WO2002061140A3 - Competitive population normalization for comparative analysis of nucleic acid samples - Google Patents

Competitive population normalization for comparative analysis of nucleic acid samples Download PDF

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Publication number
WO2002061140A3
WO2002061140A3 PCT/US2002/002892 US0202892W WO02061140A3 WO 2002061140 A3 WO2002061140 A3 WO 2002061140A3 US 0202892 W US0202892 W US 0202892W WO 02061140 A3 WO02061140 A3 WO 02061140A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
samples
targets
sample
target
Prior art date
Application number
PCT/US2002/002892
Other languages
French (fr)
Other versions
WO2002061140A9 (en
WO2002061140A2 (en
Inventor
David Brown
Matthew M Winkler
Original Assignee
Ambion Inc
David Brown
Matthew M Winkler
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 Ambion Inc, David Brown, Matthew M Winkler filed Critical Ambion Inc
Publication of WO2002061140A2 publication Critical patent/WO2002061140A2/en
Priority to US10/632,539 priority Critical patent/US20040110191A1/en
Priority to US10/632,534 priority patent/US20040058373A1/en
Publication of WO2002061140A3 publication Critical patent/WO2002061140A3/en
Publication of WO2002061140A9 publication Critical patent/WO2002061140A9/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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection

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

Abstract

Methods are disclosed that convert two or more complex nucleic acid samples into a single collection of normalized target molecules that can be used to compare the abundance of each of the targets in the original samples. Multiple RNA or DNA samples are uniquely tagged and pooled to create a sample mixture. A defined set of target within the sample mixture is converted to approximately equal amounts of nucleic acid by one of several methods employing primer extension with a set of target specific primers. The concentration of target specific primers is equal and limiting for all targets, therefore an appropriate number of primer extension cycles converts all targets to similar final concentrations of product nucleic acid. The different tags appended to the sample nucleic acids from each sample population unique. These different tags are used to generate RNA or DNA , molecules for analysis that derive form each of the input samples. The disclosed methods are primarily intended to enhance gene array analysis, however, any method used to compare multiple nucleic acid targets form different samples will benefit form the invention.
PCT/US2002/002892 2001-01-31 2002-01-31 Competitive population normalization for comparative analysis of nucleic acid samples WO2002061140A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US10/632,539 US20040110191A1 (en) 2001-01-31 2003-07-31 Comparative analysis of nucleic acids using population tagging
US10/632,534 US20040058373A1 (en) 2001-01-31 2003-07-31 Competitive amplification of fractionated targets from multiple nucleic acid samples

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US26569501P 2001-01-31 2001-01-31
US60/265,695 2001-01-31

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US10/632,539 Continuation US20040110191A1 (en) 2001-01-31 2003-07-31 Comparative analysis of nucleic acids using population tagging

Publications (3)

Publication Number Publication Date
WO2002061140A2 WO2002061140A2 (en) 2002-08-08
WO2002061140A3 true WO2002061140A3 (en) 2003-10-16
WO2002061140A9 WO2002061140A9 (en) 2003-11-27

Family

ID=23011511

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/002892 WO2002061140A2 (en) 2001-01-31 2002-01-31 Competitive population normalization for comparative analysis of nucleic acid samples

Country Status (1)

Country Link
WO (1) WO2002061140A2 (en)

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8206913B1 (en) 2003-03-07 2012-06-26 Rubicon Genomics, Inc. Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process
DE602004029560D1 (en) * 2003-03-07 2010-11-25 Rubicon Genomics Inc AMPLIFICATION AND ANALYSIS OF TOTAL GENOME AND TOTAL TRANSCRIPTIBLE LIBRARIES PRODUCED BY A DNA POLYMERIZATION PROCEDURE
EP1766061B1 (en) * 2004-05-20 2013-07-17 Quest Diagnostics Investments Incorporated Single label comparative hybridization
US7393665B2 (en) 2005-02-10 2008-07-01 Population Genetics Technologies Ltd Methods and compositions for tagging and identifying polynucleotides
US20060223066A1 (en) 2005-03-29 2006-10-05 Applera Corporation Methods for normalizing and for identifying small nucleic acids
JP4658660B2 (en) * 2005-03-30 2011-03-23 株式会社日立ハイテクノロジーズ Nucleic acid detection method
US7507539B2 (en) 2007-07-30 2009-03-24 Quest Diagnostics Investments Incorporated Substractive single label comparative hybridization
US9695416B2 (en) 2012-07-18 2017-07-04 Siemens Healthcare Diagnostics Inc. Method of normalizing biological samples
EP2749654A1 (en) * 2012-12-28 2014-07-02 Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. Method of analysis of composition of nucleic acid mixtures

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997027317A1 (en) * 1996-01-23 1997-07-31 Affymetrix, Inc. Nucleic acid analysis techniques
EP0870842A2 (en) * 1997-04-07 1998-10-14 Japan Science and Technology Corporation Adaptor-tagged competitive PCR
WO2000005409A1 (en) * 1998-07-21 2000-02-03 Pharmagene Laboratories Ltd. Quantitative analysis of gene expression using pcr

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997027317A1 (en) * 1996-01-23 1997-07-31 Affymetrix, Inc. Nucleic acid analysis techniques
EP0870842A2 (en) * 1997-04-07 1998-10-14 Japan Science and Technology Corporation Adaptor-tagged competitive PCR
WO2000005409A1 (en) * 1998-07-21 2000-02-03 Pharmagene Laboratories Ltd. Quantitative analysis of gene expression using pcr

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
ZIMMERMANN K ET AL: "TECHNICAL ASPECTS OF QUANTITATIVE COMPETITIVE PCR", BIOTECHNIQUES, EATON PUBLISHING, NATICK, US, vol. 21, no. 2, 1 August 1996 (1996-08-01), pages 268 - 270,272,27, XP000597689, ISSN: 0736-6205 *

Also Published As

Publication number Publication date
WO2002061140A9 (en) 2003-11-27
WO2002061140A2 (en) 2002-08-08

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