WO2002018659A3 - Method for determining alleles - Google Patents

Method for determining alleles Download PDF

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Publication number
WO2002018659A3
WO2002018659A3 PCT/US2001/041956 US0141956W WO0218659A3 WO 2002018659 A3 WO2002018659 A3 WO 2002018659A3 US 0141956 W US0141956 W US 0141956W WO 0218659 A3 WO0218659 A3 WO 0218659A3
Authority
WO
WIPO (PCT)
Prior art keywords
primers
primer
alleles
identifying
separating
Prior art date
Application number
PCT/US2001/041956
Other languages
French (fr)
Other versions
WO2002018659A2 (en
Inventor
Xiangjun Liu
Original Assignee
Haplogen Llc
Xiangjun Liu
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 Haplogen Llc, Xiangjun Liu filed Critical Haplogen Llc
Priority to JP2002522564A priority Critical patent/JP2004520812A/en
Priority to AU2001289177A priority patent/AU2001289177A1/en
Priority to CA002421078A priority patent/CA2421078A1/en
Publication of WO2002018659A2 publication Critical patent/WO2002018659A2/en
Publication of WO2002018659A3 publication Critical patent/WO2002018659A3/en

Links

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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

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

Abstract

The present invention provides methods and kits for separating and identifying alleles, and thereby the haplotype, in genomic DNA samples. The method generally involves hybridizing primers specific to polymorphic sites within the alleles to the DNA sample, elongating the primers by one or more nucleic acids, separating the elongated primers and identifying the alleles utilizing the elongated primer. The method also allows for a ligation of two primers, their separation and subsequent use in identifying the targeted allele. The method further provides that another primer can be used as a blocking site for elongation of the first primer such that a stretch of DNA that includes a polymorphic site is replicated and identified. The unextended or extended primers can be labeled so that the primer can be easily separated and/or identified.
PCT/US2001/041956 2000-08-30 2001-08-30 Method for determining alleles WO2002018659A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
JP2002522564A JP2004520812A (en) 2000-08-30 2001-08-30 Methods for determining alleles
AU2001289177A AU2001289177A1 (en) 2000-08-30 2001-08-30 Method for determining alleles
CA002421078A CA2421078A1 (en) 2000-08-30 2001-08-30 Method for determining alleles

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US22899400P 2000-08-30 2000-08-30
US60/228,994 2000-08-30

Publications (2)

Publication Number Publication Date
WO2002018659A2 WO2002018659A2 (en) 2002-03-07
WO2002018659A3 true WO2002018659A3 (en) 2003-07-31

Family

ID=22859388

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/041956 WO2002018659A2 (en) 2000-08-30 2001-08-30 Method for determining alleles

Country Status (5)

Country Link
JP (1) JP2004520812A (en)
CN (1) CN1293204C (en)
AU (1) AU2001289177A1 (en)
CA (1) CA2421078A1 (en)
WO (1) WO2002018659A2 (en)

Families Citing this family (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2005525787A (en) * 2001-10-24 2005-09-02 シンギュレックス・インコーポレイテッド Detection method of gene haplotype by interaction with probe
ATE520707T1 (en) 2001-11-13 2011-09-15 Univ Pennsylvania METHOD FOR THE DETECTION AND/OR IDENTIFICATION OF ADENO-ASSOCIATED VIRUS (AAV) SEQUENCES AND ISOLATION OF NEW SEQUENCES IDENTIFIED THEREFROM
AU2002360291A1 (en) 2001-12-17 2003-06-30 The Trustees Of The University Of Pennsylvania Adeno-associated virus (aav) serotype 8 sequences
ES2526341T3 (en) 2001-12-17 2015-01-09 The Trustees Of The University Of Pennsylvania Sequences of serotype 9 of adeno-associated virus (AAV), vectors containing them, and uses thereof
JP3752466B2 (en) 2002-04-24 2006-03-08 株式会社日立製作所 Genetic testing method
EP1536021A1 (en) * 2003-11-27 2005-06-01 Consortium National de Recherche en Genomique (CNRG) Method for HLA typing
GB0406863D0 (en) * 2004-03-26 2004-04-28 Qiagen As Nucleic acid sequencing
US20050282195A1 (en) * 2004-04-30 2005-12-22 Applera Corporation Compositions, methods, and kits for (MIS)ligating oligonucleotides
GB0600116D0 (en) * 2006-01-05 2006-02-15 Univ Cardiff Allele-specific sequencing
CA2695549C (en) * 2007-08-07 2019-01-08 Monsanto Technology Llc Methods and compositions for selecting soybean plants resistant to southern root knot nematode
EP2411543B1 (en) * 2009-03-27 2017-04-19 Life Technologies Corporation Methods, compositions, and kits for detecting allelic variants
JP2011072222A (en) * 2009-09-29 2011-04-14 Kitasato Otsuka Biomedical Assay Kenkyusho:Kk Method for detecting target nucleic acid
CA2792433C (en) 2010-03-08 2016-10-11 Gerassimos Makrigiorgos Full cold-pcr enrichment with reference blocking sequence
CA2828535A1 (en) * 2011-02-28 2012-09-07 Transgenomic, Inc. Kit and method for sequencing a target dna in a mixed population
DK2691541T3 (en) 2011-03-31 2018-01-22 Dana Farber Cancer Inst Inc PROCEDURE FOR ENRICHMENT OF SINGLE DRAWED MUTANTS SEQUENCES FROM A MIXTURE OF WILD TYPE AND MUTANTS
US9133490B2 (en) 2012-05-16 2015-09-15 Transgenomic, Inc. Step-up method for COLD-PCR enrichment
US10913977B2 (en) 2013-07-24 2021-02-09 Dana-Farber Cancer Institute, Inc. Methods and compositions to enable enrichment of minor DNA alleles by limiting denaturation time in PCR or simply enable enrichment of minor DNA alleles by limiting the denaturation time in PCR
KR102390075B1 (en) 2014-03-09 2022-04-26 더 트러스티스 오브 더 유니버시티 오브 펜실베니아 Compositions useful in treatment of ornithine transcarbamylase (otc) deficiency
US11371090B2 (en) 2016-12-12 2022-06-28 Dana-Farber Cancer Institute, Inc. Compositions and methods for molecular barcoding of DNA molecules prior to mutation enrichment and/or mutation detection
WO2019023243A1 (en) 2017-07-24 2019-01-31 Dana-Farber Cancer Institute, Inc. Methods and compositions for selecting and amplifying dna targets in a single reaction mixture
CN118207338A (en) * 2024-05-20 2024-06-18 杭州迪谱医学检验实验室有限公司 Multiple hypersensitive somatic mutation detection method based on nucleic acid mass spectrum

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1990009455A1 (en) * 1989-02-13 1990-08-23 Geneco Pty Ltd Detection of a nucleic acid sequence or a change therein
WO1993025563A1 (en) * 1992-06-17 1993-12-23 City Of Hope A method of detecting and discriminating between nucleic acid sequences
US5468611A (en) * 1990-06-27 1995-11-21 The Blood Center Research Foundation, Inc. Method for HLA typing
WO1996026291A1 (en) * 1995-02-24 1996-08-29 The University Of Nottingham Mutation detection using solid phase pcr
WO1997031256A2 (en) * 1996-02-09 1997-08-28 Cornell Research Foundation, Inc. Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2266847A1 (en) * 1996-09-24 1998-04-02 Rapigene, Inc. Compositions and methods for enhancing hybridization specificity

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1990009455A1 (en) * 1989-02-13 1990-08-23 Geneco Pty Ltd Detection of a nucleic acid sequence or a change therein
US5468611A (en) * 1990-06-27 1995-11-21 The Blood Center Research Foundation, Inc. Method for HLA typing
WO1993025563A1 (en) * 1992-06-17 1993-12-23 City Of Hope A method of detecting and discriminating between nucleic acid sequences
WO1996026291A1 (en) * 1995-02-24 1996-08-29 The University Of Nottingham Mutation detection using solid phase pcr
WO1997031256A2 (en) * 1996-02-09 1997-08-28 Cornell Research Foundation, Inc. Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
KAWAI S ET AL: "A SIMPLE METHOD OF HLA-DRB TYPING USING ENZYMATICALLY AMPLIFIED DNA AND IMMOBILIZED PROBES ON MICROTITER PLATE", HUMAN IMMUNOLOGY, NEW YORK, NY, US, vol. 41, no. 2, 1994, pages 121 - 126, XP000890112, ISSN: 0198-8859 *
NEWTON C R ET AL: "ANALYSIS OF ANY POINT MUTATION IN DNA. THE AMPLIFICATION REFRACTORY MUTATION SYSTEM (ARMS)", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 17, no. 7, 11 April 1989 (1989-04-11), pages 2503 - 2516, XP000141596, ISSN: 0305-1048 *
NICKERSON D A ET AL: "AUTOMATED DNA DIAGNOSTICS USING AN ELISA-BASED OLIGONUCLEOTIDE LIGATION ASSAY", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 87, no. 22, 1 November 1990 (1990-11-01), pages 8923 - 8927, XP000209335, ISSN: 0027-8424 *
PASTINEN TOMI ET AL: "A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays.", GENOME RESEARCH, vol. 10, no. 7, July 2000 (2000-07-01), pages 1031 - 1042, XP002228091, ISSN: 1088-9051 *
PREZANT T R ET AL: "TRAPPED-OLIGONUCLEOTIDE NUCLEOTIDE INCORPORATION (TONI) ASSAY, A SIMPLE METHOD FOR SCREENING POINT MUTATIONS", HUMAN MUTATION, WILEY-LISS, NEW YORK, NY, US, vol. 1, no. 2, 1992, pages 159 - 164, XP000571693, ISSN: 1059-7794 *
TOBE V O ET AL: "SINGLE-WELL GENOTYPING OF DIALLELIC SEQUENCE VARIATIONS BY A TWO-COLOR ELISA-BASED OLIGONUCLEOTIDE LIGATION ASSAY", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 24, no. 19, 1996, pages 3728 - 3732, XP000978683, ISSN: 0305-1048 *

Also Published As

Publication number Publication date
JP2004520812A (en) 2004-07-15
CN1501982A (en) 2004-06-02
AU2001289177A1 (en) 2002-03-13
CA2421078A1 (en) 2002-03-07
CN1293204C (en) 2007-01-03
WO2002018659A2 (en) 2002-03-07

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