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WO2000055364A3 - Genetic analysis - Google Patents

Genetic analysis Download PDF

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Publication number
WO2000055364A3
WO2000055364A3 PCT/GB2000/000916 GB0000916W WO0055364A3 WO 2000055364 A3 WO2000055364 A3 WO 2000055364A3 GB 0000916 W GB0000916 W GB 0000916W WO 0055364 A3 WO0055364 A3 WO 0055364A3
Authority
WO
WIPO (PCT)
Prior art keywords
depletion
population
inter
perfectly matched
matched duplex
Prior art date
Application number
PCT/GB2000/000916
Other languages
French (fr)
Other versions
WO2000055364A2 (en
Inventor
Michael Alan Reeve
Nicholas Ian Workman
Luis Martin-Parras
Original Assignee
Amersham Pharm Biotech Uk Ltd
Michael Alan Reeve
Nicholas Ian Workman
Martin Parras Luis
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 Amersham Pharm Biotech Uk Ltd, Michael Alan Reeve, Nicholas Ian Workman, Martin Parras Luis filed Critical Amersham Pharm Biotech Uk Ltd
Priority to JP2000605780A priority Critical patent/JP2002538837A/en
Priority to CA002362771A priority patent/CA2362771A1/en
Priority to EP00909502A priority patent/EP1173609A2/en
Priority to AU31782/00A priority patent/AU3178200A/en
Publication of WO2000055364A2 publication Critical patent/WO2000055364A2/en
Publication of WO2000055364A3 publication Critical patent/WO2000055364A3/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
    • C12Q1/6813—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
    • C12Q1/6813—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)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (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)
  • Sampling And Sample Adjustment (AREA)

Abstract

A method is described for use in whole genome analysis. The method - termed inter-population perfectly matched duplex depletion - can overcome many of the limitations of current approaches based upon SNPs and linkage disequilibrium within isolated populations. Inter-population perfectly matched duplex depletion isolates a fragment (or fragments) containing differences between the 'affected' and 'unaffected' populations or cells. A convenient method - terminal restriction site profiling arrays (TRSPAs) - is described for the analysis of such fragments. A totally diagnostic internal control DNA is also described which allows both the extent and exact nature of any partial digestion to be unambiguously determined for inter-population perfectly matched duplex depletion or TRSPA restriction.
PCT/GB2000/000916 1999-03-12 2000-03-10 Genetic analysis WO2000055364A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
JP2000605780A JP2002538837A (en) 1999-03-12 2000-03-10 Genetic analysis
CA002362771A CA2362771A1 (en) 1999-03-12 2000-03-10 Genetic analysis
EP00909502A EP1173609A2 (en) 1999-03-12 2000-03-10 Genetic analysis
AU31782/00A AU3178200A (en) 1999-03-12 2000-03-10 Genetic analysis

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EP99301933.0 1999-03-12
EP99301933 1999-03-12

Publications (2)

Publication Number Publication Date
WO2000055364A2 WO2000055364A2 (en) 2000-09-21
WO2000055364A3 true WO2000055364A3 (en) 2001-10-11

Family

ID=8241266

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2000/000916 WO2000055364A2 (en) 1999-03-12 2000-03-10 Genetic analysis

Country Status (5)

Country Link
EP (1) EP1173609A2 (en)
JP (1) JP2002538837A (en)
AU (1) AU3178200A (en)
CA (1) CA2362771A1 (en)
WO (1) WO2000055364A2 (en)

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9206418B2 (en) 2011-10-19 2015-12-08 Nugen Technologies, Inc. Compositions and methods for directional nucleic acid amplification and sequencing
US9650628B2 (en) 2012-01-26 2017-05-16 Nugen Technologies, Inc. Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library regeneration
US9745614B2 (en) 2014-02-28 2017-08-29 Nugen Technologies, Inc. Reduced representation bisulfite sequencing with diversity adaptors
US9822408B2 (en) 2013-03-15 2017-11-21 Nugen Technologies, Inc. Sequential sequencing
US9957549B2 (en) 2012-06-18 2018-05-01 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
US11028430B2 (en) 2012-07-09 2021-06-08 Nugen Technologies, Inc. Methods for creating directional bisulfite-converted nucleic acid libraries for next generation sequencing

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
EP1885882B1 (en) * 2005-05-10 2011-01-26 State of Oregon acting by & through the State Board of Higher Eduction on behalf of the University of Oregon Methods of mapping polymorphisms and polymorphism microarrays
GB2487341A (en) * 2009-11-02 2012-07-18 Nugen Technologies Inc Compositions and methods for targeted nucleic acid sequence selection and amplification
JP6525473B2 (en) 2013-11-13 2019-06-05 ニューゲン テクノロジーズ， インコーポレイテッド Compositions and methods for identifying replicate sequencing leads
CA2957633A1 (en) 2014-08-06 2016-02-11 Nugen Technologies, Inc. Digital measurements from targeted sequencing
US11099202B2 (en) 2017-10-20 2021-08-24 Tecan Genomics, Inc. Reagent delivery system
US12059674B2 (en) 2020-02-03 2024-08-13 Tecan Genomics, Inc. Reagent storage system

Citations (12)

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Publication number Priority date Publication date Assignee Title
EP0226288A2 (en) * 1985-10-09 1987-06-24 Collaborative Research Inc. Means and method of testing for cystic fibrosis based on genetic linkage
US4771384A (en) * 1986-07-24 1988-09-13 Dnastar, Inc. System and method for fragmentation mapping
WO1989001526A1 (en) * 1987-08-07 1989-02-23 Genelabs Incorporated Coincidence cloning method and library
EP0466404A1 (en) * 1990-07-13 1992-01-15 Life Technologies, Inc. Size markers for electrophoretic analysis of DNA
WO1993017126A1 (en) * 1992-02-19 1993-09-02 The Public Health Research Institute Of The City Of New York, Inc. Novel oligonucleotide arrays and their use for sorting, isolating, sequencing, and manipulating nucleic acids
WO1994011383A1 (en) * 1992-11-12 1994-05-26 Cold Spring Harbor Laboratory A representational approach to dna analysis
US5376526A (en) * 1992-05-06 1994-12-27 The Board Of Trustees Of The Leland Stanford Junior University Genomic mismatch scanning
WO1995011971A1 (en) * 1993-10-28 1995-05-04 Life Technologies, Inc. Nucleic acid marker ladder for estimating mass
WO1995012688A1 (en) * 1993-01-11 1995-05-11 United States Biochemical Corporation Methods of analysis and manipulation of dna utilizing mismatch repair systems
WO1997029211A1 (en) * 1996-02-09 1997-08-14 The Government Of The United States Of America, Represented By The Secretary, Department Of Health And Human Services RESTRICTION DISPLAY (RD-PCR) OF DIFFERENTIALLY EXPRESSED mRNAs
US5710000A (en) * 1994-09-16 1998-01-20 Affymetrix, Inc. Capturing sequences adjacent to Type-IIs restriction sites for genomic library mapping
US5750335A (en) * 1992-04-24 1998-05-12 Massachusetts Institute Of Technology Screening for genetic variation

Patent Citations (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0226288A2 (en) * 1985-10-09 1987-06-24 Collaborative Research Inc. Means and method of testing for cystic fibrosis based on genetic linkage
US4771384A (en) * 1986-07-24 1988-09-13 Dnastar, Inc. System and method for fragmentation mapping
WO1989001526A1 (en) * 1987-08-07 1989-02-23 Genelabs Incorporated Coincidence cloning method and library
EP0466404A1 (en) * 1990-07-13 1992-01-15 Life Technologies, Inc. Size markers for electrophoretic analysis of DNA
WO1993017126A1 (en) * 1992-02-19 1993-09-02 The Public Health Research Institute Of The City Of New York, Inc. Novel oligonucleotide arrays and their use for sorting, isolating, sequencing, and manipulating nucleic acids
US5750335A (en) * 1992-04-24 1998-05-12 Massachusetts Institute Of Technology Screening for genetic variation
US5376526A (en) * 1992-05-06 1994-12-27 The Board Of Trustees Of The Leland Stanford Junior University Genomic mismatch scanning
WO1994011383A1 (en) * 1992-11-12 1994-05-26 Cold Spring Harbor Laboratory A representational approach to dna analysis
WO1995012688A1 (en) * 1993-01-11 1995-05-11 United States Biochemical Corporation Methods of analysis and manipulation of dna utilizing mismatch repair systems
WO1995011971A1 (en) * 1993-10-28 1995-05-04 Life Technologies, Inc. Nucleic acid marker ladder for estimating mass
US5710000A (en) * 1994-09-16 1998-01-20 Affymetrix, Inc. Capturing sequences adjacent to Type-IIs restriction sites for genomic library mapping
WO1997029211A1 (en) * 1996-02-09 1997-08-14 The Government Of The United States Of America, Represented By The Secretary, Department Of Health And Human Services RESTRICTION DISPLAY (RD-PCR) OF DIFFERENTIALLY EXPRESSED mRNAs

Non-Patent Citations (7)

* Cited by examiner, † Cited by third party
Title
ELLIS L A ET AL: "MUTS BINDING PROTECTS HETERODUPLEX DNA FROM EXONUCLEASE DIGESTION IN VITRO: A SIMPLE METHOD FOR DETECTING MUTATIONS", NUCLEIC ACIDS RESEARCH, vol. 22, no. 13, 11 July 1994 (1994-07-11), pages 2710/2711, XP002021164 *
ESPOSITO J J AND KNIGHT J C: "Orthopoxvirus DNA: A comparison of restriction profiles and maps", VIROLOGY, vol. 143, 1985, pages 230 - 251, XP000951520 *
KNEHR M ET AL.: "Isolation and characterization of a cDNA encoding rat liver cytosolic epoxide hydrolase and its functional expression in Escherichia coli", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 268, no. 23, 1993, pages 17623 - 17627, XP002165725 *
KOROLIK V ET AL.: "Differentiation of Campylobacter jejuni and Campylobacter coli strains by using restriction endonuclease DNA profiles and DNA fragment polymorphisms", JOURNAL OF CLINICAL MICROBIOLOGY, vol. 33, no. 5, 1995, pages 1136 - 1140, XP000951519 *
MASATO ORITA ET AL: "DETECTION OF POLYMORPHISMS OF HUMAN DNA BY GEL ELECTROPHORESIS AS SINGLE-STRAND CONFORMATION POLYMORPHISMS", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, vol. 86, no. 8, 1 April 1989 (1989-04-01), pages 2766 - 2770, XP000310584 *
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Cited By (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9206418B2 (en) 2011-10-19 2015-12-08 Nugen Technologies, Inc. Compositions and methods for directional nucleic acid amplification and sequencing
US9650628B2 (en) 2012-01-26 2017-05-16 Nugen Technologies, Inc. Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library regeneration
US10036012B2 (en) 2012-01-26 2018-07-31 Nugen Technologies, Inc. Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library generation
US10876108B2 (en) 2012-01-26 2020-12-29 Nugen Technologies, Inc. Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library generation
US9957549B2 (en) 2012-06-18 2018-05-01 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
US11028430B2 (en) 2012-07-09 2021-06-08 Nugen Technologies, Inc. Methods for creating directional bisulfite-converted nucleic acid libraries for next generation sequencing
US9822408B2 (en) 2013-03-15 2017-11-21 Nugen Technologies, Inc. Sequential sequencing
US10760123B2 (en) 2013-03-15 2020-09-01 Nugen Technologies, Inc. Sequential sequencing
US9745614B2 (en) 2014-02-28 2017-08-29 Nugen Technologies, Inc. Reduced representation bisulfite sequencing with diversity adaptors

Also Published As

Publication number Publication date
WO2000055364A2 (en) 2000-09-21
AU3178200A (en) 2000-10-04
CA2362771A1 (en) 2000-09-21
JP2002538837A (en) 2002-11-19
EP1173609A2 (en) 2002-01-23

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