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WO2000058519A2 - Caracterisation de polymorphismes d'un seul nucleotide, dans des regions de codage de genes humains - Google Patents

Caracterisation de polymorphismes d'un seul nucleotide, dans des regions de codage de genes humains Download PDF

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Publication number
WO2000058519A2
WO2000058519A2 PCT/US2000/008440 US0008440W WO0058519A2 WO 2000058519 A2 WO2000058519 A2 WO 2000058519A2 US 0008440 W US0008440 W US 0008440W WO 0058519 A2 WO0058519 A2 WO 0058519A2
Authority
WO
WIPO (PCT)
Prior art keywords
allele
nucleic acid
polymoφhic
nucleotide
gene
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/US2000/008440
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English (en)
Other versions
WO2000058519A3 (fr
Inventor
David Altshuler
Michele Cargill
George Q. Daley
James S. Ireland
Eric S. Lander
Robert J. Lipshutz
Nila Patil
Pamela Sklar
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.)
Affymetrix Inc
Whitehead Institute for Biomedical Research
Original Assignee
Affymetrix Inc
Whitehead Institute for Biomedical Research
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
Application filed by Affymetrix Inc, Whitehead Institute for Biomedical Research filed Critical Affymetrix Inc
Priority to AU40500/00A priority Critical patent/AU4050000A/en
Publication of WO2000058519A2 publication Critical patent/WO2000058519A2/fr
Publication of WO2000058519A3 publication Critical patent/WO2000058519A3/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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Classifications

    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • 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
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • Candidate SNPs were either validated (if found by VDAs) or identified (if implicated by DHPLC) by DNA sequencing. For this pu ⁇ ose, sequences were amplified with PCR primers tailed with standard Ml 3 sequencing sites (-21 forward and -28 reverse) and conventional dye-primer sequencing was performed on ABI 377 sequencers. For candidate SNPs discovered by VDAs, one individual was chosen (a candidate homozygous variant, when available, or a candidate heterozygote) and sequencing was performed on one strand to confirm by visual inspection the presence of the SNP at the indicated position.
  • the proportion of non-synonymous SNPs expected to cause a non-conservative amino acid substitution was determined based on the actual codon usage in the 106 genes studied, the known frequencies of transitions and transversions, and the definition of non-conservative changes employed in the BLOSUM62 matrix. This implies that non-conservative cSNPs survive to be detected in such a survey at only about half of the rate of conservative, non-synonymous cSNPs.
  • the various types of SNPs differ not only in the rate of their occurrence, but also in the frequency of their minor alleles. This can be seen in several ways.
  • Polymo ⁇ hisms are detected in a target nucleic acid from an individual being analyzed.
  • genomic DNA virtually any biological sample (other than pure red blood cells) is suitable.
  • tissue samples include whole blood, semen, saliva, tears, urine, fecal material, sweat, buccal, skin and hair.
  • tissue sample must be obtained from an organ in which the target nucleic acid is expressed.
  • the target nucleic acid is a cytochrome P450
  • the liver is a suitable source.
  • Many of the methods described below require amplification of DNA from target samples. This can be accomplished by e.g., PCR. See generally PCR Technology: Principles and Applications for DNA Amplification (ed.
  • the invention further provides variant forms of nucleic acids and corresponding proteins.
  • the nucleic acids comprise one of the sequences described in Figures 5A-5QQQQQQ, column 11, in which the polymo ⁇ hic position is occupied by one of the alternative bases for that position.
  • Some nucleic acids encode full-length variant forms of proteins.
  • variant proteins have the prototypical amino acid sequences encoded by nucleic acid sequences shown in Figures 5A-5QQQQQQ, column 11, (read so as to be in- frame with the full-length coding sequence of which it is a component) except at an amino acid encoded by a codon including one of the polymo ⁇ hic positions shown in Figures 5A- 5QQQQQQ. That position is occupied by the amino acid coded by the corresponding codon in any of the alternative forms shown in Figures 5 A-
  • the present invention includes biologically active fragments of the polypeptides, or analogs thereof, including organic molecules which simulate the interactions of the peptides.
  • biologically active fragments include any portion of the full-length polypeptide which confers a biological function on the variant gene product, including ligand binding, and antibody binding.
  • Ligand binding includes binding by nucleic acids, proteins or polypeptides, small biologically active molecules, or large cellular structures.
  • Polyclonal and/or monoclonal antibodies that specifically bind to variant gene products but not to corresponding prototypical gene products are also provided. Antibodies can be made by injecting mice or other animals with the variant gene product or synthetic peptide fragments thereof.

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention concerne des segments d'acides nucléiques du génome humain, notamment des segments d'acides nucléiques provenant de la région de codage d'un gène, y compris des sites polymorphes. L'invention concerne également des amorces et sondes, spécifiques d'allèles, et s'hybridant à des régions flanquant ces sites ou contenant ceux-ci. On utilise ces acides nucléiques, amorces et sondes dans des applications telles que des corrélations de phénotypes, dans la médecine légale, la recherche de paternité, la médecine et l'analyse génétique.
PCT/US2000/008440 1999-03-31 2000-03-30 Caracterisation de polymorphismes d'un seul nucleotide, dans des regions de codage de genes humains Ceased WO2000058519A2 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU40500/00A AU4050000A (en) 1999-03-31 2000-03-30 Charaterization of single nucleotide polymorphisms in coding regions of human genes

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US12724899P 1999-03-31 1999-03-31
US60/127,248 1999-03-31

Publications (2)

Publication Number Publication Date
WO2000058519A2 true WO2000058519A2 (fr) 2000-10-05
WO2000058519A3 WO2000058519A3 (fr) 2001-08-23

Family

ID=22429104

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/008440 Ceased WO2000058519A2 (fr) 1999-03-31 2000-03-30 Caracterisation de polymorphismes d'un seul nucleotide, dans des regions de codage de genes humains

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AU (1) AU4050000A (fr)
WO (1) WO2000058519A2 (fr)

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002022887A1 (fr) * 2000-09-15 2002-03-21 Genaissance Pharmaceuticals, Inc. Haplotypes du gene htr5a
WO2001066801A3 (fr) * 2000-03-08 2003-01-09 Complexe Hospitalier De La Sag Polymorphismes de recepteurs de lipoproteines tres basse densite et utilisations associees
WO2002012499A3 (fr) * 2000-08-04 2003-08-28 Genaissance Pharmaceuticals Haplotypes du gene ntf3
WO2003089897A3 (fr) * 2001-10-09 2003-12-04 Vitivity Inc Diagnostic et traitement de maladie vasculaire
US7332597B2 (en) 2004-06-28 2008-02-19 University Of Kentucky Research Foundation Primers and probe to identify mycobacterium tuberculosis complex
US7910303B2 (en) * 2006-10-20 2011-03-22 Celera Corporation Genetic polymorphisms associated with venous thrombosis, methods of detection and uses thereof

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5830655A (en) 1995-05-22 1998-11-03 Sri International Oligonucleotide sizing using cleavable primers
US6958214B2 (en) 2000-07-10 2005-10-25 Sequenom, Inc. Polymorphic kinase anchor proteins and nucleic acids encoding the same
WO2003093296A2 (fr) 2002-05-03 2003-11-13 Sequenom, Inc. Muteines de proteines d'ancrage de kinase, leurs peptides, et procedes associes
CN108048575B (zh) * 2017-11-03 2021-06-15 中南大学湘雅医院 一种用于产前无创亲子鉴定的试剂盒及方法

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5705388A (en) * 1994-12-23 1998-01-06 Ribozyme Pharmaceuticals, Inc. CETP Ribozymes
WO1998020165A2 (fr) * 1996-11-06 1998-05-14 Whitehead Institute For Biomedical Research Marqueurs bialleliques

Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001066801A3 (fr) * 2000-03-08 2003-01-09 Complexe Hospitalier De La Sag Polymorphismes de recepteurs de lipoproteines tres basse densite et utilisations associees
US6833240B2 (en) 2000-03-08 2004-12-21 Mcgill University Very low density lipoprotein receptor polymorphisms and uses therefor
WO2002012499A3 (fr) * 2000-08-04 2003-08-28 Genaissance Pharmaceuticals Haplotypes du gene ntf3
WO2002022887A1 (fr) * 2000-09-15 2002-03-21 Genaissance Pharmaceuticals, Inc. Haplotypes du gene htr5a
WO2003089897A3 (fr) * 2001-10-09 2003-12-04 Vitivity Inc Diagnostic et traitement de maladie vasculaire
US7332597B2 (en) 2004-06-28 2008-02-19 University Of Kentucky Research Foundation Primers and probe to identify mycobacterium tuberculosis complex
US7910303B2 (en) * 2006-10-20 2011-03-22 Celera Corporation Genetic polymorphisms associated with venous thrombosis, methods of detection and uses thereof

Also Published As

Publication number Publication date
AU4050000A (en) 2000-10-16
WO2000058519A3 (fr) 2001-08-23

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