AU2003208480A1 - 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: AU2003208480A1
Authority: AU; Australia
Prior art keywords: fragments; nucleic acid; restriction; immobilized; sequence
Prior art date: 2002-03-05
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.): Abandoned

Application number

AU2003208480A

Other languages

English (en)

Inventor

Laurent Farinelli

Ilia Leview

Pascal Mayer

Magne Osteras

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.)

Solexa Ltd Great Britain

Lynx Therapeutics Inc

Original Assignee

Solexa Ltd Great Britain

Lynx Therapeutics Inc

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.)

2002-03-05

Filing date

2003-03-05

Publication date

2003-09-16

2002-03-05 Priority claimed from GB0205153A external-priority patent/GB0205153D0/en

2003-03-05 Application filed by Solexa Ltd Great Britain, Lynx Therapeutics Inc filed Critical Solexa Ltd Great Britain

2003-09-16 Publication of AU2003208480A1 publication Critical patent/AU2003208480A1/en

Status Abandoned legal-status Critical Current

Links

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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
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- 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
- 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
- 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)
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Proteomics, Peptides & Aminoacids (AREA)
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Analytical Chemistry (AREA)
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Molecular Biology (AREA)
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Biophysics (AREA)
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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)

AU2003208480A 2002-03-05 2003-03-05 Methods for detecting genome-wide sequence variations associated with a phenotype Abandoned AU2003208480A1 (en)

Applications Claiming Priority (5)

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
PCT/GB2003/000941 WO2003074734A2 (fr)	2002-03-05	2003-03-05	Procedes de detection de variations de sequence a l'echelle du genome associees a un phenotype

Publications (1)

Publication Number	Publication Date
AU2003208480A1 true AU2003208480A1 (en)	2003-09-16

Family

ID=27790185

Family Applications (1)

Application Number	Title	Priority Date	Filing Date
AU2003208480A Abandoned AU2003208480A1 (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 (fr)
JP (1)	JP2005518811A (fr)
KR (1)	KR20050008651A (fr)
AU (1)	AU2003208480A1 (fr)
CA (1)	CA2478722A1 (fr)
WO (1)	WO2003074734A2 (fr)

Families Citing this family (39)

* Cited by examiner, † Cited by third party
Publication number	Priority date	Publication date	Assignee	Title
EP1682680B2 (fr)	2003-10-31	2018-03-21	AB Advanced Genetic Analysis Corporation	Procedes de production d'une etiquette appariee a partir d'une sequence d'acides nucleiques et methodes d'utilisation associees
EP3175914A1 (fr)	2004-01-07	2017-06-07	Illumina Cambridge Limited	Perfectionnements apportés ou se rapportant à des réseaux moléculaires
US20050176019A1 (en) *	2004-02-10	2005-08-11	Beutel Bruce A.	Method for identification of the location of mutations in whole genomes
US20080096255A1 (en) *	2004-07-02	2008-04-24	Matthias Harbers	Method for Preparing Sequence Tags
CA2615323A1 (fr)	2005-06-06	2007-12-21	454 Life Sciences Corporation	Sequencage d'extremites appariees
GB0514935D0 (en)	2005-07-20	2005-08-24	Solexa Ltd	Methods for sequencing a polynucleotide template
GB0514910D0 (en)	2005-07-20	2005-08-24	Solexa Ltd	Method for sequencing a polynucleotide template
DE602007009634D1 (de) *	2006-01-04	2010-11-18	Si Lok	Verfahren zur zuordnung von nukleinsäuren und zur identifikation fein strukturierter variationen in nukleinsäuren sowie hilfsmittel dafür
US8192930B2 (en)	2006-02-08	2012-06-05	Illumina Cambridge Limited	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
US7901889B2 (en)	2007-07-26	2011-03-08	Pacific Biosciences Of California, Inc.	Molecular redundant sequencing
US20090093378A1 (en) *	2007-08-29	2009-04-09	Helen Bignell	Method for sequencing a polynucleotide template
WO2012044847A1 (fr)	2010-10-01	2012-04-05	Life Technologies Corporation	Adaptateurs d'acides nucléiques et leurs utilisations
US8530197B2 (en)	2008-01-09	2013-09-10	Applied Biosystems, Llc	Method of making a paired tag library for nucleic acid sequencing
US8202691B2 (en)	2008-01-25	2012-06-19	Illumina, Inc.	Uniform fragmentation of DNA using binding proteins
US12060554B2 (en)	2008-03-10	2024-08-13	Illumina, Inc.	Method for selecting and amplifying polynucleotides
WO2011025477A1 (fr)	2009-08-25	2011-03-03	Illumina, Inc.	Procédés de sélection et damplification de polynucléotides
WO2010048337A2 (fr)	2008-10-22	2010-04-29	Illumina, Inc.	Préservation d'informations liées à une méthylation d'adn génomique
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
US20220213540A1 (en) *	2019-04-22	2022-07-07	POSTECH Research and Business Development Foundation	Novel probe set for isothermal one-pot reaction, and uses thereof
JP2023517157A (ja)	2020-03-09	2023-04-24	イルミナ，インコーポレイテッド	ポリヌクレオチドを配列決定するための方法
AU2022409487A1 (en)	2021-12-16	2024-01-18	Illumina, Inc.	Hybrid clustering
US20240279733A1 (en)	2021-12-17	2024-08-22	Illumina, Inc.	Orthogonal hybridization
WO2023175021A1 (fr)	2022-03-15	2023-09-21	Illumina, Inc.	Procédés de préparation de banques de structures en boucle d'embranchement
WO2023175037A2 (fr)	2022-03-15	2023-09-21	Illumina, Inc.	Séquençage simultané de brins de complément avant et inverse sur des polynucléotides séparés pour la détection de méthylation
KR20250075532A (ko)	2022-09-19	2025-05-28	일루미나, 인코포레이티드	고정된 프라이머를 포함하는 변형가능한 중합체
US20240102067A1 (en)	2022-09-26	2024-03-28	Illumina, Inc.	Resynthesis Kits and Methods
US20240110221A1 (en)	2022-09-30	2024-04-04	Illumina, Inc.	Methods of modulating clustering kinetics
US20240124914A1 (en)	2022-09-30	2024-04-18	Illumina, Inc.	Thermophilic compositions for nucleic acid amplification
US20240124929A1 (en)	2022-09-30	2024-04-18	Illumina, Inc.	Mesophilic compositions for nucleic acid amplification
US20240110234A1 (en)	2022-09-30	2024-04-04	Illumina, Inc.	Amplification Compositions and Methods
WO2024256580A1 (fr)	2023-06-14	2024-12-19	Illumina, Inc.	Séquençage simultané avec des anneaux spatialement séparés
WO2024256581A1 (fr)	2023-06-14	2024-12-19	Illumina, Inc.	Identification de cytosines modifiées
WO2025062002A1 (fr)	2023-09-20	2025-03-27	Illumina, Inc.	Séquençage simultané à l'aide d'une traduction de coupure simple brin
WO2025062001A1 (fr)	2023-09-20	2025-03-27	Illumina, Inc.	Séquençage optimisé d'acides nucléiques
WO2025072683A1 (fr)	2023-09-29	2025-04-03	Illumina, Inc.	Supports solides et procédés pour l'amplification par invasion de brin
US20250207193A1 (en)	2023-12-22	2025-06-26	Illumina, Inc.	Reusable flow cells and methods of using them for nucleic acid sequencing

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number	Priority date	Publication date	Assignee	Title
AU631562B2 (en) *	1988-02-22	1992-12-03	Pioneer Hi-Bred International, Inc.	Genetic linkages between agronomically important genes and restriction fragment length polymorphisms
AU672760B2 (en) *	1991-09-24	1996-10-17	Keygene N.V.	Selective restriction fragment amplification: a general method for DNA fingerprinting
US5710000A (en) *	1994-09-16	1998-01-20	Affymetrix, Inc.	Capturing sequences adjacent to Type-IIs restriction sites for genomic library mapping
WO2000014282A1 (fr) *	1998-09-04	2000-03-16	Lynx Therapeutics, Inc.	Procede de depistage de polymorphisme genique
ATE317024T1 (de) *	1999-12-29	2006-02-15	Keygene Nv	Verfahren zur erzeugung von oligonukleotiden, im besonderen zur detektion amplifizierter restriktionsfragmente, die durch aflp erhalten wurden
EP2206791B1 (fr) *	2000-04-10	2016-07-13	Taxon Biosciences, Inc.	Procédés pour l'étude et l'analyse génétique de populations

2003
- 2003-03-05 AU AU2003208480A patent/AU2003208480A1/en not_active Abandoned
- 2003-03-05 JP JP2003573179A patent/JP2005518811A/ja not_active Withdrawn
- 2003-03-05 WO PCT/GB2003/000941 patent/WO2003074734A2/fr not_active Ceased
- 2003-03-05 KR KR10-2004-7013908A patent/KR20050008651A/ko not_active Withdrawn
- 2003-03-05 EP EP03706768A patent/EP1483404A2/fr not_active Withdrawn
- 2003-03-05 CA CA002478722A patent/CA2478722A1/fr not_active Abandoned

Also Published As

Publication number	Publication date
EP1483404A2 (fr)	2004-12-08
KR20050008651A (ko)	2005-01-21
CA2478722A1 (fr)	2003-09-12
WO2003074734A3 (fr)	2004-02-19
WO2003074734A2 (fr)	2003-09-12
JP2005518811A (ja)	2005-06-30

Publication	Publication Date	Title
US20040002090A1 (en)	2004-01-01	Methods for detecting genome-wide sequence variations associated with a phenotype
AU2003208480A1 (en)	2003-09-16	Methods for detecting genome-wide sequence variations associated with a phenotype
US5861245A (en)	1999-01-19	Arbitrarily primed polymerase chain reaction method for fingerprinting genomes
CN101374963B (zh)	2014-06-04	用于基于aflp的高通量多态性检测的方法
US10095832B2 (en)	2018-10-09	Strategies for high throughput identification and detection of polymorphisms
US4683195A (en)	1987-07-28	Process for amplifying, detecting, and/or-cloning nucleic acid sequences
US5851762A (en)	1998-12-22	Genomic mapping method by direct haplotyping using intron sequence analysis
US11319589B2 (en)	2022-05-03	Methods of determining the presence or absence of a plurality of target polynucleotides in a sample
EP1960541B1 (fr)	2013-04-24	Procede de tri a haut debit de populations de marquage de transposons et d'identification a grande echelle de sequences paralleles de sites d'insertion
CA2087042C (fr)	2006-04-04	Methode de cartographie genomique par haplotypage direct a l'aide de l'analyse de la sequence des introns
WO2000056923A2 (fr)	2000-09-28	Analyse genetique
IE83464B1 (en)	2004-06-02	Process for amplifying and detecting nucleic acid sequences
IE19930227A1 (en)	1986-09-28	Kit for use in amplifying and detecting nucleic acid sequences
IE83456B1 (en)	2004-06-02	Kit for use in amplifying and detecting nucleic acid sequences

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2006-08-03	MK1	Application lapsed section 142(2)(a) - no request for examination in relevant period