WO2010077288A3 - Methods for identifying differences in alternative splicing between two rna samples - Google Patents

Methods for identifying differences in alternative splicing between two rna samples Download PDF

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Publication number
WO2010077288A3
WO2010077288A3 PCT/US2009/006450 US2009006450W WO2010077288A3 WO 2010077288 A3 WO2010077288 A3 WO 2010077288A3 US 2009006450 W US2009006450 W US 2009006450W WO 2010077288 A3 WO2010077288 A3 WO 2010077288A3
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WO
WIPO (PCT)
Prior art keywords
methods
alternative splicing
rna samples
identifying differences
subpopulation
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/US2009/006450
Other languages
French (fr)
Other versions
WO2010077288A2 (en
Inventor
Gene Yeo
Jonathan Scolnick
Fred H. Gage
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Salk Institute for Biological Studies
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Salk Institute for Biological Studies
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 Salk Institute for Biological Studies filed Critical Salk Institute for Biological Studies
Publication of WO2010077288A2 publication Critical patent/WO2010077288A2/en
Publication of WO2010077288A3 publication Critical patent/WO2010077288A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1072—Differential gene expression library synthesis, e.g. subtracted libraries, differential screening
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biomedical Technology (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Plant Pathology (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Provided are methods of separating one or more alternate isoform of a target gene, which alternate isoform is present in a sample population of RNAs but not in a subtractive population of RNAs. Compositions comprising a subpopulation of RNA:cDNA duplexes and a subpopulation of unhybridized RNA fragments are also provided.
PCT/US2009/006450 2008-12-09 2009-12-08 Methods for identifying differences in alternative splicing between two rna samples Ceased WO2010077288A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US20137208P 2008-12-09 2008-12-09
US61/201,372 2008-12-09

Publications (2)

Publication Number Publication Date
WO2010077288A2 WO2010077288A2 (en) 2010-07-08
WO2010077288A3 true WO2010077288A3 (en) 2010-11-04

Family

ID=42310447

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2009/006450 Ceased WO2010077288A2 (en) 2008-12-09 2009-12-08 Methods for identifying differences in alternative splicing between two rna samples

Country Status (1)

Country Link
WO (1) WO2010077288A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012116248A1 (en) * 2011-02-24 2012-08-30 Massachusetts Institute Of Technology ALTERNATIVELY SPLICED mRNA ISOFORMS AS PROGNOSTIC INDICATORS FOR METASTATIC CANCER
EP2847353B1 (en) 2012-05-10 2022-01-19 The General Hospital Corporation Methods for determining a nucleotide sequence
US20150337364A1 (en) * 2014-01-27 2015-11-26 ArcherDX, Inc. Isothermal Methods and Related Compositions for Preparing Nucleic Acids
JP7016215B2 (en) 2014-01-27 2022-02-04 ザ ジェネラル ホスピタル コーポレイション How to Prepare Nucleic Acids for Sequencing
CN105063074B (en) * 2015-06-16 2019-03-05 青岛耐德生物技术有限公司 A kind of method of artificial reconstructed functional protein
CA3037185A1 (en) 2016-09-15 2018-03-22 ArcherDX, Inc. Methods of nucleic acid sample preparation
JP6997773B2 (en) 2016-09-15 2022-01-18 アーチャーディーエックス， エルエルシー Method for preparing nucleic acid sample for analysis of cell-free DNA

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030165931A1 (en) * 1998-03-11 2003-09-04 Bruno Tocque Qualitative differential screening
US20030219805A1 (en) * 2002-03-13 2003-11-27 Zvi Kelman Detection of alternative and aberrant mRNA splicing
US20070003929A1 (en) * 2002-12-12 2007-01-04 Yoshihide Hayashizaki Method for identifying, analyzing and/or cloning nucleic acid isoforms
US20080153086A1 (en) * 2003-08-08 2008-06-26 Wong Albert J Method For Rapid Identification of Alternative Splicing
WO2008119767A2 (en) * 2007-03-30 2008-10-09 Oryzon Genomics, S. A. Method of nucleic acid analysis.

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030165931A1 (en) * 1998-03-11 2003-09-04 Bruno Tocque Qualitative differential screening
US20030219805A1 (en) * 2002-03-13 2003-11-27 Zvi Kelman Detection of alternative and aberrant mRNA splicing
US20070003929A1 (en) * 2002-12-12 2007-01-04 Yoshihide Hayashizaki Method for identifying, analyzing and/or cloning nucleic acid isoforms
US20080153086A1 (en) * 2003-08-08 2008-06-26 Wong Albert J Method For Rapid Identification of Alternative Splicing
WO2008119767A2 (en) * 2007-03-30 2008-10-09 Oryzon Genomics, S. A. Method of nucleic acid analysis.

Also Published As

Publication number Publication date
WO2010077288A2 (en) 2010-07-08

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