WO1999045153A3 - An iterative and regenerative dna sequencing method - Google Patents

An iterative and regenerative dna sequencing method Download PDF

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Publication number
WO1999045153A3
WO1999045153A3 PCT/US1999/004883 US9904883W WO9945153A3 WO 1999045153 A3 WO1999045153 A3 WO 1999045153A3 US 9904883 W US9904883 W US 9904883W WO 9945153 A3 WO9945153 A3 WO 9945153A3
Authority
WO
WIPO (PCT)
Prior art keywords
dna
segments
iterative
automation
sequence
Prior art date
Application number
PCT/US1999/004883
Other languages
French (fr)
Other versions
WO1999045153A2 (en
Inventor
Douglas H Jones
Original Assignee
Univ Iowa Res Found
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 Univ Iowa Res Found filed Critical Univ Iowa Res Found
Priority to AU30695/99A priority Critical patent/AU3069599A/en
Publication of WO1999045153A2 publication Critical patent/WO1999045153A2/en
Publication of WO1999045153A3 publication Critical patent/WO1999045153A3/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
    • C12Q1/6869—Methods for sequencing
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • 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
    • 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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation

Abstract

An iterative and regenerative method for sequencing DNA is described. This method sequences DNA in discrete intervals starting at one end of a double stranded DNA segment. This method overcomes problems inherent in other sequencing methods, including the need for gel resolution of DNA fragments and the generation of artifacts caused by single-stranded DNA secondary structures. A particular advantage of this invention is that it can create offset collections of DNA segments and sequence the segments in parallel to provide continuous sequence information over long intervals. This method is also suitable for automation and multiplex automation to sequence large sets of segments.
PCT/US1999/004883 1998-03-05 1999-03-04 An iterative and regenerative dna sequencing method WO1999045153A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU30695/99A AU3069599A (en) 1998-03-05 1999-03-04 An iterative and regenerative dna sequencing method

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US09/035,183 1998-03-05
US09/035,183 US6258533B1 (en) 1996-11-01 1998-03-05 Iterative and regenerative DNA sequencing method

Publications (2)

Publication Number Publication Date
WO1999045153A2 WO1999045153A2 (en) 1999-09-10
WO1999045153A3 true WO1999045153A3 (en) 1999-10-21

Family

ID=21881154

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1999/004883 WO1999045153A2 (en) 1998-03-05 1999-03-04 An iterative and regenerative dna sequencing method

Country Status (3)

Country Link
US (3) US6258533B1 (en)
AU (1) AU3069599A (en)
WO (1) WO1999045153A2 (en)

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US9012144B2 (en) 2003-11-12 2015-04-21 Fluidigm Corporation Short cycle methods for sequencing polynucleotides
US9540689B2 (en) 1998-05-01 2017-01-10 Life Technologies Corporation Method of determining the nucleotide sequence of oligonucleotides and DNA molecules

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US5710000A (en) * 1994-09-16 1998-01-20 Affymetrix, Inc. Capturing sequences adjacent to Type-IIs restriction sites for genomic library mapping
US6780591B2 (en) 1998-05-01 2004-08-24 Arizona Board Of Regents Method of determining the nucleotide sequence of oligonucleotides and DNA molecules
US7056661B2 (en) * 1999-05-19 2006-06-06 Cornell Research Foundation, Inc. Method for sequencing nucleic acid molecules
US7501245B2 (en) 1999-06-28 2009-03-10 Helicos Biosciences Corp. Methods and apparatuses for analyzing polynucleotide sequences
US20030044785A1 (en) * 2001-05-01 2003-03-06 American Type Culture Collection Method for identifying and genotyping microorganisms
DE10144132A1 (en) * 2001-09-07 2003-03-27 Axaron Bioscience Ag Generating and sequencing nucleic acid tags of uniform length, useful e.g. in expression analysis, by cutting double stranded DNA with restriction enzyme then concatamerization
US6902914B2 (en) * 2001-09-28 2005-06-07 Sigma-Aldrich, Co. Recombinant DNA processes using a dNTP mixture containing modified nucleotides
AU2003210259A1 (en) * 2002-02-21 2003-09-09 Nanogen Recognomics Gmbh Method for detecting single nucleotide polymorphisms
AU2003249681A1 (en) * 2002-05-31 2003-12-19 Diversa Corporation Multiplexed systems for nucleic acid sequencing
WO2004020015A2 (en) * 2002-08-29 2004-03-11 Becton Dickinson And Company Microprotrusion arrays and methods for using same to deliver substances into tissue
US7049073B2 (en) 2002-10-30 2006-05-23 The University Of Chicago Double stranded nucleic acid biochips
GB0308851D0 (en) * 2003-04-16 2003-05-21 Lingvitae As Method
WO2005080605A2 (en) 2004-02-19 2005-09-01 Helicos Biosciences Corporation Methods and kits for analyzing polynucleotide sequences
US7476503B2 (en) * 2004-09-17 2009-01-13 Pacific Biosciences Of California, Inc. Apparatus and method for performing nucleic acid analysis
US7170050B2 (en) 2004-09-17 2007-01-30 Pacific Biosciences Of California, Inc. Apparatus and methods for optical analysis of molecules
DE102004049532A1 (en) * 2004-10-09 2006-04-13 Fischer, Achim, Dr. Sequencing of Nucleic Acids via Beach Displacement
US7476504B2 (en) * 2005-01-31 2009-01-13 Pacific Biosciences Of California, Inc. Use of reversible extension terminator in nucleic acid sequencing
GB0504182D0 (en) * 2005-03-01 2005-04-06 Lingvitae As Method
US7666593B2 (en) 2005-08-26 2010-02-23 Helicos Biosciences Corporation Single molecule sequencing of captured nucleic acids
US20080131937A1 (en) * 2006-06-22 2008-06-05 Applera Corporation Conversion of Target Specific Amplification to Universal Sequencing
WO2008045575A2 (en) * 2006-10-13 2008-04-17 J. Craig Venter Institute, Inc. Sequencing method
CA2719747C (en) 2008-03-28 2018-02-20 Pacific Biosciences Of California, Inc. Compositions and methods for nucleic acid sequencing
ES2752025T3 (en) 2008-07-25 2020-04-02 Wagner Richard W Protein screening methods
JP5795313B2 (en) * 2009-07-29 2015-10-14 パイロベット ピーティーイー エルティーディーＰｙｒｏｂｅｔｔ Ｐｔｅ Ｌｔｄ Methods and apparatus for performing assays
WO2011053987A1 (en) * 2009-11-02 2011-05-05 Nugen Technologies, Inc. Compositions and methods for targeted nucleic acid sequence selection and amplification
CA2852949A1 (en) 2011-10-19 2013-04-25 Nugen Technologies, Inc. Compositions and methods for directional nucleic acid amplification and sequencing
EP3578697B1 (en) 2012-01-26 2024-03-06 Tecan Genomics, Inc. Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library generation
US8597882B2 (en) * 2012-02-03 2013-12-03 Pyrobett Pte. Ltd. Method and apparatus for conducting an assay
US9957549B2 (en) 2012-06-18 2018-05-01 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
US20150011396A1 (en) 2012-07-09 2015-01-08 Benjamin G. Schroeder Methods for creating directional bisulfite-converted nucleic acid libraries for next generation sequencing
CN104619863A (en) * 2012-07-13 2015-05-13 生命技术公司 Human identifiation using a panel of SNPs
EP2971130A4 (en) 2013-03-15 2016-10-05 Nugen Technologies Inc Sequential sequencing
CN105849264B (en) 2013-11-13 2019-09-27 纽亘技术公司 For identifying the composition and method that repeat sequencing reading
US9745614B2 (en) 2014-02-28 2017-08-29 Nugen Technologies, Inc. Reduced representation bisulfite sequencing with diversity adaptors
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CA3028002A1 (en) 2016-06-27 2018-01-04 Juno Therapeutics, Inc. Method of identifying peptide epitopes, molecules that bind such epitopes and related uses
US11099202B2 (en) 2017-10-20 2021-08-24 Tecan Genomics, Inc. Reagent delivery system
US11851679B2 (en) 2017-11-01 2023-12-26 Juno Therapeutics, Inc. Method of assessing activity of recombinant antigen receptors
WO2022035834A1 (en) * 2020-08-10 2022-02-17 Integral Molecular, Inc. Methods and compositions for making antibody libraries and antibodies isolated from the same
US20220336052A1 (en) * 2021-04-19 2022-10-20 University Of Utah Research Foundation Systems and methods for facilitating rapid genome sequence analysis

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Cited By (2)

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Publication number Priority date Publication date Assignee Title
US9540689B2 (en) 1998-05-01 2017-01-10 Life Technologies Corporation Method of determining the nucleotide sequence of oligonucleotides and DNA molecules
US9012144B2 (en) 2003-11-12 2015-04-21 Fluidigm Corporation Short cycle methods for sequencing polynucleotides

Also Published As

Publication number Publication date
US20030044784A1 (en) 2003-03-06
WO1999045153A2 (en) 1999-09-10
US6258533B1 (en) 2001-07-10
US20030175780A1 (en) 2003-09-18
AU3069599A (en) 1999-09-20

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