU_0050244_0 chr4: 148585059-148685550 0.63 −3.63
    PROTEIN DOWNREG. TU_0031913_0 chr14: 20554755-20563715 0.64 −3.63
    PROTEIN DOWNREG. TU_0065343_0 chr1: 148501147-148501585 0.37 −3.63
    PROTEIN DOWNREG. TU_0084948_0 chr5: 50715235-50726033 0.68 −3.64
    PROTEIN DOWNREG. TU_0090542_0 chr11: 8672475-8549482 0.64 −3.64
    PROTEIN DOWNREG. TU_0120044_0 chr2: 155422693-155423038 0.26 −3.64
    PROTEIN DOWNREG. TU_0023267_0 chr19: 40937280-40940189 0.52 −3.84
    PROTEIN DOWNREG. TU_0023553_0 chr19: 4543319-43434071 0.51 −3.85
    PROTEIN DOWNREG. TU_0115806_0 chr2: 37722515-37725553 0.60 −3.65
    PROTEIN DOWNREG. TU_0085256_0 chr5: 59099579-55100724 0.53 −3.65
    PROTEIN DOWNREG. TU_0038056_0 chr9: 48563574-48623119 0.68 −3.65
    PROTEIN DOWNREG. TU_0022088_0 chr10: 168647988-16923718 0.55 −3.65
    ncRNA DOWNREG. TU_0088408_0 chr12: 129197899-129212499 0.58 −3.85
    PROTEIN DOWNREG. TU_0059155_0 chr1: 16397144-16405288 0.61 −3.85
    PROTEIN DOWNREG. TU_0046595_0 chr4: 3264594-3411502 0.68 −3.65
    PROTEIN DOWNREG. TU_0039476_0 chr8: 108331106-108578694 0.58 −3.66
    PROTEIN DOWNREG. TU_0091498_0 chr11: 46834081-46889744 0.65 −3.66
    PROTEIN DOWNREG. TU_0098359_0 chr8: 68585438-64499042 0.45 −3.66
    PROTEIN DOWNREG. TU_0046627_0 chr4: 3795533-3740037 0.45 −3.67
    NOVEL DOWNREG. TU_0103946_0 chr9: 116821701-116822181 0.48 −3.67
    PROTEIN DOWNREG. TU_0008057_0 chr7: 5519816-5836775 0.62 −3.67
    PROTEIN DOWNREG. TU_0180219_0 chr8: 143549604-143556275 0.59 −3.67
    PROTEIN DOWNREG. TU_0087532_0 chr5: 157802644-137810548 0.53 −3.68
    PROTEIN DOWNREG. TU_0066743_0 chr1: 154859563-154862200 0.43 −3.68
    PROTEIN DOWNREG. TU_0052586_0 chr16: 19637116-19779369 0.64 −3.68
    PROTEIN DOWNREG. TU_0075308_0 chr10: 88708340-88712998 0.51 −3.68
    PROTEIN DOWNREG. TU_0032240_0 chr14: 22894093-22905632 0.57 −3.68
    PROTEIN DOWNREG. TU_0046399_0 chr4: 2031053-2040569 0.44 −3.70
    PROTEIN DOWNREG. TU_0081487_0 chr12: 104248577-104289423 0.56 −3.70
    PROTEIN DOWNREG. TU_0096978_0 chr8: 22133174-22140355 0.47 −3.70
    PROTEIN DOWNREG. TU_0054692_0 chr16: 83411105-83900616 0.62 −3.70
    PROTEIN DOWNREG. TU_0067818_0 chr1: 180509414-180511335 0.72 −3.71
    PROTEIN DOWNREG. TU_0098841_0 chr8: 92088228-92039575 0.39 −3.71
    PROTEIN DOWNREG. TU_0121595_0 chr2: 262193170-262196672 0.62 −3.71
    PROTEIN DOWNREG. TU_0023218_0 chr18: 40679964-40694184 0.55 −3.71
    PROTEIN DOWNREG. TU_0112386_0 chr15: 71818130-71820041 0.55 −3.71
    PROTEIN DOWNREG. TU_0024601_0 chr19: 51603296-51609005 0.56 −3.71
    PROTEIN DOWNREG. TU_0055238_0 chr18: 2561572-2605627 0.59 −3.71
    PROTEIN DOWNREG. TU_0085908_0 chr5: 78401241-78420780 0.52 −3.72
    ncRNA DOWNREG. TU_0111315_0 chr15: 61676589-61681634 0.55 −3.72
    PROTEIN DOWNREG. TU_0111311_0 chr15: 61676589-61681634 0.55 −3.72
    PROTEIN DOWNREG. TU_0023241_0 chr19: 40856254-40861198 0.41 −3.72
    PROTEIN DOWNREG. TU_0068139_0 chr8: 199127296-199147465 0.42 −3.72
    ncRNA DOWNREG. TU_0102684_0 chr9: 70336502-70344481 0.56 −3.73
    PROTEIN DOWNREG. TU_0068764_0 chr1: 207854842-207892483 0.49 −3.73
    PROTEIN DOWNREG. TU_0053636_0 chr18: 55846971-55853340 0.58 −3.74
    PROTEIN DOWNREG. TU_0084025_0 chr5: 6501949-6545706 0.54 −3.74
    NOVEL DOWNREG. TU_0032151_0 chr14: 22508055-22508830 0.58 −3.74
    PROTEIN DOWNREG. TU_0014650_0 chr17: 6295379-6305574 0.62 −3.74
    PROTEIN DOWNREG. TU_0076124_0 chr10: 104619299-104651033 0.60 −3.75
    PROTEIN DOWNREG. TU_0085198_0 chr5: 58300638-58305429 0.60 −3.75
    PROTEIN DOWNREG. TU_0102686_0 chr9: 70837677-70344573 0.55 −3.76
    PROTEIN DOWNREG. TU_0112385_0 chr15: 71818130-71831566 0.54 −3.76
    PROTEIN DOWNREG. TU_0100875_0 chr21: 32705500-32809639 0.61 −3.78
    PROTEIN DOWNREG. TU_0085928_0 chr1: 151800274-151855449 0.49 −3.78
    PROTEIN DOWNREG. TU_0063298_0 chr1: 62474433-62474872 0.36 −3.78
    PROTEIN DOWNREG. TU_0100861_0 chr21: 32604246-32608457 0.62 −3.79
    PROTEIN DOWNREG. TU_0101015_0 chr21: 35010886-35012375 0.55 −3.79
    ncRNA DOWNREG. TU_0081086_0 chrX: 133993992-133995935 0.73 −3.79
    PROTEIN DOWNREG. TU_0068759_0 chr1: 207669209-207672813 0.45 −3.79
    NOVEL DOWNREG. TU_0069253_0 chr1: 223741202-223745600 0.62 −3.79
    PROTEIN DOWNREG. TU_0020150_0 chr19: 3877291-3879097 0.52 −3.79
    ncRNA DOWNREG. TU_0084059_0 chr5: 9599140-9608833 0.50 −3.80
    PROTEIN DOWNREG. TU_0016922_0 chr17: 38430856-38435173 0.51 −3.80
    PROTEIN DOWNREG. TU_0013053_0 chr7: 134114695-134205949 0.58 −3.81
    PROTEIN DOWNREG. TU_0017406_0 chr17: 43458534-43470076 0.58 −3.81
    PROTEIN DOWNREG. TU_0014681_0 chr17: 6295379-6305877 0.50 −3.81
    PROTEIN DOWNREG. TU_0058447_0 chr1: 9040090-9052238 0.36 −3.81
    PROTEIN DOWNREG. TU_0085624_0 chr18: 11872611-11875972 0.64 −3.82
    PROTEIN DOWNREG. TU_0003717_0 chr6: 43381215-43381963 0.49 −3.82
    NOVEL DOWNREG. TU_0016578_0 chr17: 35883208-35884855 0.52 −3.82
    PROTEIN DOWNREG. TU_0101224_0 chr21: 40161189-40223184 0.50 −3.82
    PROTEIN DOWNREG. TU_0064871_0 chr1: 115391459-115433611 0.59 −3.83
    PROTEIN DOWNREG. TU_0097462_0 chr8: 37773618-37822041 0.55 −3.85
    PROTEIN DOWNREG. TU_0066742_0 chr1: 154860755-154862200 0.42 −3.83
    PROTEIN DOWNREG. TU_0090638_0 chr11: 14242208-14246823 0.55 −3.83
    PROTEIN DOWNREG. TU_0046628_0 chr4: 3735533-3740037 0.46 −3.83
    PROTEIN DOWNREG. TU_0024608_0 chr19: 51842692-51911641 0.53 −3.83
    PROTEIN DOWNREG. TU_0071146_0 chr20: 25381375-25432639 0.58 −3.84
    PROTEIN DOWNREG. TU_0080097_0 chr12: 55301840-55307803 0.56 −3.85
    PROTEIN DOWNREG. TU_0062615_0 chr1: 48974664-48997227 0.51 −3.85
    PROTEIN DOWNREG. TU_0013669_0 chr7: 150272983-150305963 0.52 −3.86
    PROTEIN DOWNREG. TU_0102682_0 chr9: 70197177-70337519 0.56 −3.86
    PROTEIN DOWNREG. TU_0104855_0 chr9: 131689287-131691419 0.64 −3.86
    PROTEIN DOWNREG. TU_0116336_0 chr2: 48677181-48685259 0.65 −3.86
    PROTEIN DOWNREG. TU_0116619_0 chr2: 60532830-60533546 0.47 −3.87
    PROTEIN DOWNREG. TU_0034462_0 chr14: 69415893-69568826 0.48 −3.87
    PROTEIN DOWNREG. TU_0067213_0 chr1: 163086189-163087684 0.59 −3.87
    PROTEIN DOWNREG. TU_0066337_0 chr1: 148457403-148475119 0.56 −3.87
    NOVEL DOWNREG. TU_0062461_0 chr1: 46461750-46463004 0.51 −3.88
    PROTEIN DOWNREG. TU_0080098_0 chr12: 56302807-56307767 0.56 −3.88
    PROTEIN DOWNREG. TU_0034421_0 chr14: 68410559-68412495 0.62 −3.88
    PROTEIN DOWNREG. TU_0016601_0 chr17: 36911114-36929728 0.39 −3.88
    PROTEIN DOWNREG. TU_0079221_0 chr12: 51194638-51200498 0.43 −3.89
    PROTEIN DOWNREG. TU_0112752_0 chr15: 76184009-76210733 0.55 −3.90
    PROTEIN DOWNREG. TU_0028410_0 chrX: 48910899-48929704 0.68 −3.91
    PROTEIN DOWNREG. TU_0076488_0 chr10: 123227854-123347940 0.55 −3.92
    NOVEL DOWNREG. TU_0093208_0 chr11: 65396933-65397655 0.45 −3.92
    PROTEIN DOWNREG. TU_0078229_0 chr12: 27016771-27017190 0.47 −3.92
    PROTEIN DOWNREG. TU_0064620_0 chr1: 111962701-112059304 0.61 −3.92
    PROTEIN DOWNREG. TU_0005224_0 chr8: 107917248-108088034 0.60 −3.93
    PROTEIN DOWNREG. TU_0023668_0 chr19: 44114820-44158190 0.56 −3.93
    PROTEIN DOWNREG. TU_0041856_0 chr3: 190990156-191097717 0.44 −3.93
    PROTEIN DOWNREG. TU_0107364_0 chr22: 36658502-36671784 0.62 −3.93
    PROTEIN DOWNREG. TU_0079224_0 chr12: 61194638-61199100 0.43 −3.94
    PROTEIN DOWNREG. TU_0027357_0 chrX: 17728093-17737982 0.57 −3.94
    PROTEIN DOWNREG. TU_0071013_0 chr20: 19141491-19652034 0.55 −3.95
    PROTEIN DOWNREG. TU_0060281_0 chr1: 27204050-27211524 0.48 −3.95
    PROTEIN DOWNREG. TU_0096007_0 chr11: 119482708-119514087 0.45 −3.95
    PROTEIN DOWNREG. TU_0058810_0 chr1: 11631006-11637486 0.50 −3.95
    ncRNA DOWNREG. TU_0102668_0 chr9: 67902293-67904671 0.52 −3.96
    PROTEIN DOWNREG. TU_0103226_0 chr9: 93524079-93559558 0.55 −3.96
    PROTEIN DOWNREG. TU_0098334_0 chr8: 68508843-68581618 0.43 −3.96
    NOVEL DOWNREG. TU_0084068_0 chr5: 9602147-9603383 0.49 −3.96
    ncRNA DOWNREG. TU_0018887_0 chr17: 73068191-73068655 0.29 −3.97
    PROTEIN DOWNREG. TU_0020916_0 chr19: 9720305-9727293 0.55 −3.97
    PROTEIN DOWNREG. TU_0018819_0 chr7: 72184546-72195820 0.59 −3.97
    NOVEL DOWNREG. TU_0042081_0 chr3: 197374550-197376798 0.46 −3.97
    PROTEIN DOWNREG. TU_0065854_0 chr1: 149850009-149852298 0.46 −3.98
    PROTEIN DOWNREG. TU_0111301_0 chr18: 81676588-51684928 0.54 −3.98
    PROTEIN DOWNREG. TU_0073443_0 chr10: 5556713-3558609 0.43 −3.99
    PROTEIN DOWNREG. TU_0030581_0 chrX: 118096546-118104692 0.38 −3.99
    PROTEIN DOWNREG. TU_0019780_0 chr
    Figure US20130267443A1-20131010-P00899
    : 120
    Figure US20130267443A1-20131010-P00899
    -120
    Figure US20130267443A1-20131010-P00899
    		 0.55 −4.00
    PROTEIN DOWNREG. TU_0081660_0 chr12: 108705678-108718771 0.50 −4.00
    PROTEIN DOWNREG. TU_0046397_0 chr4: 2932589-2050090 0.46 −4.00
    PROTEIN DOWNREG. TU_0122440_0 chr2: 219991398-219999705 0.53 −4.01
    PROTEIN DOWNREG. TU_0011534_0 chr7: 99085437-99096154 0.36 −4.01
    PROTEIN DOWNREG. TU_0047205_0 chr4: 37815997-37817290 0.59 −4.02
    PROTEIN DOWNREG. TU_0017005_0 chr17: 39308253-39337366 0.52 −4.02
    PROTEIN DOWNREG. TU_0052436_0 chr16: 15704459-15858435 0.54 −4.03
    PROTEIN DOWNREG. TU_0014762_0 chr17: 7128572-7131411 0.46 −4.03
    PROTEIN DOWNREG. TU_0080075_0 chr12: 56290183-56301803 0.53 −4.03
    PROTEIN DOWNREG. TU_0083295_0 chr5: 177597111-177621358 0.48 −4.03
    PROTEIN DOWNREG. TU_0062594_0 chr16: 19775320-19780719 0.68 −4.03
    PROTEIN DOWNREG. TU_0068168_0 chr1: 199700556-199742901 0.61 −4.04
    ncRNA DOWNREG. TU_0102657_0 chr9: 67902293-67908869 0.54 −4.04
    PROTEIN DOWNREG. TU_0088729_0 chr8: 43825496-43526789 0.55 −4.04
    PROTEIN DOWNREG. TU_0071246_0 chr20: 29913077-29921837 0.42 −4.05
    NOVEL DOWNREG. TU_0050224_0 chr4: 147115887-147190781 0.25 −4.06
    PROTEIN DOWNREG. TU_0110166_0 chr15: 48172154-43198892 0.49 −4.07
    PROTEIN DOWNREG. TU_0030085_0 chrX: 101782933-101800062 0.56 −4.07
    PROTEIN DOWNREG. TU_0021042_0 chr19: 10435466-10441506 0.61 −4.08
    PROTEIN DOWNREG. TU_0097463_0 chr8: 37812227-37826549 0.58 −4.08
    PROTEIN DOWNREG. TU_0101682_0 chr9: 734412-736069 0.67 −4.08
    PROTEIN DOWNREG. TU_0030157_0 chrX: 102750729-102751737 0.44 −4.09
    NOVEL DOWNREG. TU_0098190_0 chr8: 61704765-61708199 0.40 −4.09
    PROTEIN DOWNREG. TU_0082947_0 chr1: 53744955-53838542 0.42 −4.09
    PROTEIN DOWNREG. TU_0078008_0 chr12: 21679541-21762042 0.57 −4.09
    PROTEIN DOWNREG. TU_0017582_0 chr17: 45858594-45907395 0.54 −4.09
    PROTEIN DOWNREG. TU_0080022_0 chr6: 1555144-1659122 0.53 −4.09
    PROTEIN DOWNREG. TU_0031424_0 chrX: 149482223-149433104 0.47 −4.10
    PROTEIN DOWNREG. TU_0065603_0 chr1: 149275738-149286201 0.42 −4.10
    PROTEIN DOWNREG. TU_0037859_0 chr3: 45240966-45242817 0.49 −4.11
    PROTEIN DOWNREG. TU_0162271_0 chr9: 34511045-34512853 0.50 −4.11
    PROTEIN DOWNREG. TU_0035605_0 chr14: 95254401-93273368 0.49 −4.11
    PROTEIN DOWNREG. TU_0064621_0 chr1: 112047963-1120
    Figure US20130267443A1-20131010-P00899
    		 0.54 −4.11
    ncRNA DOWNREG. TU_0031098_0 chrX: 134057388-134058604 0.47 −4.11
    PROTEIN DOWNREG. TU_0018799_0 chr17: 72061371-72080938 0.61 −4.11
    PROTEIN DOWNREG. TU_0011129_0 chr7: 94135058-94136943 0.41 −4.11
    NOVEL DOWNREG. TU_0036396_0 chr14: 104617328-104619095 0.41 −4.12
    PROTEIN DOWNREG. TU_0056255_0 chr5: 92944260-92956054 0.57 −4.12
    ncRNA DOWNREG. TU_0074501_0 chr10: 60429298-60431031 0.42 −4.12
    PROTEIN DOWNREG. TU_0073757_0 chr10: 17672347-17899481 0.56 −4.13
    PROTEIN DOWNREG. TU_0015457_0 chr17: 195
    Figure US20130267443A1-20131010-P00899
    1898-19287156    		 0.45 −4.13
    PROTEIN DOWNREG. TU_0122402_0 chr2: 219821926-219824741 0.61 −4.13
    PROTEIN DOWNREG. TU_0116618_0 chr2: 60932830-60633902 0.49 −4.13
    PROTEIN DOWNREG. TU_0029963_0 chrX: 100220537-100238065 0.51 −4.15
    PROTEIN DOWNREG. TU_0028949_0 chrK: 64964077-64878513 0.61 −4.15
    PROTEIN DOWNREG. TU_0082443_0 chr5: 154178336-164210363 0.57 −4.16
    PROTEIN DOWNREG. TU_0107372_0 chr22: 36668731-36871784 0.56 −4.17
    PROTEIN DOWNREG. TU_0016330_0 chr17: 38070936-35071660 0.57 −4.17
    PROTEIN DOWNREG. TU_0016596_0 chr17: 36923524-36946925 0.58 −4.17
    PROTEIN DOWNREG. TU_0014764_0 chr17: 7131441-7134452 0.45 −4.18
    PROTEIN DOWNREG. TU_0070473_0 chr20: 2621571-2702522 0.60 −4.18
    PROTEIN DOWNREG. TU_0053602_0 chr1: 149282296-149268718 0.40 −4.19
    PROTEIN DOWNREG. TU_0105435_0 chr9: 138997874-138999099 0.37 −4.19
    PROTEIN DOWNREG. TU_0015445_0 chr17: 19415396-19422513 0.46 −4.20
    PROTEIN DOWNREG. TU_0013012_0 chr17: 74597027-74930278 0.42 −4.21
    PROTEIN DOWNREG. TU_0048538_0 chr4: 21336928-81344460 0.41 −4.22
    PROTEIN DOWNREG. TU_0098385_0 chr8: 68508843-68509222 0.41 −4.22
    PROTEIN DOWNREG. TU_0076499_0 chr10: 225227854-123248042 0.53 −4.23
    PROTEIN DOWNREG. TU_0117482_0 chr2: 73973697-71000287 0.56 −4.23
    PROTEIN DOWNREG. TU_0114778_0 chr2: 20264034-20288661 0.45 −4.24
    PROTEIN DOWNREG. TU_0016318_0 chr17: 33917848-33935788 0.53 −4.25
    PROTEIN DOWNREG. TU_0071893_0 chr20: 34603301-34611746 0.59 −4.25
    PROTEIN DOWNREG. TU_0073523_0 chr10: 8136827-8157157 0.44 −4.26
    PROTEIN DOWNREG. TU_0064500_0 chr1: 110861354-110079791 0.42 −4.27
    PROTEIN DOWNREG. TU_0064862_0 chr1: 149
    Figure US20130267443A1-20131010-P00899
    50009-149952444    		 0.41 −4.27
    PROTEIN DOWNREG. TU_0030064_0 chrX: 101268429-101269091 0.44 −4.28
    PROTEIN DOWNREG. TU_0060278_0 chr1: 27192773-27200190 0.51 −4.28
    PROTEIN DOWNREG. TU_0000013_0 chr6: 1287191-1259372 0.36 −4.29
    PROTEIN DOWNREG. TU_0120707_0 chr2: 17686568-176869190 0.45 −4.31
    PROTEIN DOWNREG. TU_0016744_0 chr17: 37790358-37809206 0.54 −4.31
    PROTEIN DOWNREG. TU_0016827_0 chr17: 38085330-38071660 0.53 −4.31
    PROTEIN DOWNREG. TU_0056190_0 chr18: 26824024-26842486 0.43 −4.33
    PROTEIN DOWNREG. TU_0096964_0 chr8: 22027917-22043914 0.47 −4.35
    PROTEIN DOWNREG. TU_0030062_0 chrX: 101267701-101269091 0.41 −4.35
    ncRNA DOWNREG. TU_0120713_0 chr2: 176930391-176969560 0.49 −4.35
    PROTEIN DOWNREG. TU_0011537_0 chr7: 99589728-99111736 0.39 −4.39
    PROTEIN DOWNREG. TU_0107366_0 chr22: 36038731-36673469 0.54 −4.39
    PROTEIN DOWNREG. TU_0065341_0 chr1: 148496851-148500610 0.35 −4.39
    PROTEIN DOWNREG. TU_0013076_0 chr17: 12510065-12612990 0.50 −4.40
    PROTEIN DOWNREG. TU_0087752_0 chr5: 199206352-199211418 0.44 −4.40
    PROTEIN DOWNREG. TU_0108990_0 chr15: 34970176-35180015 0.51 −4.41
    PROTEIN DOWNREG. TU_0062566_0 chr1: 47037330-47057598 0.43 −4.42
    PROTEIN DOWNREG. TU_0018825_0 chr17: 2192513-2192794 0.47 −4.43
    PROTEIN DOWNREG. TU_0002566_0 chr6: 55797424-55798978 0.37 −4.44
    PROTEIN DOWNREG. TU_0074074_0 chr10: 29814868-29815135 0.26 −4.44
    PROTEIN DOWNREG. TU_0110179_0 chr15: 45196205-45255205 0.43 −4.46
    PROTEIN DOWNREG. TU_0082372_0 chr12: 116130336-116130610 0.41 −4.47
    ncRNA DOWNREG. TU_0102658_0 chr9: 67902293-67908683 0.46 −4.48
    PROTEIN DOWNREG. TU_0024160_0 chr19: 48777171-48778386 0.51 −4.49
    PROTEIN DOWNREG. TU_0031081_0 chrX: 133993992-134013925 0.64 −4.49
    PROTEIN DOWNREG. TU_0015447_0 chr17: 19421649-19423000 0.46 −4.50
    PROTEIN DOWNREG. TU_0016834_0 chr17: 38072130-38072515 0.54 −4.50
    PROTEIN DOWNREG. TU_0120709_0 chr2: 176677352-176697902 0.49 −4.50
    PROTEIN DOWNREG. TU_0041205_0 chr3: 171619688-171634575 0.48 −4.53
    PROTEIN DOWNREG. TU_0110178_0 chr15: 43196270-43241274 0.43 −4.54
    PROTEIN DOWNREG. TU_0084473_0 chr1: 110000292-110079791 0.51 −4.58
    ncRNA DOWNREG. TU_0120715_0 chr2: 176692475-176697902 0.50 −4.58
    PROTEIN DOWNREG. TU_0110180_0 chr15: 43196205-43243358 0.43 −4.63
    PROTEIN DOWNREG. TU_0024922_0 chr19: 54255568-54259943 0.42 −4.64
    ncRNA DOWNREG. TU_0119818_0 chr2: 38109039-38116939 0.32 −4.64
    ncRNA DOWNREG. TU_0067289_0 chr1: 166307141-166318970 0.48 −4.69
    NOVEL DOWNREG. TU_0095765_0 chr11: 117640504-117642734 0.36 −4.69
    PROTEIN DOWNREG. TU_0058445_0 chr1: 9017797-9040122 0.33 −4.70
    PROTEIN DOWNREG. TU_0047068_0 chr4: 23402764-23403824 0.41 −4.72
    PROTEIN DOWNREG. TU_0018882_0 chr17: 38260060-38263683 0.51 −4.82
    NOVEL DOWNREG. TU_0098382_0 chr8: 68494189-68495887 0.23 −4.83
    PROTEIN DOWNREG. TU_0110177_0 chr15: 43196768-43245735 0.47 −4.86
    PROTEIN DOWNREG. TU_0089598_0 chr11: 303980-310982 0.35 −4.87
    PROTEIN DOWNREG. TU_0107527_0 chr22: 37740155-37746215 0.44 −4.88
    PROTEIN DOWNREG. TU_0107528_0 chr22: 37741248-37746215 0.43 −4.90
    PROTEIN DOWNREG. TU_0032311_0 chr14: 23612588-23617134 0.32 −5.04
    Figure US20130267443A1-20131010-P00899
    indicates data missing or illegible when filed
  • TABLE 5
    Fold change
    Expected score Observed (PCA vs q-value
    PCAT ID Gene Chromosomal Location (dExp) score (d) Benign (%)
    PCAT-1 TU_0099866_0 chr8: 128087842-128095202 −2.2654014 5.444088 6.9071784 0
    PCAT-2 TU_0090142_0 chr11: 4745677-4760303 −2.4408573 4.6781354 11.39658 0
    PCAT-3 TU_0054605_0 chr16: 82380336-82394836 −2.1786723 4.4612455 5.8916535 0
    PCAT-4 TU_0090140_0 chr11: 4748163-4759145 −2.1153826 4.4345 7.1933164 0
    PCAT-5 TU_0078286_0 chr12: 2393286-32405731 −1.9164219 4.312603 3.5655262 0
    PCAT-6 TU_0090864_0 chr6: 128084589-128103681 −1.7214081 4.265536 3.8937242 0
    PCAT-7 TU_0084308_0 chr5: 15938756-15949124 −1.9636476 4.124071 4.747601 0
    PCAT-8 TU_0084303_0 chr6: 15899476-15955226 −2.0245786 4.0520086 7.1035067 0
    PCAT-9 TU_0082746_0 chr12: 120197102-120197416 −1.861408 3.7551165 5.1431665 0
    PCAT-10 TU_0078296_0 chr12: 32394534-32405549 −1.5944241 3.6902914 3.034359 0
    PCAT-11 TU_0078290_0 chr12: 32394534-32410898 −1.5337954 3.675318 3.1572607 0
    PCAT-12 TU_0002597_0 chr12: 32394534-32410898 −1.6263148 3.6469774 3.352418 0
    PCAT-13 TU_0049368_0 chr6: 34335202-34338521 −1.6894234 3.6079373 2.8299546 0
    PCAT-14 TU_0106548_0 chr4: 106772318-106772770 −1.939075 3.591398 5.3962547 0
    PCAT-15 TU_0078293_0 chr22: 22209111-22212055 −1.5212961 3.5705945 2.9213174 0
    PCAT-16 TU_0099834_0 chr8: 128301495-128307576 −1.4445064 3.5658643 2.516981 0
    PCAT-17 TU_0112014_0 chr15: 67722165-67739990 −1.6326295 3.562463 3.694224 0
    PCAT-18 TU_0084306_0 chr5: 15896315-15947086 −1.845 3.5603588 5.746707 0
    PCAT-19 TU_0124240_0 chr2: 1534883-1538193 −1.6870209 3.5233572 4.339847 0
    PCAT-20 TU_0008439_0 chr7: 24236191-24236455 −1.6302066 3.5071697 6.6821446 0
    PCAT-21 TU_0078299_0 chr12: 32200296-32292169 −1.7297353 3.606232 3.2923664 0
    PCAT-22 TU_0000033_0 chr6: 1619606-1668581 −1.7680657 3.434185 2.2470813 0
    PCAT-23 TU_0096472_0 chr11: 133844590-133862924 −1.8782617 3.410356 5.9854193 0
    PCAT-24 TU_0114259_0 chr2: 1686782-1687314 −1.6662377 3.3919659 5.080926 0
    PCAT-25 TU_0096473_0 chr11: 133844500-133862995 −1.8963361 3.859823 6.1071715 0
    PCAT-26 TU_0100362_0 chr8: 144914456-144930753 −1.6521469 3.3805158 3.8420231 0
    PCAT-27 TU_0040394_0 chr3: 135418632-133441252 −1.6208396 3.3201025 2.8724674 0
    PCAT-28 TU_0043432_0 chr13: 34062994-34056503 −1.6739871 3.2037551 3.2093527 0
    PCAT-29 TU_0112020_0 chr15: 67764259-67801825 −1.5603316 3.1967351 3.593551 0
    PCAT-30 TU_0042717_0 chr13: 23149908-23200198 −1.0654948 3.1685438 4.9633407 0
    PCAT-31 TU_0078232_0 chr12: 62290485-62406307 −1.4503008 3.151879 2.8011364 0
    PCAT-32 TU_0084146_0 chr5: 14025126-14062770 −1.6452767 3.1257985 2.6193055 0
    PCAT-33 TU_0066168_0 chr18: 22477042-22477666 −1.5381516 3.0557241 3.1951044 0
    PCAT-34 TU_0040383_0 chr3: 133360941-133429262 −1.5558791 3.0416508 3.7478442 0
    PCAT-35 TU_0112025_0 chr15: 67780574-87782345 −1.6815977 3.0412362 3.433415 0
    PCAT-36 TU_0041688_0 chr3: 186743298-186741933 −1.4748297 3.0062308 2.543468 0
    PCAT-37 TU_0103642_0 chr9: 109187089-109187455 −1.7387192 2.998958 6.6124363 0
    PCAT-38 TU_0040375_0 chr3: 133280694-133394609 −1.5469999 2.9753568 3.9068055 0
    PCAT-39 TU_0047312_0 chr4: 19217689-39222163 −1.6388936 2.9124916 3.6121209 0
    PCAT-40 TU_0106545_0 chr22: 22218478-22219162 −1.7586407 2.889856 3.7357745 0
    PCAT-41 TU_0054541_0 chr16: 79408800-79435066 −1.7485934 2.8699164 6.647557 0
    PCAT-42 TU_0060446_0 chr1: 28438629-28450156 −1.4880521 2.857332 1.0824111 0
    PCAT-43 TU_0072907_0 chr20: 55759486-55771563 −1.5254781 2.7966201 2.812179 0
    PCAT-44 TU_0043453_0 chr13: 33844637-33845921 −1.5793877 2.7919009 3.6403422 0
    PCAT-45 TU_0038678_0 chr3: 53515951-53517078 −1.7047809 2.7858517 3.6909987 0
    PCAT-46 TU_0101786_0 chr9: 3408690-3415374 −1.4780945 2.7822099 3.3066912 0
    PCAT-47 TU_0101709_0 chr9: 3411967-3415374 −1.4852373 2.7622206 3.1886175 0
    PCAT-48 TU_0166544_0 chr22: 22210421-22220506 −1.6153399 2.7578155 3.7418716 0
    PCAT-49 TU_0046121_0 chr4: 766363-766599 −1.5697786 2.7573307 1.485532 0
    PCAT-50 TU_0106542_0 chr22: 22211315-22220506 −1.6098742 2.755221 3.3781004 0
    PCAT-51 TU_0106541_0 chr22: 22209111-22219162 −1.6593723 2.7341027 3.664146 0
    PCAT-52 TU_0044453_0 chr13: 51505777-51524522 −1.3416 2.732019 2.536953 0
    PCAT-53 TU_0104717_0 chr9: 130697833-130698832 −1.2938 2.7219732 2.3344588 0
    PCAT-54 TU_0039014_0 chr5: 176014905-176015351 −1.3967873 2.7047258 3.7803582 0
    PCAT-55 TU_0168452_0 chr15: 19344745-19362916 −1.5839852 2.6759455 1.8484153 0
    PCAT-56 TU_0112053_0 chr15: 67645590-67775246 −1.4386703 2.668052 3.045022 0
    PCAT-57 TU_0078286_0 chr12: 32395588-32405731 −1.3580605 2.6660874 2.6121044 0
    PCAT-58 TU_0078303_0 chr12: 32274210-32274530 −1.5020599 2.65856 3.3306372 0
    PCAT-59 TU_0112054_0 chr15: 67644390-67650387 −1.5175762 2.8509888 2.9933636 0
    PCAT-60 TU_0071087_0 chr20: 21428679-21429454 −1.4916688 2.649109 4.6481714 0
    PCAT-61 TU_0072906_0 chr20: 95759768-55770657 −1.5059631 2.645004 2.95756 0
    PCAT-62 TU_0054240_0 chr16: 70155175-70173873 −1.4715649 2.6437716 3.5309577 0
    PCAT-63 TU_0047330_0 chr4: 39217641-39222163 −1.5139307 2.6277235 3.0695639 0
    PCAT-64 TU_0055435_0 chr18: 6715938-6719172 −1.6048826 2.6173768 2.9221427 0
    PCAT-65 TU_0079791_0 chr12: 54971063-54971481 −1.4415668 2.6010823 2.0141602 0
    PCAT-66 TU_0043411_0 chr13: 33918267-33926769 −1.495064 2.5991623 3.3860362 0
    PCAT-67 TU_0056121_0 chr18: 20196762-20197522 −1.2526748 2.5938754 1.7191441 0
    PCAT-68 TU_0043412_0 chr13: 33918267-33935946 −1.5891836 2.5901399 4.2804045 0
    PCAT-69 TU_0065837_0 chr1: 149791252-149795934 −1.3852053 2.5882297 2.9343975 0
    PCAT-70 TU_0043461_0 chr13: 33825711-33845275 −1.5994886 2.5853698 4.3461533 0
    PCAT-71 TU_0006453_0 chr6: 144659813-144660143 −1.4985942 2.5744107 2.2007995 0
    PCAT-72 TU_0048596_0 chr4: 30329017-80348259 −1.5744382 2.5690413 2.8022916 0
    PCAT-73 TU_0084140_0 chr5: 14003669-14054874 −1.4040573 2.5472755 2.5979325 0
    PCAT-74 TU_0082982_0 chr12: 121776584-121777370 −1.5293782 2.5458217 2.6197503 0
    PCAT-75 TU_0013212_0 chr7: 13890883-139001515 −1.2298403 2.544434 1.6879753 0
    PCAT-76 TU_0072912_0 chr20: 55779532-55780817 −1.4302964 2.5406737 3.2653345 0
    PCAT-77 TU_0112281_0 chr15: 70586704-70590792 −1.4590155 2.5875097 2.4288568 0
    PCAT-78 TU_0048787_0 chr4: 88120068-88124880 −1.3735119 2.5328946 2.233808 0
    PCAT-79 TU_0108455_0 chr15: 19358626-19365341 −1.6651321 2.5261333 1.9462687 0
    PCAT-80 TU_0091997_0 chr11: 58560356-58573012 −1.3149038 2.5185204 2.1176686 0
    PCAT-81 TU_0122655_0 chr2: 202985284-202998634 −1.4014161 2.476237 2.2194188 0.859614
    PCAT-82 TU_0071798_0 chr20: 33775260-33778511 −1.3388665 2.4848917 1.65688733 0.850371
    PCAT-83 TU_0049200_0 chr4: 102469973-102476087 −1.3222212 2.456723 1.9456172 0.841324
    PCAT-84 TU_0121714_0 chr2: 203295212-203314865 −1.3457565 2.4496663 1.7624274 0.832468
    PCAT-85 TU_0098937_0 chr2: 95748751-95751821 −1.4532137 2.42248 2.2326834 0.823797
    PCAT-86 TU_0108453_0 chr15: 19356996-19364013 −1.8033699 2.4094539 3.839975 0.767811
    PCAT-87 TU_0114170_0 chr15: 99659312-99669199 −1.4358851 2.4062114 2.1252658 0.768711
    PCAT-88 TU_0089906_0 chr11: 1042845-1045705 −1.3899238 2.401665 2.839095.5 0.767811
    PCAT-89 TU_0001559_0 chr6: 30283700-30286011 −1.3517065 2.3987799 1.5110766 0.767811
    PCAT-90 TU_0050557_0 chr4: 159976338-160016453 −1.17525 2.398688 2.0524442 0.767811
    PCAT-91 TU_0078294_0 chr12: 32395632-32413084 −1.4560982 2.3969867 2.1863208 0.767811
    PCAT-92 TU_0044933_0 chr13: 94755992-94760688 −1.2905197 2.3965187 2.189938 0.767811
    PCAT-93 TU_0017730_0 chr17: 52346638-52346880 −1.4169512 2.3874857 1.4708191 0.760428
    PCAT-94 TU_0039020_0 chr3: 66578629-66507777 −1.2662895 2.3720088 1.7112708 0.712473
    PCAT-95 TU_0049213_0 chr4: 102461960-102476087 −1.2725139 2.3871806 1.8878821 0.712473
    PCAT-96 TU_0093070_0 chr11: 64945809-64961189 −1.2954472 2.3645105 1.9128969 0.712473
    PCAT-97 TU_0051063_0 chr4: 187244297-187244767 1.8922851 −2.8485844 0.50983155 0.732264
    PCAT-98 TU_0098190_0 chr8: 61704765-61708199 1.9825526 −2.8612607 0.4027831 0.732264
    PCAT-99 TU_0038811_0 chr3: 57890130-57890884 1.9820296 −2.8837616 0.44431657 0.732264
    PCAT-100 TU_0020814_0 chr19: 9718812-9721799 1.8433232 −2.9248087 0.50623006 0.732264
    PCAT-101 TU_0112056_0 chr15: 89658838-69678409 1.837821 −3.0355222 0.48161976 0
    PCAT-102 TU_0056396_0 chr14: 104617328-104619095 1.549786 −3.1192882 0.45514825 0
    PCAT-103 TU_0095765_0 chr11: 117640504-117642734 2.1002219 −3.2632742 0.38160667 0
    PCAT-104 TU_0050224_0 chr4: 147115887-147190781 2.1981242 −3.2975357 0.28569755 0
    PCAT-105 TU_0112089_0 chr15: 69667695-60691724 1.8148681 −3.3816626 0.43567468 0
    PCAT-106 TU_0098382_0 chr8: 68494189-68495887 2.5433978 −4.0586042 0.30793378 0
  • TABLE 6
    Median Maximum
    Expression Expression
    PCAT ID Gene Chromosomal Location Outlier Score (RPKM) (RPKM)
    PCAT-107 TU_0029004_0 chrX: 66691350-56692032 130.7343145 1 90.921
    PCAT-108 TU_0054542_0 chr16: 79420131-79423590 227.0430857 5.60998 135.85
    PCAT-109 TU_0120899_0 chr2: 180689090-180696402 223.5416436 1.0525222 94.6932
    PCAT-110 TU_0054540_0 chr16: 79419351-79423673 119.050847 4.161985 94.4461
    PCAT-111 TU_0120918_0 chr2: 181297540-181400892 112.710111 1.4533705 92.1795
    PCAT-112 TU_0054538_0 chr16: 79408946-79450819 93.01851659 1.830343 93.1207
    PCAT-113 TU_0059541_0 chr2: 20685471-20686432 68.3572507 1.783109 1375.15
    PCAT-114 TU_0120524_0 chr2: 181331111-181427485 63.95455962 1.3891845 365.202
    PCAT-115 TU_0074308_0 chr10: 42652247-42653596 60.91841567 1.393607 65.7712
    PCAT-116 TU_0049192_0 chr4: 102257900-102306678 59.24997694 1.3854525 69.2423
    PCAT-117 TU_0054537_0 chr16: 79406933-79430041 53.04481877 1.8534395 42.751
    PCAT-118 TU_0120900_0 chr2: 180916864-180985957 55.8438747 1 67.6582
    PCAT-119 TU_0114527_0 chr2: 10858318-10858530 54.76455104 1.2969775 35.0059
    PCAT-120 TU_0120923_0 chr2: 181328093-181419226 52.9783227 1.2821 232.556
    PCAT-121 TU_0049231_0 chr4: 102257900-102259695 52.77001947 1.34042 67.6276
  • TABLE 7
    Median Maximum
    Outlier Expression Expression
    Rank Gene Chromosomal location Score (RPKM) (RPKM)
    1 CRISP3 chr6: 49803053-49813070 294.56446 1.5414775 478.812
    2 SPINK1 chr5: 147184335-147191453 177.19518 2.484455 624.733
    3 TU_0029004_0 chrX: 66691350-66692032 130.73491 1 90.921
    4 TU_0054542_0 chr16: 79420131-79423590 127.0431 5.60998 135.85
    5 TU_0120899_0 chr2: 180689090-180696402 123.54164 1.0525222 94.6932
    6 ERG chr21: 38673821-38792298 119.446 3.421615 178.826
    7 TU_0054540_0 chr16: 79419351-79423673 119.09085 4.161985 94.4461
    8 ERG chr21: 38673821-38792298 117.60294 3.470755 176.186
    9 ERG chr21: 38673821-38955574 117.26408 3.385695 170.663
    10 ERG chr21: 38673821-38955574 116.33448 3.40077 170.443
    11 TU_0120918_0 chr2: 181297540-181400892 112.71011 1.4533705 92.1795
    12 C7orf68 chr7: 127883119-127885708 105.18504 6.835525 336.148
    13 CSRP3 chr11: 19160153-19180106 101.12947 1 148.45
    14 C7orf68 chr7: 127883119-127885708 100.63202 7.08303 337.76
    15 COL2A1 chr12: 46653014-46684552 99.166329 1.2285615 96.0977
    16 C1orf64 chr1: 16203317-16205771 98.085922 3.62012 252.013
    17 TU_0054538_0 chr16: 79403946-79450819 98.018517 1.830343 93.1207
    18 COL2A1 chr12: 46653014-46684552 97.347905 1.2416035 94.6672
    19 CSRP3 chr11: 19160153-19180165 96.730187 1 141.963
    20 COL9A2 chr1: 40538749-40555526 74.408443 19.24815 570.961
    21 PLA2G7 chr6: 46780012-46811389 69.521175 10.83567 97.8331
    22 AGT chr1: 228904891-228916959 69.319886 4.797365 189.281
    23 TU_0059541_0 chr1: 20685471-20686432 68.357251 1.783109 1375.15
    24 ETV1 chr7: 13897382-13992664 68.218569 1.932797 138.519
    25 ETV1 chr7: 13897382-13992664 67.723331 1.9899945 142.406
    26 ETV1 chr7: 13897382-13992664 67.680571 1.9915925 143.632
    27 PLA2G7 chr6: 46780011-46811110 67.089039 10.62 95.3551
    28 ETV1 chr7: 13897382-13997390 66.381191 2.097225 143.975
    29 ETV1 chr7: 13897382-13997575 65.563724 2.074935 141.069
    30 MUC6 chr11: 1002823-1026706 64.7328 1.466194 351.862
    31 TU_0120924_0 chr2: 181331111-181427485 63.95456 1.3891845 365.202
    32 ETV1 chr7: 13897382-13996167 63.929225 2.05648 135.131
    33 ETV1 chr7: 13897382-13996167 62.424072 2.03086 131.644
    34 TU_0074308_0 chr10: 42652247-42653596 60.918416 1.393607 65.7712
    35 TU_0049192_0 chr4: 102257900-102306678 59.249977 1.3854525 69.2423
    36 TU_0054537_0 chr16: 79406933-79430041 58.04482 1.8534395 42.751
    37 RGL3 chr19: 11365731-11391018 57.528689 7.660035 91.2238
    38 RGL3 chr19: 11365731-11391018 57.393056 7.6327 90.6937
    39 TMEM458 chr11: 129190950-129235108 55.887845 4.87695 60.0414
    40 TU_0120900_0 chr2: 180926364-180935967 55.843875 1 67.6582
    41 PTK6 chr20: 61630219-61639151 55.101291 3.420545 114.116
    42 TU_0114527_0 chr2: 10858318-10858530 54.764551 1.2969775 35.0059
    43 TU_0112020_0 chr15: 67764259-67801825 53.832769 2.0281615 88.99
    44 TU_0120923_0 chr2: 181328093-181419226 52.979323 1.2821 232.556
    45 TU_0049231_0 chr4: 102257900-102259695 52.770019 1.34042 67.6276
    46 MON1B chr16: 75782336-75791044 51.717027 26.00355 187.807
    47 TU_0054541_0 chr16: 79408800-79435066 50.445248 1.7164375 32.5832
    48 TU_0087466_0 chr5: 136779809-136798173 50.285169 1.2738505 42.0309
    49 DLX1 chr2: 172658453-172662647 50.043039 2.088625 43.0035
    50 TU_0108209_0 chr22: 46493579-46531245 47.753833 1.0491419 26.6643
    51 DLX1 chr2: 172658453-172662647 47.159314 1.9682735 38.4705
    52 SMC4 chr3: 161600123-161635435 47.127047 4.581655 63.2353
    53 SMC4 chr3: 161601040-161635435 46.967013 4.442065 61.2756
    54 TU_0102399_0 chr9: 35759438-35761676 46.664973 6.44675 179.711
    55 TU_0029005_0 chrX: 66690414-66704178 46.155567 1.0870047 38.3022
    56 C15orf48 chr15: 43510054-43512939 45.732195 19.02125 223.42
    57 C15orf48 chr15: 43510054-43512339 45.549287 21.28355 248.097
    58 EFNA3 chr1: 153317971-153326638 44.993943 3.68358 70.5016
    59 TU_0043412_0 chr13: 33918267-33935946 44.506741 1.311142 15.1968
    60 TU_0069093_0 chr1: 220878648-220886461 42.645673 1.443496 160.898
    61 UGT1A6 chr2: 234265059-234346684 42.500058 1.937622 45.753
    62 TU_0057051_0 chr18: 54524352-54598419 42.108622 2.418785 56.0712
    63 AMH chr19: 2200112-2203072 41.744334 2.16026 91.244
    64 TU_0120908_0 chr2: 181147971-181168431 41.650097 1.0750564 48.7957
    65 TU_0099873_0 chr8: 128138926-128140075 41.420293 1.51101 38.7353
    66 HN1 chr17: 70642938-70662369 40.495209 16.35625 110.208
    67 TU_0022570_0 chr19: 20341299-20343938 39.984803 2.912835 98.5739
    68 TU_0098937_0 chr8: 95748751-95751321 39.740546 1.4422495 51.5935
    69 TU_0040375_0 chr3: 133280694-133394609 39.664781 2.149005 90.9787
    70 HN1 chr17: 70642938-70662370 39.655603 16.34725 109.587
    71 TU_0120929_0 chr2: 181328093-181423017 39.419483 1.2116475 189.765
    72 TU_0112004_0 chr15: 67644390-67650387 39.300923 6.10665 76.723
    73 TU_0108439_0 chr15: 19293567-19296333 39.131646 1 27.7534
    74 HN1 chr17: 70642938-70662369 39.00893 15.53595 103.782
    75 SULT1C2 chr2: 108271526-108292803 39.007062 1.2259165 91.5617
    76 STX19 chr3: 95215904-95230144 38.954223 4.521255 46.0375
    77 TU_0030420_0 chrX: 112642982-112685485 38.715477 1.0890785 62.9419
    78 TU_0099875_0 chr8: 128138047-128140075 38.489447 1.393413 35.8984
    79 IJBE2T chr1: 200567406-200577717 38.387515 3.070345 85.9738
    80 SULT1C2 chr2: 108271526-108292803 37.817555 1.215033 88.0858
    81 TU_0049429_0 chr4: 109263508-109272353 37.794245 1.09915225 29.1838
    82 STMN1 chr1: 26099193-26105955 37.319869 14.3784 187.062
    83 UGT1A1 chr2: 234333657-234346684 37.267194 1.660554 35.9476
    84 LRRN1 chr3: 3816120-3864387 37.229013 3.8912 137.117
    85 TU_0886631_0 chr5: 113806149-113806936 36.896806 1.0501165 29.6561
    86 ORM2 chr9: 116131889-116135357 36.878688 3.614505 120.139
    87 TU_0084060_0 chr5: 7932238-7932523 36.807599 1 23.1979
    88 TU_0098644_0 chr8: 81204784-81207034 36.779294 1.6013735 64.9663
    89 ACSM1 chr16: 20542059-20610079 36.280896 13.3707 317.077
    90 STMN1 chr1: 26099193-26105231 35.882914 12.73275 164.721
    91 STMN1 chr1: 26099193-26105580 35.823453 14.31935 185.329
    92 TU_0120914_0 chr2: 181265370-181266053 35.551458 1.053468 30.7074
    93 UGT1A7 chr2: 234255322-234346684 35.073998 1.667349 33.4378
    94 TU_0087462_0 chr5: 136386339-136403134 34.992335 1.4450115 27.1703
    95 UGT1A3 chr2: 234302511-234346684 34.952247 1.6889365 33.4202
    96 UGT1A5 chr2: 234286376-234346684 34.950003 1.6639345 33.2718
    97 FOXD1 chr5: 72777840-72780108 34.875512 1.2373575 10.80944
    98 ADM chr11: 10283217-10285499 34.855767 11.83635 276.194
    99 PPFIA4 chr1: 201286933-201314487 34.769924 1.566044 43.9812
    100 UGT1A10 chr2: 234209861-234346690 34.738527 1.652799 32.7318
    101 UGT1A4 chr2: 234292176-234346684 34.663597 1.655824 32.9264
    102 UGT1A9 chr2: 234245282-234346690 34.648086 1.655272 32.852
    103 TU_0090142_0 chr11: 4748677-4760303 34.517072 1.6226305 51.3411
    104 TU_0082746_0 chr12: 120197102-120197416 34.499713 2.531095 59.9026
    105 UGT1A8 chr2: 234191029-234346684 34.433379 1.6498025 32.5849
    106 TU_0112207_0 chr15: 70278422-70286121 34.308752 10.40266 112.274
    107 LOC145837 chr15: 67641112-67650833 34.291574 7.59729 74.8194
    108 TU_0050712_0 chr4: 170217424-170228463 34.23107 1.504313 65.5606
    109 TU_0043410_0 chr13: 33929484-33944669 34.112491 1.393529 24.8401
    110 SNHG1 chr11: 62376035-62379936 33.971989 33.74365 270.512
    111 MUC1 chr1: 153424923-153429324 33.838228 16.3238 664.278
    112 MUC1 chr1: 153424923-153429324 33.828147 15.8436 644.44
    113 TU_0099871_0 chr8: 128138047-128143500 33.697285 1.412872 33.2958
    114 TU_0040383_0 chr3: 133360541-133429262 33.548813 2.553955 85.8384
    115 MUC1 chr1: 153424923-153429324 33.495501 15.91355 627.622
    116 TU_0049202_0 chr4: 102257900-102304755 33.391066 1.5555505 39.7522
    117 TU_0120913_0 chr2: 181254530-181266950 33.188328 1 43.8515
    118 B4GALNT4 chr11: 359794-372116 33.176248 6.3749 80.9639
    119 TU_0100059_0 chr8: 141258835-141260573 33.169029 1.3615865 44.8943
    120 TOP2A chr17: 35798321-35827695 33.132056 1.9725825 34.1032
    121 MUC1 chr1: 153424923-153429324 33.081326 15.9539 632.042
    122 TU_0001265_0 chr6: 27081719-27082291 33.045746 1.3381905 100.5401
    123 C7orf53 chr7: 111908143-111918171 33.024251 2.820945 32.2465
    124 SLC45A2 chr5: 33980477-34020537 32.952911 2.012104 54.8589
    125 TU_0099869_0 chr8: 128138047-128225937 32.928048 1.308804 30.4657
    126 UGT1A6 chr2: 234266250-234346690 32.918772 1.662221 31.4671
    127 TU_0120917_0 chr2: 181265370-181266950 32.796137 1.0771403 36.3557
    128 CACNA1D chr3: 53504070-53821532 32.608994 4.51306 44.9904
    129 UBE2C chr20: 43874661-43879003 32.456813 1.6391285 58.398
    130 ALDOC chr17: 23924259-23928078 32.455953 14.98415 228.812
    131 MUC1 chr1: 153424923-153429324 32.44845 15.5895 599.062
    132 MMP11 chr22: 22445035-22456503 32.411555 3.257735 73.9158
    133 TU_0084303_0 chr5:15899476-15955226 32.39036 2.21168 14.4385
    134 CACNA1D chr3: 53504070-53821532 32.381439 4.484655 44.6867
    135 UBE2C chr20: 43874661-43879003 32.358151 1.705223 57.8559
    136 CACNA1D chr3: 53504070-53821532 32.353332 4.463805 44.2455
    137 FGFRL1 chr4: 995609-1010686 32.275762 26.0133 450.449
    138 FGFRL1 chr4: 996251-1010686 32.075261 27.0148 468.809
    139 FGFRL1 chr4: 995759-1010686 32.069901 26.92945 457.246
    140 MUC1 chr1: 153424923-153429324 32.011017 15.3218 586.058
    141 TU_0099922_0 chr8: 128979617-128981414 31.833339 3.32544 32.6893
    142 TU_0001173_0 chr6: 26385234-26386052 31.823293 2.339595 71.3388
    143 MUC1 chr1: 153424923-153429324 31.781267 15.22945 587.582
    144 TMEM178 chr2: 39746141-39798605 31.614406 13.40605 182.08
    145 UBE2C chr20: 43874661-43879003 31.37539 1.7154185 58.1531
    146 KCNC2 chr12: 73720162-73889778 31.294059 1.8783795 104.225
    147 MAGEC2 chrX: 141117794-141120742 31.286618 1 34.1099
    148 SERHL2 chr22: 41279868-41300332 31.131788 3.670135 61.9969
    149 KCNC2 chr12: 7.3720162-73889778 31.126593 1.868714 108.199
    150 GRAMD4 chr22: 45401321-45454352 31.063732 5.977725 79.8338
  • Table 8 shows the number of cancer-associated lncRNAs nominated for four major cancer types. The number validated is indicated in the column on the right. This table reflects ongoing efforts.
  • TABLE 8
    # of cancer-specific
    in cRNAs nominated # validated to date
    Prostate cancer
    121 11
    Breast cancer 6 6
    Lung cancer 36 32
    Pancreatic cancer 34 0
    • Example 2 SchLAP-1 ncRNA Methods Cell Lines
  • All cell lines were obtained from the American Type Culture Collection (Manassas, Va.). Cell lines were maintained using standard media and conditions. SChLAP-1 or control expressing cell lines were generated by cloning SChLAP-1 or control into the pLenti6 vector (Invitrogen). Stably-transfected RWPE, HME and MCF7 cells were selected using blasticidin (Invitrogen). For LNCAP and 22Rv1 cells with stable knockdown of SChLAP-1, cells were transfected with SChLAP-1 or non-targeting shRNA lentiviral constructs for 48 hours. GFP+ cells were drug-selected using puromycin.
  • RNA Isolation; cDNA Synthesis; and PCR Experiments
  • RNA isolation and cDNA synthesis was performed according standard protocols. Quantitative PCR was performed using Power SYBR Green Mastermix (Applied Biosystems, Foster City, Calif.), using GAPDH and HMBS as housekeeping control genes. The relative quantity of the target gene was completed for each sample using the ΔΔCt method.
    • Murine Intracardiac and Subcutaneous In Vivo Models
  • Intracardiac injection model: 5×105 cells were introduced to CB-17 severe combine immunodeficient mice (CB-17 SCID) at 6 weeks of age. Beginning one week post injection, bioluminescent imaging of mice was performed weekly using a CCD IVIS system with a 50-mm lens (Xenogen Corp.) and the results were analyzed using LivingImage software (Xenogen). Subcutaneous injection model: 1×106 cells were introduced to mice (CB-17 SCID), ages 5-7 weeks, with a matrigel scaffold (BD Matrigel Matrix, BD Biosciences) in the posterior dorsal flank region (n=10 per cell line). Tumors were measured weekly using a digital caliper, and endpoint was determined as a tumor volume of 1000 mm3.
    • Immunoblot Analysis
  • Cells were lysed in RIPA lysis buffer (Sigma, St. Louis, Mo.) supplemented with HALT protease inhibitor (Fisher). Western blotting analysis was performed with standard protocols using Polyvinylidene Difluoride membrane (GE Healthcare, Piscataway, N.J.) and the signals visualized by enhanced chemiluminescence system as described by the manufacturer (GE Healthcare).
  • siRNA Knockdown, Proliferation and Invasion Studies
  • Cells were plated in 100 mM plates at a desired concentration and transfected with 20 uM experimental siRNA oligos or non-targeting controls according to standard protocols. 72 hours post-transfection with siRNA, cells were trypsinized, counted with a Coulter counter, and diluted to 1 million cells/mL. Proliferation assays were performed with a Coulter counter, and invasion of cells through Matrigel (BD Biosciences) was performed according to standard protocols
    • RNA Immunoprecipitation
  • RIP assays were performed using a Millipore EZ-Magna RIP RNA-Binding Protein Immunoprecipitation kit (Millipore, #17-701) according to the manufacturer's instructions.
    • Mayo Clinic Cohort Analyses
  • Formalin-fixed paraffin embedded (FFPE) samples from 235 prostate cancer patients from the Mayo Clinic43 were processed for total RNA using the RNeasy FFPE nucleic acid extraction kit (Qiagen). RNA was subjected to whole-transcriptome amplification using the WT-Ovation FFPE system (NuGen, San Carlos, Calif.), biotin-labelled with the Encore Biotin Module (NuGen), and hybridized to Affymetrix Human Exon (HuEx) 1.0 ST GeneChips (Affymetrix, Santa Clara Calif.). Microarray data was analyzed as detailed previously (Vergara et al. Front Genet. 3, 23, (2012), and SChLAP-1 expression was determined by Partition Around Medoids (PAM) unsupervised clustering using probe selection region 2518129.
    • Statistical Analyses for Experimental Studies
  • All data are presented as means±S.E.M. All experimental assays were performed in duplicate or triplicate. Statistical analyses shown in figures represent Fisher's exact tests or two-tailed Student t-tests, as indicated.
    • Results
  • RNA-Seq has been used to profile >100 prostate cell lines and tissues, including both localized and metastatic prostate cancers (Prensner, et al. Nat Biotechnol 29, 742-749, (2011)). Given that only a fraction of prostate cancers present with aggressive clinical features (Cooperberg et al., J Clin Oncol 23, 8146-8151 (2005)), cancer outlier profile analysis (COPA; Tomlins et al., Tomlins, S. A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor Tomlins et al., Science 310, 644-648, science 310 644-648 (2005)) was performed to nominate intergenic lncRNAs selectively upregulated in a subset of cancers. PCAT-109 and PCAT-114 showed striking outlier profiles and ranked among the best outliers in prostate cancer when compared to protein-coding genes (FIG. 40 a). Notably, both are located in a “gene desert” on Chromosome 2q31.3, a region with previously unknown ties to prostate cancer (FIG. 40 b and FIG. 43).
  • Efforts to validate PCAT-109 by PCR and rapid amplification of cDNA ends (RACE) failed, partly due to the fact that this gene is not robustly expressed in any prostate cell lines (FIG. 40 b and data not shown). By contrast, in the PCAT-114 region, PCR experiments and 5′ and 3′ RACE defined a 1.4 kb, poly-adenylated gene composed of up to seven exons and spanning nearly 200 kb on Ch2q31.3 (FIG. 40 c and FIG. 44). This gene was named Second Chromosome Locus Associated with Prostate-1 (SChLAP-1) after its genomic location. To further characterize this gene, a published ChIP-Seq dataset of prostate cancer (Yu et al. Cancer Cell 17, 443-454 (2010)) was used and it was found that the transcriptional start site (TSS) of SChLAP-1 was marked by tri-methylation of H3K4 (H3K4me3) and its gene body harbored tri-methylation of H3K36 (H3K36me3) (FIG. 40 c), an epigenetic signature consistent with canonical protein-coding genes and lncRNAs (Guttman et al., Nature 458, 223-227 (2009)). PCR assays defined numerous splicing isoforms of this gene of which three (termed isoforms #1, #2, and #3, respectively) constituted the vast majority (>90%) of transcripts in the cell (FIG. 40 d).
  • Using quantitative PCR (qPCR), it was validated that SChLAP-1 was highly expressed in ˜20% of prostate cancers, including metastatic prostate cancer (FIG. 40 e). Moreover, examination of SChLAP-1 expression in an RNA-seq compendium of >600 samples, representing >30 tissue types, demonstrated that SChLAP-1 expression was relatively absent in other tumor types (FIG. 4), demonstrating prostate cancer specific activity. To establish SChLAP-1 as a non-coding gene, three isoforms ( isoforms 1, 2 and 3) were cloned and in vitro translation assays were performed, which were negative. It was also found that SChLAP-1 expression in prostate cell lines was predominantly located in the nucleus (FIG. 400, while most protein-coding mRNAs are located in the cytoplasm, where they engage the ribosomal translation machinery.
  • To elucidate the functional role for SChLAP-1 in prostate cancer, siRNA knockdowns of this gene was performed using two independent siRNAs as well as siRNA to EZH2, which is essential for cancer cell invasion (Kleer, et al. Proc Natl Acad Sci USA 100, 11606-11611, (2003); Varambally, S. et al. Nature 419, 624-629, (2002)) as a positive control. In three prostate cancer cell lines but not breast and lung cancer cells, knockdown of SChLAP-1 dramatically impaired cell invasion in vitro at a level comparable to EZH2 (FIG. 41 a). SChLAP-1 knockdown also impaired cell proliferation in prostate cells but not nonprostate cells. To confirm this phenotype, the three most abundant SChLAP-1 isoforms were overexpressed in RWPE benign immortalized prostate cells at physiologic levels similar to the LNCaP cell line. While SChLAP-1 overexpression did not impact cell proliferation, RWPE cells expressing all three SChLAP-1 isoforms, but not control cells, exhibited the ability to invade through Matrigel model basement membrane matrix in vitro (FIG. 41 b). Overexpression of SChLAP-1 in HME benign breast or MCF7 breast cancer cells did not induce cell invasion, consistent with its prostate-specific expression pattern. These data support a lineage-specific role for SChLAP-1.
  • To characterize specific regions of SChLAP-1 essential for its function, deletion constructs tiling every 250 bp were overexpressed in RWPE cells. Deletion of a single 250 bp region (bp 1001-1250 for SChLAP-1 isoform #1) shared by all three major isoforms abrogated SChLAP-1 mediated invasion in RWPE (FIG. 41 c). In silico modeling with RNAfold22 of the SChLAP-1 RNA structure indicated the presence of a RNA hairpin in this region that is lost specifically in deletion construct #5 (FIG. 41 d), implicating this secondary structure in the function of the molecule.
  • Xenograft analysis of 22Rv1 cells stably knocking down SChLAP-1 further confirmed that this gene is necessary for appropriate cancer cell metastatic seeding in vivo. To test this, intracardiac injection of tumor cells was performed and luciferase signal from mouse lungs and distant metastases was monitored. These experiments showed that 22Rv1 shSChLAP-1 cells displayed impaired metastatic seeding at both proximal (lungs) and distal sites (FIG. 41 e). 22Rv1 shSChLAP-1 cells displayed both fewer gross metastatic sites overall (an average 3.66 metastatic sites in shNT mice vs. 2.07 metastatic sites in shSChLAP-1 #1 and 1.07 sites in shSChLAP-1 #2 mice, p<0.05, Student's t-test) as well as smaller metastatic tumors when they did form (FIG. 41 f). shSChLAP-1 subcutaneous xenografts displayed slower tumor progression in vivo, though this was due to delayed tumor engraftment rather than altered tumor growth kinetics. Together, these in vitro and in vivo data support a prostate-specific role for SChLAP-1 in cancer cell invasion, metastasis, and aggressiveness.
  • To interrogate SChLAP-1 function, microarray profiling of 22Rv1 and LNCaP prostate cancer cells treated with SChLAP-1 or control siRNAs was performed, which revealed 165 upregulated and 264 downregulated genes in a highly significant manner (q-value <0.001), indicating that SChLAP-1 contributes to the positive and negative regulation of numerous genes.
  • After ranking genes according to differential expression by Significance Analysis of Microarrays (SAM) (Tusher et al., Proc Natl Acad Sci USA 98, 5116-5121, (2001)), Proc Natl Acad Sci USA 102, 15545-15550 (2005)) was used to search for enrichment across the Molecular Signatures Database (MSigDB) (Liberzon, A. et al. Bioinformatics 27, 1739-1740, (2011)). Among the highest ranked concepts genes positively or negatively correlated with BRM, an enzymatic subunit of the SWI/SNF chromatin remodeling complex (Roberts et al., Nat Rev Cancer 4, 133-142 (2004)) were observed (FIG. 42 a, left). This gene set was generated through an analysis of the SWI/SNF complex in human prostate cancer samples (Shen, H. et al. Cancer Res 68, 10154-10162, (2008)), making it an attractive biological insight due to the tissue-specific functions of this complex. This analysis was mirrored by generating gene signatures positive and negatively correlated to BRM in the RNA-Seq dataset and the enrichment for SChLAP-1-regulated genes was confirmed (FIG. 42 a, right). SChLAP-1-regulated genes were inversely correlated with both BRM datasets (FIG. 42 a). These results demonstrate that SChLAP-1 and SWI/SNF regulate gene transcription in opposing manners, leading to an antagonism of SWI/SNF activity by SChLAP-1.
  • The SWI/SNF complex operates as a large, multi-protein system that utilizes ATPase enzymatic activity to physically move nucleosomes and, in doing so, regulates gene transcription (Roberts, C. W. & Orkin, S. H. Nat Rev Cancer 4, 133-142, (2004)). Several SWI/SNF complex members are the target of recurrent, inactivating mutations in cancer, including ARID1A (Wiegand, K. C. et al. N Engl J Med 363, 1532-1543, (2010); Jones, S. et al. Science 330, 228-231 (2010)), PBRM1 (Varela, I. et al. Nature 469, 539-542 (2011)), and SNF5 (Versteege, I. et al. Nature 394, 203-206, (1998)), and numerous studies demonstrate that loss of SWI/SNF functionality promotes cancer Progression (Robers et al., supra; Reisman, D., Glaros, S. & Thompson, E. A. Oncogene 28, 1653-1668, (2009)). While SWI/SNF mutations are not commonly observed in prostate cancer, several reports indicate that down-regulation of SWI/SNF complex members, particularly BRM, characterizes some subsets of prostate cancer (Sun, A. et al. Prostate 67, 203-213, (2007); Shen, H. et al. Cancer Res 68, 10154-10162, (2008)), and mice with a prostate-specific BRM deletion exhibit prostatic hyperplasia and castration-resistant cellular proliferation (Shen et al., supra). Thus, antagonism of SWI/SNF activity by SChLAP-1 is consistent with the oncogenic behavior of SChLAP-1 and the tumor suppressive behavior of the SWI-SNF complex.
  • To test whether SChLAP-1 antagonizes SWI/SNF-mediated gene expression regulation, siRNA knockdown of three key components of the SWI-SNF complex: BRM (also known as SMARCA2), BRG1 (also known as SMARCA4), and SNF5 (also known as SMARCB1) was performed. Like BRM, BRG1 serves as an enzymatic subunit of SWI/SNF complex activity, and SNF5 is an essential subunit thought to bind histone proteins (Dechassa, M. L. et al. Mol Cell Biol 28, 6010-6021, (2008)). Knockdown of BRM, BRG1, and SNF5 in two prostate cell lines, 22Rv1 and LNCaP, followed by expression microarray profiling generated highly overlapping sets of up- and down-regulated genes, demonstrating that these factors have broad commonalities in their function in prostate cells. Knockdown of BRM, BRG1 and SNF5 also increased the invasiveness and proliferation rate of 22Rv1 cells, consistent with the role of SWI/SNF in tumor suppression. Comparison of genes commonly regulated by knockdown of all SWI/SNF proteins (BRM, BRG1, and SNF5) to genes regulated by SChLAP1 demonstrated an antagonistic relationship where SChLAP1 knockdown affected the same genes as SWI/SNF but in the opposing direction (FIG. 42 b). These microarray data were used to generate gene signatures for up- and down-regulated genes upon knockdown of each SWI/SNF protein (BRM, BRG1, and SNF5) and SChLAP-1. The significance of the overlap was quantitated using GSEA. Performing this analysis across two cell lines (22Rv1 and LNCaP) showed that SWI/SNF and SChLAP-1 affect gene expression in a highly significant and opposing manner in 23 of 24 total GSEA comparisons (FDR <0.05) (FIG. 42 c). Together, these data demonstrate that SChLAP-1 functions to modulate SWI/SNF complex activity in prostate cancer.
  • To examine the mechanism of SChLAP-1 regulation of the SWI/SNF complex, it was examined whether SChLAP-1 regulated SWI/SNF complex genes themselves. Using Western blots, no change in BRM, BRG1, or SNF5 protein abundance following SChLAP-1 knockdown or overexpression was detected, demonstrating that SChLAP-1 regulates SWI/SNF activity post-translationally. Motivated by reports of lncRNAs coordinating the function of epigenetic complexes through direct RNA-protein binding, RNA immunoprecipitation assays (RIP) were performed for SNF5, a core subunit essential for both BRG1 and BRM function, in 22Rv1 and LNCaP cells. It was found that endogenous SChLAP-1, but not other prostate-specific lncRNAs such as PCA3 and PCAT-1, robustly bound SNF5 protein (FIG. 42 d). RIP for androgen receptor (AR) and SNRNP70, which specifically binds to the U1 snRNP, served as additional negative controls for these experiments (FIG. 42 d).
  • The role of SChLAP-1-SWI/SNF interactions in the functional role of SChLAP-1 in inducing cell invasion was tested by evaluating SChLAP-1-SNF5 binding in the RWPE-SChLAP-1 overexpression model, including overexpression of SChLAP-1 deletion construct #5, which failed to induce cell invasion (FIG. 41 c). Overexpression of both SChLAP-1 isoform #1 and isoform #2 robustly bound to SNF5, whereas deletion construct 5 (which lacks bps 1001-1250 in SChLAP-1 isoform #1) failed to bind SNF5 (FIG. 42 e). As controls, AK093002 and LOC145837, two lncRNAs upregulated in subsets of prostate cancer that are endogenously expressed in RWPE were measured. Control RIP experiments for SNRNP70 demonstrated uniformly strong binding of this protein to U1 in all RWPE cell lines evaluated. Thus, SChLAP-1 regulates SWI/SNF complex activity by directly binding to SWI/SNF proteins through an interaction dependent on base pairs 1001-1250 of the RNA.
  • To explore a potential link between SChLAP-1 and aggressive prostate cancer associations between SChLAP-1 and gene expression phenotypes curated from published microarray profiling data were explored. Given that SChLAP-1 is currently not measured by microarray platforms, a signature of genes with expression significantly correlated or anti-correlated to SChLAP-1 expression in localized tumors was designed and used as a surrogate for SChLAP-1 expression level. The SChLAP-1 signature was examined using Oncomine concept analysis (Rhodes, D. R. et al. Neoplasia 9, 166-180 (2007)) and network representations of the significantly enriched concepts (p-value <1e-6, odds ratio >3.0) were generated. The networks revealed an association with concepts related to prostate cancer progression (FIG. 43 a). Genes positively correlated with SChLAP-1 were over-expressed in metastatic and high-grade localized tumors. Conversely, genes negatively correlated with SChLAP-1 were under-expressed in metastatic and high-grade localized tumors.
  • The analysis was expanded to include four known cancer genes: EZH2, a known metastasis gene (Kleer, C. G. et al. Proc Natl Acad Sci USA 100; 11606-11611, (2003); Varambally, S. et al. Nature 419, 624-629, (2002)) PCA3, a lncRNA biomarker over-expressed in prostate cancer and used in prostate cancer diagnosis (de Kok, J. B. et al. Cancer Res 62, 2695-2698 (2002); Tomlins, S. A. et al. Sci Transl Med 3, 94ra72, (2011)), AMACR, a tissue biomarker of prostate cancer (Rubin et al., JAMA 287, 1662-1670 (2002)), and BRM, a SWI/SNF enzymatic subunit under-expressed in advanced prostate cancer (Shen et al., supra). Control genes were also analyzed: the nucleoporin genes NUP133 and NUP155, as well as B-actin (ACTB). The expression profiles of each of these seven genes was used to derive correlated and anti-correlated gene sets in the same manner as for SChLAP-1.
  • The statistical association between each dataset in the clinical concept compendium was analyzed with the gene signatures derived from correlation analysis, including signatures from the RNA-Seq cohort delineating localized cancer vs. benign tissues, high grade localized prostate cancer (Gleason ≧8 vs. Gleason 6), and metastatic vs. primary tumors. Odds ratios, p-values, and q-values were calculated for each comparison (one-sided Fisher's exact test). A heat-map visualization of statistically significant comparisons (q-value <0.01) confirmed a strong association of SChLAP-1-correlated genes with high-grade and metastatic cancers as well as poor clinical outcomes (FIG. 43 b). In this respect, SChLAP-1 was highly similar to EZH2, the positive control, which is widely associated with aggressive, lethal prostate cancer, whereas PCA3 and AMACR, two biomarkers not associated with disease progression, strongly associated with Cancer vs. Normal concepts but not concepts associated with aggressive disease. Kaplan-Meier analysis of publicly-available datasets for biochemical recurrence (Glinsky et al., J Clin Invest 113, 913-923, (2004)) and overall survival (Setlur, S. R. et al. J Natl Cancer Inst 100, 815-825, (2008)) similarly showed significant associations (log rank test, p<0.01) between the SChLAP-1 signature and more rapid disease recurrence and decreased survival probability.
  • In order to link SChLAP-1 expression with clinical outcomes directly, Affymetrix exon microarrays, which harbor probes mapping to SChLAP-1 exons was used to profile its expression in a prospectively-designed study of 235 high-risk prostate cancer patients who underwent radical prostatectomy between 2000-2006 at the Mayo Clinic (Buerki, C. et al. ASCO Annual Meeting, Abstract #4565 (2012). Nakagawa, T. et al. PLoS One 3, e2318, (2008)). Unsupervised clustering was used to define patients into low and high SChLAP-1 expression groups and the prognostic utility of SChLAP-1 was evaluated with three clinical endpoints: biochemical recurrence (BCR), clinical progression to systemic disease (CP), and prostate cancer-specific mortality (PCSM). At the time of this analysis, patients had a median follow-up of 8.1 years.
  • Kaplan-Meier analyses show SChLAP-1 as a powerful single-gene predictor of aggressive prostate cancer (FIG. 43 c-e). SChLAP-1 expression was highly significant when distinguishing CP and PCSM (p=0.00005 and p=0.002, respectively); patients with high SChLAP-1 expression had 5-year CP- and PCSM-free survival of only 65% and 85%, respectively, compared to 85% and 95% for patients with low SChLAP-1 expression (FIGS. 43 d and 43 e). For the BCR endpoint, high SChLAP-1 expression in patient primary tumor specimens was associated with a rapid median time-to-progression (1.9 vs 5.5 years for SChLAP-1 high and low patients, respectively) (FIG. 43 c). These data demonstrate that SChLAP-1 expression retains its prognostic utility for defining a subgroup of patients more likely to experience BCR, CP, and PCSM even in high-risk patients, where most individuals experienced disease recurrence within ten years post-prostatectomy (FIG. 43 c). To independently validate these findings, the prognostic value of SChLAP-1 for BCR was assessed using qPCR on a University of Michigan cohort and confirmed that SChLAP-1 positive patients are at markedly higher risk for BCR.
  • Multivariable and univariable regression analyses of the Mayo Clinic data demonstrated that SChLAP-1 expression is an independent predictor of prostate cancer aggressiveness with highly significant hazard ratios for predicting BCR, CP, and PCSM (HR or 3.045, 0.563, and 4.339, respectively, p<0.01) which were comparable to other clinical factors such as Gleason score and advanced clinical stage. Finally, receiver-operator curves (ROC) demonstrated the discriminative ability of SChLAP-1 expression in the Mayo Clinic dataset with area-under-the-curve (AUC) values of 0.63, 0.65, and 0.74 for the 5-year prediction of BCR, CP, and PCSM, which were either equivalent to, or slightly higher than, the AUC values for Gleason score (0.59, 0.65, and 0.71, respectively).
  • Thus, these data demonstrate that SChLAP-1 expression either out-performs, or is comparable to, standard clinical parameters such as clinical stage, lymph node invasion, pre-operative serum PSA, surgical margin status (SMS) and Gleason score for the prediction of CP, PCSM, and BCR. The particularly strong prognostic value of SChLAP-1 expression for CP and PCSM is important, as it is known that patients who develop BCR do not necessarily progress further to lethal or clinically significant recurrent disease: that is, many patients who experience BCR nevertheless die with prostate cancer but not from it (Simmons et al., Eur Urol 51, 1175-1184, (2007); Boorjian, S. A. et al. Eur Urol 59, 893-899, (2011)). As such, CP and PCSM represent more stringent criteria to define aggressive prostate cancer. Taken together, the findings indicate that measurement of SChLAP-1 expression in the early development of prostate cancer serves as a valuable biomarker to stratify patient outcomes.
  • To explore this, SChLAP-1 expression was measured in urine sediment RNA from 111 biopsy-confirmed prostate cancer patients with Gleason score. These RNA samples were collected at the time of PSA screening as described previously (Tomlins, S. A. et al. Sci Transl Med 3, 94ra72, (2011)). It was found that SChLAP-1 was significantly higher in Gleason 7 patients vs. Gleason 6 patients (Welch's Two Sample t-test, p=0.01498). These data support the utility of SChLAP-1 as a prognostic screening biomarker for aggressive prostate cancer (Prensner et al., Sci Transl Med 4, 127rv123, (2012)).
  • In conclusion, this example describes a lineage-specific lncRNA that is highly expressed in 15-30% of prostate cancers but not other tissue or cancer types. In the tissue sets, the sensitivity ranges from 20-35% and the specificity ranges from 94-100%. SChLAP-1 is highly expressed in a subset of cancers and is thus a highly specific marker for those cancers. SChLAP-1 directly binds a core subunit in the SWI/SNF complex, leading to reversion of SWI/SNF mediated gene expression (FIG. 44 f). In model systems, SChLAP-1 coordinates prostate cancer cell invasion in vitro and metastatic spread in vivo, and in patient tissue samples SChLAP-1 expression characterizes a metastatic-like gene expression profile associated with high-grade localized prostate cancers and poor clinical outcomes. It was further demonstrated that patients with high SChLAP-1 expression are at markedly increased risk for developing metastatic and lethal prostate cancer.
  • Table 9 shows genes correlated with SChLAP-1.
  • TABLE 9
    locus nearest_ref_id r p qval
    chr12: 57180908-57181574 HSD17B6 −0.546164551 0.001483863 0.063564631
    chr10: 100995269-100995619 HPSE2 −0.529744166 0 0
    chr9: 4585311-4587469 SLC1A1 −0.528631581 0 0
    chr12: 104234726-104234975 NT5DC3 −0.52574655 0 0
    chr1: 85358698-85358896 LPAR3 −0.519067947 0 0
    chr7: 12692212-12693228 SCIN −0.513485431 0 0
    chr1: 204328821-204329044 PLEKHA6 −0.512422441 0 0
    chr22: 31674282-31676066 LIMK2 −0.50924733 0 0
    chr16: 85121881-85127826 KIAA0513 −0.506320229 0 0
    chr11: 126310080-126310239 ST3GAL4 −0.506170919 0 0
    chr2: 102855651-102856462 IL1RL2 −0.499389029 0 0
    chr2: 100759172-100759201 AFF3 −0.498848742 0 0
    chr3: 87039767-87040269 VGLL3 −0.4955607 0.001996514 0.07433842
    chr10: 106058885-106059616 GSTO2 −0.481459111 0 0
    chr18: 78005159-78005429 PARD6G −0.480259815 0.001816685 0.07142087
    chr5: 14692962-14699820 FAM105B −0.478056706 0.001989958 0.07433842
    chr11: 124955849-124959131 SLC37A2 −0.477004111 0 0
    chr11: 134134801-134135749 ACAD8 −0.474921728 0 0
    chr12: 104159806-104160505 STAB2 −0.474825465 0 0
    chr13: 24462816-24463558 MIPEP −0.47377468 0.000330132 0.017740189
    chr15: 89738457-89745591 ABHD2 −0.473687887 0.001901732 0.07290082
    chr16: 22295207-22297954 EEF2K −0.471488569 0 0
    chr6: 159185526-159185908 SYTL3 −0.470902458 0 0
    chr2: 204399833-204400133 RAPH1 −0.469048813 0 0
    chr21: 35987058-35987441 RCAN1 −0.468923289 0 0
    chr2: 242089022-242089679 PASK −0.468525633 0 0
    chr1: 153603987-153604513 S100A1 −0.467663305 0 0
    chr9: 77502739-77503010 TRPM6 −0.466199058 0 0
    chr5: 66458974-66465423 MAST4 −0.464838512 0 0
    chr12: 112247346-112247782 ALDH2 −0.464258794 0 0
    chr20: 33460449-33460663 GGT7 −0.464248542 0 0
    chr16: 84695183-84701292 KLHL36 −0.462458945 0.001623427 0.067166971
    chr5: 55218223-55218678 IL31RA −0.462369779 0 0
    chrX: 63615219-63615333 MTMR8 −0.462171273 0 0
    chr16: 84538206-84538296 KIAA1609 −0.461782241 0 0
    chrX: 18671551-18671749 CDKL5 −0.461589982 0 0
    chr10: 94050682-94050844 CPEB3 −0.461125435 0 0
    chr18: 11908199-11908779 MPPE1 −0.460707259 0 0
    chr3: 189839991-189840226 LEPREL1 −0.459922767 0.002264726 0.074896868
    chr1: 154321315-154323783 ATP8B2 −0.459778607 0 0
    chr4: 100009839-100009952 ADH5 −0.459096821 0 0
    chr2: 202028557-202029033 CFLAR −0.454603271 0 0
    chr11: 130272233-130273133 RP11- −0.453760945 0 0
    121M22.1
    chr4: 106924870-106925184 NPNT −0.453089747 0.001896636 0.07290082
    chr17: 53809031-53809482 TMEM100 −0.452269788 0 0
    chr18: 19102618-19102791 GREB1L −0.45014015 0 0
    chr7: 128461852-128462186 CCDC136 −0.449966828 0 0
    chr4: 113206795-113207059 TIFA −0.44794294 0 0
    chr13: 111955337-111958084 ARHGEF7 −0.447155527 0 0
    chr7: 103086544-103086624 SLC26A5 −0.446130747 0.001571059 0.065901041
    chr2: 199436579-199437305 PLCL1 −0.445732252 0 0
    chr7: 99526462-99527243 GJC3 −0.44536614 0 0
    chr17: 1613360-1613651 TLCD2 −0.444818675 0.001340945 0.059259314
    chr11: 44640598-44641913 CD82 −0.444058521 0 0
    chr11: 134094990-134095348 NCAPD3 −0.443736551 0 0
    chr1: 152297664-152297679 FLG −0.442245082 0 0
    chr18: 8406106-8406859 PTPRM −0.442183213 0 0
    chr11: 74178676-74178774 KCNE3 −0.44185294 0 0
    chr17: 7951703-7952452 ALOX15B −0.440459014 0 0
    chr3: 49213037-49213918 KLHDC8B −0.440313623 0 0
    chr2: 219696460-219696809 PRKAG3 −0.440081326 0 0
    chr14: 23778024-23780968 BCL2L2 −0.438071628 0 0
    chr8: 11182824-11182938 AF131216.6 −0.437271292 0.00048729 0.025803614
    chr14: 77843278-77843396 TMED8 −0.436273666 0.002421059 0.07683164
    chr8: 22926263-22926692 TNFRSF10B −0.433462746 0 0
    chr11: 118550247-118550399 TREH −0.432052092 0 0
    chr8: 22471420-22474170 RP11-582J16.5 −0.431261913 0 0
    chr14: 76668033-76669134 C14orf118 −0.431248632 0 0
    chr7: 83277743-83278479 SEMA3E −0.430438439 0 0
    chr8: 109095151-109095913 RSPO2 −0.428973643 0 0
    chr6: 42931272-42931618 GNMT −0.427598114 0.000130606 0.007299047
    chr1: 24795475-24799466 NIPAL3 −0.426835742 0 0
    chrX: 148713225-148713568 TMEM185A −0.426606945 0 0
    chr6: 52860046-52860176 GSTA4 −0.426487126 0.002511383 0.077005838
    chr11: 4903048-4904113 OR51T1 −0.42646843 0.002258333 0.074896868
    chr20: 45362394-45364965 SLC2A10 −0.426321136 0.002038631 0.074404864
    chr14: 21167513-21168761 RNASE4 −0.425769874 0.00199731 0.07433842
    chrX: 23783663-23784592 ACOT9 −0.424946982 0 0
    chr12: 22218054-22218608 CMAS −0.424346307 0.001493347 0.063820363
    chr13: 114203739-114204542 TMCO3 −0.423927242 0.001408993 0.06151812
    chr7: 127233551-127233665 GCC1 −0.423122614 0 0
    chr1: 168211738-168212378 SFT2D2 −0.422864243 0.001012021 0.048756847
    chr7: 80551580-80551675 SEMA3C −0.421618187 0.000762726 0.03891404
    chr5: 149011544-149014531 ARHGEF37 −0.421113016 0.00166369 0.068211282
    chr6: 125583979-125585553 TPD52L1 −0.420885828 0 0
    chr22: 39190072-39190148 SUN2 −0.420660125 0 0
    chr14: 75201584-75203421 FCF1 −0.420391618 0 0
    chr4: 142133947-142134031 RNF150 −0.420201646 0.002267743 0.074896868
    chr6: 159420466-159421219 RSPH3 −0.419873459 0 0
    chr7: 142637438-142637955 C7orf34 −0.419724438 0.001112591 0.052900521
    chr1: 38019606-38019905 SNIP1 −0.417392665 0 0
    chr12: 112590538-112591407 TRAFD1 −0.416676004 0.001376789 0.060695692
    chr8: 11643471-11644855 NEIL2 −0.415555366 0.000979486 0.047441064
    chrX: 99986990-99987110 SYTL4 −0.4151136 0 0
    chr1: 11865403-11866977 MTHFR −0.414935432 0 0
    chr17: 19578870-19580909 ALDH3A2 −0.414755637 0 0
    chr1: 11322501-11322608 MTOR −0.414459145 0 0
    chr22: 29449566-29453475 ZNRF3 −0.414121517 0 0
    chr6: 3157640-3157809 TUBB2A −0.413596935 0 0
    chr17: 12893348-12894960 ARHGAP44 −0.413315388 0 0
    chr1: 110888929-110889299 RBM15 −0.413119683 0 0
    chr7: 227553-229557 AC145676.2 −0.412677313 0 0
    chr21: 39288186-39288749 KCNJ6 −0.412229747 0.00154936 0.065292417
    chr13: 21635484-21635718 LATS2 −0.412031798 0 0
    chr3: 68981390-68981761 FAM19A4 −0.411387043 0.002212811 0.074896868
    chr17: 56032585-56032684 CUEDC1 −0.411227218 0.000689134 0.035558916
    chr11: 94861540-94865809 ENDOD1 −0.411164472 0 0
    chr9: 5339535-5339873 RLN1 −0.410338259 0.001605749 0.066739616
    chr8: 22291403-22291642 SLC39A14 −0.409172508 0.002273186 0.074896868
    chrX: 2799092-2800859 GYG2 −0.409121519 0 0
    chr5: 10649377-10650308 ANKRD33B −0.408925428 0 0
    chr3: 33138210-33138293 TMPPE −0.408755569 0.002067948 0.074404864
    chr17: 74639589-74639894 ST6GALNAC1 −0.408601974 0 0
    chr4: 108871400-108874613 CYP2U1 −0.408590838 0 0
    chr13: 24476755-24476794 C1QTNF9B −0.4085811 0 0
    chr2: 222438569-222438922 EPHA4 −0.408496252 0.002565861 0.077672883
    chr7: 99573567-99573780 AZGP1 −0.408221377 0.001762692 0.070831349
    chr11: 134188770-134189458 GLB1L3 −0.407453053 0 0
    chr15: 90286522-90286868 WDR93 −0.407011464 0 0
    chr3: 132086547-132087142 ACPP −0.40512191 0 0
    chr1: 154437609-154441926 IL6R −0.404694713 0 0
    chr16: 13328886-13329566 SHISA9 −0.404456273 0.00120856 0.054952728
    chr3: 184999697-184999778 EHHADH −0.404337224 0 0
    chr7: 30168881-30170096 PLEKHA8 −0.404069681 0.001124581 0.053024689
    chr2: 231742722-231743963 ITM2C −0.404000609 0.001502313 0.064052833
    chr15: 43212635-43213007 TTBK2 −0.403995065 0 0
    chr5: 78531633-78531861 DMGDH −0.403410254 0.001386979 0.060862399
    chr8: 105478884-105479281 DPYS −0.403219685 0.006490479 0.118025771
    chr20: 49307662-49308065 FAM65C −0.40278536 0.001873108 0.072385669
    chr16: 46796951-46797158 MYLK3 −0.402096842 0.002040434 0.074404864
    chr12: 27167010-27167367 TM7SF3 −0.401727922 0.003064993 0.083839548
    chr4: 89205557-89205921 PPM1K −0.400464856 0.001268359 0.057164267
    chr6: 160199690-160200144 ACAT2 −0.400341345 0.002969949 0.083014679
    chr2: 179914566-179914813 CCDC141 −0.400161772 0 0
    chr18: 48604625-48611415 SMAD4 −0.4000199 0.002020762 0.074404864
    chr6: 134373515-134373774 SLC2A12 −0.399516711 0 0
    chr2: 239198539-239198743 PER2 −0.398648438 0.001529527 0.064908426
    chr3: 195808701-195809060 TFRC −0.398416367 0.001122515 0.053024689
    chr10: 128994260-128994422 FAM196A −0.397675255 0 0
    chr19: 18474200-18480763 PGPEP1 −0.397511696 0.001654324 0.067980724
    chr12: 89913184-89918583 GALNT4 −0.3971679 0.000720157 0.036845671
    chr8: 27168317-27168836 TRIM35 −0.39698147 0 0
    chr12: 112459953-112461255 ERP29 −0.396890381 0 0
    chr6: 160534453-160534539 IGF2R −0.396621725 0 0
    chr2: 70052587-70053596 ANXA4 −0.396576146 0 0
    chr14: 25518412-25519503 STXBP6 −0.396022636 0.00593713 0.114006188
    chr15: 90358003-90358094 ANPEP −0.39538808 0.001716149 0.069576817
    chr2: 219157188-219157309 TMBIM1 −0.394985318 0.00305971 0.083821279
    chr2: 103459870-103460352 TMEM182 −0.393872182 0 0
    chr1: 24861582-24863506 RCAN3 −0.392511497 0 0
    chrX: 19140559-19140755 GPR64 −0.39247745 0 0
    chr2: 130886644-130886795 POTEF −0.392414695 0.000955249 0.046515259
    chr2: 231911596-231914434 C2orf72 −0.391887127 0 0
    chr8: 142201372-142205907 DENND3 −0.391794001 0.001844172 0.072262867
    chr12: 47226109-47226191 SLC38A4 −0.391782093 0.002190198 0.074896868
    chr4: 8442374-8442450 ACOX3 −0.391346718 0.005560396 0.110932307
    chr17: 65052160-65052913 CACNG1 −0.39017191 0.001934814 0.073518881
    chr22: 34318608-34318829 LARGE −0.390149896 0.002219852 0.074896868
    chr10: 30404295-30404423 KIAA1462 −0.390135064 0 0
    chrX: 12738647-12742642 FRMPD4 −0.390006756 0.002157606 0.074896868
    chr4: 75971372-75975325 PARM1 −0.38979558 0.005925405 0.114006188
    chr21: 47575383-47575481 FTCD −0.389547561 0 0
    chr4: 6619106-6625089 MAN2B2 −0.38950881 0.001332285 0.059043466
    chr16: 4986984-4987136 PPL −0.389314121 0 0
    chr5: 140389211-140391929 PCDHA4 −0.389058019 0 0
    chr1: 150980723-150980854 FAM63A −0.388539406 0.002205328 0.074896868
    chr1: 94312625-94312706 BCAR3 −0.388149966 0 0
    chr3: 48340444-48340743 ZNF589 −0.388018199 0.002300474 0.074896868
    chr11: 62323634-62323719 AHNAK −0.387645912 0.002464434 0.07690982
    chr12: 13366614-13369708 EMP1 −0.387372671 0.001560707 0.065618351
    chr16: 56458984-56459448 AMFR −0.387021554 0.003775885 0.092303358
    chr17: 17875575-17875784 TOM1L2 −0.386445952 0.001581429 0.066031038
    chr10: 115489069-115490662 CASP7 −0.386338815 0.000117675 0.006596685
    chr13: 36871773-36871977 C13orf38 −0.386125524 0 0
    chr10: 73610938-73611126 PSAP −0.386051278 0 0
    chr12: 63543646-63544722 AVPR1A −0.385980337 0 0
    chrX: 70321926-70323385 FOXO4 −0.385961192 0 0
    chr6: 149394968-149398126 UST −0.385088054 0.000264232 0.014369004
    chr12: 6346928-6347427 CD9 −0.385058406 0.002081356 0.074416668
    chr20: 52686971-52687304 BCAS1 −0.384835934 0.001858984 0.072287892
    chr6: 36891122-36892331 C6orf89 −0.384372572 0.000705143 0.036281919
    chr18: 55253785-55254004 FECH −0.384344223 0.002210942 0.074896868
    chr12: 108154733-108155049 PRDM4 −0.384286586 0 0
    chr4: 87769891-87770416 SLC10A6 −0.383888948 0 0
    chr4: 166418663-166419472 CPE −0.38344051 0 0
    chr10: 115423569-115423805 NRAP −0.383262593 0.001199197 0.054952728
    chr18: 59560027-59560992 RNF152 −0.382492767 0.002621541 0.078272928
    chr21: 34185901-34186053 C21orf62 −0.382395766 0 0
    chr1: 114515645-114520426 HIPK1 −0.382102457 0.003983912 0.094835898
    chr1: 235813848-235814054 GNG4 −0.382028045 0.006734515 0.120383578
    chr20: 36151068-36152092 NNAT −0.381520055 0 0
    chr4: 141677069-141677274 TBC1D9 −0.381389837 0.007537688 0.126765765
    chr15: 90293739-90294541 MESP1 −0.381319191 0 0
    chr17: 65026581-65029518 CACNG4 −0.380258212 0.003303945 0.085620014
    chr21: 43735402-43735761 TFF3 −0.37982593 0 0
    chrX: 71363102-71363424 NHSL2 −0.379789027 0.003306045 0.085620014
    chr9: 117568082-117568406 TNFSF15 −0.379635338 0.001517712 0.064557866
    chr4: 111563074-111563279 PITX2 −0.379432657 0.003164641 0.084777841
    chr7: 7575380-7575484 COL28A1 −0.379174401 0.003048335 0.083821279
    chr1: 19983358-19984945 NBL1 −0.379105575 0.005009103 0.104695438
    chr17: 7990613-7991022 ALOX12B −0.37885261 0.004112088 0.09575366
    chr4: 114899592-114900883 ARSJ −0.378760672 0.008790649 0.13508
    chr17: 19237268-19240028 EPN2 −0.378663398 0 0
    chr1: 162749901-162750237 DDR2 −0.378539319 0.004597198 0.100359255
    chr10: 117704168-117708503 ATRNL1 −0.378216284 0 0
    chr15: 39887562-39891119 THBS1 −0.378209064 0 0
    chr7: 51384289-51384515 COBL −0.378105277 0 0
    chr7: 6590638-6591067 GRID2IP −0.378036482 0 0
    chr13: 36047925-36050832 MAB21L1 −0.377665681 0.002616639 0.078272928
    chr5: 171433461-171433877 FBXW11 −0.377240049 0.001478969 0.063564631
    chr16: 20911525-20911706 DCUN1D3 −0.377176749 0.001548826 0.065292417
    chr2: 61148897-61150645 REL −0.377068408 0 0
    chr2: 175351600-175351822 GPR155 −0.376758939 0.001703413 0.069486359
    chr4: 110222878-110223813 COL25A1 −0.376530527 0 0
    chr16: 16317255-16317351 ABCC6 −0.376524916 0.002250961 0.074896868
    chr14: 55611833-55612147 LGALS3 −0.376477741 0.001813224 0.07142087
    chr11: 6631692-6632102 ILK −0.376273373 0 0
    chr20: 8000084-8000476 TMX4 −0.37620338 0.002797436 0.080691396
    chr2: 23929350-23931481 KLHL29 −0.375178691 0.003023736 0.0837197
    chr11: 30608288-30608419 MPPED2 −0.375114316 0.002532313 0.077155474
    chr8: 30585046-30585443 GSR −0.375065559 0.000240196 0.013260404
    chr9: 91606384-91611055 C9orf47 −0.375058726 0.001854016 0.072262867
    chr18: 71958981-71959251 CYB5A −0.374903816 0.002292426 0.074896868
    chr10: 43623559-43625799 RET −0.374655986 0.00408246 0.095677062
    chr6: 143266235-143266338 HIVEP2 −0.374655117 0.004838503 0.102307014
    chr11: 74022456-74022702 P4HA3 −0.37407796 0.003297931 0.085620014
    chr1: 184006228-184006863 GLT25D2 −0.373798797 0 0
    chr14: 21161705-21162338 ANG −0.373610746 0.000947353 0.046379462
    chr15: 55581913-55582001 RAB27A −0.372372329 0.004349301 0.09789861
    chr21: 48084206-48085036 PRMT2 −0.372320011 0.002611429 0.078272928
    chr12: 130387805-130388211 TMEM132D −0.372252514 0.002436548 0.07683164
    chr16: 66516774-66519747 AC132186.2 −0.372011859 0 0
    chr3: 119483898-119485949 C3orf15 −0.371762952 0.002076929 0.074404864
    chr11: 71707240-71708643 RNF121 −0.371621829 0 0
    chr16: 71883526-71891231 ATXN1L −0.371120686 0 0
    chr19: 38886119-38886868 SPRED3 −0.370771544 0.002710805 0.07954175
    chr15: 78461263-78464291 IDH3A −0.370762369 0.005599722 0.111134243
    chr17: 42255572-42256451 ASB16 −0.370554636 0.002239895 0.074896868
    chr19: 57351949-57352097 ZIM2 −0.370474327 0.009388443 0.140270167
    chr15: 32695347-32695396 RP13- −0.370325092 0.000183582 0.010196928
    395E19.1
    chr1: 214725657-214725792 PTPN14 −0.369408066 0.005749033 0.112400084
    chr15: 84962535-84966399 CSPG4P5 −0.369128441 0.002286269 0.074896868
    chr18: 19284464-19284766 ABHD3 −0.369063411 0.002353978 0.075673086
    chr3: 113005521-113006303 BOC −0.36895421 0.001134915 0.053127463
    chr22: 30685281-30685616 GATSL3 −0.368746426 0.001870578 0.072385669
    chr15: 42783294-42783336 ZFP106 −0.368565346 0.003731514 0.091793135
    chr19: 48700486-48700877 C19orf68 −0.36851038 0 0
    chrX: 120181461-120183794 GLUD2 −0.368504069 0.003279187 0.085620014
    chrX: 47064319-47065264 INE1 −0.368175848 0.001988041 0.07433842
    chr5: 125930698-125931110 ALDH7A1 −0.367952163 0.002483797 0.076926292
    chr12: 10374385-10375727 GABARAPL1 −0.367831123 0.005297504 0.108851661
    chr1: 209907648-209908295 HSD11B1 −0.367714675 0.003052939 0.083821279
    chr22: 40366908-40369725 GRAP2 −0.367292326 0.003208892 0.085084821
    chr2: 171572768-171574588 SP5 −0.367283441 0.002630479 0.078272928
    chr10: 102745374-102745628 SEMA4G −0.366880776 0 0
    chr11: 33757927-33757991 CD59 −0.366726455 0.003215396 0.085133002
    chr16: 69152257-69152622 HAS3 −0.366420617 0.00095903 0.046574504
    chr9: 119158787-119164601 PAPPA −0.365815146 0.00627853 0.116920758
    chr2: 227659704-227664475 IRS1 −0.365509755 0.002014141 0.074404864
    chr19: 46148530-46148726 EML2 −0.364924449 0 0
    chr21: 38639538-38640262 DSCR3 −0.364678478 0.004475788 0.098672627
    chr7: 79082335-79082890 MAGI2 −0.364612272 0.005047787 0.105261723
    chr12: 102079359-102079796 MYBPC1 −0.364376297 0.007651984 0.127947875
    chr12: 57350933-57351418 RDH16 −0.364373561 0.004448539 0.098538814
    chr15: 42500278-42500514 VPS39 −0.364232582 0.002353503 0.075673086
    chr14: 81864638-81864927 STON2 −0.364230778 0.004382182 0.098116492
    chr7: 91771776-91772266 CYP51A1 −0.364210127 0 0
    chr3: 159614511-159615149 SCHIP1 −0.364186792 0.002167089 0.074896868
    chr2: 238820169-238820756 RAMP1 −0.363626284 0.00164314 0.067674286
    chr22: 36054661-36057404 APOL6 −0.363509609 0.00456657 0.099888173
    chr12: 78604177-78606790 NAV3 −0.363115626 0.003889133 0.094210495
    chr15: 71407467-71407839 CT62 −0.362619907 0.000302258 0.016339042
    chr1: 182359631-182361341 GLUL −0.362222252 0.00311835 0.084283617
    chr6: 144385587-144385735 PLAGL1 −0.36221699 0.006059476 0.11560742
    chr18: 57364443-57364574 CCBE1 −0.361989182 0.001160655 0.0540538
    chr9: 108536145-108538893 TMEM38B −0.36183798 0.003196865 0.085052362
    chr7: 121784214-121784334 AASS −0.361635356 0.001030161 0.049499517
    chr2: 230135729-230136001 PID1 −0.361364734 0.007876988 0.129133025
    chr4: 37687821-37687998 RELL1 −0.361328155 0.004421037 0.098285551
    chr16: 69166386-69166487 CHTF8 −0.360655997 0.00397391 0.094764506
    chr1: 184943433-184943682 FAM129A −0.360529444 0.003171679 0.084841251
    chr12: 56112874-56113871 BLOC1S1 −0.360332424 0.002460351 0.07690982
    chr5: 40691880-40693837 PTGER4 −0.360302037 0 0
    chr20: 48098450-48099184 KCNB1 −0.360156699 0.005928121 0.114006188
    chr14: 91282518-91282761 TTC7B −0.36000688 0.002911014 0.08228265
    chr2: 169721343-169722024 NOSTRIN −0.359423859 0.002183004 0.074896868
    chr19: 47290656-47291851 SLC1A5 −0.358711445 0 0
    chr2: 111875192-111875799 ACOXL −0.358659464 0.00272735 0.079641256
    chr7: 84815993-84816171 SEMA3D −0.358554714 0.008937979 0.1364206
    chr16: 75528837-75529282 CHST6 −0.358161822 0 0
    chr1: 46216268-46216322 IPP −0.358130707 0.002061859 0.074404864
    chr15: 30706317-30706463 AC019322.1 −0.35739784 0.003295666 0.085620014
    chr9: 4662297-4665256 PPAPDC2 −0.357393072 0.008539527 0.133479717
    chr14: 23904828-23904927 MYH7 −0.357022956 0.000251827 0.013818534
    chr5: 42887392-42887494 SEPP1 −0.356433723 0.004618262 0.10049394
    chr10: 53455246-53459355 CSTF2T −0.356077989 0.005394785 0.109381082
    chr1: 82456074-82458107 LPHN2 −0.35586493 0.00872594 0.134884462
    chr20: 5170747-5178533 CDS2 −0.355827803 0.001959211 0.074231845
    chr14: 20881563-20881580 TEP1 −0.355558706 0 0
    chr17: 62207335-62207502 ERN1 −0.355198611 0.003341644 0.085969228
    chr22: 24890657-24891042 C22orf45 −0.355112593 0.006216471 0.116920758
    chr7: 148112508-148118090 CNTNAP2 −0.355018684 0.003900583 0.094210495
    chrX: 100786630-100788446 ARMCX4 −0.354773706 0.001780023 0.071212674
    chr9: 100845127-100845357 NANS −0.354741743 0.00322612 0.085267223
    chr11: 85338261-85338966 DLG2 −0.35458979 0.007531741 0.126765765
    chr10: 36810648-36813162 NAMPTL −0.354542215 0.003272356 0.085620014
    chr3: 51418480-51421629 DOCK3 −0.354499487 0.009000821 0.136900167
    chr11: 119170204-119177651 CBL −0.354474684 0 0
    chr7: 92465791-92465908 CDK6 −0.354190236 0.007309538 0.124777387
    chrX: 110463585-110464173 PAK3 −0.353473303 0.00372339 0.091761103
    chr1: 213445866-213448116 RPS6KC1 −0.353132762 0.008090944 0.130860029
    chr1: 203144678-203144941 MYBPH −0.353031224 0 0
    chr12: 110205816-110208312 C12orf34 −0.352927122 0.003855714 0.093875787
    chr1: 54483764-54483856 LDLRAD1 −0.352368395 0.002200147 0.074896868
    chr8: 92052871-92053292 TMEM55A −0.352125583 0.00424435 0.096531516
    chr15: 90890818-90892669 GABARAPL3 −0.352096621 0.004075199 0.09564239
    chr5: 126801297-126801429 MEGF10 −0.351979071 0.005769117 0.112671479
    chr7: 66273872-66276446 KCTD7 −0.351787458 0.008500777 0.133361292
    chr12: 101521638-101522419 ANO4 −0.351661205 0.00536422 0.109252525
    chr6: 3231790-3231964 TUBB2B −0.350836048 0.00415823 0.095871025
    chr14: 76446884-76448092 TGFB3 −0.350820631 0.007016608 0.121921113
    chr2: 178972980-178973081 PDE11A −0.350337632 0.005792206 0.113000905
    chr11: 114121047-114121398 ZBTB16 −0.349982548 0.007051836 0.122091644
    chr3: 97471032-97471304 EPHA6 −0.349748772 0.004669226 0.100960902
    chr18: 72775105-72777628 ZNF407 −0.349595533 0.011713078 0.154835981
    chr17: 40540296-40540449 STAT3 −0.349348115 0 0
    chr16: 90095315-90096309 C16orf3 −0.349062505 0.002890689 0.082124567
    chr17: 76899215-76899297 AC100788.1 −0.349055229 0.004954969 0.104163323
    chr2: 11780416-11782914 GREB1 −0.348390425 0.004885601 0.103182756
    chr3: 169487108-169487683 AC078802.1 −0.348375436 0.006616271 0.118981508
    chr15: 64126025-64126147 HERC1 −0.348284478 0.004634897 0.10069813
    chr7: 102301592-102301847 RP11-577H5.4 −0.348203645 0 0
    chr2: 169764077-169766505 G6PC2 −0.347521745 0.000531991 0.027845969
    chr10: 127697622-127698161 FANK1 −0.346440794 0.003260067 0.085620014
    chr1: 68153343-68154021 GADD45A −0.346346476 0.008456687 0.133216661
    chr14: 93651154-93651260 MOAP1 −0.34606439 0 0
    chr9: 102625901-102629173 NR4A3 −0.346030498 0.004972561 0.10429172
    chr20: 42939615-42939809 FITM2 −0.345997257 0.004756964 0.101816018
    chr2: 239139841-239140318 AC016757.3 −0.3458947 0.004187488 0.096032
    chr4: 175443509-175444305 HPGD −0.345861904 0.002242854 0.074896868
    chr1: 24740163-24743424 C1orf201 −0.345686354 0.005986125 0.114759271
    chr1: 113499460-113499635 SLC16A1 −0.345488279 0.009716079 0.142148692
    chr10: 14816251-14816896 FAM107B −0.345316938 0.001800119 0.071315614
    chr12: 85429981-85430055 TSPAN19 −0.345103145 0.006226591 0.116920758
    chr16: 88634958-88636548 C16orf85 −0.345097604 0.001129539 0.053024689
    chr4: 100212053-100212185 ADH1A −0.344998373 0.004254851 0.096531516
    chr8: 1728415-1734738 CLN8 −0.344633185 0.010423843 0.14552518
    chr11: 67124213-67124443 POLD4 −0.344486773 0.002625331 0.078272928
    chr14: 102964439-102968809 TECPR2 −0.344287946 0.00249821 0.076926292
    chr19: 45826078-45826233 CKM −0.344265976 0.002432096 0.07683164
    chr6: 20212366-20212670 MBOAT1 −0.343916793 0.005876217 0.113663186
    chr9: 130869307-130871524 SLC25A25 −0.343624793 0 0
    chr9: 86258343-86259045 C9orf103 −0.343444827 0.002600596 0.078272928
    chr11: 626020-626078 CDHR5 −0.343187787 0.008441373 0.133216661
    chr16: 88729418-88729518 MVD −0.343137668 0.004619966 0.10049394
    chr12: 52470569-52471278 C12orf44 −0.343056136 0.000630237 0.032893644
    chr3: 143767509-143767561 C3orf58 −0.342328768 0.006331044 0.117217889
    chr16: 76592386-76593135 CNTNAP4 −0.342102919 0.000790908 0.040014672
    chr6: 139113885-139114456 CCDC28A −0.341986012 0.006517637 0.118025771
    chr17: 33513317-33516364 UNC45B −0.341937241 0.003818629 0.093222797
    chr10: 135336774-135337062 RP11- −0.341903564 0.006813291 0.120821721
    108K14.4
    chr2: 242162600-242164792 ANO7 −0.341869694 0.007132564 0.123028262
    chr4: 7940727-7942023 AC097381.1 −0.341732589 0.008108444 0.131026389
    chr19: 35614344-35615227 FXYD3 −0.341197928 0.006740632 0.120383578
    chr10: 81373492-81375197 SFTPA1 −0.341146486 0.001850992 0.072262867
    chr11: 125301061-125303285 PKNOX2 −0.341144084 0.003301426 0.085620014
    chr8: 27401960-27403081 EPHX2 −0.34107733 0.004448705 0.098538814
    chr16: 81411019-81413940 GAN −0.341026233 0.002661769 0.078610908
    chr2: 179695391-179695529 TTN −0.340871763 0.003439286 0.087240779
    chr3: 49761030-49761384 GMPPB −0.340818196 0.006392303 0.117755656
    chr11: 125366403-125369424 AP000708.1 −0.340419481 0.007994613 0.12969294
    chr8: 27337285-27337400 CHRNA2 −0.340317829 0.01017339 0.143603022
    chr6: 170713850-170716153 FAM120B −0.340145296 0.006394353 0.117755656
    chr19: 52034835-52035110 SIGLEC6 −0.339935646 0.00249674 0.076926292
    chr2: 169952053-169952677 DHRS9 −0.339663644 0 0
    chr8: 121825324-121825513 SNTB1 −0.339220559 0.013026815 0.159180228
    chr10: 61122866-61122939 FAM13C −0.339116788 0.012107259 0.155429477
    chr7: 98030113-98030380 AC093799.1 −0.339089857 0.002803296 0.080691396
    chr5: 131630870-131631008 P4HA2 −0.338862866 0.004018835 0.095037797
    chrX: 112083679-112084043 AMOT −0.338743263 0.009557513 0.141580566
    chr3: 113346492-113348425 SIDT1 −0.338182328 0.016461828 0.175467239
    chr1: 111893880-111895635 C1orf88 −0.337856332 0.00901587 0.136919096
    chr13: 111521577-111522162 C13orf29 −0.33775445 0.002559298 0.077611339
    chr1: 201860927-201861434 SHISA4 −0.337716435 0.002153764 0.074896868
    chr11: 134019040-134021896 JAM3 −0.337708293 0.002445067 0.07690982
    chr7: 49951629-49952138 VWC2 −0.33764517 0.005162659 0.106835773
    chr12: 46663762-46663800 SLC38A1 −0.33763681 0.009933718 0.143081782
    chr17: 71258247-71258491 CPSF4L −0.337524821 0.006504807 0.118025771
    chr1: 156108870-156109880 LMNA −0.337501786 0 0
    chr19: 30205813-30206364 C19orf12 −0.337294662 0.009407927 0.140292428
    chr7: 134264258-134264592 AKR1B15 −0.337020674 0.005585004 0.111106714
    chr7: 4897363-4901625 PAPOLB −0.336643583 0.009833222 0.142636167
    chr2: 11317862-11319000 PQLC3 −0.33652056 0.013477235 0.162218034
    chr14: 39900767-39901704 FBXO33 −0.336362403 0.004102791 0.09575366
    chr9: 131703723-131704320 PHYHD1 −0.336138287 0 0
    chr1: 221915322-221915518 DUSP10 −0.33590192 0.012733827 0.158213348
    chr3: 41301355-41301587 CTNNB1 −0.335633668 0.006267131 0.116920758
    chr4: 31144094-31144728 PCDH7 −0.335237096 0.005140064 0.106574171
    chr1: 203765436-203769686 ZBED6 −0.335082465 0.003469323 0.087293121
    chr19: 3543826-3544028 C19orf71 −0.334820013 0.004225675 0.096464363
    chr22: 43117170-43117304 A4GALT −0.33461522 0 0
    chr15: 99791359-99791422 TTC23 −0.334607361 0.009988191 0.143216183
    chr16: 5064859-5069156 SEC14L5 −0.334522135 0 0
    chr5: 32786339-32787256 NPR3 −0.334311711 0.005412112 0.10946569
    chr2: 160918805-160919121 PLA2R1 −0.334063845 0.005422954 0.109562966
    chr4: 108955394-108956331 HADH −0.334047223 0.005989748 0.114759271
    chr3: 14814297-14814541 C3orf20 −0.333760773 0.004507549 0.099237103
    chr20: 55100838-55100981 GCNT7 −0.333749414 0.008434475 0.133216661
    chr10: 43762292-43762367 RASGEF1A −0.333319387 0.001430906 0.06194304
    chr5: 80561957-80562216 CKMT2 −0.333284313 0.005483096 0.109968839
    chr6: 41031839-41032465 APOBEC2 −0.333213576 0.004677515 0.10098106
    chr9: 5304369-5304969 RLN2 −0.333058195 0.005460123 0.109968839
    chr1: 181057637-181059977 IER5 −0.332972834 0 0
    chr12: 50236168-50236912 BCDIN3D −0.332717732 0.007849382 0.129133025
    chr14: 95942014-95942173 C14orf49 −0.332614322 0.008380922 0.133216661
    chr13: 24247510-24250232 TNFRSF19 −0.332405917 0.0118646 0.155153269
    chr3: 38178355-38178733 ACAA1 −0.332380373 0.005375471 0.109333343
    chr10: 62761156-62761198 RHOBTB1 −0.332293978 0.008639609 0.134263631
    chr14: 24114350-24114848 DHRS2 −0.332200435 0.009216563 0.138576518
    chr19: 53077329-53077383 ZNF808 −0.332184126 0.004142985 0.095871025
    chrX: 67944146-67945684 STARD8 −0.332156945 0.005297851 0.108851661
    chr22: 17612504-17612994 AC006946.15 −0.332029863 0.002076087 0.074404864
    chr15: 100273489-100273766 LYSMD4 −0.33196355 0.004818502 0.102159863
    chr19: 57802066-57805436 ZNF460 −0.331805696 0.0062541 0.116920758
    chr1: 110052041-110052360 AMIGO1 −0.331748977 0.007140297 0.12304479
    chr19: 40931773-40931932 SERTAD1 −0.331603747 0.004097877 0.09575366
    chr1: 235667440-235667781 B3GALNT2 −0.331355681 0.006921811 0.121704609
    chr5: 180631588-180632293 TRIM7 −0.331070531 0.00478817 0.102074564
    chr7: 134849169-134850650 TMEM140 −0.330961226 0.006462905 0.118025771
    chr1: 203054618-203055164 MYOG −0.330806046 0 0
    chr22: 24836550-24838328 ADORA2A −0.330604462 0.009903173 0.143081782
    chr14: 59950207-59951148 C14orf149 −0.330342745 0.011107988 0.150003266
    chr17: 62833173-62833243 AC103810.1 −0.330067269 0.004228881 0.096464363
    chr3: 159614511-159615155 IQCJ-SCHIP1 −0.329859948 0.000512092 0.026881861
    chr22: 43411026-43411151 PACSIN2 −0.329641143 0.00529232 0.108851661
    chr3: 143566989-143567373 SLC9A9 −0.329499509 0.00957653 0.141580566
    chr6: 147705849-147708707 STXBP5 −0.329411447 0.005615759 0.111134243
    chr10: 43991463-43991517 ZNF487P −0.329209459 0.004820294 0.102159863
    chr6: 123384818-123385612 CLVS2 −0.328460279 0.004405369 0.098228128
    chr2: 168114366-168116263 XIRP2 −0.328456174 0.001905952 0.07290082
    chr11: 70281131-70282690 CTTN −0.328378509 0.005485425 0.109968839
    chr1: 39876150-39882154 KIAA0754 −0.328304607 0.009074575 0.137166781
    chr21: 47648347-47648738 LSS −0.32811765 0.006302121 0.116920758
    chr8: 75233143-75233563 JPH1 −0.327851537 0.005395884 0.109381082
    chr17: 46135656-46138906 NFE2L1 −0.327788072 0.002131117 0.074896868
    chr3: 196065134-196065374 TM4SF19 −0.327643438 0.004075715 0.09564239
    chr17: 11461070-11462196 SHISA6 −0.327641088 0.003501168 0.08783387
    chr7: 97841565-97842271 BHLHA15 −0.327621915 0.007927854 0.129538147
    chr11: 4730834-4731698 AC103710.1 −0.327522873 0.003710943 0.091703214
    chr10: 75457290-75457639 AGAP5 −0.327417008 0.00230532 0.074904336
    chr2: 204599506-204602557 CD28 −0.327340798 0.003182194 0.084997327
    chr1: 200143090-200146552 NR5A2 −0.327072728 0.000350694 0.01878955
    chr5: 140890513-140892542 PCDHGC3 −0.326986718 0 0
    chr17: 4926762-4931696 KIF1C −0.326823547 0.00581312 0.11307866
    chr2: 182794287-182795465 SSFA2 −0.326707409 0.006909184 0.121600292
    chr6: 159240348-159240444 EZR −0.326642824 0.006782665 0.120633891
    chr8: 12613432-12613582 LONRF1 −0.326542762 0.001910521 0.07290082
    chr11: 111789401-111789574 AP000907.1 −0.326455419 0.006026463 0.115098472
    chr8: 74235147-74237516 RDH10 −0.326283654 0 0
    chr9: 36276890-36277053 GNE −0.326253035 0.007726033 0.128531382
    chr11: 66725792-66725847 PC −0.32597854 0.002534333 0.077155474
    chr14: 23834216-23834961 EFS −0.325910554 0.005541994 0.110736224
    chr17: 46198596-46200105 SNX11 −0.325404034 0.00435117 0.09789861
    chr22: 50450973-50451088 IL17REL −0.325024492 0.006764548 0.120633891
    chr21: 34265885-34266043 C21orf49 −0.324901611 0.003697375 0.091617209
    chr5: 135223720-135224326 SLC25A48 −0.324491441 0.004700972 0.101165586
    chr11: 31451817-31453396 DNAJC24 −0.324035319 0.007961992 0.12969294
    chr16: 69117387-69119083 TMCO7 −0.323930714 0.001996814 0.07433842
    chr11: 5256444-5256600 HBD −0.323415761 0.006496377 0.118025771
    chr11: 60543077-60544205 MS4A15 −0.323306954 0.005827077 0.113194863
    chr19: 34991033-34992085 WTIP −0.323288091 0.003628394 0.09052543
    chr21: 33765077-33765335 URB1 −0.322605234 0.007661761 0.127947875
    chr11: 107590341-107590419 SLN −0.32259301 0.003198302 0.085052362
    chr1: 16332413-16335302 C1orf64 −0.322571114 0.003329308 0.085908111
    chr14: 52793938-52795324 PTGER2 −0.32254401 0.00584014 0.113206474
    chr7: 100734918-100735017 TRIM56 −0.32209346 0.006276926 0.116920758
    chr4: 6302383-6304992 WFS1 −0.321869596 0.006860626 0.121215509
    chr14: 65007185-65009955 HSPA2 −0.321607655 0.004372355 0.098043319
    chr10: 92680757-92681033 ANKRD1 −0.32149868 0.004154414 0.095871025
    chr2: 169887734-169887832 ABCB11 −0.321337647 0 0
    chr2: 100937876-100939195 LONRF2 −0.321330932 0.006819887 0.120821721
    chr3: 9934492-9936033 JAGN1 −0.32116212 0.00609355 0.116013774
    chr7: 1097127-1098897 GPR146 −0.320796122 0.005512112 0.110317975
    chr22: 24236884-24237414 MIF −0.320238374 0.003304999 0.085620014
    chr10: 17171642-17171830 CUBN −0.3201406 0.006228317 0.116920758
    chr11: 70052238-70053496 FADD −0.320086207 0.005320566 0.109004718
    chr10: 120355027-120355160 PRLHR −0.319837349 0.001458704 0.062932162
    chr1: 6674509-6674667 KLHL21 −0.319337027 0.004808398 0.102159863
    chr1: 167095023-167098402 DUSP27 −0.31926543 0.003356573 0.086049007
    chr5: 176730009-176730745 RAB24 −0.319255928 0.003368433 0.086049007
    chr20: 55093142-55093943 C20orf43 −0.319042706 0.006112598 0.116162907
    chr5: 140389211-140391929 PCDHA13 −0.318776843 0.005901557 0.113959318
    chr4: 186320723-186321782 ANKRD37 −0.318309287 0.006407439 0.117791816
    chrX: 138790264-138790386 MCF2 −0.318200097 0.003906063 0.094217569
    chr12: 124242473-124245549 ATP6V0A2 −0.318185391 0.005692545 0.112019177
    chr2: 211179634-211179914 MYL1 −0.318151264 0.004475644 0.098672627
    chr1: 232172439-232177018 DISC1 −0.317969164 0.006350874 0.117465307
    chr9: 99381500-99382112 CDC14B −0.317910194 0.004163307 0.095871025
    chr1: 223175726-223179337 DISP1 −0.317844696 0.003050324 0.083821279
    chr12: 53646601-53648189 MFSD5 −0.317723142 0 0
    chr22: 50050271-50051190 C22orf34 −0.317628122 0.004257102 0.096531516
    chr6: 30523907-30525008 GNL1 −0.317139954 0 0
    chr3: 11596284-11599139 ATG7 −0.3169458 0.002281379 0.074896868
    chr16: 71264464-71264625 HYDIN −0.316806117 0.004731057 0.101554491
    chr11: 125136535-125136741 RP11- −0.316600832 0.003883559 0.094210495
    687M24.6
    chr12: 113797134-113797298 SLC24A6 −0.315121613 0.004109022 0.09575366
    chr11: 66113960-66115163 B3GNT1 −0.314657476 0.00480751 0.102159863
    chr7: 128498389-128499328 FLNC −0.312046294 0.006196778 0.116920758
    chr11: 35441454-35441610 SLC1A2 −0.311887865 0.004570119 0.099888173
    chr20: 61167650-61167971 C20orf166 −0.311455851 0.006090275 0.116013774
    chrX: 37312388-37316548 PRRG1 −0.311450759 0.002311383 0.074967239
    chr6: 3152721-3153812 BPHL −0.311242496 0.003734797 0.091793135
    chr7: 31697884-31698334 CCDC129 −0.311051556 0.002109037 0.074896868
    chr1: 26393826-26394927 TRIM63 −0.309913705 0.005735635 0.112400084
    chr20: 6034475-6034695 LRRN4 −0.309273385 0.001724002 0.069739517
    chr5: 80689806-80689998 ACOT12 −0.308117282 0.003117847 0.084283617
    chr8: 33330581-33330940 FUT10 −0.307474854 0.003443905 0.087240779
    chr1: 182558301-182558391 RNASEL −0.307317477 0.005481298 0.109968839
    chr7: 107443555-107443670 SLC26A3 −0.307261592 0.003057062 0.083821279
    chr10: 76868766-76868976 DUSP13 −0.306383849 0.004406938 0.098228128
    chr19: 54984210-54984411 CDC42EP5 −0.305854117 0.002282771 0.074896868
    chrX: 118699087-118699397 CXorf56 −0.304902726 0.002049412 0.074404864
    chr11: 34492914-34493609 CAT −0.303602311 0.004918322 0.103512716
    chr15: 101454905-101456831 ALDH1A3 −0.303374031 0.005729864 0.112400084
    chr17: 10325246-10325267 MYH8 −0.303265671 0.001915237 0.072927569
    chr1: 45792544-45794347 HPDL −0.302015312 0.005632886 0.111327654
    chr1: 162838442-162838605 C1orf110 −0.300571972 0 0
    chr6: 39869588-39872648 DAAM2 −0.299895021 0.00330218 0.085620014
    chr11: 68855342-68858072 TPCN2 −0.299814629 0.004906377 0.103387608
    chr2: 28634745-28640179 FOSL2 −0.299377859 0.004661807 0.100960902
    chr22: 20137990-20138399 AC006547.14 −0.295216407 0.002654087 0.078584121
    chr19: 4867620-4867780 PLIN3 −0.292601141 0.005346359 0.109247654
    chrX: 152760831-152760978 HAUS7 −0.289026884 0.00546317 0.109968839
    chr7: 54636701-54638773 VSTM2A −0.286077172 0.004209951 0.096303956
    chr5: 180000987-180005405 CNOT6 0.280162496 0.004272958 0.096770254
    chr8: 56685785-56685966 TMEM68 0.280739417 0.004369285 0.098043319
    chr14: 97031291-97033425 PAPOLA 0.28154747 0.002912941 0.08228265
    chr8: 66545953-66546442 ARMC1 0.281785249 0.005362125 0.109252525
    chr15: 49170297-49172190 EID1 0.288853949 0.005164445 0.106835773
    chr1: 226496809-226497570 LIN9 0.291829568 0.004543724 0.099671077
    chr17: 57970057-57970296 TUBD1 0.293182401 0.004441351 0.098538814
    chr4: 148593017-148593195 TMEM184C 0.293710605 0 0
    chr15: 38776455-38779911 FAM98B 0.294672563 0.002073568 0.074404864
    chr20: 47712344-47713489 CSE1L 0.296532783 0.002844634 0.081237547
    chr5: 56558420-56560505 GPBP1 0.297506006 0 0
    chr12: 58350469-58351052 XRCC6BP1 0.298404618 0.005616981 0.111134243
    chr19: 44284854-44285409 KCNN4 0.299794156 0.001595016 0.066445584
    chr17: 30325676-30328064 SUZ12 0.300313931 0.002768918 0.080210303
    chr5: 140698056-140700330 TAF7 0.30034378 0.004413046 0.098228128
    chr1: 185069331-185071740 RNF2 0.300817006 0.002256081 0.074896868
    chr17: 58023911-58027925 RPS6KB1 0.301654892 0.002463315 0.07690982
    chr1: 151881835-151882284 THEM4 0.303048607 0.003891008 0.094210495
    chr3: 196555189-196559518 PAK2 0.304684107 0.00565642 0.111550003
    chr3: 56655559-56655846 CCDC66 0.305496446 0.004722128 0.101500611
    chr9: 130457272-130457460 STXBP1 0.306449217 0.002610067 0.078272928
    chr6: 84418064-84419410 SNAP91 0.306744409 0.00289378 0.082124567
    chr18: 267965-268059 THOC1 0.308452954 0.002246863 0.074896868
    chr11: 126174102-126174213 RP11-712L6.5 0.308555738 0.001968874 0.074231845
    chr1: 92764481-92764544 GLMN 0.309420667 0.005838193 0.113206474
    chr5: 68709857-68710628 RAD17 0.309947634 0.002036157 0.074404864
    chr12: 51566083-51566926 TFCP2 0.310337811 0.002022616 0.074404864
    chr12: 133532828-133532892 ZNF605 0.310370533 0.005741782 0.112400084
    chr3: 69129484-69129559 UBA3 0.311955874 0.004476434 0.098672627
    chr2: 44222912-44223144 LRPPRC 0.311969209 0.005806947 0.11307866
    chr12: 106697789-106698057 CKAP4 0.31330448 0.005323305 0.109004718
    chr19: 11978120-11980306 ZNF439 0.31399977 0.000679969 0.03518595
    chr17: 30714772-30714780 ZNF207 0.314664535 0.004663714 0.100960902
    chr3: 178984436-178984790 KCNMB3 0.315313767 0.000492826 0.026020926
    chr3: 3192223-3192563 TRNT1 0.315943006 0.005904075 0.113959318
    chr2: 37193372-37193615 STRN 0.316227369 0.004355122 0.09789861
    chr19: 34718269-34720420 LSM14A 0.316229966 0.005347198 0.109247654
    chr5: 86708251-86708836 CCNH 0.31651571 0.002288526 0.074896868
    chr19: 12662143-12662327 ZNF564 0.316577163 0.001969925 0.074231845
    chr19: 23941548-23941693 ZNF681 0.316870966 0.003718019 0.091753239
    chr2: 203103162-203103331 SUMO1 0.317470493 0.00313409 0.08454882
    chr11: 85563599-85565986 AP000974.1 0.31748757 0.00585565 0.113386114
    chr14: 39649706-39652422 PNN 0.317832199 0.006385595 0.117755656
    chr8: 142012112-142012315 PTK2 0.318325276 0.003146205 0.084658552
    chr20: 57617753-57617964 SLMO2 0.319001046 0.005278416 0.108821635
    chr13: 47371239-47371367 ESD 0.319016641 0.003463992 0.087293121
    chr21: 40721385-40721573 HMGN1 0.319212709 0 0
    chr7: 79846618-79848718 GNAI1 0.320340043 0.004411903 0.098228128
    chr19: 57764440-57774106 ZNF805 0.320363681 0.005385112 0.109381082
    chr16: 3367189-3368574 ZNF75A 0.320482104 0.002181862 0.074896868
    chr15: 60771201-60771344 NARG2 0.321091259 0.004175977 0.095889084
    chr17: 8286474-8286568 RPL26 0.321101419 0.003760575 0.092052993
    chr6: 168720067-168720434 DACT2 0.321179692 0.002407179 0.076804143
    chr14: 35008760-35008943 EAPP 0.321340899 0.004534668 0.099592725
    chr2: 99921102-99921205 LYG1 0.321471395 0.0062296 0.116920758
    chr13: 41701704-41706882 KBTBD6 0.321594919 0.004173426 0.095889084
    chr5: 140602930-140605858 PCDHB14 0.322104178 0.006233177 0.116920758
    chr12: 75905292-75905416 KRR1 0.322196506 0 0
    chr7: 29552179-29553944 CHN2 0.322296255 0.002750261 0.080052876
    chr19: 19843764-19843921 ZNF14 0.322336899 0.004015145 0.095037797
    chr11: 75851754-75854239 UVRAG 0.322461087 0.005592429 0.111132704
    chr3: 93747210-93747454 STX19 0.322908263 0.006898306 0.121600292
    chr17: 65739858-65740318 NOL11 0.323132613 0.00348465 0.087540376
    chr16: 28331396-28335170 SBK1 0.324007796 0.005584472 0.111106714
    chr11: 125825711-125826214 RP11- 0.324171654 0.007187233 0.123441982
    680F20.6
    chrY: 21765682-21768160 CYorf15B 0.324250683 0 0
    chr15: 59949322-59949740 GTF2A2 0.324886639 0.00679345 0.120633891
    chr8: 141524392-141527236 CHRAC1 0.325103238 0.006576969 0.1185295
    chr1: 46153654-46153785 GPBP1L1 0.325228449 0.00663606 0.119219352
    chr18: 33558797-33559241 C18orf21 0.325286794 0.00452516 0.099504209
    chr19: 35174896-35177302 ZNF302 0.325802707 0.003260401 0.085620014
    chr4: 170192009-170192256 SH3RF1 0.326613568 0.008264705 0.132373754
    chr10: 74927623-74927853 ECD 0.326731314 0.005005407 0.104695438
    chr5: 170738392-170739138 TLX3 0.326740102 0.007724752 0.128531382
    chr2: 217069910-217071026 XRCC5 0.327063734 0.004964977 0.104253046
    chr16: 3458320-3459370 ZNF174 0.32719442 0.005999522 0.114825412
    chr8: 82644987-82645138 ZFAND1 0.327291564 0.004906685 0.103387608
    chr2: 238166072-238166319 AC112715.2 0.327628695 0.006988291 0.121921113
    chr22: 41252434-41253026 ST13 0.327785232 0.006664518 0.119612287
    chr19: 21950228-21950330 ZNF100 0.328529297 7.16E−05 0.00404126
    chr1: 95007092-95007356 F3 0.328897709 0.003923792 0.0943921
    chr12: 72070468-72074419 THAP2 0.328949319 0.000936046 0.045949726
    chr13: 37633616-37633850 FAM48A 0.329201798 0 0
    chr2: 136481506-136482840 R3HDM1 0.329264663 0.004476477 0.098672627
    chr9: 66553673-66555928 RP11- 0.329390698 0.004136364 0.095871025
    262H14.4
    chr13: 41345120-41345309 MRPS31 0.329399968 0.001803178 0.071315614
    chr17: 4994791-4999668 ZFP3 0.329822496 0.00706482 0.122091644
    chr1: 151141461-151142773 SCNM1 0.330275788 0.004023788 0.095037797
    chr11: 32623824-32627808 EIF3M 0.330560474 0.007052809 0.122091644
    chr8: 42029046-42029191 AP3M2 0.330606328 0.005212564 0.107708532
    chr11: 64338450-64340347 SLC22A11 0.330712435 0.003990159 0.094844827
    chr3: 32814948-32815367 CNOT10 0.330830953 0 0
    chrX: 15682840-15683154 TMEM27 0.330831688 0.006114174 0.116162907
    chr19: 36909393-36909558 ZFP82 0.330854448 0.000308635 0.016634253
    chr14: 23240642-23241007 OXA1L 0.330898021 0.009077491 0.137166781
    chr7: 64291828-64294054 ZNF138 0.33092203 0.004247302 0.096531516
    chr14: 30661071-30661104 PRKD1 0.331146193 0.007424771 0.125564356
    chr9: 100777645-100778225 ANP32B 0.331404852 0.008878 0.136076888
    chr6: 10419650-10419892 TFAP2A 0.331452981 0.00775069 0.128531382
    chr15: 23334999-23335196 AC091565.1 0.331545817 0.002559555 0.077611339
    chr17: 58156056-58156292 HEATR6 0.331671707 0.00624891 0.116920758
    chr11: 73964536-73965748 PPME1 0.33178239 0.011463933 0.153440983
    chr19: 56347701-56348128 NLRP11 0.332151069 0.003966634 0.094764506
    chr3: 64009480-64009658 PSMD6 0.332227431 0.004735818 0.101554491
    chr15: 40331293-40331389 SRP14 0.332257211 0.009745137 0.142230949
    chr15: 29409264-29410518 APBA2 0.332585829 0.00820806 0.132028532
    chr10: 60588520-60591195 BICC1 0.332588003 0.005814869 0.11307866
    chr16: 47177489-47177908 NETO2 0.33260473 0.002989626 0.083076103
    chr10: 124713530-124713919 C10orf88 0.332876872 0.002993704 0.083076103
    chr9: 127951840-127952218 PPP6C 0.332984853 0.003994731 0.094844827
    chr1: 151735802-151736040 MRPL9 0.333136616 0.004195675 0.096098418
    chr4: 120325655-120326749 AC110373.1 0.333522527 0.004232896 0.096464363
    chr1: 152020297-152020383 S100A11 0.333566613 0.007853817 0.129133025
    chrX: 24094838-24096088 EIF2S3 0.333582575 0.003071993 0.083904667
    chr2: 207582984-207583120 DYTN 0.333890074 0.014367499 0.165520063
    chr4: 146048677-146050331 ABCE1 0.333925697 0.003089387 0.084000815
    chr2: 109492543-109493034 CCDC138 0.333976981 0.004349929 0.09789861
    chr2: 231989685-231989832 HTR2B 0.334198112 0.004153272 0.095871025
    chr11: 59436353-59436471 PATL1 0.334333206 0.007983468 0.12969294
    chr11: 58384668-58388515 ZFP91 0.334555856 0 0
    chr12: 120315052-120315095 CIT 0.334566849 0.012110335 0.155429477
    chr9: 97090889-97090926 FAM22F 0.334602902 0.008513342 0.133361292
    chr8: 103136797-103137135 NCALD 0.334783433 0 0
    chr2: 99797169-99797521 MITD1 0.33494044 0.001482186 0.063564631
    chr5: 140579182-140582618 PCDHB11 0.335046305 0.003710523 0.091703214
    chr11: 66610639-66610987 C11orf80 0.335296837 0.003954429 0.094764506
    chr12: 93894951-93897545 MRPL42 0.335324039 0.002410305 0.076804143
    chr20: 21695108-21696620 PAX1 0.335448884 0.007190531 0.123441982
    chr5: 134735438-134735604 H2AFY 0.335582907 0.007328985 0.124979581
    chr1: 235611984-235612283 TBCE 0.335596516 0.003395192 0.086368012
    chr19: 51538050-51538486 KLK12 0.335737191 0.00967498 0.142148692
    chr18: 12884071-12884337 PTPN2 0.336004992 0.002423347 0.07683164
    chr9: 19102521-19103117 HAUS6 0.336050358 0.00392889 0.0943921
    chr16: 4322658-4323001 TFAP4 0.336101155 0.005641999 0.111386545
    chr6: 32938355-32938493 HLA-DMA 0.336336244 0.01336062 0.16167151
    chr6: 108508504-108510013 NR2E1 0.336437613 0.012157358 0.155429477
    chr12: 6756489-6756626 ACRBP 0.336450652 0.009063847 0.137166781
    chr11: 3400267-3400448 ZNF195 0.336605687 0.002843888 0.081237547
    chr1: 25558934-25558993 SYF2 0.336667727 0.004644165 0.10077894
    chr7: 16872879-16873057 AGR2 0.336738631 2.81E−05 0.001591309
    chr12: 118405880-118406788 KSR2 0.336775902 0.007835265 0.129133025
    chr19: 56988640-56988770 ZNF667 0.336884962 0.004098152 0.09575366
    chr15: 83209176-83209208 RPS17L 0.336885484 0.003539674 0.08867737
    chr10: 5498550-5500426 NET1 0.33716755 0.005108136 0.10615454
    chr17: 50237283-50237377 CA10 0.337244385 0.008810051 0.135263703
    chr4: 159825617-159829201 FNIP2 0.33761486 0.01001205 0.143216183
    chr5: 159855608-159855748 PTTG1 0.337619827 0.012232275 0.155522345
    chr14: 36982316-36982990 SFTA3 0.337685044 0.009064788 0.137166781
    chr9: 140194082-140196703 NRARP 0.337748136 0.00700953 0.121921113
    chr9: 104499562-104500862 GRIN3A 0.337777935 0.003309214 0.085620014
    chr9: 125084818-125085743 MRRF 0.338049105 0.001250772 0.056511886
    chr3: 167196633-167196792 SERPINI2 0.338488624 0.002335643 0.075350427
    chr5: 98134164-98134347 RGMB 0.338500085 0 0
    chr17: 6920575-6920844 AC040977.1 0.33861797 0.005612306 0.111134243
    chr5: 154393314-154397692 KIF4B 0.33863313 0.006124103 0.116167412
    chr1: 145440852-145442635 TXNIP 0.33868063 0.009449784 0.140634887
    chr2: 113332423-113334673 POLR1B 0.338711651 0.005564022 0.110932307
    chr5: 1886975-1887350 IRX4 0.338712821 0.002923933 0.082464901
    chr2: 74729793-74732192 LBX2 0.338737246 0.010063139 0.14338159
    chr3: 138663065-138665982 FOXL2 0.33877365 0.005017129 0.104742652
    chr9: 88897292-88897676 ISCA1 0.339022749 0.006559848 0.1185295
    chr10: 98273267-98273675 TLL2 0.339042421 0.003673076 0.091389151
    chr2: 30862982-30867091 LCLAT1 0.339179902 0.006299765 0.116920758
    chr3: 197682620-197683481 RPL35A 0.33923522 0.002247057 0.074896868
    chr5: 140571941-140575215 PCDHB10 0.339319919 0.004991115 0.104560114
    chr6: 3982908-3984372 AL138831.1 0.339526883 0.002639458 0.078334109
    chr5: 171221568-171221602 C5orf50 0.339540771 0.004766959 0.101816018
    chr4: 76911848-76912115 SDAD1 0.339847696 0.004162516 0.095871025
    chr1: 92852567-92853730 RPAP2 0.340299513 0.00346415 0.087293121
    chr17: 45899031-45899200 OSBPL7 0.34043401 0 0
    chr16: 81110740-81110818 C16orf46 0.340560273 0.00461508 0.10049394
    chr19: 55325296-55325972 KIR2DL4 0.340589063 0.002577114 0.077883735
    chr5: 114598408-114598569 PGGT1B 0.340742067 0.003243526 0.085503862
    chr6: 37225338-37225931 TMEM217 0.34102065 0.005320913 0.109004718
    chr9: 131456919-131458679 SET 0.34104979 0.00334917 0.086040971
    chr7: 130144779-130146133 MEST 0.341209576 0.002501724 0.076926292
    chr1: 32798617-32799236 HDAC1 0.341243395 0.008437076 0.133216661
    chr7: 117068123-117068177 ASZ1 0.341268169 0.018375867 0.183687882
    chr1: 166818174-166825581 POGK 0.341341081 0.002180119 0.074896868
    chr3: 169801692-169803191 GPR160 0.341411568 0 0
    chr1: 173793699-173793858 CENPL 0.341600458 0.004386422 0.098116492
    chr9: 37356831-37358146 ZCCHC7 0.341832318 0.002878016 0.081933244
    chr6: 153452258-153452384 RGS17 0.341997405 0.007479401 0.126251813
    chr19: 2877270-2878501 ZNF556 0.342151748 0.009710946 0.142148692
    chr6: 150292504-150294844 ULBP1 0.342179031 0.007550635 0.126866028
    chr1: 25824754-25826700 TMEM57 0.342284881 0.004046878 0.095335211
    chr13: 26594025-26599989 ATP8A2 0.342473022 0.004835519 0.102307014
    chr19: 12551725-12551926 ZNF443 0.342588553 0.00297085 0.083014679
    chr1: 146253037-146253110 WI2- 0.342683663 0.012131595 0.155429477
    3658N16.1
    chr16: 18473011-18473188 RP11- 0.342756738 0.007019189 0.121921113
    1212A22.4
    chr6: 74233169-74233520 EEF1A1 0.342860281 0.003454471 0.087293121
    chr2: 102003478-102004057 CREG2 0.342980433 0.007909977 0.129431455
    chr5: 113831591-113832321 KCNN2 0.343097059 0.004322128 0.097640305
    chr22: 24125597-24126503 MMP11 0.343244705 0.006555426 0.1185295
    chr22: 38878500-38879452 KDELR3 0.343585262 0.005483917 0.109968839
    chr14: 64108016-64108125 WDR89 0.343869473 0.002621089 0.078272928
    chr14: 20825209-20826063 PARP2 0.34415271 0.009261923 0.139028346
    chr8: 42229080-42229326 POLB 0.344522366 0.008229294 0.132039458
    chr12: 110318076-110318293 GLTP 0.344549419 0.004690493 0.101059823
    chr11: 114320567-114321001 REXO2 0.344608407 0.007037485 0.122083904
    chr11: 132204939-132206716 NTM 0.344711378 0.005128034 0.106446266
    chr19: 58513763-58514717 ZNF606 0.344730774 0.003193862 0.085052362
    chr10: 12291579-12292588 CDC123 0.344789304 0.005742969 0.112400084
    chr1: 40758116-40759856 ZMPSTE24 0.345388616 0.00276453 0.080210303
    chr12: 53873189-53874945 PCBP2 0.345510005 0.00245255 0.07690982
    chr11: 4673715-4676718 OR51E1 0.345933376 0.003329808 0.085908111
    chr1: 43727512-43727589 EBNA1BP2 0.346047624 0.002367912 0.075986532
    chr12: 104359293-104359486 C12orf73 0.346225796 0.003975695 0.094764506
    chr3: 52029746-52029958 RPL29 0.346304272 0 0
    chr19: 34302695-34306668 KCTD15 0.346487607 0.007147226 0.123047454
    chr12: 102224336-102224716 GNPTAB 0.346582993 0.002656535 0.078584121
    chr1: 186282812-186283694 PRG4 0.347040363 0.001203172 0.054952728
    chr20: 57485737-57486247 GNAS 0.347157354 0.011944047 0.155429477
    chr5: 72875701-72877794 UTP15 0.347177955 0 0
    chr19: 1652298-1652326 TCF3 0.347341283 0.003229855 0.085267223
    chr8: 17104183-17104387 CNOT7 0.347410862 0.003680922 0.091459073
    chr4: 88312012-88312538 HSD17B11 0.347520476 0.008454701 0.133216661
    chr16: 67418772-67419106 LRRC36 0.347808564 0.005934616 0.114006188
    chr12: 70747608-70748773 CNOT2 0.348186738 0.001273157 0.057173139
    chr1: 52552383-52556388 BTF3L4 0.348370433 0.002680623 0.078783422
    chr17: 36294031-36294915 TBC1D3F 0.34873563 0.002667289 0.078646054
    chr22: 31363051-31364284 MORC2 0.348951739 0.003750785 0.092052993
    chr15: 52356098-52358462 MAPK6 0.34926453 0.007410428 0.125555604
    chr10: 50970284-50970425 OGDHL 0.349324408 0.00510169 0.106142027
    chr6: 7417563-7418270 RIOK1 0.349666416 0.007217973 0.12367929
    chr12: 69783926-69784576 YEATS4 0.350000562 0.008141607 0.131445347
    chr13: 100622380-100624163 ZIC5 0.35012692 0.008295958 0.132523738
    chr9: 95244574-95244788 ASPN 0.350256133 0.003759281 0.092052993
    chr8: 101965496-101965616 YWHAZ 0.350510592 0.005746975 0.112400084
    chr20: 55840760-55841685 BMP7 0.350559373 0.002260921 0.074896868
    chr2: 47614696-47614740 EPCAM 0.350697329 0.005088462 0.105988221
    chr9: 139304779-139305061 SDCCAG3 0.350723691 0.003054233 0.083821279
    chr16: 332614-333003 ARHGDIG 0.350753346 0.010006296 0.143216183
    chr19: 19007369-19007488 LASS1 0.351329035 0.010345517 0.145135442
    chr9: 33917015-33920402 UBE2R2 0.351623699 0.003205954 0.085084821
    chr10: 33625122-33625190 NRP1 0.351650511 0.000150014 0.008357973
    chr4: 70079719-70080449 UGT2B11 0.351862854 0.007741352 0.128531382
    chr7: 99679923-99680171 ZNF3 0.352255056 0.010014015 0.143216183
    chr17: 40169357-40169715 DNAJC7 0.352324455 0.001535738 0.065020053
    chr6: 88376735-88377169 ORC3 0.352508512 0 0
    chr1: 2564304-2564481 MMEL1 0.352661402 0 0
    chr17: 74944721-74946465 MGAT5B 0.352666207 0.004035915 0.095200415
    chr19: 52511393-52511483 ZNF615 0.352758492 0.000854457 0.042519208
    chr12: 54678041-54680872 HNRNPA1 0.352793166 0 0
    chr21: 45079266-45079374 HSF2BP 0.352847214 0.003836372 0.093530226
    chr6: 76425100-76427997 SENP6 0.352949584 0.002051473 0.074404864
    chr8: 86129188-86129387 E2F5 0.352950312 0.002863213 0.081639789
    chr16: 19716437-19716880 C16orf62 0.353016377 0 0
    chr1: 148025760-148025863 NBPF14 0.353092408 0.004067093 0.09564239
    chr7: 155255065-155257526 EN2 0.353146057 0.007860271 0.129133025
    chr14: 70826235-70826444 COX16 0.353343863 0.002633087 0.078272928
    chr5: 140588268-140591696 PCDHB12 0.353452742 0.002137676 0.074896868
    chr6: 97345541-97345757 NDUFAF4 0.353576318 0.000829729 0.041516184
    chr19: 21560190-21562104 ZNF738 0.3536571 0.005514988 0.110317975
    chr5: 140557370-140560081 PCDHB8 0.353698505 0.00831499 0.13259453
    chr4: 55161291-55161439 FIP1L1 0.353817549 0.004681278 0.10098106
    chr17: 79771349-79771889 GCGR 0.354035638 0.005445589 0.109898029
    chr19: 52793318-52795977 ZNF766 0.354073875 0.002226165 0.074896868
    chr1: 63788729-63790797 FOXD3 0.354149363 0.005405168 0.109447113
    chr1: 147954634-147955419 PPIAL4A 0.354222847 0.002675456 0.078759014
    chr12: 122496997-122499948 BCL7A 0.354825754 0.002231741 0.074896868
    chr9: 123605014-123605229 PSMD5 0.355144141 0 0
    chr2: 233412778-233415226 TIGD1 0.355197399 0.004022874 0.095037797
    chr22: 49246569-49246724 FAM19A5 0.355373328 0.00336784 0.086049007
    chr17: 41154888-41154956 RPL27 0.355442918 0.002963896 0.083014679
    chr12: 123741359-123742506 C12orf65 0.355530218 0.013002282 0.159180228
    chr6: 31937586-31940069 DOM3Z 0.355568549 0.006009592 0.114897067
    chr17: 5322673-5323000 NUP88 0.355910655 0.002129205 0.074896868
    chr8: 26227649-26230196 PPP2R2A 0.356005328 0.00272447 0.079641256
    chr2: 74734702-74735707 PCGF1 0.356137025 0.006485052 0.118025771
    chr10: 70968355-70968855 SUPV3L1 0.35616511 0 0
    chrX: 70519791-70521018 NONO 0.35629128 0.003965269 0.094764506
    chr2: 44547337-44548633 SLC3A1 0.356342942 0.013472925 0.162218034
    chr7: 87536502-87538856 DBF4 0.356363925 0.006137741 0.116167412
    chr19: 37019120-37019562 ZNF260 0.356458224 0.002725493 0.079641256
    chr1: 149899617-149900236 SF3B4 0.356570693 0.002827474 0.081130196
    chr4: 83822235-83822319 SEC31A 0.35704326 0.003360274 0.086049007
    chr8: 19615360-19615540 CSGALNACT1 0.357581398 0 0
    chr6: 44221225-44221620 HSP90AB1 0.357638149 0.004764199 0.101816018
    chr8: 54934622-54935089 TCEA1 0.357638989 0.003470001 0.087293121
    chr4: 13485699-13485989 RAB28 0.358225721 0.00029466 0.015975864
    chr10: 61665879-61666414 CCDC6 0.358410884 0.004770436 0.101816018
    chr15: 82939013-82939159 RP13-98N21.1 0.358524403 0.003390575 0.086368012
    chr5: 170837530-170838141 NPM1 0.358661212 0.003112663 0.084283617
    chr5: 138665033-138667360 MATR3 0.358905176 0 0
    chr1: 150443036-150449042 RPRD2 0.358931012 0.001044122 0.049906291
    chr19: 39303481-39303740 LGALS4 0.359501829 0.002800501 0.080691396
    chr7: 143002032-143004789 CASP2 0.359779958 0.0052784 0.108821635
    chr14: 64804615-64805317 AL161756.1 0.360196944 0.001852672 0.072262867
    chr17: 44833167-44834830 NSF 0.360685738 0.004164634 0.095871025
    chr11: 114284677-114284925 RBM7 0.360737625 0 0
    chr2: 180725827-180726232 ZNF385B 0.360753689 0.000458772 0.024364569
    chr19: 51587392-51587502 KLK14 0.361259901 0.009570729 0.141580566
    chr19: 52868950-52870375 ZNF610 0.361291389 0.001739732 0.070219452
    chr14: 21737456-21737638 HNRNPC 0.361477927 0.002287559 0.074896868
    chr11: 117155801-117157161 RNF214 0.361847621 0.00250308 0.076926292
    chr13: 79979835-79980612 RBM26 0.36206404 0.00677961 0.120633891
    chr5: 32601110-32604185 SUB1 0.362303909 0 0
    chr6: 53787432-53788919 LRRC1 0.362759243 0.001706266 0.069486359
    chr11: 22644078-22647387 FANCF 0.363489573 0 0
    chr20: 52844491-52844591 PFDN4 0.363560498 0 0
    chr6: 30613671-30614600 ATAT1 0.363580156 0.003898538 0.094210495
    chr16: 70605575-70608820 SF3B3 0.363659853 0.008588833 0.134075072
    chr16: 3355211-3355645 TIGD7 0.363725026 0 0
    chr1: 161135146-161135513 USP21 0.363771581 0.002323203 0.075082439
    chr8: 101733618-101735037 PABPC1 0.364174471 0.002118261 0.074896868
    chr1: 151688094-151689290 CELF3 0.364376964 0.002952999 0.083014679
    chr9: 133376362-133376661 ASS1 0.364697462 0.00725575 0.124092447
    chr12: 3048476-3050306 TULP3 0.364753258 0.006132467 0.116167412
    chr4: 111120255-111120355 ELOVL6 0.364868424 0.003051244 0.083821279
    chr9: 19378705-19380252 RPS6 0.365038972 0.002300966 0.074896868
    chr10: 121302101-121302220 RGS10 0.365192 0.002278591 0.074896868
    chr16: 277240-279462 LUC7L 0.365306003 0.003898555 0.094210495
    chr19: 24309055-24312643 ZNF254 0.365391007 0.00247424 0.076926292
    chrX: 152241317-152243401 AC152006.1 0.365477178 0.002089412 0.074557938
    chr1: 116609639-116612675 SLC22A15 0.365617395 0.005365482 0.109252525
    chr15: 69113036-69113236 ANP32A 0.366537633 0.002497996 0.076926292
    chr11: 6463716-6463847 HPX 0.36658236 0.003082241 0.084000815
    chr17: 4269565-4269969 UBE2G1 0.366624907 0 0
    chr17: 30228554-30228731 UTP6 0.366824192 0.003624029 0.09052543
    chr5: 178157556-178157703 ZNF354A 0.367356176 0.002058499 0.074404864
    chr14: 21464685-21465189 METTL17 0.367400305 0.002197521 0.074896868
    chr1: 144828540-144830302 NBPF9 0.3679992 0.000828298 0.041516184
    chr16: 3284635-3285456 ZNF200 0.368145566 0.004814693 0.102159863
    chr19: 33078158-33078322 PDCD5 0.368297261 0.004138572 0.095871025
    chr1: 17766040-17766220 RCC2 0.36830465 0.006298625 0.116920758
    chr22: 31740317-31742218 PATZ1 0.368414717 0 0
    chr4: 96075698-96079599 BMPR1B 0.368570648 0 0
    chr2: 190339938-190340291 WDR75 0.368575508 0.001803079 0.071315614
    chr15: 52970768-52970820 KIAA1370 0.369520608 0.001991434 0.07433842
    chr3: 62359972-62359999 FEZF2 0.370011496 0.006297319 0.116920758
    chr14: 36789665-36789882 MBIP 0.370390986 0.002395341 0.076596085
    chr9: 131303380-131304567 GLE1 0.370432615 0.001207478 0.054952728
    chr19: 36726560-36729673 ZNF146 0.37076253 0.001797055 0.071315614
    chr11: 76731317-76737841 ACER3 0.371547935 0.002473745 0.076926292
    chr5: 44816544-44820530 MRPS30 0.372171618 0.001169204 0.054060041
    chr20: 50418817-50419014 SALL4 0.372219721 0.002515478 0.077005838
    chr2: 175113179-175113426 OLA1 0.372322556 0 0
    chr11: 43876693-43878167 HSD17B12 0.372729256 0.002281533 0.074896868
    chr6: 111214678-111216916 AMD1 0.372775014 0 0
    chr2: 44999174-44999731 CAMKMT 0.372782137 0.002908212 0.08228265
    chr17: 30380284-30380517 LRRC37B 0.374033979 0.002518387 0.077005838
    chr14: 91883974-91884152 CCDC88C 0.374642963 0.000670737 0.034807417
    chr1: 85514078-85514182 MCOLN3 0.374684625 0.003969808 0.094764506
    chr11: 26744853-26744974 SLC5A12 0.375189064 0.010525668 0.146272153
    chr3: 52089865-52090566 DUSP7 0.375203447 0.002453789 0.07690982
    chr11: 102340904-102341115 TMEM123 0.375721711 0.00219416 0.074896868
    chr6: 27368071-27371683 ZNF391 0.375903341 0 0
    chr7: 19156293-19157295 TWIST1 0.376075851 0.000868692 0.043055081
    chrX: 129063311-129063737 UTP14A 0.376243265 0.002051346 0.074404864
    chr21: 18965469-18965897 CXADR 0.377652362 0 0
    chr5: 68665483-68665840 TAF9 0.37769513 0.00220028 0.074896868
    chr7: 149470196-149470568 ZNF467 0.377842565 0.002987109 0.083076103
    chr14: 89088611-89088615 ZC3H14 0.377843839 0 0
    chr6: 137112847-137113656 MAP3K5 0.378372715 0.003924303 0.0943921
    chr1: 155707947-155708803 DAP3 0.378584615 0 0
    chr12: 118500157-118500235 WSB2 0.378701761 0.003285179 0.085620014
    chr12: 122985186-122985518 ZCCHC8 0.37906625 0 0
    chr20: 13797763-13799067 C20orf7 0.379646265 0.002733521 0.079693317
    chr20: 20693017-20693266 RALGAPA2 0.379953096 0.000392922 0.02099011
    chr17: 27940371-27941779 ANKRD13B 0.379965854 0 0
    chr2: 24991089-24993571 NCOA1 0.380049681 0.003108189 0.084283617
    chr1: 2706067-2706280 TTC34 0.380131608 0.00112532 0.053024689
    chr11: 61136068-61136683 TMEM138 0.380382477 0.002431464 0.07683164
    chr5: 72801016-72801460 BTF3 0.380632257 0.004553657 0.099768482
    chr12: 26277650-26278060 BHLHE41 0.380649557 0.000869967 0.043055081
    chr11: 77348634-77348850 CLNS1A 0.381389378 0 0
    chr11: 64940653-64940715 SPDYC 0.381489194 0.001862618 0.072287892
    chr1: 169555466-169555826 F5 0.382149137 0 0
    chr1: 113212613-113214241 CAPZA1 0.382444099 0 0
    chr11: 118888070-118889401 RPS25 0.38247485 0 0
    chr6: 119228566-119230332 ASF1A 0.382887636 0 0
    chr9: 96082648-96082854 WNK2 0.383066155 0.002147218 0.074896868
    chr16: 48419114-48419361 SIAH1 0.38346374 0 0
    chr6: 117252493-117253326 RFX6 0.383666724 0.003137472 0.08454882
    chr5: 140890513-140892546 PCDHGA1 0.384828032 0 0
    chr1: 203821268-203823252 ZC3H11A 0.385182686 0 0
    chr12: 57125273-57125412 NACA 0.386358061 0.002030959 0.074404864
    chr19: 11849631-11849824 ZNF823 0.386599542 0 0
    chr22: 41255552-41258130 DNAJB7 0.386599867 0 0
    chr9: 86595417-86595569 HNRNPK 0.38694272 0 0
    chr12: 21391912-21392180 SLCO1B1 0.38730007 0 0
    chr4: 165878099-165880274 C4orf39 0.387654409 0 0
    chr13: 53216540-53217919 HNRNPA1L2 0.387659039 0.003340795 0.085969228
    chr7: 16921567-16921611 AGR3 0.387702629 0.003578066 0.089515727
    chr10: 27035261-27035727 PDSS1 0.388612797 0.002981744 0.083076103
    chr12: 15114470-15114662 ARHGDIB 0.388654077 0 0
    chr9: 74525549-74525847 FAM108B1 0.389098607 0 0
    chr4: 77996624-77997158 CCNI 0.389315949 0 0
    chr22: 29137756-29138410 CHEK2 0.389761154 0.00049489 0.026054161
    chr4: 69696317-69696914 UGT2B10 0.390049265 0.00315215 0.08468855
    chr4: 44700560-44702943 GUF1 0.390286785 0.001037899 0.049739741
    chr4: 169931098-169931426 CBR4 0.390480296 0.002223282 0.074896868
    chr1: 46158875-46160115 TMEM69 0.390570946 0.000653249 0.033997013
    chr19: 11494768-11495018 EPOR 0.390666769 0.001169718 0.054060041
    chr6: 32151657-32152101 AGER 0.39120754 0.002536025 0.077155474
    chrX: 51238802-51239448 NUDT11 0.392382255 0 0
    chr11: 1481729-1483919 BRSK2 0.392392838 0.001425388 0.061936163
    chr10: 35927176-35930362 FZD8 0.392659985 0.002373224 0.07602269
    chr5: 34924951-34926101 BRIX1 0.392764346 0.000257339 0.014078459
    chr11: 108810972-108811657 DDX10 0.393686876 0 0
    chr6: 151422661-151423023 MTHFD1L 0.393780109 0 0
    chr5: 179498455-179499118 RNF130 0.39413346 0.002300383 0.074896868
    chr2: 207653542-207657233 FASTKD2 0.395080106 0.002995917 0.083076103
    chr1: 32801547-32801980 MARCKSL1 0.395222571 0 0
    chr15: 58073773-58074960 GRINL1A 0.395317713 0 0
    chr5: 150080493-150080669 RBM22 0.395392528 0.00249879 0.076926292
    chr11: 58345458-58345693 LPXN 0.395428297 0.003088638 0.084000815
    chr1: 167757056-167761156 MPZL1 0.395807291 0 0
    chr1: 154531383-154531504 UBE2Q1 0.395931922 0 0
    chr21: 27107163-27107984 ATP5J 0.395993559 0.001203617 0.054952728
    chr1: 84963111-84963473 RPF1 0.396095665 0 0
    chr14: 20925149-20925933 APEX1 0.396178148 0.001190996 0.05490369
    chr6: 116914142-116918838 RWDD1 0.396503437 0.002228124 0.074896868
    chr9: 33798853-33799230 PRSS3 0.397409769 0 0
    chr9: 74597572-74600970 C9orf85 0.397495381 0 0
    chr11: 62507447-62507756 TTC9C 0.397920759 0 0
    chr6: 47009926-47010099 GPR110 0.397964341 0.002809976 0.080755689
    chr1: 236385090-236385165 GPR137B 0.398121433 0.002838645 0.081237547
    chr6: 107979410-107981357 SOBP 0.39849222 0 0
    chr1: 151220338-151222012 PIP5K1A 0.398670482 0.001578429 0.066031038
    chr12: 21242841-21243179 RP11-545J16.1 0.398687934 0.002064621 0.074404864
    chr1: 154243356-154243986 UBAP2L 0.398763956 0.001640837 0.067674286
    chr2: 9613044-9613230 CPSF3 0.398839677 0.000818676 0.04119004
    chr6: 28097207-28097860 ZSCAN16 0.399313964 0 0
    chr5: 68849396-68853931 OCLN 0.399353915 0 0
    chr1: 183567145-183567381 SMG7 0.399418476 0 0
    chr12: 50492729-50494495 SMARCD1 0.399921615 0 0
    chr10: 33171620-33171802 C10orf68 0.39996233 0 0
    chr7: 23571407-23571660 TRA2A 0.400855902 0.001909912 0.07290082
    chr1: 2520848-2522908 C1orf93 0.401674406 0.000832687 0.041549723
    chr21: 33103975-33104431 SCAF4 0.401930251 0.00367158 0.091389151
    chr6: 30530165-30531500 PRR3 0.402082178 0.003156645 0.08468855
    chr2: 223520734-223521056 FARSB 0.402157653 0.001309609 0.058443307
    chr12: 96437066-96437298 LTA4H 0.402185173 0 0
    chr5: 140041763-140042064 IK 0.402703343 0.001774987 0.071167982
    chr1: 155248165-155248282 CLK2 0.40304566 0.002943221 0.082880196
    chr10: 71871273-71872032 H2AFY2 0.403191879 0 0
    chr13: 103491900-103493885 BIVM 0.40403719 0.000414281 0.022066226
    chr1: 228353174-228353213 C1orf148 0.404051637 0.000953353 0.046515259
    chr2: 42719976-42721237 KCNG3 0.404235536 0.0011298 0.053024689
    chr1: 54879028-54879152 SSBP3 0.404739966 0.001387273 0.060862399
    chr3: 195310748-195311076 APOD 0.405410563 0 0
    chr9: 129458572-129463311 LMX1B 0.406246618 0.002026027 0.074404864
    chr11: 93583577-93583697 C11orf90 0.406962716 0.002608771 0.078272928
    chr12: 56693943-56694176 CS 0.407050318 0 0
    chr22: 44258093-44258398 SULT4A1 0.407538876 0 0
    chr19: 14201749-14201848 SAMD1 0.407614144 0 0
    chr17: 44632896-44633016 LRRC37A2 0.40823187 0.00107377 0.051188688
    chr7: 33148832-33149013 RP9 0.408861449 0 0
    chr19: 20046830-20046860 ZNF93 0.409274151 0 0
    chr15: 77241410-77242601 RCN2 0.409441008 0.001415528 0.061655257
    chr1: 26233278-26233482 STMN1 0.409501544 0 0
    chr1: 222886085-222886552 AIDA 0.410481766 0.00279499 0.080691396
    chr13: 100637576-100639018 ZIC2 0.410515198 0.001274851 0.057173139
    chr2: 181940922-181941312 UBE2E3 0.410818774 0.002071907 0.074404864
    chr8: 97273728-97273838 MTERFD1 0.411514119 0 0
    chr6: 80751835-80752244 TTK 0.412567895 0.000782933 0.039721802
    chr11: 49229843-49230222 FOLH1 0.412864835 0.000915002 0.045038408
    chr11: 18127453-18127638 SAAL1 0.412967343 0.001716101 0.069576817
    chr2: 74718607-74722013 TTC31 0.413386439 0.002320775 0.075082439
    chr2: 172952730-172954405 DLX1 0.413626042 0 0
    chr1: 156051335-156051789 MEX3A 0.414113678 0 0
    chr20: 45985400-45985567 ZMYND8 0.414360157 0.003386848 0.086368012
    chr6: 20490398-20493945 E2F3 0.414889711 0 0
    chr9: 17502548-17503921 CNTLN 0.415096245 0 0
    chr11: 125933120-125933230 CDON 0.415241654 0.003399941 0.086368012
    chr16: 1374730-1377019 UBE2I 0.415614971 0.000805294 0.04062931
    chr4: 85418711-85419603 NKX6-1 0.415770608 0.002969533 0.083014679
    chr1: 2345035-2345236 PEX10 0.415818061 0.00226998 0.074896868
    chr13: 37583320-37583750 EXOSC8 0.41616237 0 0
    chr6: 114332294-114332472 HDAC2 0.41634724 0 0
    chr11: 94730187-94732682 KDM4D 0.416396892 0 0
    chr7: 96639107-96640351 DLX6 0.416500311 0 0
    chr1: 43316593-43318148 ZNF691 0.417052551 0 0
    chr6: 30620387-30620987 C6orf136 0.417479864 0 0
    chr1: 38455541-38456593 SF3A3 0.419671206 0 0
    chr16: 3450944-3451030 ZNF434 0.421275822 0 0
    chr2: 27886195-27886676 SUPT7L 0.421878368 0 0
    chr3: 131221573-131221827 MRPL3 0.422205914 0.004302763 0.097323884
    chr6: 117890782-117891021 DCBLD1 0.422518501 0 0
    chr6: 37298819-37300746 TBC1D22B 0.422672614 0 0
    chr19: 52531494-52531680 ZNF614 0.422808785 0.001307515 0.058443307
    chr12: 76478346-76478813 NAP1L1 0.423706864 0 0
    chr6: 110797724-110797844 SLC22A16 0.424337101 0 0
    chr17: 38290531-38293040 MSL1 0.425415614 0 0
    chr2: 71192087-71192555 ATP6V1B1 0.425997989 0 0
    chr1: 236645566-236648026 EDARADD 0.426385524 0 0
    chr1: 90398625-90402170 LRRC8D 0.4277395 0 0
    chr15: 34880591-34880704 GOLGA8A 0.428326543 0.001214634 0.055015953
    chr17: 27277912-27278789 PHF12 0.428389454 0.001210213 0.054952728
    chr7: 50632981-50633154 DDC 0.428397647 0 0
    chr10: 122348814-122349367 PPAPDC1A 0.428573634 0.002188707 0.074896868
    chr12: 54428061-54429145 HOXC5 0.429414056 0.001786691 0.071315614
    chr3: 63849179-63849579 THOC7 0.429484227 0 0
    chr17: 57351011-57353322 GDPD1 0.430283967 0 0
    chr19: 11529921-11530018 RGL3 0.432861793 7.75E−05 0.004357466
    chr12: 54423414-54424607 HOXC6 0.432933362 0.001968332 0.074231845
    chr6: 107372260-107372546 C6orf203 0.433507583 0.000780773 0.039721802
    chr17: 27169675-27169841 C17orf63 0.43537005 0 0
    chr12: 2113366-2113701 DCP1B 0.438106424 0.002757557 0.080136814
    chr20: 62168437-62168723 PTK6 0.438444953 0.002433076 0.07683164
    chr20: 524315-524482 CSNK2A1 0.438596671 0 0
    chr2: 40006253-40006407 THUMPD2 0.438989821 0 0
    chr1: 38061359-38061540 GNL2 0.439023194 0 0
    chr7: 40899914-40900362 C7orf10 0.439295183 0.001314219 0.058505314
    chr12: 54448633-54449814 HOXC4 0.440488904 0.00162294 0.067166971
    chr2: 86422460-86422893 IMMT 0.440753615 0.000251254 0.013818534
    chr4: 147442769-147443123 SLC10A7 0.441806672 0.001164603 0.054060041
    chr1: 145368440-145370303 NBPF10 0.441846603 0 0
    chr6: 46669594-46672056 TDRD6 0.442466815 0 0
    chr5: 136933886-136934068 SPOCK1 0.443225182 0 0
    chr4: 39529418-39529931 UGDH 0.444185722 0 0
    chr8: 145979576-145981802 ZNF251 0.445163073 0.001145009 0.05346221
    chr11: 381668-382116 B4GALNT4 0.445270209 0 0
    chr5: 68737358-68740157 MARVELD2 0.446183422 0.001432367 0.06194304
    chr1: 150325308-150325671 PRPF3 0.447239122 0 0
    chr3: 53845139-53846490 CACNA1D 0.448853672 0 0
    chr9: 126030714-126030855 STRBP 0.449208753 0 0
    chrX: 109683117-109683461 AMMECR1 0.449831614 0.003696425 0.091617209
    chr5: 74072428-74072737 NSA2 0.450170336 0.000888381 0.043846937
    chr19: 19654489-19657468 CILP2 0.451206343 0 0
    chr22: 19770836-19771116 TBX1 0.45229799 0.00133281 0.059043466
    chr16: 11945264-11945442 RSL1D1 0.453363354 0 0
    chr12: 56509926-56509935 PA2G4 0.453629094 0.001682554 0.068829349
    chr11: 18063910-18063973 TPH1 0.454146123 0.001759224 0.070831349
    chr6: 111137010-111137161 CDK19 0.461218971 0 0
    chr5: 11903928-11904155 CTNND2 0.46164781 0 0
    chr9: 23825803-23826335 ELAVL2 0.461847559 0.001878907 0.072455602
    chr5: 137910926-137911133 HSPA9 0.462177989 0 0
    chr16: 15224943-15225458 PKD1P6 0.463922149 0 0
    chr10: 115991244-115992063 TDRD1 0.464073889 0 0
    chr11: 49059029-49059579 AC084851.1 0.464703457 0.000995607 0.048093643
    chrX: 135962755-135962939 RBMX 0.467663273 0 0
    chr15: 74005274-74006859 CD276 0.469036908 0.001399893 0.061268074
    chr6: 76624529-76629254 MYO6 0.472241272 0 0
    chr6: 105627707-105627870 POPDC3 0.474183404 0 0
    chr1: 224517772-224518089 NVL 0.474352541 0.000217576 0.012048295
    chr9: 93405033-93405386 DIRAS2 0.476231667 0 0
    chr20: 1373477-1373806 FKBP1A 0.477529689 0 0
    chr9: 131262345-131263239 ODF2 0.479887989 0 0
    chr10: 124923335-124924886 BUB3 0.481360778 0.000709825 0.03641962
    chr5: 133304136-133304478 C5orf15 0.481540922 0 0
    chr1: 84855461-84855640 SAMD13 0.483533428 0 0
    chr5: 79865972-79866307 ANKRD34B 0.48535555 0 0
    chr3: 132004083-132004254 CPNE4 0.487204732 0 0
    chr1: 40783259-40783488 COL9A2 0.488099327 0 0
    chr6: 111346605-111347303 RPF2 0.488404844 0 0
    chr12: 82152992-82153332 PPFIA2 0.488405043 0 0
    chr1: 76076724-76076801 SLC44A5 0.48908972 0.00026347 0.014369004
    chr11: 94965320-94965705 SESN3 0.490557941 0 0
    chr5: 102611597-102614361 C5orf30 0.50386609 0 0
    chr1: 166845396-166845564 TADA1 0.508490879 0 0
    chr6: 28200339-28201260 ZNF193 0.511690319 0 0
    chr4: 122617735-122618268 ANXA5 0.516661902 0 0
    chr2: 203630168-203634480 FAM117B 0.517778257 0 0
    chr15: 82554954-82555104 EFTUD1 0.51899271 0 0
    chr6: 46703286-46703430 PLA2G7 0.519577791 0 0
    chr6: 24785865-24786327 GMNN 0.522285573 0 0
    chr3: 175520792-175523428 NAALADL2 0.531051532 0 0
    chr1: 70587462-70589164 LRRC7 0.531438025 0 0
    chr6: 38997880-38998301 DNAH8 0.533275843 0 0
    chr1: 31769457-31769662 SNRNP40 0.533891931 0 0
    chr3: 3886047-3889387 LRRN1 0.539082031 0 0
    chr17: 4545517-4545589 ALOX15 0.542179201 0 0
    chr18: 55143668-55158530 ONECUT2 0.543914583 0 0
    chr18: 63547636-63552376 CDH7 0.547130694 0 0
    chr11: 129728468-129729898 TMEM45B 0.551304803 0 0
    chr17: 38821255-38821393 SMARCE1 0.554810297 0 0
    chr6: 107436293-107436473 BEND3 0.555214105 0 0
    chr1: 180991774-180992047 STX6 0.555781993 0.001806154 0.071315614
    chr9: 114361882-114362135 PTGR1 0.556369465 0 0
    chr3: 193855471-193856521 HES1 0.556473721 0 0
    chr6: 38670746-38670917 GLO1 0.559523889 0 0
    chr2: 71159896-71160576 VAX2 0.561327888 0 0
    chr8: 136668468-136668965 KHDRBS3 0.563811465 0 0
    chr9: 79634570-79635869 FOXB2 0.583315396 0 0
    chr1: 31712340-31712401 NKAIN1 0.590810474 0 0
    chr6: 107780193-107780768 PDSS2 0.595945426 0 0
    chr2: 181780999-181782519 SCHLAP1 1 0 0
    locus pglobal qglobal prank padj
    chr12: 57180908-57181574 2.21E−06 0.002893994 0.000660684 0.001483863
    chr10: 100995269-100995619 4.25E−06 0.003261046 0.000935969 0.000935969
    chr9: 4585311-4587469 4.60E−06 0.003261046 0.001046083 0.001046083
    chr12: 104234726-104234975 4.88E−06 0.003261046 0.001266311 0.001266311
    chr1: 85358698-85358896 5.53E−06 0.003261046 0.001541596 0.001541596
    chr7: 12692212-12693228 6.48E−06 0.003676617 0.00165171 0.00165171
    chr1: 204328821-204329044 6.68E−06 0.003676889 0.001706767 0.001706767
    chr22: 31674282-31676066 8.12E−06 0.004015199 0.001871937 0.001871937
    chr16: 85121881-85127826 8.39E−06 0.004015199 0.001926994 0.001926994
    chr11: 126310080-126310239 8.40E−06 0.004015199 0.001982051 0.001982051
    chr2: 102855651-102856462 9.02E−06 0.004201028 0.002037108 0.002037108
    chr2: 100759172-100759201 9.27E−06 0.004210011 0.002092165 0.002092165
    chr3: 87039767-87040269 1.09E−05 0.004810345 0.002257336 0.002257336
    chr10: 106058885-106059616 1.52E−05 0.00641619 0.002202279 0.002202279
    chr18: 78005159-78005429 1.56E−05 0.006424942 0.00236745 0.00236745
    chr5: 14692962-14699820 1.76E−05 0.007084909 0.002422507 0.002422507
    chr11: 124955849-124959131 1.97E−05 0.007236461 0.002312393 0.002312393
    chr11: 134134801-134135749 2.40E−05 0.008231158 0.002587678 0.002587678
    chr12: 104159806-104160505 2.45E−05 0.008235358 0.002642735 0.002642735
    chr13: 24462816-24463558 2.88E−05 0.009222872 0.002807906 0.002807906
    chr15: 89738457-89745591 2.89E−05 0.009222872 0.003028134 0.003028134
    chr16: 22295207-22297954 3.24E−05 0.009557199 0.002862963 0.002862963
    chr6: 159185526-159185908 3.32E−05 0.009557199 0.002973077 0.002973077
    chr2: 204399833-204400133 4.11E−05 0.010718571 0.003248362 0.003248362
    chr21: 35987058-35987441 4.13E−05 0.010718571 0.003303419 0.003303419
    chr2: 242089022-242089679 4.23E−05 0.01082872 0.003358476 0.003358476
    chr1: 153603987-153604513 4.69E−05 0.011520023 0.00346859 0.00346859
    chr9: 77502739-77503010 5.03E−05 0.012121545 0.003523647 0.003523647
    chr5: 66458974-66465423 5.40E−05 0.012121545 0.003578704 0.003578704
    chr12: 112247346-112247782 5.50E−05 0.012121545 0.003633761 0.003633761
    chr20: 33460449-33460663 5.50E−05 0.012121545 0.003688818 0.003688818
    chr16: 84695183-84701292 6.03E−05 0.012724535 0.004404559 0.004404559
    chr5: 55218223-55218678 6.09E−05 0.012724535 0.00401916 0.00401916
    chrX: 63615219-63615333 6.18E−05 0.012761283 0.004074217 0.004074217
    chr16: 84538206-84538296 6.44E−05 0.013127093 0.004129274 0.004129274
    chrX: 18671551-18671749 6.50E−05 0.013127093 0.004184331 0.004184331
    chr10: 94050682-94050844 6.65E−05 0.0132686 0.004239388 0.004239388
    chr18: 11908199-11908779 6.74E−05 0.013313983 0.004294445 0.004294445
    chr3: 189839991-189840226 7.07E−05 0.013784792 0.0051203 0.0051203
    chr1: 154321315-154323783 7.13E−05 0.013784792 0.004349502 0.004349502
    chr4: 100009839-100009952 7.21E−05 0.013789835 0.004404559 0.004404559
    chr2: 202028557-202029033 9.16E−05 0.016804159 0.004514673 0.004514673
    chr11: 130272233-130273133 9.42E−05 0.016939391 0.00456973 0.00456973
    chr4: 106924870-106925184 9.56E−05 0.017026472 0.005395584 0.005395584
    chr17: 53809031-53809482 9.71E−05 0.017086351 0.004624787 0.004624787
    chr18: 19102618-19102791 0.00010456 0.017905164 0.004734901 0.004734901
    chr7: 128461852-128462186 0.000105283 0.017905164 0.004789958 0.004789958
    chr4: 113206795-113207059 0.000110766 0.018214263 0.004900072 0.004900072
    chr13: 111955337-111958084 0.000113277 0.018370082 0.005010186 0.005010186
    chr7: 103086544-103086624 0.000118707 0.018912891 0.005615812 0.005615812
    chr2: 199436579-199437305 0.000122153 0.019126366 0.0051203 0.0051203
    chr7: 99526462-99527243 0.000124666 0.019242801 0.005175356 0.005175356
    chr17: 1613360-1613651 0.000126503 0.019242801 0.005670869 0.005670869
    chr11: 44640598-44641913 0.00013486 0.020077586 0.005340527 0.005340527
    chr11: 134094990-134095348 0.000136153 0.020105287 0.005395584 0.005395584
    chr1: 152297664-152297679 0.000144867 0.020358172 0.005560755 0.005560755
    chr18: 8406106-8406859 0.000145 0.020358172 0.005615812 0.005615812
    chr11: 74178676-74178774 0.000145712 0.020358172 0.005725926 0.005725926
    chr17: 7951703-7952452 0.000150385 0.020596714 0.005780983 0.005780983
    chr3: 49213037-49213918 0.000150553 0.020596714 0.00583604 0.00583604
    chr2: 219696460-219696809 0.000150821 0.020596714 0.005891097 0.005891097
    chr14: 23778024-23780968 0.000162326 0.021533748 0.005946154 0.005946154
    chr8: 11182824-11182938 0.000166756 0.021533748 0.006331553 0.006331553
    chr14: 77843278-77843396 0.000174114 0.021961395 0.007763035 0.007763035
    chr8: 22926263-22926692 0.000198143 0.024649764 0.006221439 0.006221439
    chr11: 118550247-118550399 0.000206789 0.025550394 0.006276496 0.006276496
    chr8: 22471420-22474170 0.000215369 0.025749707 0.006331553 0.006331553
    chr14: 76668033-76669134 0.000215491 0.025749707 0.00638661 0.00638661
    chr7: 83277743-83278479 0.00021898 0.025995608 0.006441667 0.006441667
    chr8: 109095151-109095913 0.000231367 0.027287785 0.006496724 0.006496724
    chr6: 42931272-42931618 0.000243869 0.027410832 0.006661895 0.006661895
    chr1: 24795475-24799466 0.00024945 0.027410832 0.006661895 0.006661895
    chrX: 148713225-148713568 0.000251178 0.027410832 0.006772009 0.006772009
    chr6: 52860046-52860176 0.00025189 0.027410832 0.008974288 0.008974288
    chr11: 4903048-4904113 0.000252001 0.027410832 0.008809117 0.008809117
    chr20: 45362394-45364965 0.000253538 0.027410832 0.008809117 0.008809117
    chr14: 21167513-21168761 0.00025544 0.027452953 0.008809117 0.008809117
    chrX: 23783663-23784592 0.000269284 0.028436048 0.006992237 0.006992237
    chr12: 22218054-22218608 0.00028048 0.029277918 0.008258548 0.008258548
    chr13: 114203739-114204542 0.0002876 0.029849598 0.008148434 0.008148434
    chr7: 127233551-127233665 0.000296624 0.030160322 0.007212465 0.007212465
    chr1: 168211738-168212378 0.000297236 0.030160322 0.007873149 0.007873149
    chr7: 80551580-80551675 0.000309825 0.030524412 0.007818092 0.007818092
    chr5: 149011544-149014531 0.000312739 0.030524412 0.008974288 0.008974288
    chr6: 125583979-125585553 0.000314397 0.030524412 0.007377636 0.007377636
    chr22: 39190072-39190148 0.00031763 0.030524412 0.007542807 0.007542807
    chr14: 75201584-75203421 0.000321289 0.030617528 0.007597864 0.007597864
    chr4: 142133947-142134031 0.00032197 0.030617528 0.010185542 0.010185542
    chr6: 159420466-159421219 0.000327348 0.030966787 0.007652921 0.007652921
    chr7: 142637438-142637955 0.000329233 0.030983765 0.008423719 0.008423719
    chr1: 38019606-38019905 0.000356182 0.03317611 0.007763035 0.007763035
    chr12: 112590538-112591407 0.000369367 0.0338033 0.009084402 0.009084402
    chr8: 11643471-11644855 0.000381186 0.0338033 0.008699003 0.008699003
    chrX: 99986990-99987110 0.000382884 0.0338033 0.008093377 0.008093377
    chr1: 11865403-11866977 0.000384771 0.0338033 0.008203491 0.008203491
    chr17: 19578870-19580909 0.000386887 0.0338033 0.008258548 0.008258548
    chr1: 11322501-11322608 0.000388904 0.0338033 0.008313605 0.008313605
    chr22: 29449566-29453475 0.000393128 0.033840648 0.008368662 0.008368662
    chr6: 3157640-3157809 0.000399369 0.033903107 0.008423719 0.008423719
    chr17: 12893348-12894960 0.000403186 0.033903107 0.00858889 0.00858889
    chr1: 110888929-110889299 0.00040617 0.033963425 0.008643946 0.008643946
    chr7: 227553-229557 0.000407643 0.033963425 0.008699003 0.008699003
    chr21: 39288186-39288749 0.000413797 0.034004231 0.01040577 0.01040577
    chr13: 21635484-21635718 0.000415622 0.034004231 0.008809117 0.008809117
    chr3: 68981390-68981761 0.000421217 0.034068108 0.011561967 0.011561967
    chr17: 56032585-56032684 0.000423903 0.034068108 0.00930463 0.00930463
    chr11: 94861540-94865809 0.000425781 0.034068108 0.008919231 0.008919231
    chr9: 5339535-5339873 0.000433669 0.034246655 0.010846226 0.010846226
    chr8: 22291403-22291642 0.00045167 0.035043161 0.01222265 0.01222265
    chrX: 2799092-2800859 0.000454498 0.035043161 0.008974288 0.008974288
    chr5: 10649377-10650308 0.000458355 0.035043161 0.009029345 0.009029345
    chr3: 33138210-33138293 0.000460544 0.035043161 0.012057479 0.012057479
    chr17: 74639589-74639894 0.000462776 0.035043161 0.009139459 0.009139459
    chr4: 108871400-108874613 0.000462962 0.035043161 0.009194516 0.009194516
    chr13: 24476755-24476794 0.000463125 0.035043161 0.009249573 0.009249573
    chr2: 222438569-222438922 0.000463739 0.035043161 0.012883334 0.012883334
    chr7: 99573567-99573780 0.000464978 0.035043161 0.011617024 0.011617024
    chr11: 134188770-134189458 0.00047331 0.035377477 0.00930463 0.00930463
    chr15: 90286522-90286868 0.000481285 0.035534876 0.009359687 0.009359687
    chr3: 132086547-132087142 0.000517458 0.037444565 0.009579915 0.009579915
    chr1: 154437609-154441926 0.00052751 0.037486096 0.009634972 0.009634972
    chr16: 13328886-13329566 0.000529298 0.037486096 0.010901283 0.010901283
    chr3: 184999697-184999778 0.000530546 0.037486096 0.009745086 0.009745086
    chr7: 30168881-30170096 0.000535569 0.037486096 0.01095634 0.01095634
    chr2: 231742722-231743963 0.000536517 0.037486096 0.011947366 0.011947366
    chr15: 43212635-43213007 0.000536607 0.037486096 0.0098552 0.0098552
    chr5: 78531633-78531861 0.000556206 0.038412018 0.011727138 0.011727138
    chr8: 105478884-105479281 0.000559086 0.038464661 0.014535044 0.014535044
    chr20: 49307662-49308065 0.000567068 0.038720521 0.012883334 0.012883334
    chr16: 46796951-46797158 0.000586403 0.039611265 0.013488961 0.013488961
    chr12: 27167010-27167367 0.000588837 0.039611265 0.014590101 0.014590101
    chr4: 89205557-89205921 0.000614304 0.040555725 0.011617024 0.011617024
    chr6: 160199690-160200144 0.000617597 0.040555725 0.014865386 0.014865386
    chr2: 179914566-179914813 0.000622444 0.040555725 0.010075428 0.010075428
    chr18: 48604625-48611415 0.00062436 0.040555725 0.013764246 0.013764246
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    chr2: 239198539-239198743 0.00065163 0.041198377 0.012828277 0.012828277
    chr3: 195808701-195809060 0.000653258 0.041198377 0.01150691 0.01150691
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    chr19: 18474200-18480763 0.000672614 0.041773747 0.013268733 0.013268733
    chr12: 89913184-89918583 0.00067673 0.041773747 0.010846226 0.010846226
    chr8: 27168317-27168836 0.000679602 0.041773747 0.01040577 0.01040577
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    chr2: 70052587-70053596 0.000692281 0.041773747 0.010736112 0.010736112
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    chr15: 90358003-90358094 0.0007237 0.042677179 0.014259759 0.014259759
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    chr2: 103459870-103460352 0.000751677 0.043341943 0.011011397 0.011011397
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    chrX: 19140559-19140755 0.000784366 0.043808512 0.011286682 0.011286682
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    chr2: 231911596-231914434 0.000799811 0.043922586 0.011451853 0.011451853
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    chr22: 34318608-34318829 0.000854631 0.045631286 0.016737323 0.016737323
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    chrX: 12738647-12742642 0.000858999 0.045631286 0.016682266 0.016682266
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    chr21: 47575383-47575481 0.000873685 0.045863418 0.011727138 0.011727138
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    chr5: 140389211-140391929 0.000891792 0.046411507 0.011837252 0.011837252
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    chr1: 94312625-94312706 0.000930104 0.047587285 0.011892309 0.011892309
    chr3: 48340444-48340743 0.00093681 0.047661833 0.018003634 0.018003634
    chr11: 62323634-62323719 0.000950347 0.047947664 0.018333976 0.018333976
    chr12: 13366614-13369708 0.00096088 0.048344752 0.015360899 0.015360899
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    chr17: 17875575-17875784 0.000989388 0.049024274 0.015636183 0.015636183
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    chr6: 36891122-36892331 0.001065356 0.050387852 0.013378847 0.013378847
    chr18: 55253785-55254004 0.001065873 0.050387852 0.018554204 0.018554204
    chr12: 108154733-108155049 0.001068068 0.050387852 0.012608049 0.012608049
    chr4: 87769891-87770416 0.001091989 0.051250108 0.012663106 0.012663106
    chr4: 166418663-166419472 0.001102949 0.051612302 0.012718163 0.012718163
    chr10: 115423569-115423805 0.001107713 0.051612302 0.0149755 0.0149755
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    chr21: 34185901-34186053 0.001141255 0.052744562 0.012883334 0.012883334
    chr1: 114515645-114520426 0.001150361 0.053030454 0.021417167 0.021417167
    chr1: 235813848-235814054 0.001155036 0.053111188 0.021747509 0.021747509
    chr20: 36151068-36152092 0.001172766 0.053570624 0.012938391 0.012938391
    chr4: 141677069-141677274 0.00118035 0.053586679 0.021967737 0.021967737
    chr15: 90293739-90294541 0.001183079 0.053586679 0.013048505 0.013048505
    chr17: 65026581-65029518 0.00122096 0.054621439 0.021527281 0.021527281
    chr21: 43735402-43735761 0.001229156 0.054707452 0.01332379 0.01332379
    chrX: 71363102-71363424 0.001229655 0.054707452 0.021637395 0.021637395
    chr9: 117568082-117568406 0.001233934 0.054707452 0.016902494 0.016902494
    chr4: 111563074-111563279 0.001237943 0.054707452 0.021692452 0.021692452
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    chr1: 19983358-19984945 0.001250341 0.054730647 0.022463249 0.022463249
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    chr4: 114899592-114900883 0.001263618 0.054730647 0.023013819 0.023013819
    chr17: 19237268-19240028 0.001267584 0.054730647 0.013433904 0.013433904
    chr1: 162749901-162750237 0.001272199 0.054730647 0.022738534 0.022738534
    chr10: 117704168-117708503 0.001284378 0.054730647 0.013488961 0.013488961
    chr15: 39887562-39891119 0.001284498 0.054730647 0.013544018 0.013544018
    chr7: 51384289-51384515 0.001289026 0.054730647 0.013654132 0.013654132
    chr7: 6590638-6591067 0.001292708 0.054730647 0.013709189 0.013709189
    chr13: 36047925-36050832 0.001312128 0.055295099 0.021417167 0.021417167
    chr5: 171433461-171433877 0.001336152 0.055965232 0.01734295 0.01734295
    chr16: 20911525-20911706 0.001337274 0.055965232 0.017673292 0.017673292
    chr2: 61148897-61150645 0.001345056 0.056118504 0.013819303 0.013819303
    chr2: 175351600-175351822 0.001359864 0.056348645 0.018499147 0.018499147
    chr4: 110222878-110223813 0.001371014 0.056348645 0.013929417 0.013929417
    chr16: 16317255-16317351 0.00137118 0.056348645 0.02081154 0.02081154
    chr14: 55611833-55612147 0.001372424 0.056348645 0.018994659 0.018994659
    chr11: 6631692-6632102 0.001375926 0.056348645 0.013984474 0.013984474
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    chr2: 23929350-23931481 0.001423641 0.057443033 0.022903705 0.022903705
    chr11: 30608288-30608419 0.001425187 0.057443033 0.021967737 0.021967737
    chr8: 30585046-30585443 0.001429341 0.057443033 0.014369873 0.014369873
    chr9: 91606384-91611055 0.001429513 0.057443033 0.019380058 0.019380058
    chr18: 71958981-71959251 0.001437928 0.057629628 0.021527281 0.021527281
    chr10: 43623559-43625799 0.001443629 0.057629628 0.024335187 0.024335187
    chr6: 143266235-143266338 0.001443676 0.057629628 0.024610472 0.024610472
    chr11: 74022456-74022702 0.001472566 0.058397855 0.023839674 0.023839674
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    chr11: 71707240-71708643 0.001592571 0.06115405 0.014314816 0.014314816
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    chr19: 38886119-38886868 0.001644515 0.061976164 0.023564389 0.023564389
    chr15: 78461263-78464291 0.00164469 0.061976164 0.026152067 0.026152067
    chr17: 42255572-42256451 0.001656546 0.062263442 0.021967737 0.021967737
    chr19: 57351949-57352097 0.00165917 0.062263442 0.026592523 0.026592523
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    chr18: 19284464-19284766 0.001741729 0.064353713 0.022848648 0.022848648
    chr3: 113005521-113006303 0.001746759 0.064353713 0.016957551 0.016957551
    chr22: 30685281-30685616 0.001754562 0.064510342 0.020371084 0.020371084
    chr15: 42783294-42783336 0.001766266 0.064581327 0.025986896 0.025986896
    chr19: 48700486-48700877 0.001770365 0.064581327 0.014535044 0.014535044
    chrX: 120181461-120183794 0.001770715 0.064581327 0.025491384 0.025491384
    chrX: 47064319-47065264 0.00178612 0.065012604 0.020866597 0.020866597
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    chr22: 40366908-40369725 0.001844113 0.066010185 0.025821725 0.025821725
    chr2: 171572768-171574588 0.001844519 0.066010185 0.024445301 0.024445301
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    chr11: 33757927-33757991 0.001876261 0.066300655 0.02609701 0.02609701
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    chr9: 119158787-119164601 0.001925722 0.067433539 0.028079062 0.028079062
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    chr21: 38639538-38640262 0.002001389 0.068739822 0.027913891 0.027913891
    chr7: 79082335-79082890 0.002005363 0.068739822 0.028244233 0.028244233
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    chr12: 57350933-57351418 0.002026872 0.068739822 0.028024005 0.028024005
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    chr14: 81864638-81864927 0.002034942 0.068739822 0.028134119 0.028134119
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    chr2: 238820169-238820756 0.002074537 0.069507577 0.019875571 0.019875571
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    chr18: 57364443-57364574 0.002188416 0.071361233 0.017783406 0.017783406
    chr9: 108536145-108538893 0.002195984 0.071479663 0.027528492 0.027528492
    chr7: 121784214-121784334 0.002205346 0.071655996 0.017287893 0.017287893
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    chr7: 84815993-84816171 0.002433204 0.075804938 0.031933051 0.031933051
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    chr9: 4662297-4665256 0.002522928 0.077274787 0.03231845 0.03231845
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    chr22: 24890657-24891042 0.002694653 0.079550065 0.032758905 0.032758905
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    chrX: 100786630-100788446 0.002728068 0.079648701 0.021582338 0.021582338
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    chr11: 119170204-119177651 0.002753152 0.079738981 0.015636183 0.015636183
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    chr1: 203144678-203144941 0.002856557 0.081129471 0.01569124 0.01569124
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    chr17: 40540296-40540449 0.003184574 0.085285307 0.015966525 0.015966525
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    chr17: 76899215-76899297 0.003211516 0.085528988 0.034190387 0.034190387
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    chr1: 113499460-113499635 0.003587275 0.091208876 0.038870231 0.038870231
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    chr11: 67124213-67124443 0.003683245 0.092274168 0.02884986 0.02884986
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    chr9: 130869307-130871524 0.003772717 0.093229751 0.01624181 0.01624181
    chr9: 86258343-86259045 0.003800119 0.09365204 0.028794803 0.028794803
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    chr16: 76592386-76593135 0.003922446 0.095100371 0.018003634 0.018003634
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    chr7: 4897363-4901625 0.004590477 0.1005752 0.044596157 0.044596157
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    chr16: 5064859-5069156 0.004874777 0.102956744 0.016682266 0.016682266
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    chr22: 43411026-43411151 0.005558398 0.108672962 0.041953422 0.041953422
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    chr8: 75233143-75233563 0.005847533 0.111316988 0.042944448 0.042944448
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    chr5: 159855608-159855748 0.004502947 0.099271066 0.045036613 0.045036613
    chr14: 36982316-36982990 0.004496721 0.099271066 0.043935473 0.043935473
    chr9: 140194082-140196703 0.004490551 0.099271066 0.041788251 0.041788251
    chr9: 104499562-104500862 0.004488935 0.099271066 0.034080273 0.034080273
    chr9: 125084818-125085743 0.004454398 0.099254224 0.020536255 0.020536255
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    chr5: 98134164-98134347 0.004395858 0.098637481 0.016462038 0.016462038
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    chr2: 113332423-113334673 0.004367673 0.098553166 0.039145516 0.039145516
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    chr3: 138663065-138665982 0.004361352 0.098553166 0.038209547 0.038209547
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    chr3: 197682620-197683481 0.004331408 0.098553166 0.026757694 0.026757694
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    chr16: 81110740-81110818 0.004190181 0.097074302 0.036667951 0.036667951
    chr19: 55325296-55325972 0.00418778 0.097074302 0.029125145 0.029125145
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    chr1: 32798617-32799236 0.00411599 0.096482536 0.041182624 0.041182624
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    chr1: 166818174-166825581 0.004110184 0.096482536 0.025656555 0.025656555
    chr3: 169801692-169803191 0.004104013 0.096482536 0.016296867 0.016296867
    chr1: 173793699-173793858 0.004081228 0.096315629 0.035842097 0.035842097
    chr9: 37356831-37358146 0.004050647 0.095937748 0.030446512 0.030446512
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    chr19: 12551725-12551926 0.003964282 0.095242391 0.030831911 0.030831911
    chr1: 146253037-146253110 0.003951763 0.095100371 0.041402852 0.041402852
    chr16: 18473011-18473188 0.003944395 0.095100371 0.039090459 0.039090459
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    chr2: 102003478-102004057 0.003919321 0.095100371 0.039530914 0.039530914
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    chr22: 24125597-24126503 0.003890015 0.095018782 0.038429775 0.038429775
    chr22: 38878500-38879452 0.003855253 0.094370558 0.036998293 0.036998293
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    chr14: 20825209-20826063 0.003783766 0.09337573 0.039861256 0.039861256
    chr8: 42229080-42229326 0.003752975 0.092868242 0.039145516 0.039145516
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    chr11: 114320567-114321001 0.003745569 0.092868242 0.038264604 0.038264604
    chr11: 132204939-132206716 0.003738017 0.092868242 0.036227495 0.036227495
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    chr19: 34302695-34306668 0.003572035 0.091143709 0.037328635 0.037328635
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    chr5: 72875701-72877794 0.00349355 0.090400812 0.016076639 0.016076639
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    chr8: 17104183-17104387 0.003462106 0.090089159 0.032153279 0.032153279
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    chr16: 67418772-67419106 0.003414593 0.089108124 0.03578704 0.03578704
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    chr22: 31363051-31364284 0.003316793 0.087182226 0.032098222 0.032098222
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    chr13: 100622380-100624163 0.003203139 0.085528988 0.03650278 0.03650278
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    chr8: 101965496-101965616 0.00316881 0.085014912 0.034740957 0.034740957
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    chr2: 47614696-47614740 0.003153567 0.084982538 0.034080273 0.034080273
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    chr7: 99679923-99680171 0.002977233 0.08168847 0.036227495 0.036227495
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    chr21: 45079266-45079374 0.002931642 0.081412629 0.031492595 0.031492595
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    chr8: 86129188-86129387 0.002913777 0.081412629 0.028519518 0.028519518
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    chr4: 55161291-55161439 0.002837998 0.081115772 0.032373507 0.032373507
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    chr1: 147954634-147955419 0.002795098 0.080555005 0.027418378 0.027418378
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    chr22: 49246569-49246724 0.002711088 0.079550065 0.029950999 0.029950999
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    chr8: 19615360-19615540 0.002555298 0.077741827 0.015415956 0.015415956
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    chr8: 54934622-54935089 0.002552422 0.077741827 0.029510543 0.029510543
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    chr19: 52868950-52870375 0.002286182 0.072893957 0.020701426 0.020701426
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    chr10: 121302101-121302220 0.002017084 0.068739822 0.023454275 0.023454275
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    chr11: 6463716-6463847 0.00193868 0.067488924 0.025931839 0.025931839
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    chr17: 30228554-30228731 0.001926885 0.067433539 0.026812751 0.026812751
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    chr9: 131303380-131304567 0.001740684 0.064353713 0.01734295 0.01734295
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    chr11: 26744853-26744974 0.001508748 0.059059014 0.025546441 0.025546441
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    chr11: 102340904-102341115 0.001485218 0.058516288 0.021031768 0.021031768
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    chr7: 19156293-19157295 0.001471295 0.058397855 0.015526069 0.015526069
    chrX: 129063311-129063737 0.001461047 0.058195149 0.020371084 0.020371084
    chr21: 18965469-18965897 0.001396915 0.056634289 0.014094588 0.014094588
    chr5: 68665483-68665840 0.001392548 0.056583554 0.020646369 0.020646369
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    chr14: 89088611-89088615 0.001383605 0.056348645 0.014039531 0.014039531
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    chr1: 155707947-155708803 0.001353654 0.056261816 0.01387436 0.01387436
    chr12: 118500157-118500235 0.001347116 0.056118504 0.022793591 0.022793591
    chr12: 122985186-122985518 0.001329462 0.055895875 0.013764246 0.013764246
    chr20: 13797763-13799067 0.001301059 0.054956129 0.021472224 0.021472224
    chr20: 20693017-20693266 0.001289806 0.054730647 0.014204702 0.014204702
    chr17: 27940371-27941779 0.001287374 0.054730647 0.013599075 0.013599075
    chr2: 24991089-24993571 0.001282497 0.054730647 0.021857623 0.021857623
    chr1: 2706067-2706280 0.001276855 0.054730647 0.015471012 0.015471012
    chr11: 61136068-61136683 0.001269747 0.054730647 0.020591312 0.020591312
    chr5: 72801016-72801460 0.001259835 0.054730647 0.022518306 0.022518306
    chr12: 26277650-26278060 0.001259656 0.054730647 0.014700215 0.014700215
    chr11: 77348634-77348850 0.001244205 0.054730647 0.013378847 0.013378847
    chr11: 64940653-64940715 0.00123731 0.054707452 0.018223862 0.018223862
    chr1: 169555466-169555826 0.00121279 0.054389907 0.013268733 0.013268733
    chr1: 113212613-113214241 0.00120243 0.054058764 0.013213676 0.013213676
    chr11: 118888070-118889401 0.001202139 0.054058764 0.013158619 0.013158619
    chr6: 119228566-119230332 0.001187702 0.053662274 0.013103562 0.013103562
    chr9: 96082648-96082854 0.001181597 0.053586679 0.018884546 0.018884546
    chr16: 48419114-48419361 0.001173876 0.053570624 0.012993448 0.012993448
    chr6: 117252493-117253326 0.001165397 0.0534523 0.020921654 0.020921654
    chr5: 140890513-140892546 0.001117453 0.051908714 0.012828277 0.012828277
    chr1: 203821268-203823252 0.001108231 0.051612302 0.01277322 0.01277322
    chr12: 57125273-57125412 0.001072585 0.05046987 0.018058691 0.018058691
    chr19: 11849631-11849824 0.001062858 0.050387852 0.012552992 0.012552992
    chr22: 41255552-41258130 0.001062854 0.050387852 0.012497935 0.012497935
    chr9: 86595417-86595569 0.001048739 0.050126946 0.012442878 0.012442878
    chr12: 21391912-21392180 0.00104238 0.05009999 0.012387821 0.012387821
    chr4: 165878099-165880274 0.001026914 0.049738242 0.012332764 0.012332764
    chr13: 53216540-53217919 0.001026838 0.049738242 0.019985685 0.019985685
    chr7: 16921567-16921611 0.001026105 0.049738242 0.020095799 0.020095799
    chr10: 27035261-27035727 0.000990592 0.049024274 0.019325001 0.019325001
    chr12: 15114470-15114662 0.000989776 0.049024274 0.012057479 0.012057479
    chr9: 74525549-74525847 0.000977152 0.048758299 0.012002423 0.012002423
    chr4: 77996624-77997158 0.000969463 0.048641844 0.011947366 0.011947366
    chr22: 29137756-29138410 0.000946731 0.047898273 0.012442878 0.012442878
    chr4: 69696317-69696914 0.0009412 0.047751429 0.01915983 0.01915983
    chr4: 44700560-44702943 0.000934167 0.047660883 0.013378847 0.013378847
    chr4: 169931098-169931426 0.000927605 0.047587285 0.017453064 0.017453064
    chr1: 46158875-46160115 0.000926916 0.047587285 0.012387821 0.012387821
    chr19: 11494768-11495018 0.000922982 0.047587285 0.013654132 0.013654132
    chr6: 32151657-32152101 0.000903309 0.046876568 0.018003634 0.018003634
    chrX: 51238802-51239448 0.00086822 0.045708659 0.011672081 0.011672081
    chr11: 1481729-1483919 0.000867469 0.045708659 0.01442493 0.01442493
    chr10: 35927176-35930362 0.000859214 0.045631286 0.017398007 0.017398007
    chr5: 34924951-34926101 0.000856629 0.045631286 0.011892309 0.011892309
    chr11: 108810972-108811657 0.000832793 0.045017925 0.011561967 0.011561967
    chr6: 151422661-151423023 0.000829888 0.044994788 0.01150691 0.01150691
    chr5: 179498455-179499118 0.000820915 0.044641533 0.016902494 0.016902494
    chr2: 207653542-207657233 0.000797601 0.043922586 0.017508121 0.017508121
    chr1: 32801547-32801980 0.000791124 0.043808512 0.011396796 0.011396796
    chr15: 58073773-58074960 0.000790373 0.043808512 0.011341739 0.011341739
    chr5: 150080493-150080669 0.000787766 0.043808512 0.01679238 0.01679238
    chr11: 58345458-58345693 0.000786872 0.043808512 0.017453064 0.017453064
    chr1: 167757056-167761156 0.000777688 0.043808512 0.011176568 0.011176568
    chr1: 154531383-154531504 0.000777153 0.043808512 0.011121511 0.011121511
    chr21: 27107163-27107984 0.000776889 0.043808512 0.012828277 0.012828277
    chr1: 84963111-84963473 0.00077556 0.043808512 0.011066454 0.011066454
    chr14: 20925149-20925933 0.000771737 0.043808512 0.012718163 0.012718163
    chr6: 116914142-116918838 0.000766759 0.043808512 0.015856411 0.015856411
    chr9: 33798853-33799230 0.000744555 0.043068013 0.01095634 0.01095634
    chr9: 74597572-74600970 0.000742855 0.043068013 0.010901283 0.010901283
    chr11: 62507447-62507756 0.000734445 0.042755513 0.010846226 0.010846226
    chr6: 47009926-47010099 0.000734128 0.042755513 0.016351924 0.016351924
    chr1: 236385090-236385165 0.000728916 0.04274929 0.016351924 0.016351924
    chr6: 107979410-107981357 0.000718577 0.042513049 0.010791169 0.010791169
    chr1: 151220338-151222012 0.000717051 0.042513049 0.013709189 0.013709189
    chr12: 21242841-21243179 0.000716921 0.042513049 0.015195728 0.015195728
    chr1: 154243356-154243986 0.000713525 0.042513049 0.01387436 0.01387436
    chr2: 9613044-9613230 0.000708342 0.042460748 0.011617024 0.011617024
    chr6: 28097207-28097860 0.000690497 0.041773747 0.010625998 0.010625998
    chr5: 68849396-68853931 0.000689997 0.041773747 0.010570941 0.010570941
    chr1: 183567145-183567381 0.000687128 0.041773747 0.010515884 0.010515884
    chr12: 50492729-50494495 0.000677636 0.041773747 0.010350713 0.010350713
    chr10: 33171620-33171802 0.000677312 0.041773747 0.010295656 0.010295656
    chr7: 23571407-23571660 0.000656983 0.041289887 0.013929417 0.013929417
    chr1: 2520848-2522908 0.000641426 0.040735055 0.011011397 0.011011397
    chr21: 33103975-33104431 0.00063637 0.040555725 0.015526069 0.015526069
    chr6: 30530165-30531500 0.000634398 0.040555725 0.015360899 0.015360899
    chr2: 223520734-223521056 0.000632879 0.040555725 0.012002423 0.012002423
    chr12: 96437066-96437298 0.000632631 0.040555725 0.010185542 0.010185542
    chr5: 140041763-140042064 0.000626233 0.040555725 0.013158619 0.013158619
    chr1: 155248165-155248282 0.000619771 0.040555725 0.014810329 0.014810329
    chr10: 71871273-71872032 0.000616327 0.040555725 0.010020371 0.010020371
    chr13: 103491900-103493885 0.000597551 0.039755743 0.010350713 0.010350713
    chr1: 228353174-228353213 0.00059719 0.039755743 0.010846226 0.010846226
    chr2: 42719976-42721237 0.000592999 0.039744051 0.011176568 0.011176568
    chr1: 54879028-54879152 0.000588247 0.039611265 0.011837252 0.011837252
    chr3: 195310748-195311076 0.000575152 0.039125424 0.009965314 0.009965314
    chr9: 129458572-129463311 0.000561861 0.038509773 0.013268733 0.013268733
    chr11: 93583577-93583697 0.00054174 0.037555812 0.014039531 0.014039531
    chr12: 56693943-56694176 0.000538947 0.037505344 0.009910257 0.009910257
    chr22: 44258093-44258398 0.000530737 0.037486096 0.009800143 0.009800143
    chr19: 14201749-14201848 0.000530518 0.037486096 0.009690029 0.009690029
    chr17: 44632896-44633016 0.000525864 0.037486096 0.010625998 0.010625998
    chr7: 33148832-33149013 0.000509039 0.036982719 0.009524858 0.009524858
    chr19: 20046830-20046860 0.000499745 0.036453301 0.009469801 0.009469801
    chr15: 77241410-77242601 0.000497827 0.036453301 0.011176568 0.011176568
    chr1: 26233278-26233482 0.000496568 0.036453301 0.009414744 0.009414744
    chr1: 222886085-222886552 0.000478764 0.035493035 0.013213676 0.013213676
    chr13: 100637576-100639018 0.00047822 0.035493035 0.010625998 0.010625998
    chr2: 181940922-181941312 0.000472014 0.035377477 0.012332764 0.012332764
    chr8: 97273728-97273838 0.000459439 0.035043161 0.009084402 0.009084402
    chr6: 80751835-80752244 0.000437005 0.034360736 0.009579915 0.009579915
    chr11: 49229843-49230222 0.00043239 0.034246655 0.009690029 0.009690029
    chr11: 18127453-18127638 0.00043097 0.034246655 0.011011397 0.011011397
    chr2: 74718607-74722013 0.000425021 0.034068108 0.011947366 0.011947366
    chr2: 172952730-172954405 0.000421691 0.034068108 0.008864174 0.008864174
    chr1: 156051335-156051789 0.000415016 0.034004231 0.00875406 0.00875406
    chr20: 45985400-45985567 0.000413714 0.034004231 0.011892309 0.011892309
    chr6: 20490398-20493945 0.000402697 0.033903107 0.008533833 0.008533833
    chr9: 17502548-17503921 0.000399995 0.033903107 0.008478776 0.008478776
    chr11: 125933120-125933230 0.000398772 0.033903107 0.011561967 0.011561967
    chr16: 1374730-1377019 0.000390959 0.033814213 0.008919231 0.008919231
    chr4: 85418711-85419603 0.000388972 0.0338033 0.011396796 0.011396796
    chr1: 2345035-2345236 0.000387542 0.0338033 0.011066454 0.011066454
    chr13: 37583320-37583750 0.000383013 0.0338033 0.008148434 0.008148434
    chr6: 114332294-114332472 0.00038083 0.0338033 0.00803832 0.00803832
    chr11: 94730187-94732682 0.000380412 0.0338033 0.007983263 0.007983263
    chr7: 96639107-96640351 0.000379524 0.0338033 0.007928206 0.007928206
    chr1: 43316593-43318148 0.000374998 0.0338033 0.007873149 0.007873149
    chr6: 30620387-30620987 0.000368399 0.0338033 0.007818092 0.007818092
    chr1: 38455541-38456593 0.000337962 0.031641224 0.007707978 0.007707978
    chr16: 3450944-3451030 0.000317223 0.030524412 0.00748775 0.00748775
    chr2: 27886195-27886676 0.000315018 0.030524412 0.007432693 0.007432693
    chr3: 131221573-131221827 0.000312506 0.030524412 0.010130485 0.010130485
    chr6: 117890782-117891021 0.000309822 0.030524412 0.007322579 0.007322579
    chr6: 37298819-37300746 0.00030641 0.030524412 0.007267522 0.007267522
    chr19: 52531494-52531680 0.000301647 0.030437889 0.008148434 0.008148434
    chr12: 76478346-76478813 0.000294718 0.030160322 0.007157408 0.007157408
    chr6: 110797724-110797844 0.000290236 0.029952049 0.007102351 0.007102351
    chr17: 38290531-38293040 0.000275367 0.028910303 0.007047294 0.007047294
    chr2: 71192087-71192555 0.00026727 0.028388448 0.00693718 0.00693718
    chr1: 236645566-236648026 0.000264197 0.028227163 0.006882123 0.006882123
    chr1: 90398625-90402170 0.000252946 0.027410832 0.006827066 0.006827066
    chr15: 34880591-34880704 0.000250304 0.027410832 0.007542807 0.007542807
    chr17: 27277912-27278789 0.000250154 0.027410832 0.00748775 0.00748775
    chr7: 50632981-50633154 0.000250135 0.027410832 0.006716952 0.006716952
    chr10: 122348814-122349367 0.000249544 0.027410832 0.008533833 0.008533833
    chr12: 54428061-54429145 0.000246644 0.027410832 0.007983263 0.007983263
    chr3: 63849179-63849579 0.000246543 0.027410832 0.006606838 0.006606838
    chr17: 57351011-57353322 0.000236747 0.027410832 0.006551781 0.006551781
    chr19: 11529921-11530018 0.000212432 0.02572268 0.006331553 0.006331553
    chr12: 54423414-54424607 0.00021234 0.02572268 0.007818092 0.007818092
    chr6: 107372260-107372546 0.000211601 0.02572268 0.006661895 0.006661895
    chr17: 27169675-27169841 0.000193726 0.024266551 0.006166382 0.006166382
    chr12: 2113366-2113701 0.000172975 0.021961395 0.007818092 0.007818092
    chr20: 62168437-62168723 0.000168353 0.021533748 0.007763035 0.007763035
    chr20: 524315-524482 0.000167895 0.021533748 0.006111325 0.006111325
    chr2: 40006253-40006407 0.000165764 0.021533748 0.006056268 0.006056268
    chr1: 38061359-38061540 0.000165526 0.021533748 0.006001211 0.006001211
    chr7: 40899914-40900362 0.000163423 0.021533748 0.006496724 0.006496724
    chr12: 54448633-54449814 0.000153417 0.020640881 0.006772009 0.006772009
    chr2: 86422460-86422893 0.000152321 0.020640881 0.006001211 0.006001211
    chr4: 147442769-147443123 0.000145311 0.020358172 0.006111325 0.006111325
    chr1: 145368440-145370303 0.000145073 0.020358172 0.005670869 0.005670869
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    chr5: 136933886-136934068 0.000138325 0.020261212 0.005450641 0.005450641
    chr4: 39529418-39529931 0.000133517 0.020041937 0.00528547 0.00528547
    chr8: 145979576-145981802 0.000127134 0.019242801 0.005615812 0.005615812
    chr11: 381668-382116 0.000126188 0.019242801 0.005230413 0.005230413
    chr5: 68737358-68740157 0.000121712 0.019126366 0.005560755 0.005560755
    chr1: 150325308-150325671 0.00011576 0.018606562 0.005065243 0.005065243
    chr3: 53845139-53846490 0.000111313 0.018214263 0.004955129 0.004955129
    chr9: 126030714-126030855 0.000110375 0.018214263 0.004845015 0.004845015
    chrX: 109683117-109683461 0.000107624 0.018099813 0.005946154 0.005946154
    chr5: 74072428-74072737 0.000105481 0.017905164 0.005065243 0.005065243
    chr19: 19654489-19657468 9.78E−05 0.017086351 0.004679844 0.004679844
    chr22: 19770836-19771116 9.30E−05 0.016887835 0.004845015 0.004845015
    chr16: 11945264-11945442 8.79E−05 0.016293883 0.004459616 0.004459616
    chr12: 56509926-56509935 8.68E−05 0.016256711 0.004900072 0.004900072
    chr11: 18063910-18063973 8.50E−05 0.016078925 0.004900072 0.004900072
    chr6: 111137010-111137161 5.67E−05 0.012121545 0.003964103 0.003964103
    chr5: 11903928-11904155 5.64E−05 0.012121545 0.003909046 0.003909046
    chr9: 23825803-23826335 5.63E−05 0.012121545 0.004404559 0.004404559
    chr5: 137910926-137911133 5.62E−05 0.012121545 0.003853989 0.003853989
    chr16: 15224943-15225458 5.55E−05 0.012121545 0.003798932 0.003798932
    chr10: 115991244-115992063 5.54E−05 0.012121545 0.003743875 0.003743875
    chr11: 49059029-49059579 5.36E−05 0.012121545 0.003798932 0.003798932
    chrX: 135962755-135962939 4.64E−05 0.011520023 0.003413533 0.003413533
    chr15: 74005274-74006859 4.35E−05 0.010985753 0.003633761 0.003633761
    chr6: 76624529-76629254 3.98E−05 0.010632462 0.003193305 0.003193305
    chr6: 105627707-105627870 3.80E−05 0.010304253 0.003138248 0.003138248
    chr1: 224517772-224518089 3.80E−05 0.010304253 0.003138248 0.003138248
    chr9: 93405033-93405386 3.72E−05 0.010304253 0.003083191 0.003083191
    chr20: 1373477-1373806 3.37E−05 0.009557199 0.003028134 0.003028134
    chr9: 131262345-131263239 3.28E−05 0.009557199 0.00291802 0.00291802
    chr10: 124923335-124924886 3.21E−05 0.009557199 0.002973077 0.002973077
    chr5: 133304136-133304478 3.20E−05 0.009557199 0.002807906 0.002807906
    chr1: 84855461-84855640 2.97E−05 0.009293059 0.002752849 0.002752849
    chr5: 79865972-79866307 2.72E−05 0.008978177 0.002697792 0.002697792
    chr3: 132004083-132004254 2.23E−05 0.007783374 0.002532621 0.002532621
    chr1: 40783259-40783488 2.03E−05 0.007236461 0.002477564 0.002477564
    chr6: 111346605-111347303 2.02E−05 0.007236461 0.002422507 0.002422507
    chr12: 82152992-82153332 2.02E−05 0.007236461 0.00236745 0.00236745
    chr1: 76076724-76076801 2.00E−05 0.007236461 0.00236745 0.00236745
    chr11: 94965320-94965705 1.94E−05 0.007236461 0.002257336 0.002257336
    chr5: 102611597-102614361 1.15E−05 0.00499128 0.002147222 0.002147222
    chr1: 166845396-166845564 7.77E−06 0.004015199 0.00181688 0.00181688
    chr6: 28200339-28201260 7.13E−06 0.003810198 0.001761823 0.001761823
    chr4: 122617735-122618268 5.57E−06 0.003261046 0.001596653 0.001596653
    chr2: 203630168-203634480 5.50E−06 0.003261046 0.001486539 0.001486539
    chr15: 82554954-82555104 5.43E−06 0.003261046 0.001431482 0.001431482
    chr6: 46703286-46703430 5.40E−06 0.003261046 0.001376425 0.001376425
    chr6: 24785865-24786327 5.24E−06 0.003261046 0.001321368 0.001321368
    chr3: 175520792-175523428 4.73E−06 0.003261046 0.001211254 0.001211254
    chr1: 70587462-70589164 4.71E−06 0.003261046 0.001156197 0.001156197
    chr6: 38997880-38998301 4.60E−06 0.003261046 0.00110114 0.00110114
    chr1: 31769457-31769662 4.57E−06 0.003261046 0.000991026 0.000991026
    chr3: 3886047-3889387 3.97E−06 0.003261046 0.000880912 0.000880912
    chr17: 4545517-4545589 3.58E−06 0.003261046 0.000825855 0.000825855
    chr18: 55143668-55158530 3.36E−06 0.003261046 0.000770798 0.000770798
    chr18: 63547636-63552376 2.83E−06 0.003261046 0.000715741 0.000715741
    chr11: 129728468-129729898 2.23E−06 0.002893994 0.000660684 0.000660684
    chr17: 38821255-38821393 2.07E−06 0.002893994 0.000605627 0.000605627
    chr6: 107436293-107436473 2.06E−06 0.002893994 0.00055057 0.00055057
    chr1: 180991774-180992047 2.03E−06 0.002893994 0.00055057 0.001806154
    chr9: 114361882-114362135 2.00E−06 0.002893994 0.000495513 0.000495513
    chr3: 193855471-193856521 2.00E−06 0.002893994 0.000440456 0.000440456
    chr6: 38670746-38670917 1.86E−06 0.002893994 0.000385399 0.000385399
    chr2: 71159896-71160576 1.78E−06 0.002893994 0.000330342 0.000330342
    chr8: 136668468-136668965 1.67E−06 0.002893994 0.000275285 0.000275285
    chr9: 79634570-79635869 5.60E−07 0.002542246 0.000220228 0.000220228
    chr1: 31712340-31712401 0 0 0.000165171 0.000165171
    chr6: 107780193-107780768 0 0 0.000165171 0.000165171
    chr2: 181780999-181782519 0 0 0.000165171 0.000165171
  • All publications, patents, patent applications and accession numbers mentioned in the above specification are herein incorporated by reference in their entirety. Although the invention has been described in connection with specific embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications and variations of the described compositions and methods of the invention will be apparent to those of ordinary skill in the art and are intended to be within the scope of the following claims.

Claims (21)

1.-272. (canceled)
273. A system for analyzing a cancer, comprising:
a. a probe set comprising a plurality of probes, wherein the plurality of probes comprises a sequence that hybridizes to at least a portion of one or more target molecules selected from the group comprising PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9; and
b. a computer model or algorithm for analyzing an expression level and/or expression profile of a target molecule hybridized to the probe in a sample from a subject suffering from a cancer.
274. The system claim 273, wherein PCAT is selected from the group comprising PCAT1, PCAT2, PCAT3, PCAT4, PCAT5, PCAT6, PCAT7, PCAT8, PCAT9, PCAT10, PCAT11, PCAT12, PCAT13, PCAT14, PCAT15, PCAT16, PCAT17, PCAT18, PCAT19, PCAT20, PCAT21, PCAT22, PCAT23, PCAT24, PCAT25, PCAT26, PCAT27, PCAT28, PCAT29, PCAT30, PCAT31, PCAT32, PCAT33, PCAT34, PCAT35, PCAT36, PCAT37, PCAT38, PCAT39, PCAT40, PCAT41, PCAT42, PCAT43, PCAT44, PCAT45, PCAT46, PCAT47, PCAT48, PCAT49, PCAT50, PCAT51, PCAT52, PCAT53, PCAT54, PCAT55, PCAT56, PCAT57, PCAT58, PCAT59, PCAT60, PCAT61, PCAT62, PCAT63, PCAT64, PCAT65, PCAT66, PCAT67, PCAT68, PCAT69, PCAT70, PCAT71, PCAT72, PCAT73, PCAT74, PCAT75, PCAT76, PCAT77, PCAT78, PCAT79, PCAT80, PCAT81, PCAT82, PCAT83, PCAT84, PCAT85, PCAT86, PCAT87, PCAT88, PCAT89, PCAT90, PCAT91, PCAT92, PCAT93, PCAT94, PCAT95, PCAT96, PCAT97, PCAT98, PCAT99, PCAT100, PCAT101, PCAT102, PCAT103, PCAT104, PCAT105, PCAT106, PCAT107, PCAT108, PCAT109, PCAT110, PCAT111, PCAT112, PCAT113, PCAT114, PCAT115, PCAT116, PCAT117, PCAT118, PCAT119, PCAT120, and PCAT121.
275. The system of claim 273, further comprising an electronic memory for capturing and storing an expression profile.
276. The system of claim 273, further comprising a computer-processing device, optionally connected to a computer network.
277. The system of claim 276, further comprising a software module executed by the computer-processing device to analyze an expression profile.
278. The system of claim 276, further comprising a software module executed by the computer-processing device to compare the expression profile to a standard or control.
279. The system of claim 276, further comprising a software module executed by the computer-processing device to determine the expression level of the target.
280. The system of claim 276, further comprising a software module executed by the computer-processing device to transmit an analysis of the expression profile to the subject or a medical professional treating the subject.
281. The system of claim 276, further comprising a software module executed by the computer-processing device to transmit a diagnosis or prognosis to the subject or a medical professional treating the subject.
282. The system of claim 273, further comprising a machine to isolate the target or the probe from the sample, a machine to sequence the target or the probe, and/or a machine to amplify the target or the probe.
283. The system of claim 273, wherein the plurality of probes comprises a sequence that hybridizes to at least a portion of two or more target molecules selected from the group comprising PCAT, SChLAP-1, TU0011194, TU0019356, TU0024146, TU0009141, TU0062051, TU0021861, M41, ENST-75, and SEQ ID NOs: 1-9.
284. The system of claim 273, wherein the cancer is selected from the group comprising prostate, lung, breast, and pancreatic cancer.
285. The system of claim 273, wherein the plurality of probes comprises a sequence that hybridizes to at least a portion of one or more target molecules selected from the group comprising and SEQ ID NOs: 1-9, PCAT1, PCAT14, PCAT43, PCAT 109, and SChLAP-1.
286. The system of claim 285, wherein the cancer is a prostate cancer.
287. The system of claim 273, wherein the plurality of probes comprises a sequence that hybridizes to at least a portion of one or more target molecules selected from the group comprising M41 and ENST-75.
288. The system of claim 287, wherein the cancer is a lung cancer.
289. The system of claim 273, wherein the plurality of probes comprises a sequence that hybridizes to at least a portion of one or more target molecules selected from the group comprising TU0011194, TU0019356 and TU0024146.
290. The system of claim 288, wherein the cancer is a breast cancer or prostate.
291. The system of claim 273, wherein the plurality of probes is attached to one or more solid supports.
292. The system of claim 291, wherein the one or more solid supports is a bead, array, microarray, well, plate, chip, or a combination thereof.
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