WO2003014295A3 - Method and system for identifying splice variants of a gene - Google Patents

Method and system for identifying splice variants of a gene Download PDF

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Publication number
WO2003014295A3
WO2003014295A3 PCT/US2002/023819 US0223819W WO03014295A3 WO 2003014295 A3 WO2003014295 A3 WO 2003014295A3 US 0223819 W US0223819 W US 0223819W WO 03014295 A3 WO03014295 A3 WO 03014295A3
Authority
WO
WIPO (PCT)
Prior art keywords
exon
sample
splice variants
gene
splice
Prior art date
Application number
PCT/US2002/023819
Other languages
French (fr)
Other versions
WO2003014295A2 (en
WO2003014295A9 (en
Inventor
Jonathan Bingham
Subha Srinivasan
Original Assignee
Jivan Biolog Inc
Jonathan Bingham
Subha Srinivasan
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 Jivan Biolog Inc, Jonathan Bingham, Subha Srinivasan filed Critical Jivan Biolog Inc
Priority to EP02752593A priority Critical patent/EP1466010A4/en
Priority to AU2002355529A priority patent/AU2002355529A1/en
Publication of WO2003014295A2 publication Critical patent/WO2003014295A2/en
Publication of WO2003014295A3 publication Critical patent/WO2003014295A3/en
Publication of WO2003014295A9 publication Critical patent/WO2003014295A9/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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • 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
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S707/00—Data processing: database and file management or data structures
    • Y10S707/99941—Database schema or data structure
    • Y10S707/99943—Generating database or data structure, e.g. via user interface

Abstract

A method and system for identifying mRNA present in a sample. A splice variant technique selects a set of possible exon-exon junctions based on exons of expected mRNA transcripts. The splice varianttechnique then selects indicator polynucleotides for the exon-exon junctions and detects the expressionlevel of the indicator polynucleotides in the sample. The splice variant technique then may use a mathematical algorithm to identify possible splice variants in the sample from the observed expressionlevels.
PCT/US2002/023819 2001-07-25 2002-07-25 Method and system for identifying splice variants of a gene WO2003014295A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP02752593A EP1466010A4 (en) 2001-07-25 2002-07-25 Method and system for identifying splice variants of a gene
AU2002355529A AU2002355529A1 (en) 2001-07-25 2002-07-25 Method and system for identifying splice variants of a gene

Applications Claiming Priority (12)

Application Number Priority Date Filing Date Title
US30791101P 2001-07-25 2001-07-25
US60/307,911 2001-07-25
US32991401P 2001-10-17 2001-10-17
US60/329,914 2001-10-17
US34328601P 2001-12-21 2001-12-21
US34329801P 2001-12-21 2001-12-21
US34326901P 2001-12-21 2001-12-21
US60/343,298 2001-12-21
US60/343,286 2001-12-21
US60/343,269 2001-12-21
US10/146,720 2002-05-14
US10/146,720 US7340349B2 (en) 2001-07-25 2002-05-14 Method and system for identifying splice variants of a gene

Publications (3)

Publication Number Publication Date
WO2003014295A2 WO2003014295A2 (en) 2003-02-20
WO2003014295A3 true WO2003014295A3 (en) 2003-11-27
WO2003014295A9 WO2003014295A9 (en) 2006-12-28

Family

ID=27558330

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/023819 WO2003014295A2 (en) 2001-07-25 2002-07-25 Method and system for identifying splice variants of a gene

Country Status (4)

Country Link
US (2) US7340349B2 (en)
EP (1) EP1466010A4 (en)
AU (1) AU2002355529A1 (en)
WO (1) WO2003014295A2 (en)

Families Citing this family (4)

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Publication number Priority date Publication date Assignee Title
US7361488B2 (en) * 2000-02-07 2008-04-22 Illumina, Inc. Nucleic acid detection methods using universal priming
US20030170637A1 (en) * 2002-03-06 2003-09-11 Pirrung Michael C. Method of analyzing mRNA splice variants
US20040234963A1 (en) * 2003-05-19 2004-11-25 Sampas Nicholas M. Method and system for analysis of variable splicing of mRNAs by array hybridization
US7962291B2 (en) 2005-09-30 2011-06-14 Affymetrix, Inc. Methods and computer software for detecting splice variants

Citations (1)

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US6171793B1 (en) * 1999-04-19 2001-01-09 Affymetrix, Inc. Method for scanning gene probe array to produce data having dynamic range that exceeds that of scanner

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Also Published As

Publication number Publication date
US7340349B2 (en) 2008-03-04
AU2002355529A1 (en) 2003-02-24
WO2003014295A2 (en) 2003-02-20
EP1466010A2 (en) 2004-10-13
US20030087261A1 (en) 2003-05-08
AU2002355529A8 (en) 2003-02-24
EP1466010A4 (en) 2005-03-30
US20060142952A1 (en) 2006-06-29
WO2003014295A9 (en) 2006-12-28

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