WO2002064835A3 - Methods for nucleic acid fingerprint analysis - Google Patents

Methods for nucleic acid fingerprint analysis Download PDF

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Publication number
WO2002064835A3
WO2002064835A3 PCT/US2002/003168 US0203168W WO02064835A3 WO 2002064835 A3 WO2002064835 A3 WO 2002064835A3 US 0203168 W US0203168 W US 0203168W WO 02064835 A3 WO02064835 A3 WO 02064835A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
amplification
population
methods
complex
Prior art date
Application number
PCT/US2002/003168
Other languages
French (fr)
Other versions
WO2002064835A2 (en
Inventor
David Brown
Matthew M Winkler
Frank Lawrence
Jeffrey Shelton
Original Assignee
Ambion Inc
David Brown
Matthew M Winkler
Frank Lawrence
Jeffrey Shelton
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, Frank Lawrence, Jeffrey Shelton filed Critical Ambion Inc
Publication of WO2002064835A2 publication Critical patent/WO2002064835A2/en
Priority to US10/632,539 priority Critical patent/US20040110191A1/en
Priority to US10/632,534 priority patent/US20040058373A1/en
Publication of WO2002064835A3 publication Critical patent/WO2002064835A3/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 provided for generating nucleic acid fingerprints from complex nucleic acid populations. The methods rely on the addition of a nucleic acid tag with at least two functional domains to members of the complex population being assessed. Primers specific to the appended tag and arbitrary or adapter-specific primers are used to amplify subsets of the complex population. The amplified population is then used to generate labeled products for comparative expression analysis using the functional domain of the appended tag sequence that was not used for amplification. The separation of amplification and labeling substantially reduces the number of false positives common in amplification fingerprinting experiments by removing all amplification products from the analysis that do not derive from the anchored ends of the nucleic acid population.
PCT/US2002/003168 2001-01-31 2002-01-31 Methods for nucleic acid fingerprint analysis WO2002064835A2 (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
US26569301P 2001-01-31 2001-01-31
US60/265,693 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 (2)

Publication Number Publication Date
WO2002064835A2 WO2002064835A2 (en) 2002-08-22
WO2002064835A3 true WO2002064835A3 (en) 2003-12-11

Family

ID=23011502

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/003168 WO2002064835A2 (en) 2001-01-31 2002-01-31 Methods for nucleic acid fingerprint analysis

Country Status (1)

Country Link
WO (1) WO2002064835A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2290073A3 (en) 2004-05-28 2011-08-31 Asuragen, Inc. Methods and compositions involving microRNA
EP2302055B1 (en) 2004-11-12 2014-08-27 Asuragen, Inc. Methods and compositions involving miRNA and miRNA inhibitor molecules
US7393665B2 (en) 2005-02-10 2008-07-01 Population Genetics Technologies Ltd Methods and compositions for tagging and identifying polynucleotides
US8361714B2 (en) 2007-09-14 2013-01-29 Asuragen, Inc. Micrornas differentially expressed in cervical cancer and uses thereof
EP2201143B2 (en) 2007-09-21 2016-08-24 Katholieke Universiteit Leuven Tools and methods for genetic tests using next generation sequencing
EP2990487A1 (en) 2008-05-08 2016-03-02 Asuragen, INC. Compositions and methods related to mirna modulation of neovascularization or angiogenesis
WO2013040251A2 (en) 2011-09-13 2013-03-21 Asurgen, Inc. Methods and compositions involving mir-135b for distinguishing pancreatic cancer from benign pancreatic disease

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5262311A (en) * 1992-03-11 1993-11-16 Dana-Farber Cancer Institute, Inc. Methods to clone polyA mRNA
US5545522A (en) * 1989-09-22 1996-08-13 Van Gelder; Russell N. Process for amplifying a target polynucleotide sequence using a single primer-promoter complex
EP0870842A2 (en) * 1997-04-07 1998-10-14 Japan Science and Technology Corporation Adaptor-tagged competitive PCR
US5861245A (en) * 1990-10-15 1999-01-19 Stratagene & California Institute Of Biological Research Arbitrarily primed polymerase chain reaction method for fingerprinting genomes
US6132997A (en) * 1999-05-28 2000-10-17 Agilent Technologies Method for linear mRNA amplification
WO2000075356A1 (en) * 1999-06-04 2000-12-14 Lin Shi Lung Rna polymerase chain reaction

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5545522A (en) * 1989-09-22 1996-08-13 Van Gelder; Russell N. Process for amplifying a target polynucleotide sequence using a single primer-promoter complex
US5861245A (en) * 1990-10-15 1999-01-19 Stratagene & California Institute Of Biological Research Arbitrarily primed polymerase chain reaction method for fingerprinting genomes
US5262311A (en) * 1992-03-11 1993-11-16 Dana-Farber Cancer Institute, Inc. Methods to clone polyA mRNA
EP0870842A2 (en) * 1997-04-07 1998-10-14 Japan Science and Technology Corporation Adaptor-tagged competitive PCR
US6132997A (en) * 1999-05-28 2000-10-17 Agilent Technologies Method for linear mRNA amplification
WO2000075356A1 (en) * 1999-06-04 2000-12-14 Lin Shi Lung Rna polymerase chain reaction

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
KATO K: "ADAPTOR-TAGGED COMPETITIVE PCR: A NOVEL METHOD FOR MEASURING RELATIVE GENE EXPRESSION", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 25, no. 22, 15 November 1997 (1997-11-15), pages 4694 - 4696, XP002900285, ISSN: 0305-1048 *
PHILLIPS JENNIFER ET AL: "Antisense RNA amplification: A linear amplification method for analyzing th mRNA population from single living cells.", METHODS, A COMPANION TO METHODS IN ENZYMOLOGY, vol. 10, no. 3, 1996, pages 283 - 288, XP002248904, ISSN: 1046-2023 *
SHULDINER A R ET AL: "RNA TEMPLATE-SPECIFIC POLYMERASE CHAIN REACTION RS-PCR A NOVEL STRATEGY TO REDUCE DRAMATICALLY FALSE POSITIVES", GENE (AMSTERDAM), vol. 91, no. 1, 1990, pages 139 - 142, XP001153862, ISSN: 0378-1119 *
WELSH J ET AL: "FINGERPRINTING GENOMES USING PCR WITH ARBITRARY PRIMERS", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 18, no. 24, 25 December 1990 (1990-12-25), pages 7213 - 7218, XP000310554, ISSN: 0305-1048 *
WELSH JOHN ET AL: "Nucleic acid fingerprinting by PCR-based methods: Applications to problems in aging and mutagenesis.", MUTATION RESEARCH, vol. 338, no. 1-6, 1995, pages 215 - 229, XP009014423, ISSN: 0027-5107 *

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Publication number Publication date
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