WO2002016645A3 - Polymorphic dna fragments and uses thereof - Google Patents

Polymorphic dna fragments and uses thereof Download PDF

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Publication number
WO2002016645A3
WO2002016645A3 PCT/US2001/026115 US0126115W WO0216645A3 WO 2002016645 A3 WO2002016645 A3 WO 2002016645A3 US 0126115 W US0126115 W US 0126115W WO 0216645 A3 WO0216645 A3 WO 0216645A3
Authority
WO
WIPO (PCT)
Prior art keywords
pools
attached
microparticles
reference library
frequencies
Prior art date
Application number
PCT/US2001/026115
Other languages
French (fr)
Other versions
WO2002016645A2 (en
Inventor
Sydney Brenner
Original Assignee
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.)
Filing date
Publication date
Application filed by Lynx Therapeutics Inc filed Critical Lynx Therapeutics Inc
Priority to AU2001285155A priority Critical patent/AU2001285155A1/en
Publication of WO2002016645A2 publication Critical patent/WO2002016645A2/en
Publication of WO2002016645A3 publication Critical patent/WO2002016645A3/en

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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
    • C12Q1/6809—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
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • 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
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors

Abstract

The invention provides methods and materials for generating a reference library of restriction fragments from pooled nucleic acids that contain a sequence polymorphism. An important aspect of the invention is the use of the reference population of restriction fragments to compare the frequencies of polymorphic sequences between different populations pools. Such comparisons may be accomplished by competitively hybridizing DNA from the respective pools which has been enriched for the presence of a restriction site polymorphism with DNA from the reference population. Preferably, such competitive hybridization reactions are carried out on the reference library attached to one or more solid phase supports. Most preferably, members of the reference library are attached to individual microparticles so that each microparticle has a unique fragment attached. After competitive hybridization, the microparticles may be anaylzed and sorted to identify those microparticles carrying sequences for which the pools being compared exhibit different polymorphic frequencies.
PCT/US2001/026115 2000-08-21 2001-08-21 Polymorphic dna fragments and uses thereof WO2002016645A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2001285155A AU2001285155A1 (en) 2000-08-21 2001-08-21 Polymorphic dna fragments and uses thereof

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US22705800P 2000-08-21 2000-08-21
US60/227,058 2000-08-21

Publications (2)

Publication Number Publication Date
WO2002016645A2 WO2002016645A2 (en) 2002-02-28
WO2002016645A3 true WO2002016645A3 (en) 2003-04-03

Family

ID=22851571

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/026115 WO2002016645A2 (en) 2000-08-21 2001-08-21 Polymorphic dna fragments and uses thereof

Country Status (3)

Country Link
US (1) US20030032020A1 (en)
AU (1) AU2001285155A1 (en)
WO (1) WO2002016645A2 (en)

Families Citing this family (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6872529B2 (en) * 2001-07-25 2005-03-29 Affymetrix, Inc. Complexity management of genomic DNA
EP1713936B1 (en) * 2004-02-12 2009-12-09 Population Genetics Technologies Ltd Corporation of Great Britain Genetic analysis by sequence-specific sorting
US7407757B2 (en) * 2005-02-10 2008-08-05 Population Genetics Technologies Genetic analysis by sequence-specific sorting
WO2009031054A2 (en) * 2007-06-29 2009-03-12 Population Genetics Technologies Ltd. Methods and compositions for isolating nucleic acid sequence variants
WO2009040682A2 (en) * 2007-09-26 2009-04-02 Population Genetics Technologies Ltd. Methods and compositions for reducing the complexity of a nucleic acid sample
US20110059453A1 (en) * 2009-08-23 2011-03-10 Affymetrix, Inc. Poly(A) Tail Length Measurement by PCR

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1995025538A1 (en) * 1994-03-18 1995-09-28 The General Hospital Corporation Cleaved amplified rflp detection methods
EP0735144A1 (en) * 1995-03-28 1996-10-02 Research Development Corporation Of Japan Method for molecular indexing categorising of expressed genes using restriction enzymes
WO1998012352A1 (en) * 1996-09-18 1998-03-26 The General Hospital Corporation Cleaved amplified rflp detection methods
WO1998040515A1 (en) * 1997-03-10 1998-09-17 Mansour Samadpour Method for the identification of genetic subtypes
WO1999023256A1 (en) * 1997-10-30 1999-05-14 Cold Spring Harbor Laboratory Probe arrays and methods of using probe arrays for distinguishing dna
WO2000050632A2 (en) * 1999-02-22 2000-08-31 Lynx Therapeutics, Inc. Polymorphic dna fragments and uses thereof

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6013445A (en) * 1996-06-06 2000-01-11 Lynx Therapeutics, Inc. Massively parallel signature sequencing by ligation of encoded adaptors
US6352842B1 (en) * 1995-12-07 2002-03-05 Diversa Corporation Exonucease-mediated gene assembly in directed evolution
EP0912761A4 (en) * 1996-05-29 2004-06-09 Cornell Res Foundation Inc Detection of nucleic acid sequence differences using coupled ligase detection and polymerase chain reactions
US6480791B1 (en) * 1998-10-28 2002-11-12 Michael P. Strathmann Parallel methods for genomic analysis
US6534293B1 (en) * 1999-01-06 2003-03-18 Cornell Research Foundation, Inc. Accelerating identification of single nucleotide polymorphisms and alignment of clones in genomic sequencing
US6475736B1 (en) * 2000-05-23 2002-11-05 Variagenics, Inc. Methods for genetic analysis of DNA using biased amplification of polymorphic sites
AU2001293163A1 (en) * 2000-09-27 2002-04-08 Lynx Therapeutics, Inc. Method for determining relative abundance of nucleic acid sequences

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1995025538A1 (en) * 1994-03-18 1995-09-28 The General Hospital Corporation Cleaved amplified rflp detection methods
EP0735144A1 (en) * 1995-03-28 1996-10-02 Research Development Corporation Of Japan Method for molecular indexing categorising of expressed genes using restriction enzymes
WO1998012352A1 (en) * 1996-09-18 1998-03-26 The General Hospital Corporation Cleaved amplified rflp detection methods
WO1998040515A1 (en) * 1997-03-10 1998-09-17 Mansour Samadpour Method for the identification of genetic subtypes
WO1999023256A1 (en) * 1997-10-30 1999-05-14 Cold Spring Harbor Laboratory Probe arrays and methods of using probe arrays for distinguishing dna
WO2000050632A2 (en) * 1999-02-22 2000-08-31 Lynx Therapeutics, Inc. Polymorphic dna fragments and uses thereof

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
LISITSYN N ET AL: "CLONING THE DIFFERENCES BETWEEN TWO COMPLEX GENOMES", SCIENCE,US,AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE,, vol. 259, no. 5097, 12 February 1993 (1993-02-12), pages 946 - 951, XP000196441, ISSN: 0036-8075 *

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Publication number Publication date
WO2002016645A2 (en) 2002-02-28
AU2001285155A1 (en) 2002-03-04
US20030032020A1 (en) 2003-02-13

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