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WO1997037041A3 - Dna sequencing by mass spectrometry - Google Patents

Dna sequencing by mass spectrometry Download PDF

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Publication number
WO1997037041A3
WO1997037041A3 PCT/US1997/004394 US9704394W WO9737041A3 WO 1997037041 A3 WO1997037041 A3 WO 1997037041A3 US 9704394 W US9704394 W US 9704394W WO 9737041 A3 WO9737041 A3 WO 9737041A3
Authority
WO
WIPO (PCT)
Prior art keywords
mass spectrometry
chain
mass
nucleoside triphosphates
dna sequencing
Prior art date
Application number
PCT/US1997/004394
Other languages
French (fr)
Other versions
WO1997037041A2 (en
WO1997037041A9 (en
Inventor
Hubert Koester
Original Assignee
Sequenom 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
Priority claimed from US08/617,010 external-priority patent/US6194144B1/en
Application filed by Sequenom Inc filed Critical Sequenom Inc
Priority to AU22175/97A priority Critical patent/AU2217597A/en
Publication of WO1997037041A2 publication Critical patent/WO1997037041A2/en
Publication of WO1997037041A3 publication Critical patent/WO1997037041A3/en
Publication of WO1997037041A9 publication Critical patent/WO1997037041A9/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
    • C12Q1/6872—Methods for sequencing involving mass spectrometry

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  • Life Sciences & Earth Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Physics & Mathematics (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (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)

Abstract

The invention describes a new method to sequence DNA. The improvements over the existing DNA sequencing technologies are high speed, high throughput, no electrophoresis and gel reading artifacts due to the complete absence of an electrophoretic step, and no costly reagents involving various substitutions with stable isotopes. The invention utilizes the Sanger sequencing strategy and assembles the sequence information by analysis of the nested fragments obtained by base-specific chain termination via their different molecular masses using mass spectrometry, as for example, MALDI or ES mass spectrometry. A futher increase in throughtput can be obtained by introducing mass-modifications in the oligonucleotide primer, chain-terminating nucleoside triphosphates and/or in the chain-elongating nucleoside triphosphates, as well as using integrated tag sequences which allow multiplexing by hybridization of tag specific probes with mass differentiated molecular weights.
PCT/US1997/004394 1996-03-18 1997-03-18 Dna sequencing by mass spectrometry WO1997037041A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU22175/97A AU2217597A (en) 1996-03-18 1997-03-18 Dna sequencing by mass spectrometry

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US08/617,010 1996-03-18
US08/617,010 US6194144B1 (en) 1993-01-07 1996-03-18 DNA sequencing by mass spectrometry
US54783596A 1996-08-20 1996-08-20
US5/547,835 1996-08-20

Publications (3)

Publication Number Publication Date
WO1997037041A2 WO1997037041A2 (en) 1997-10-09
WO1997037041A3 true WO1997037041A3 (en) 1997-12-04
WO1997037041A9 WO1997037041A9 (en) 1997-12-31

Family

ID=27068672

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1997/004394 WO1997037041A2 (en) 1996-03-18 1997-03-18 Dna sequencing by mass spectrometry

Country Status (2)

Country Link
AU (1) AU2217597A (en)
WO (1) WO1997037041A2 (en)

Cited By (18)

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US6958214B2 (en) 2000-07-10 2005-10-25 Sequenom, Inc. Polymorphic kinase anchor proteins and nucleic acids encoding the same
US7074563B2 (en) 1995-03-17 2006-07-11 Sequenom, Inc. Mass spectrometric methods for detecting mutations in a target nucleic acid
US7132519B2 (en) 1996-12-10 2006-11-07 Sequenom, Inc. Releasable nonvolatile mass-label molecules
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
US7198893B1 (en) 1996-11-06 2007-04-03 Sequenom, Inc. DNA diagnostics based on mass spectrometry
US7297518B2 (en) 2001-03-12 2007-11-20 California Institute Of Technology Methods and apparatus for analyzing polynucleotide sequences by asynchronous base extension
US7319003B2 (en) 1992-11-06 2008-01-15 The Trustees Of Boston University Arrays of probes for positional sequencing by hybridization
US7332275B2 (en) 1999-10-13 2008-02-19 Sequenom, Inc. Methods for detecting methylated nucleotides
US7397546B2 (en) 2006-03-08 2008-07-08 Helicos Biosciences Corporation Systems and methods for reducing detected intensity non-uniformity in a laser beam
US7462449B2 (en) 1999-06-28 2008-12-09 California Institute Of Technology Methods and apparatuses for analyzing polynucleotide sequences
US7608394B2 (en) 2004-03-26 2009-10-27 Sequenom, Inc. Methods and compositions for phenotype identification based on nucleic acid methylation
US7820378B2 (en) 2002-11-27 2010-10-26 Sequenom, Inc. Fragmentation-based methods and systems for sequence variation detection and discovery
USRE44693E1 (en) 1996-11-06 2014-01-07 Sequenom, Inc. Beads bound to a solid support and to nucleic acids
US8962247B2 (en) 2008-09-16 2015-02-24 Sequenom, Inc. Processes and compositions for methylation-based enrichment of fetal nucleic acid from a maternal sample useful for non invasive prenatal diagnoses
US8999266B2 (en) 2000-10-30 2015-04-07 Agena Bioscience, Inc. Method and apparatus for delivery of submicroliter volumes onto a substrate
US9249456B2 (en) 2004-03-26 2016-02-02 Agena Bioscience, Inc. Base specific cleavage of methylation-specific amplification products in combination with mass analysis
US9394565B2 (en) 2003-09-05 2016-07-19 Agena Bioscience, Inc. Allele-specific sequence variation analysis
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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Cited By (22)

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US7319003B2 (en) 1992-11-06 2008-01-15 The Trustees Of Boston University Arrays of probes for positional sequencing by hybridization
US7419787B2 (en) 1995-03-17 2008-09-02 Sequenom, Inc. Mass spectrometric methods for detecting mutations in a target nucleic acid
US7074563B2 (en) 1995-03-17 2006-07-11 Sequenom, Inc. Mass spectrometric methods for detecting mutations in a target nucleic acid
US7198893B1 (en) 1996-11-06 2007-04-03 Sequenom, Inc. DNA diagnostics based on mass spectrometry
USRE44693E1 (en) 1996-11-06 2014-01-07 Sequenom, Inc. Beads bound to a solid support and to nucleic acids
US7501251B2 (en) 1996-11-06 2009-03-10 Sequenom, Inc. DNA diagnostics based on mass spectrometry
US7132519B2 (en) 1996-12-10 2006-11-07 Sequenom, Inc. Releasable nonvolatile mass-label molecules
US9540689B2 (en) 1998-05-01 2017-01-10 Life Technologies Corporation Method of determining the nucleotide sequence of oligonucleotides and DNA molecules
US7462449B2 (en) 1999-06-28 2008-12-09 California Institute Of Technology Methods and apparatuses for analyzing polynucleotide sequences
US7332275B2 (en) 1999-10-13 2008-02-19 Sequenom, Inc. Methods for detecting methylated nucleotides
US6958214B2 (en) 2000-07-10 2005-10-25 Sequenom, Inc. Polymorphic kinase anchor proteins and nucleic acids encoding the same
US8999266B2 (en) 2000-10-30 2015-04-07 Agena Bioscience, Inc. Method and apparatus for delivery of submicroliter volumes onto a substrate
US7297518B2 (en) 2001-03-12 2007-11-20 California Institute Of Technology Methods and apparatus for analyzing polynucleotide sequences by asynchronous base extension
US7820378B2 (en) 2002-11-27 2010-10-26 Sequenom, Inc. Fragmentation-based methods and systems for sequence variation detection and discovery
US9394565B2 (en) 2003-09-05 2016-07-19 Agena Bioscience, Inc. Allele-specific sequence variation analysis
US7491498B2 (en) 2003-11-12 2009-02-17 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
US9012144B2 (en) 2003-11-12 2015-04-21 Fluidigm Corporation Short cycle methods for sequencing polynucleotides
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
US7608394B2 (en) 2004-03-26 2009-10-27 Sequenom, Inc. Methods and compositions for phenotype identification based on nucleic acid methylation
US9249456B2 (en) 2004-03-26 2016-02-02 Agena Bioscience, Inc. Base specific cleavage of methylation-specific amplification products in combination with mass analysis
US7397546B2 (en) 2006-03-08 2008-07-08 Helicos Biosciences Corporation Systems and methods for reducing detected intensity non-uniformity in a laser beam
US8962247B2 (en) 2008-09-16 2015-02-24 Sequenom, Inc. Processes and compositions for methylation-based enrichment of fetal nucleic acid from a maternal sample useful for non invasive prenatal diagnoses

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