WO2000050632A3 - Polymorphic dna fragments and uses thereof - Google Patents

Polymorphic dna fragments and uses thereof Download PDF

Info

Publication number
WO2000050632A3
WO2000050632A3 PCT/US2000/004349 US0004349W WO0050632A3 WO 2000050632 A3 WO2000050632 A3 WO 2000050632A3 US 0004349 W US0004349 W US 0004349W WO 0050632 A3 WO0050632 A3 WO 0050632A3
Authority
WO
WIPO (PCT)
Prior art keywords
population
restriction
restriction fragments
pools
single stranded
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/US2000/004349
Other languages
French (fr)
Other versions
WO2000050632A9 (en
WO2000050632A2 (en
Inventor
Sydney Brenner
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.)
Lynx Therapeutics Inc
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 JP2000601195A priority Critical patent/JP4669614B2/en
Priority to AU32378/00A priority patent/AU779231B2/en
Priority to CA002372131A priority patent/CA2372131A1/en
Priority to EP00910255A priority patent/EP1157131A2/en
Publication of WO2000050632A2 publication Critical patent/WO2000050632A2/en
Publication of WO2000050632A3 publication Critical patent/WO2000050632A3/en
Anticipated expiration legal-status Critical
Publication of WO2000050632A9 publication Critical patent/WO2000050632A9/en
Ceased legal-status Critical Current

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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C12Q1/683—Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips

Landscapes

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

Abstract

The invention provides methods and materials for generating a reference library of restriction fragments from pooled nucleic acids that contain a sequence polymorphism. Preferably, such a library is formed by digesting genomic DNA from a pool of individuals with a first and a second restriction endonuclease to form a population of restriction fragments; isolating restriction fragments of the population digested by both the first and second restriction endonucleases and forming a first single stranded fragment population therefrom; separately isolating restriction fragments from the population digested by the first restriction endonuclease but not the second restriction endonuclease and forming a second single stranded fragment population therefrom; hybridizing the first and second single stranded fragment populations to form a population of duplexes; and isolating the population of duplexes to form a reference library of restriction fragments that contain 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 population pools. Such comparisons may be accomplished by competively 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 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 analyzed and sorted for identifying those microparticles carrying sequences for which the pools being compared exhibit different polymorphic frequencies.
PCT/US2000/004349 1999-02-22 2000-02-18 Polymorphic dna fragments and uses thereof Ceased WO2000050632A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
JP2000601195A JP4669614B2 (en) 1999-02-22 2000-02-18 Polymorphic DNA fragments and uses thereof
AU32378/00A AU779231B2 (en) 1999-02-22 2000-02-18 Polymorphic DNA fragments and uses thereof
CA002372131A CA2372131A1 (en) 1999-02-22 2000-02-18 Polymorphic dna fragments and uses thereof
EP00910255A EP1157131A2 (en) 1999-02-22 2000-02-18 Polymorphic dna fragments and uses thereof

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US12102399P 1999-02-22 1999-02-22
US60/121,023 1999-02-22
US15848399P 1999-10-08 1999-10-08
US60/158,483 1999-10-08

Publications (3)

Publication Number Publication Date
WO2000050632A2 WO2000050632A2 (en) 2000-08-31
WO2000050632A3 true WO2000050632A3 (en) 2001-03-29
WO2000050632A9 WO2000050632A9 (en) 2001-11-01

Family

ID=26819005

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/004349 Ceased WO2000050632A2 (en) 1999-02-22 2000-02-18 Polymorphic dna fragments and uses thereof

Country Status (6)

Country Link
US (1) US20060199198A1 (en)
EP (1) EP1157131A2 (en)
JP (1) JP4669614B2 (en)
AU (1) AU779231B2 (en)
CA (1) CA2372131A1 (en)
WO (1) WO2000050632A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11104948B2 (en) 2014-02-10 2021-08-31 Vela Operations Singapore Pte. Ltd. NGS systems control and methods involving the same

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030032020A1 (en) * 2000-08-21 2003-02-13 Sydney Brenner Polymorphic DNA fragments and uses thereof
US7435572B2 (en) 2002-04-12 2008-10-14 New England Biolabs, Inc. Methods and compositions for DNA manipulation
US7141371B2 (en) 2002-09-06 2006-11-28 State Of Oregon Acting By And Through The State Board Of Higher Education On Behalf Of The University Of Oregon Methods for detecting and localizing DNA mutations by microarray
CA2513889A1 (en) * 2003-01-29 2004-08-19 454 Corporation Double ended sequencing
JP2009523404A (en) * 2003-01-30 2009-06-25 アプレラ コーポレイション Genetic polymorphism associated with rheumatoid arthritis, detection method and use thereof
WO2004081187A2 (en) * 2003-03-10 2004-09-23 Applera Corporation Genetic polymorphisms associated with myocardial infarction, methods of detection and uses thereof
US7625699B2 (en) * 2003-03-10 2009-12-01 Celera Corporation Genetic polymorphisms associated with coronary stenosis, methods of detection and uses thereof
US7811794B2 (en) * 2003-03-18 2010-10-12 Celera Corporation Genetic polymorphisms associated with rheumatoid arthritis, methods of detection and uses thereof
WO2005074511A2 (en) * 2004-01-27 2005-08-18 The Board Of Trustees Of The Leland Stanford Junior University Methods and compositions for homozygous gene inactivation using collections of pre-defined nucleotide sequences complementary to chromosomal transcripts
DK1885882T3 (en) 2005-05-10 2011-04-11 State Of Oregon Acting By & Through The State Board Of Higher Eduction On Behalf Of The University O Methods for mapping polymorphisms and polymorphism microarray
US8399188B2 (en) 2006-09-28 2013-03-19 Illumina, Inc. Compositions and methods for nucleotide sequencing
US10364465B2 (en) 2013-11-12 2019-07-30 Life Technologies Corporation Reagents and methods for sequencing
GB201411603D0 (en) * 2014-06-30 2014-08-13 Vela Operations Pte Ltd Compositions for quantitative and/or semiquantitative mutation detection methods
CA3135856A1 (en) * 2019-04-01 2020-10-08 National University Corporation Kobe University Method for constructing chimeric plasmid library

Citations (8)

* 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
WO1996012039A1 (en) * 1994-10-13 1996-04-25 Lynx Therapeutics, Inc. Massively parallel sequencing of sorted polynucleotides
WO1996012014A1 (en) * 1994-10-13 1996-04-25 Lynx Therapeutics, Inc. Molecular tagging system
EP0735144A1 (en) * 1995-03-28 1996-10-02 Research Development Corporation Of Japan Method for molecular indexing categorising of expressed genes using restriction enzymes
WO1996041011A1 (en) * 1995-06-07 1996-12-19 Lynx Therapeutics, Inc. Oligonucleotide tags for sorting and identification
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

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ATE466109T1 (en) * 1995-06-07 2010-05-15 Solexa Inc METHOD FOR IMPROVING THE EFFICIENCY OF POLYNUCLEOTIDE SEQUENCING
EP1124990B1 (en) * 1998-10-27 2006-01-18 Affymetrix, Inc. Complexity management and analysis of genomic dna

Patent Citations (8)

* 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
WO1996012039A1 (en) * 1994-10-13 1996-04-25 Lynx Therapeutics, Inc. Massively parallel sequencing of sorted polynucleotides
WO1996012014A1 (en) * 1994-10-13 1996-04-25 Lynx Therapeutics, Inc. Molecular tagging system
EP0735144A1 (en) * 1995-03-28 1996-10-02 Research Development Corporation Of Japan Method for molecular indexing categorising of expressed genes using restriction enzymes
WO1996041011A1 (en) * 1995-06-07 1996-12-19 Lynx Therapeutics, Inc. Oligonucleotide tags for sorting and identification
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

Non-Patent Citations (2)

* 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 *
QIANG LIU ET AL: "RESTRICTION INDONUCLEASE FINGERPRINTING (REF): A SENSITIVE METHOD FOR SCREENING MUTATIONS IN LONG, CONTIGUOUS SEGMENTS OF DNA", BIOTECHNIQUES,US,EATON PUBLISHING, NATICK, vol. 18, no. 3, 1 March 1995 (1995-03-01), pages 470 - 477, XP000493933, ISSN: 0736-6205 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11104948B2 (en) 2014-02-10 2021-08-31 Vela Operations Singapore Pte. Ltd. NGS systems control and methods involving the same

Also Published As

Publication number Publication date
AU3237800A (en) 2000-09-14
JP4669614B2 (en) 2011-04-13
EP1157131A2 (en) 2001-11-28
US20060199198A1 (en) 2006-09-07
AU779231B2 (en) 2005-01-13
WO2000050632A9 (en) 2001-11-01
JP2002537774A (en) 2002-11-12
CA2372131A1 (en) 2000-08-31
WO2000050632A2 (en) 2000-08-31

Similar Documents

Publication Publication Date Title
Lavrentieva et al. High polymorphism level of genomic sequences flanking insertion sites of human endogenous retroviral long terminal repeats
EP2463386A3 (en) Nucleic acid analysis by random mixtures of non-overlapping fragments
WO2004033649A3 (en) High throughput multiplex dna sequence amplifications
WO2003016565A3 (en) Dna sequence analysis
WO1999035293A3 (en) Solid phase selection of differentially expressed genes
ZA200109609B (en) Microarray-based subtractive hybridization.
CA2500783A1 (en) Microarrays having multiple oligonucleotides in single array features
WO2002097113A3 (en) Sequencing by proxy
CN101142325A (en) Method for preparing polynucleotide for analysis
Tost et al. DNA analysis by mass spectrometry—past, present and future
EP0995804A3 (en) Nucleic acid analysis using complete N-mer arrays
MXPA03000575A (en) Methods for analysis and identification of transcribed genes, and fingerprinting.
US20050009020A1 (en) Microarray method for enriching dna fragments from complex mixtures
US20080076130A1 (en) Molecular haplotyping of genomic dna
Cabe et al. Microsatellite loci from the house wren (Troglodytes aedon)
WO2001036669A3 (en) Method for the controlled implementation of complex pcr amplifications
WO2002016645A3 (en) Polymorphic dna fragments and uses thereof
WO2003018746A3 (en) Estrogen receptor alpha variants and methods of detection thereof
WO2000026415A3 (en) A method for genomic substractive hybridization
WO1997024974A3 (en) Compositions and methods for diagnosis of mutation in the von hippel-lindau tumor suppressor gene
Odeberg et al. A cDNA RDA protocol using solid-phase technology suited for analysis in small tissue samples
EP2341146A3 (en) Method for determining chromatin structure
Gaudeul et al. Isolation and characterization of microsatellites in a perennial Apiaceae, Eryngium alpinum L.
Cabe et al. Dinucleotide microsatellite loci isolated from flowering dogwood (Cornus florida L.)
Pettersson et al. Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AL AM AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ DE DK DM EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
AK Designated states

Kind code of ref document: A3

Designated state(s): AE AL AM AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ DE DK DM EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A3

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

ENP Entry into the national phase

Ref document number: 2372131

Country of ref document: CA

Ref country code: JP

Ref document number: 2000 601195

Kind code of ref document: A

Format of ref document f/p: F

Ref country code: CA

Ref document number: 2372131

Kind code of ref document: A

Format of ref document f/p: F

WWE Wipo information: entry into national phase

Ref document number: 32378/00

Country of ref document: AU

WWE Wipo information: entry into national phase

Ref document number: 2000910255

Country of ref document: EP

AK Designated states

Kind code of ref document: C2

Designated state(s): AE AL AM AT AU AZ BA BB BG BR BY CA CH CN CR CU CZ DE DK DM EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: C2

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

COP Corrected version of pamphlet

Free format text: PAGES 1/19-19/19, DRAWINGS, REPLACED BY NEW PAGES 1/19-19/19; DUE TO LATE TRANSMITTAL BY THE RECEIVING OFFICE

WWP Wipo information: published in national office

Ref document number: 2000910255

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWG Wipo information: grant in national office

Ref document number: 32378/00

Country of ref document: AU