WO2002016649A3 - Probes and decoder oligonucleotides - Google Patents

Probes and decoder oligonucleotides Download PDF

Info

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

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
    • C12Q1/6834—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

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 (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9399795B2 (en) 1998-06-24 2016-07-26 Illumina, Inc. Multiplex decoding of array sensors with microspheres

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 Oligonucleotide for assaying mycobacterium avium as atypical acid-fast bacterium, and method for detecting the same
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
AU2005322640B2 (en) * 2004-02-18 2008-09-18 Ibis Biosciences, Inc. Compositions for use in identification of bacteria
ES2625288T3 (en) 2011-04-15 2017-07-19 The Johns Hopkins University Secure Sequencing System
ES2701742T3 (en) 2012-10-29 2019-02-25 Univ Johns Hopkins Papanicolaou test for ovarian and endometrial cancers
US11286531B2 (en) 2015-08-11 2022-03-29 The Johns Hopkins University Assaying ovarian cyst fluid
SG11202001010UA (en) 2017-08-07 2020-03-30 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 (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9399795B2 (en) 1998-06-24 2016-07-26 Illumina, Inc. Multiplex decoding of array sensors with microspheres

Also Published As

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

Similar Documents

Publication Publication Date Title
WO2001094630A3 (en) Compositions and methods for array-based nucleic acid hybridization
AU2002238418A1 (en) Use of DNA repair enzymes as MMP-1 inhibitors
WO2001047944A3 (en) Nucleic acids containing single nucleotide polymorphisms and methods of use thereof
WO2001096607A3 (en) Use of nucleotide analogs in the analysis of oligonucleotide mixtures and in highly multiplexed nucleic acid sequencing
WO1997026270A3 (en) Synthesis of methoxy nucleosides and enzymatic nucleic acid molecules
AU2001271669A1 (en) Multipartite high-affinity nucleic acid probes
AU2002227156A1 (en) Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
WO2002057491A3 (en) Direct multiplex characterization of genomic dna
AU2001245945A1 (en) Detection kits, such as nucleic acid arrays, for detecting the expression of 10,000 or more drosophila genes and uses thereof
WO2003060144A3 (en) High fidelity dna polymerase compositions and uses therefor
WO1999067619A3 (en) Compounds and methods for detecting biomolecules
WO2004001062A3 (en) Multiplex nucleic acid reactions
WO2001038584A3 (en) Non-aggregating, non-quenching oligomers comprising nucleotide analogues; methods of synthesis and use thereof
AU2001268513A1 (en) Nucleic acid accessible hybridization sites
AU3623800A (en) Methods and compositions for economically synthesizing and assembling long dna sequences
AU2013202A (en) Nucleic acid amplification methods
WO2002016649A3 (en) Probes and decoder oligonucleotides
WO1999036571A3 (en) Method for the detection or nucleic acid of nucleic acid sequences
AU2001285219A1 (en) Methods and compositions for identifying nucleic acid molecules using nucleolytic activities and hybridization
WO2000029623A3 (en) Nucleic acids containing single nucleotide polymorphisms and methods of use thereof
AU2002314997A1 (en) Methods for low background cloning of dna using long oligonucleotides
EP2110432A3 (en) High fidelity DNA polymerase compositions and uses therefor
AU2001259131A1 (en) Detection of nucleotide sequence variations via the proofreading activity of polymerases
AU2003211947A1 (en) PRIMERS FOR NUCLEIC ACID AMPLIFICATION IN DETECTING HOUSEKEEPING GENE mRNA AND TEST METHOD USING THESE PRIMERS
AU2001296015A1 (en) Method of synthesizing single-stranded nucleic acid

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PH PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

122 Ep: pct application non-entry in european phase
NENP Non-entry into the national phase

Ref country code: JP