WO2003074734A3 - Methods for detecting genome-wide sequence variations associated with a phenotype - Google Patents

Methods for detecting genome-wide sequence variations associated with a phenotype Download PDF

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Publication number
WO2003074734A3
WO2003074734A3 PCT/GB2003/000941 GB0300941W WO03074734A3 WO 2003074734 A3 WO2003074734 A3 WO 2003074734A3 GB 0300941 W GB0300941 W GB 0300941W WO 03074734 A3 WO03074734 A3 WO 03074734A3
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WO
WIPO (PCT)
Prior art keywords
restriction
phenotype
methods
variations associated
sequence
Prior art date
Application number
PCT/GB2003/000941
Other languages
French (fr)
Other versions
WO2003074734A2 (en
Inventor
Pascal Mayer
Ilia Leviev
Magne Osteras
Laurent Farinelli
Original Assignee
Manteia S A
Pascal Mayer
Ilia Leviev
Magne Osteras
Laurent Farinelli
Lee Nicholas John
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 claimed from GB0205153A external-priority patent/GB0205153D0/en
Application filed by Manteia S A, Pascal Mayer, Ilia Leviev, Magne Osteras, Laurent Farinelli, Lee Nicholas John filed Critical Manteia S A
Priority to KR10-2004-7013908A priority Critical patent/KR20050008651A/en
Priority to CA002478722A priority patent/CA2478722A1/en
Priority to EP03706768A priority patent/EP1483404A2/en
Priority to JP2003573179A priority patent/JP2005518811A/en
Priority to AU2003208480A priority patent/AU2003208480A1/en
Publication of WO2003074734A2 publication Critical patent/WO2003074734A2/en
Publication of WO2003074734A3 publication Critical patent/WO2003074734A3/en

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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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/30—Phosphoric diester hydrolysing, i.e. nuclease
    • C12Q2521/301—Endonuclease

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

Abstract

The invention provides methods for determining genome-wide sequence variations associated with phenotype of a species in a hypothesis-free manner. In the methods of the invention, a set of restriction fragments for each of a sub-population of individuals having the phenotype are generated by digesting nucleic acids from the individual using one or more different restriction enzymes. A set of restriction sequence tags for the individual is then determined from the set of restriction fragments. The restriction sequence tags for the sub-population of organisms are compared and grouped into one or more groups, each of which comprising restriction sequence tags that comprise homologous sequences. The obtained one or more groups of restriction sequence tags identify the sequence variations associated with the phenotype. The methods of the invention can be used for, e.g., analysis of large numbers of sequence variants in many patient samples to identify subtle genetic risk factors.
PCT/GB2003/000941 2002-03-05 2003-03-05 Methods for detecting genome-wide sequence variations associated with a phenotype WO2003074734A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
KR10-2004-7013908A KR20050008651A (en) 2002-03-05 2003-03-05 Methods for detecting genome-wide sequence variations associated with a phenotype
CA002478722A CA2478722A1 (en) 2002-03-05 2003-03-05 Methods for detecting genome-wide sequence variations associated with a phenotype
EP03706768A EP1483404A2 (en) 2002-03-05 2003-03-05 Methods for detecting genome-wide sequence variations associated with a phenotype
JP2003573179A JP2005518811A (en) 2002-03-05 2003-03-05 A method for determining genome-wide sequence changes associated with a phenotype
AU2003208480A AU2003208480A1 (en) 2002-03-05 2003-03-05 Methods for detecting genome-wide sequence variations associated with a phenotype

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US36202302P 2002-03-05 2002-03-05
GB0205153.0 2002-03-05
GB0205153A GB0205153D0 (en) 2002-03-05 2002-03-05 Methods for detecting genome-wide sequence variations associated with a phenotype
US60/362,023 2002-03-05

Publications (2)

Publication Number Publication Date
WO2003074734A2 WO2003074734A2 (en) 2003-09-12
WO2003074734A3 true WO2003074734A3 (en) 2004-02-19

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2003/000941 WO2003074734A2 (en) 2002-03-05 2003-03-05 Methods for detecting genome-wide sequence variations associated with a phenotype

Country Status (6)

Country Link
EP (1) EP1483404A2 (en)
JP (1) JP2005518811A (en)
KR (1) KR20050008651A (en)
AU (1) AU2003208480A1 (en)
CA (1) CA2478722A1 (en)
WO (1) WO2003074734A2 (en)

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EP3175914A1 (en) 2004-01-07 2017-06-07 Illumina Cambridge Limited Improvements in or relating to molecular arrays
US20050176019A1 (en) * 2004-02-10 2005-08-11 Beutel Bruce A. Method for identification of the location of mutations in whole genomes
WO2006003721A1 (en) * 2004-07-02 2006-01-12 Kabushiki Kaisha Dnaform Method for preparing sequence tags
WO2007145612A1 (en) * 2005-06-06 2007-12-21 454 Life Sciences Corporation Paired end sequencing
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GB0514935D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Methods for sequencing a polynucleotide template
EP1969146B1 (en) * 2006-01-04 2010-10-06 Si Lok Methods for nucleic acid mapping and identification of fine-structural-variations in nucleic acids and utilities
CN101415839B (en) 2006-02-08 2012-06-27 亿明达剑桥有限公司 Method for sequencing a polynucleotide template
US7754429B2 (en) 2006-10-06 2010-07-13 Illumina Cambridge Limited Method for pair-wise sequencing a plurity of target polynucleotides
US8551704B2 (en) 2007-02-16 2013-10-08 Pacific Biosciences Of California, Inc. Controllable strand scission of mini circle DNA
CN101802220B (en) 2007-07-26 2013-07-31 加利福尼亚太平洋生物科学股份有限公司 Molecular redundant sequencing method
WO2009032167A1 (en) * 2007-08-29 2009-03-12 Illumina Cambridge Method for sequencing a polynucleotide template
EP2235217B1 (en) 2008-01-09 2016-04-20 Life Technologies Corporation Method of making a paired tag library for nucleic acid sequencing
US9540637B2 (en) 2008-01-09 2017-01-10 Life Technologies Corporation Nucleic acid adaptors and uses thereof
US8202691B2 (en) 2008-01-25 2012-06-19 Illumina, Inc. Uniform fragmentation of DNA using binding proteins
US8541207B2 (en) 2008-10-22 2013-09-24 Illumina, Inc. Preservation of information related to genomic DNA methylation
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US9012022B2 (en) 2012-06-08 2015-04-21 Illumina, Inc. Polymer coatings
US10910087B2 (en) * 2017-06-27 2021-02-02 Hyunghoon Cho Secure secret-sharing-based crowdsourcing for large-scale association studies of genomic and phenotypic data
JP7477183B2 (en) * 2019-04-22 2024-05-01 ポステック・リサーチ・アンド・ビジネス・ディベロップメント・ファウンデーション Novel isothermal single reaction probe set and its use
ES2965266T3 (en) 2020-03-09 2024-04-11 Illumina Inc Methods for polynucleotide sequencing
CA3223595A1 (en) 2021-12-16 2023-06-22 Xiaoyu Ma Hybrid clustering
CN118103528A (en) 2021-12-17 2024-05-28 因美纳有限公司 Orthogonal hybridization
AU2023233839A1 (en) 2022-03-15 2024-01-18 Illumina, Inc. Concurrent sequencing of forward and reverse complement strands on concatenated polynucleotides for methylation detection
WO2023175042A1 (en) 2022-03-15 2023-09-21 Illumina, Inc. Parallel sample and index sequencing
WO2024061799A1 (en) 2022-09-19 2024-03-28 Illumina, Inc. Deformable polymers comprising immobilised primers
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Also Published As

Publication number Publication date
JP2005518811A (en) 2005-06-30
CA2478722A1 (en) 2003-09-12
KR20050008651A (en) 2005-01-21
WO2003074734A2 (en) 2003-09-12
AU2003208480A1 (en) 2003-09-16
EP1483404A2 (en) 2004-12-08

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