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WO2002016649A3 - Probes and decoder oligonucleotides - Google Patents

Probes and decoder oligonucleotides Download PDF

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Publication number
WO2002016649A3
WO2002016649A3 PCT/US2001/026519 US0126519W WO0216649A3 WO 2002016649 A3 WO2002016649 A3 WO 2002016649A3 US 0126519 W US0126519 W US 0126519W WO 0216649 A3 WO0216649 A3 WO 0216649A3
Authority
WO
WIPO (PCT)
Prior art keywords
reactions
oligonucleotides
probes
decoder
arrays
Prior art date
Application number
PCT/US2001/026519
Other languages
French (fr)
Other versions
WO2002016649A2 (en
Inventor
Kevin Gunderson
Original Assignee
Illumina 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 Illumina Inc filed Critical Illumina Inc
Priority to AU2001288393A priority Critical patent/AU2001288393A1/en
Publication of WO2002016649A2 publication Critical patent/WO2002016649A2/en
Publication of WO2002016649A3 publication Critical patent/WO2002016649A3/en

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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
    • C12Q1/6834—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)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Saccharide Compounds (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The present invention is directed to improved methods and compositions for the use of adapter sequences on arrays in a variety of multiplexed nucleic acid reactions, including synthesis reactions, amplification reactions, and genotyping reactions.
PCT/US2001/026519 2000-08-25 2001-08-27 Probes and decoder oligonucleotides WO2002016649A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2001288393A AU2001288393A1 (en) 2000-08-25 2001-08-27 Probes and decoder oligonucleotides

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US22794800P 2000-08-25 2000-08-25
US60/227,948 2000-08-25
US22885400P 2000-08-29 2000-08-29
US60/228,854 2000-08-29

Publications (2)

Publication Number Publication Date
WO2002016649A2 WO2002016649A2 (en) 2002-02-28
WO2002016649A3 true WO2002016649A3 (en) 2003-03-13

Family

ID=26921901

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/026519 WO2002016649A2 (en) 2000-08-25 2001-08-27 Probes and decoder oligonucleotides

Country Status (2)

Country Link
AU (1) AU2001288393A1 (en)
WO (1) WO2002016649A2 (en)

Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6902921B2 (en) 2001-10-30 2005-06-07 454 Corporation Sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US6956114B2 (en) 2001-10-30 2005-10-18 '454 Corporation Sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US7033754B2 (en) 1998-06-24 2006-04-25 Illumina, Inc. Decoding of array sensors with microspheres
US7211390B2 (en) 1999-09-16 2007-05-01 454 Life Sciences Corporation Method of sequencing a nucleic acid
US7244559B2 (en) 1999-09-16 2007-07-17 454 Life Sciences Corporation Method of sequencing a nucleic acid
US7323305B2 (en) 2003-01-29 2008-01-29 454 Life Sciences Corporation Methods of amplifying and sequencing nucleic acids
US7575865B2 (en) 2003-01-29 2009-08-18 454 Life Sciences Corporation Methods of amplifying and sequencing nucleic acids

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7572642B2 (en) 2001-04-18 2009-08-11 Ambrigen, Llc Assay based on particles, which specifically bind with targets in spatially distributed characteristic patterns
US7138506B2 (en) 2001-05-09 2006-11-21 Genetic Id, Na, Inc. Universal microarray system
JP2003289869A (en) * 2002-04-02 2003-10-14 Tosoh Corp Oligonucleotides and detection methods for detection of atypical mycobacterium Mycobacterium avium
US7250496B2 (en) * 2002-11-14 2007-07-31 Rosetta Genomics Ltd. Bioinformatically detectable group of novel regulatory genes and uses thereof
US7195875B2 (en) 2003-04-18 2007-03-27 Beckman Coulter, Inc. Oligonucleotide pairs for multiplexed binding assays
WO2006071241A2 (en) * 2004-02-18 2006-07-06 Isis Pharmaceuticals, Inc. Compositions for use in identification of bacteria
EP3907297A1 (en) 2011-04-15 2021-11-10 The Johns Hopkins University Safe sequencing system
CA2889937C (en) 2012-10-29 2020-12-29 The Johns Hopkins University Papanicolaou test for ovarian and endometrial cancers
WO2017027653A1 (en) 2015-08-11 2017-02-16 The Johns Hopkins University Assaying ovarian cyst fluid
IL319255A (en) 2017-08-07 2025-04-01 Univ Johns Hopkins Methods and materials for assessing and treating cancer

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0799897A1 (en) * 1996-04-04 1997-10-08 Affymetrix, Inc. (a California Corporation) Methods and compositions for selecting tag nucleic acids and probe arrays
WO1999028505A1 (en) * 1997-12-03 1999-06-10 Curagen Corporation Methods and devices for measuring differential gene expression
WO2000047767A1 (en) * 1999-02-11 2000-08-17 Astrazeneca Ab Oligonucleotide array and methods of use

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0799897A1 (en) * 1996-04-04 1997-10-08 Affymetrix, Inc. (a California Corporation) Methods and compositions for selecting tag nucleic acids and probe arrays
WO1999028505A1 (en) * 1997-12-03 1999-06-10 Curagen Corporation Methods and devices for measuring differential gene expression
WO2000047767A1 (en) * 1999-02-11 2000-08-17 Astrazeneca Ab Oligonucleotide array and methods of use

Non-Patent Citations (7)

* Cited by examiner, † Cited by third party
Title
BEN-DOR A ET AL: "Universal DNA tag systems: a combinatorial design scheme.", JOURNAL OF COMPUTATIONAL BIOLOGY: A JOURNAL OF COMPUTATIONAL MOLECULAR CELL BIOLOGY. UNITED STATES 2000, vol. 7, no. 3-4, 2000, pages 503 - 519, XP002948494, ISSN: 1066-5277 *
BRENNER S ET AL: "Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.", NATURE BIOTECHNOLOGY. UNITED STATES JUN 2000, vol. 18, no. 6, June 2000 (2000-06-01), pages 630 - 634, XP002199492, ISSN: 1087-0156 *
FAN J B ET AL: "Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays.", GENOME RESEARCH. UNITED STATES JUN 2000, vol. 10, no. 6, June 2000 (2000-06-01), pages 853 - 860, XP002934219, ISSN: 1088-9051 *
GERRY N P ET AL: "Universal DNA microarray method for multiplex detection of low abundance point mutations.", JOURNAL OF MOLECULAR BIOLOGY. ENGLAND 17 SEP 1999, vol. 292, no. 2, 17 September 1999 (1999-09-17), pages 251 - 262, XP002214482, ISSN: 0022-2836 *
GUNDERSON K L ET AL: "Mutation detection by ligation to complete n-mer DNA arrays.", GENOME RESEARCH. UNITED STATES NOV 1998, vol. 8, no. 11, November 1998 (1998-11-01), pages 1142 - 1153, XP002130857, ISSN: 1088-9051 *
HIRSCHHORN JOEL N ET AL: "SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism genotyping", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA, NATIONAL ACADEMY OF SCIENCE. WASHINGTON, US, vol. 97, no. 22, 24 October 2000 (2000-10-24), pages 12164 - 12169, XP002158215, ISSN: 0027-8424 *
SHOEMAKER D D ET AL: "Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy.", NATURE GENETICS. UNITED STATES DEC 1996, vol. 14, no. 4, December 1996 (1996-12-01), pages 450 - 456, XP002043431, ISSN: 1061-4036 *

Cited By (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7226734B2 (en) 1998-06-24 2007-06-05 Illumina, Inc. Multiplex decoding of array sensors with microspheres
US9399795B2 (en) 1998-06-24 2016-07-26 Illumina, Inc. Multiplex decoding of array sensors with microspheres
US7033754B2 (en) 1998-06-24 2006-04-25 Illumina, Inc. Decoding of array sensors with microspheres
US7060431B2 (en) 1998-06-24 2006-06-13 Illumina, Inc. Method of making and decoding of array sensors with microspheres
US7455971B2 (en) 1998-06-24 2008-11-25 Illumina, Inc. Multiplex decoding of array sensors with microspheres
US7244559B2 (en) 1999-09-16 2007-07-17 454 Life Sciences Corporation Method of sequencing a nucleic acid
US7264929B2 (en) 1999-09-16 2007-09-04 454 Life Sciences Corporation Method of sequencing a nucleic acid
US7335762B2 (en) 1999-09-16 2008-02-26 454 Life Sciences Corporation Apparatus and method for sequencing a nucleic acid
US7211390B2 (en) 1999-09-16 2007-05-01 454 Life Sciences Corporation Method of sequencing a nucleic acid
US6902921B2 (en) 2001-10-30 2005-06-07 454 Corporation Sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US6956114B2 (en) 2001-10-30 2005-10-18 '454 Corporation Sulfurylase-luciferase fusion proteins and thermostable sulfurylase
US7323305B2 (en) 2003-01-29 2008-01-29 454 Life Sciences Corporation Methods of amplifying and sequencing nucleic acids
US7575865B2 (en) 2003-01-29 2009-08-18 454 Life Sciences Corporation Methods of amplifying and sequencing nucleic acids

Also Published As

Publication number Publication date
AU2001288393A1 (en) 2002-03-04
WO2002016649A2 (en) 2002-02-28

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