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WO2010073248A3 - Gene expression signature for classification of tissue of origin of tumor samples - Google Patents

Gene expression signature for classification of tissue of origin of tumor samples Download PDF

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Publication number
WO2010073248A3
WO2010073248A3 PCT/IL2009/001212 IL2009001212W WO2010073248A3 WO 2010073248 A3 WO2010073248 A3 WO 2010073248A3 IL 2009001212 W IL2009001212 W IL 2009001212W WO 2010073248 A3 WO2010073248 A3 WO 2010073248A3
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WO
WIPO (PCT)
Prior art keywords
classification
origin
tissue
gene expression
tumor samples
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/IL2009/001212
Other languages
French (fr)
Other versions
WO2010073248A2 (en
Inventor
Ranit Aharonov
Nitzan Rosenfeld
Shai Rosenwald
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Rosetta Genomics Ltd
Original Assignee
Rosetta Genomics Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to CN200980157378XA priority Critical patent/CN102333888B/en
Application filed by Rosetta Genomics Ltd filed Critical Rosetta Genomics Ltd
Publication of WO2010073248A2 publication Critical patent/WO2010073248A2/en
Publication of WO2010073248A3 publication Critical patent/WO2010073248A3/en
Priority to IL212979A priority patent/IL212979A/en
Priority to US13/167,489 priority patent/US8802599B2/en
Anticipated expiration legal-status Critical
Priority to US13/856,190 priority patent/US9096906B2/en
Priority to US14/320,113 priority patent/US20140315739A1/en
Priority to US14/746,487 priority patent/US20150368724A1/en
Priority to US15/853,258 priority patent/US20180127835A1/en
Priority to US15/909,145 priority patent/US20190032142A1/en
Priority to US16/226,406 priority patent/US20190241966A1/en
Ceased 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
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • 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
    • C12Q2600/178—Oligonucleotides characterized by their use miRNA, siRNA or ncRNA
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Medical Informatics (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Microbiology (AREA)
  • Bioethics (AREA)
  • General Engineering & Computer Science (AREA)
  • Artificial Intelligence (AREA)
  • Biochemistry (AREA)
  • Signal Processing (AREA)
  • Pathology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention provides a process for classification of cancers and tissues of origin through the analysis of the expression patterns of specific microRNAs and nucleic acid molecules relating thereto. Classification according to a microRNA tree-based expression framework allows optimization of treatment, and determination of specific therapy.
PCT/IL2009/001212 2007-03-27 2009-12-23 Gene expression signature for classification of tissue of origin of tumor samples Ceased WO2010073248A2 (en)

Priority Applications (9)

Application Number Priority Date Filing Date Title
CN200980157378XA CN102333888B (en) 2008-12-24 2009-12-23 Gene expression signatures for tissue-of-origin classification of tumor samples
IL212979A IL212979A (en) 2008-12-24 2011-05-18 Gene expression signature for classification of tissue of origin of tumor samples
US13/167,489 US8802599B2 (en) 2007-03-27 2011-06-23 Gene expression signature for classification of tissue of origin of tumor samples
US13/856,190 US9096906B2 (en) 2007-03-27 2013-04-03 Gene expression signature for classification of tissue of origin of tumor samples
US14/320,113 US20140315739A1 (en) 2007-03-27 2014-06-30 Gene expression signature for classification of tissue of origin of tumor samples
US14/746,487 US20150368724A1 (en) 2007-03-27 2015-06-22 Methods and materials for classification of tissue of origin of tumor samples
US15/853,258 US20180127835A1 (en) 2007-03-27 2017-12-22 Gene expression signature for classification of tissue of origin of tumor samples
US15/909,145 US20190032142A1 (en) 2007-03-27 2018-03-01 Methods and materials for classification of tissue of origin of tumor samples
US16/226,406 US20190241966A1 (en) 2007-03-27 2018-12-19 Gene Expression Signature for Classification of Tissue of Origin of Tumor Samples

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US14064208P 2008-12-24 2008-12-24
US61/140,642 2008-12-24

Related Parent Applications (4)

Application Number Title Priority Date Filing Date
PCT/IL2008/000396 Continuation-In-Part WO2008117278A2 (en) 2007-03-27 2008-03-20 Gene expression signature for classification of cancers
US12/532,940 Continuation-In-Part US20100178653A1 (en) 2007-03-27 2008-03-20 Gene expression signature for classification of cancers
US53294009A Continuation-In-Part 2007-03-27 2009-09-24
PCT/IL2011/000849 Continuation-In-Part WO2012070037A2 (en) 2007-03-27 2011-11-01 Methods and materials for classification of tissue of origin of tumor samples

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US13/167,489 Continuation-In-Part US8802599B2 (en) 2007-03-27 2011-06-23 Gene expression signature for classification of tissue of origin of tumor samples

Publications (2)

Publication Number Publication Date
WO2010073248A2 WO2010073248A2 (en) 2010-07-01
WO2010073248A3 true WO2010073248A3 (en) 2010-09-16

Family

ID=42288202

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IL2009/001212 Ceased WO2010073248A2 (en) 2007-03-27 2009-12-23 Gene expression signature for classification of tissue of origin of tumor samples

Country Status (2)

Country Link
CN (1) CN102333888B (en)
WO (1) WO2010073248A2 (en)

Cited By (11)

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US8541170B2 (en) 2008-11-17 2013-09-24 Veracyte, Inc. Methods and compositions of molecular profiling for disease diagnostics
US8669057B2 (en) 2009-05-07 2014-03-11 Veracyte, Inc. Methods and compositions for diagnosis of thyroid conditions
US9495515B1 (en) 2009-12-09 2016-11-15 Veracyte, Inc. Algorithms for disease diagnostics
US10114924B2 (en) 2008-11-17 2018-10-30 Veracyte, Inc. Methods for processing or analyzing sample of thyroid tissue
US10422009B2 (en) 2009-03-04 2019-09-24 Genomedx Biosciences Inc. Compositions and methods for classifying thyroid nodule disease
US10446272B2 (en) 2009-12-09 2019-10-15 Veracyte, Inc. Methods and compositions for classification of samples
US11217329B1 (en) 2017-06-23 2022-01-04 Veracyte, Inc. Methods and systems for determining biological sample integrity
US11639527B2 (en) 2014-11-05 2023-05-02 Veracyte, Inc. Methods for nucleic acid sequencing
US11976329B2 (en) 2013-03-15 2024-05-07 Veracyte, Inc. Methods and systems for detecting usual interstitial pneumonia
US12297505B2 (en) 2014-07-14 2025-05-13 Veracyte, Inc. Algorithms for disease diagnostics
US12534763B2 (en) 2023-03-09 2026-01-27 Veracyte, Inc. Systems and methods of diagnosing idiopathic pulmonary fibrosis

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US9096906B2 (en) 2007-03-27 2015-08-04 Rosetta Genomics Ltd. Gene expression signature for classification of tissue of origin of tumor samples
WO2009143603A1 (en) 2008-05-28 2009-12-03 Genomedx Biosciences, Inc. Systems and methods for expression-based discrimination of distinct clinical disease states in prostate cancer
WO2011154008A1 (en) * 2010-06-11 2011-12-15 Rigshospitalet Microrna classification of thyroid follicular neoplasia
WO2012010584A1 (en) * 2010-07-20 2012-01-26 Febit Holding Gmbh Complex mirna sets as novel biomarkers for gastric cancer
CA2817882C (en) 2010-11-17 2022-08-23 Asuragen, Inc. Mirnas as biomarkers for distinguishing benign from malignant thyroid neoplasms
US20130267443A1 (en) 2010-11-19 2013-10-10 The Regents Of The University Of Michigan ncRNA AND USES THEREOF
EP2643479B1 (en) * 2010-11-22 2017-09-13 Rosetta Genomics Ltd Methods and materials for classification of tissue of origin of tumor samples
EP2505663A1 (en) 2011-03-30 2012-10-03 IFOM Fondazione Istituto Firc di Oncologia Molecolare A method to identify asymptomatic high-risk individuals with early stage lung cancer by means of detecting miRNAs in biologic fluids
WO2012131670A2 (en) * 2011-03-28 2012-10-04 Rosetta Genomics Ltd Methods for lung cancer clasification
US9568483B2 (en) * 2011-04-18 2017-02-14 Cornell University Molecular subtyping, prognosis and treatment of prostate cancer
WO2012161124A1 (en) * 2011-05-20 2012-11-29 国立大学法人愛媛大学 Composition containing micro rna or expression system thereof
US8831327B2 (en) 2011-08-30 2014-09-09 General Electric Company Systems and methods for tissue classification using attributes of a biomarker enhanced tissue network (BETN)
ES2688619T3 (en) * 2011-12-22 2018-11-05 Interna Technologies B.V. MiRNA to treat head and neck cancer
EP2653558B1 (en) 2012-04-18 2015-10-07 Roche Diagniostics GmbH A method of detecting nucleic acid targets using a statistical classifier
EP3435084B1 (en) 2012-08-16 2023-02-22 Decipher Biosciences, Inc. Prostate cancer prognostics using biomarkers
CN110506127B (en) 2016-08-24 2024-01-12 维拉科特Sd公司 Use of genomic signatures to predict responsiveness to postoperative radiotherapy in prostate cancer patients
WO2018132916A1 (en) 2017-01-20 2018-07-26 Genomedx Biosciences, Inc. Molecular subtyping, prognosis, and treatment of bladder cancer
EP3593140A4 (en) 2017-03-09 2021-01-06 Decipher Biosciences, Inc. PROSTATE CANCER SUB-TYPING TO PREDICT RESPONSE TO HORMONAL THERAPY
AU2018266733A1 (en) 2017-05-12 2020-01-16 Veracyte, Inc. Genetic signatures to predict prostate cancer metastasis and identify tumor aggressiveness
WO2019028285A2 (en) 2017-08-04 2019-02-07 Genomedx, Inc. Use of immune cell-specific gene expression for prognosis of prostate cancer and prediction of responsiveness to radiation therapy
US20200005901A1 (en) * 2018-06-30 2020-01-02 20/20 Genesystems, Inc Cancer classifier models, machine learning systems and methods of use
CN110706749B (en) * 2019-09-10 2022-06-10 至本医疗科技（上海）有限公司 Cancer type prediction system and method based on tissue and organ differentiation hierarchical relation

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* Cited by examiner, † Cited by third party
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US10672504B2 (en) 2008-11-17 2020-06-02 Veracyte, Inc. Algorithms for disease diagnostics
US12305238B2 (en) 2008-11-17 2025-05-20 Veracyte, Inc. Methods for treatment of thyroid cancer
US8541170B2 (en) 2008-11-17 2013-09-24 Veracyte, Inc. Methods and compositions of molecular profiling for disease diagnostics
US10114924B2 (en) 2008-11-17 2018-10-30 Veracyte, Inc. Methods for processing or analyzing sample of thyroid tissue
US10236078B2 (en) 2008-11-17 2019-03-19 Veracyte, Inc. Methods for processing or analyzing a sample of thyroid tissue
US10422009B2 (en) 2009-03-04 2019-09-24 Genomedx Biosciences Inc. Compositions and methods for classifying thyroid nodule disease
US10934587B2 (en) 2009-05-07 2021-03-02 Veracyte, Inc. Methods and compositions for diagnosis of thyroid conditions
US8669057B2 (en) 2009-05-07 2014-03-11 Veracyte, Inc. Methods and compositions for diagnosis of thyroid conditions
US12110554B2 (en) 2009-05-07 2024-10-08 Veracyte, Inc. Methods for classification of tissue samples as positive or negative for cancer
US12297503B2 (en) 2009-05-07 2025-05-13 Veracyte, Inc. Methods for classification of tissue samples as positive or negative for cancer
US10446272B2 (en) 2009-12-09 2019-10-15 Veracyte, Inc. Methods and compositions for classification of samples
US10731223B2 (en) 2009-12-09 2020-08-04 Veracyte, Inc. Algorithms for disease diagnostics
US9856537B2 (en) 2009-12-09 2018-01-02 Veracyte, Inc. Algorithms for disease diagnostics
US9495515B1 (en) 2009-12-09 2016-11-15 Veracyte, Inc. Algorithms for disease diagnostics
US11976329B2 (en) 2013-03-15 2024-05-07 Veracyte, Inc. Methods and systems for detecting usual interstitial pneumonia
US12297505B2 (en) 2014-07-14 2025-05-13 Veracyte, Inc. Algorithms for disease diagnostics
US11639527B2 (en) 2014-11-05 2023-05-02 Veracyte, Inc. Methods for nucleic acid sequencing
US11217329B1 (en) 2017-06-23 2022-01-04 Veracyte, Inc. Methods and systems for determining biological sample integrity
US12534763B2 (en) 2023-03-09 2026-01-27 Veracyte, Inc. Systems and methods of diagnosing idiopathic pulmonary fibrosis

Also Published As

Publication number Publication date
CN102333888B (en) 2013-07-10
WO2010073248A2 (en) 2010-07-01
CN102333888A (en) 2012-01-25

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