WO2000056925A3 - Methods for single nucleotide polymorphism detection - Google Patents

Methods for single nucleotide polymorphism detection Download PDF

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Publication number
WO2000056925A3
WO2000056925A3 PCT/US2000/006135 US0006135W WO0056925A3 WO 2000056925 A3 WO2000056925 A3 WO 2000056925A3 US 0006135 W US0006135 W US 0006135W WO 0056925 A3 WO0056925 A3 WO 0056925A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleotide
particles
single nucleotide
target dna
members
Prior art date
Application number
PCT/US2000/006135
Other languages
French (fr)
Other versions
WO2000056925A2 (en
Inventor
Sharat Singh
Edwin F Ullman
Original Assignee
Aclara Biosciences 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 to US12531999P priority Critical
Priority to US60/125,319 priority
Application filed by Aclara Biosciences Inc filed Critical Aclara Biosciences Inc
Publication of WO2000056925A2 publication Critical patent/WO2000056925A2/en
Publication of WO2000056925A3 publication Critical patent/WO2000056925A3/en

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Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/6858Allele-specific amplification
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing

Abstract

Methods and compositions are provided for determining large numbers of single nucleotide polymorphisms in target DNA employing particles having (1) primers complementary to sequences in the target DNA where the next succeeding 3'-nucleotide is a potential single nucleotide polymorphism and coding composition members, where the members are unique for each primer, and (2) differentially labeled terminating nucleotides, where the label permits separation of the terminating nucleotides. Desirably the particles are separated into groups having a common prevalent next succeeding nucleotide. The particles and target DNA are combined under nucleotide extending conditions, the particles separated into groups in accordance with the terminating nucleotide and the coding members identified, so that one knows the sequence and the single nucleotide polymorophism. Various protocols are provided for the determination.
PCT/US2000/006135 1999-03-19 2000-03-08 Methods for single nucleotide polymorphism detection WO2000056925A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US12531999P true 1999-03-19 1999-03-19
US60/125,319 1999-03-19

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
AU35199/00A AU3519900A (en) 1999-03-19 2000-03-08 Methods for single nucleotide polymorphism detection

Publications (2)

Publication Number Publication Date
WO2000056925A2 WO2000056925A2 (en) 2000-09-28
WO2000056925A3 true WO2000056925A3 (en) 2002-04-11

Family

ID=22419183

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/006135 WO2000056925A2 (en) 1999-03-19 2000-03-08 Methods for single nucleotide polymorphism detection

Country Status (2)

Country Link
AU (1) AU3519900A (en)
WO (1) WO2000056925A2 (en)

Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7771934B2 (en) 2000-12-13 2010-08-10 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US7771946B2 (en) 2001-03-09 2010-08-10 Nugen Technologies, Inc. Methods, kits and compositions for single primer linear isothermal amplification of nucleic acid sequences
US7846733B2 (en) 2000-06-26 2010-12-07 Nugen Technologies, Inc. Methods and compositions for transcription-based nucleic acid amplification
US7846666B2 (en) 2008-03-21 2010-12-07 Nugen Technologies, Inc. Methods of RNA amplification in the presence of DNA
US7939258B2 (en) 2005-09-07 2011-05-10 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US8034568B2 (en) 2008-02-12 2011-10-11 Nugen Technologies, Inc. Isothermal nucleic acid amplification methods and compositions
US8465950B2 (en) 2003-04-14 2013-06-18 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
US9110075B2 (en) 2001-05-21 2015-08-18 Monogram Biosciences, Inc. Compositions for analyzing proteins

Families Citing this family (19)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6372142B1 (en) 1996-11-13 2002-04-16 Transgenomic, Inc. Column for DNA separation by matched ion polynucleotide chromatography
US7001725B2 (en) 1999-04-30 2006-02-21 Aclara Biosciences, Inc. Kits employing generalized target-binding e-tag probes
US6322980B1 (en) 1999-04-30 2001-11-27 Aclara Biosciences, Inc. Single nucleotide detection using degradation of a fluorescent sequence
US7160735B2 (en) 2000-04-28 2007-01-09 Monogram Biosciences, Inc. Tagged microparticle compositions and methods
US6627400B1 (en) 1999-04-30 2003-09-30 Aclara Biosciences, Inc. Multiplexed measurement of membrane protein populations
US7771929B2 (en) 2000-04-28 2010-08-10 Monogram Biosciences, Inc. Tag library compounds, compositions, kits and methods of use
US6673550B2 (en) 1999-04-30 2004-01-06 Aclara Biosciences, Inc. Electrophoretic tag reagents comprising fluorescent compounds
US6514700B1 (en) * 1999-04-30 2003-02-04 Aclara Biosciences, Inc. Nucleic acid detection using degradation of a tagged sequence
US6692918B2 (en) 1999-09-13 2004-02-17 Nugen Technologies, Inc. Methods and compositions for linear isothermal amplification of polynucleotide sequences
AT414787T (en) * 1999-12-10 2008-12-15 Univ Princeton Process for the selective isolation of a nucleic acid
AU4565001A (en) 2000-03-10 2001-09-24 Ana Gen Technologies Inc Mutation detection using denaturing gradients
AU6481101A (en) * 2000-05-23 2001-12-03 Variagenics Inc Methods for genetic analysis of dna to detect sequence variances
US7435541B2 (en) 2000-05-23 2008-10-14 Sequenom, Inc. Restriction enzyme genotyping
US7110885B2 (en) 2001-03-08 2006-09-19 Dnaprint Genomics, Inc. Efficient methods and apparatus for high-throughput processing of gene sequence data
AU2002305658A1 (en) 2001-05-21 2002-12-03 Aclara Biosciences, Inc. Analyzing phosphorylated proteins
AU2002344221A1 (en) 2001-05-26 2002-12-09 Aclara Biosciences, Inc. Catalytic amplification of multiplexed assay signals
US7045311B2 (en) 2001-10-25 2006-05-16 Monogram Biosciences, Inc. Whole cell assay systems for cell surface proteases
SE0300965D0 (en) * 2003-04-02 2003-04-02 Dynamic Code Ab Method to detect mutations
US20060040300A1 (en) 2004-08-09 2006-02-23 Generation Biotech, Llc Method for nucleic acid isolation and amplification

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5604097A (en) * 1994-10-13 1997-02-18 Spectragen, Inc. Methods for sorting polynucleotides using oligonucleotide tags
US5710028A (en) * 1992-07-02 1998-01-20 Eyal; Nurit Method of quick screening and identification of specific DNA sequences by single nucleotide primer extension and kits therefor
WO1998059066A1 (en) * 1997-06-25 1998-12-30 Orchid Biocomputer, Inc. Methods for the detection of multiple single nucleotide polymorphisms in a single reaction
WO1999022030A1 (en) * 1997-10-28 1999-05-06 The Regents Of The University Of California Dna polymorphism identity determination using flow cytometry
WO2000039335A1 (en) * 1998-12-24 2000-07-06 Aclara Biosciences, Inc. Individually addressable solid surfaces for multiplexed operations

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5710028A (en) * 1992-07-02 1998-01-20 Eyal; Nurit Method of quick screening and identification of specific DNA sequences by single nucleotide primer extension and kits therefor
US5604097A (en) * 1994-10-13 1997-02-18 Spectragen, Inc. Methods for sorting polynucleotides using oligonucleotide tags
WO1998059066A1 (en) * 1997-06-25 1998-12-30 Orchid Biocomputer, Inc. Methods for the detection of multiple single nucleotide polymorphisms in a single reaction
WO1999022030A1 (en) * 1997-10-28 1999-05-06 The Regents Of The University Of California Dna polymorphism identity determination using flow cytometry
WO2000039335A1 (en) * 1998-12-24 2000-07-06 Aclara Biosciences, Inc. Individually addressable solid surfaces for multiplexed operations

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
PASTINEN T ET AL: "MINISEQUENCING: A SPECIFIC TOOL FOR DNA ANALYSIS AND DIAGNOSTICS ONOLIGONUCLEOTIDE ARRAYS", GENOME RESEARCH, COLD SPRING HARBOR LABORATORY PRESS, US, vol. 7, no. 6, 1 June 1997 (1997-06-01), pages 606 - 614, XP000699761, ISSN: 1088-9051 *
PASTINEN T ET AL: "Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation", CLINICAL CHEMISTRY. PRINCIPLES AND TECHNICS, NEW YORK, HARPER & ROW, US, 1974, pages 1391 - 1397, XP002116875 *

Cited By (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7846733B2 (en) 2000-06-26 2010-12-07 Nugen Technologies, Inc. Methods and compositions for transcription-based nucleic acid amplification
US7771934B2 (en) 2000-12-13 2010-08-10 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US8334116B2 (en) 2000-12-13 2012-12-18 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
US7771946B2 (en) 2001-03-09 2010-08-10 Nugen Technologies, Inc. Methods, kits and compositions for single primer linear isothermal amplification of nucleic acid sequences
US8071311B2 (en) 2001-03-09 2011-12-06 Nugen Technologies, Inc. Methods and compositions for amplification of RNA sequences
US9181582B2 (en) 2001-03-09 2015-11-10 Nugen Technologies, Inc. Compositions for amplification of RNA sequences using composite primers
US9110075B2 (en) 2001-05-21 2015-08-18 Monogram Biosciences, Inc. Compositions for analyzing proteins
US9175325B2 (en) 2003-04-14 2015-11-03 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
US8465950B2 (en) 2003-04-14 2013-06-18 Nugen Technologies, Inc. Global amplification using a randomly primed composite primer
US8852867B2 (en) 2005-09-07 2014-10-07 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US7939258B2 (en) 2005-09-07 2011-05-10 Nugen Technologies, Inc. Nucleic acid amplification procedure using RNA and DNA composite primers
US8034568B2 (en) 2008-02-12 2011-10-11 Nugen Technologies, Inc. Isothermal nucleic acid amplification methods and compositions
US7846666B2 (en) 2008-03-21 2010-12-07 Nugen Technologies, Inc. Methods of RNA amplification in the presence of DNA

Also Published As

Publication number Publication date
AU3519900A (en) 2000-10-09
WO2000056925A2 (en) 2000-09-28

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