WO2002016648A3 - Methods for external controls for nucleic acid amplification - Google Patents

Methods for external controls for nucleic acid amplification Download PDF

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Publication number
WO2002016648A3
WO2002016648A3 PCT/US2001/026499 US0126499W WO0216648A3 WO 2002016648 A3 WO2002016648 A3 WO 2002016648A3 US 0126499 W US0126499 W US 0126499W WO 0216648 A3 WO0216648 A3 WO 0216648A3
Authority
WO
WIPO (PCT)
Prior art keywords
target
primers
nucleic acid
methods
acid amplification
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/US2001/026499
Other languages
French (fr)
Other versions
WO2002016648A2 (en
Inventor
Christian Heid
Kenneth J Livak
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.)
Applied Biosystems Inc
Original Assignee
PE Corp
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 PE Corp filed Critical PE Corp
Priority to EP01964412A priority Critical patent/EP1339870B1/en
Priority to AU85267/01A priority patent/AU8526701A/en
Priority to AT01964412T priority patent/ATE288964T1/en
Priority to DE60108897T priority patent/DE60108897T2/en
Priority to CA002386913A priority patent/CA2386913A1/en
Priority to JP2002522318A priority patent/JP2004507248A/en
Publication of WO2002016648A2 publication Critical patent/WO2002016648A2/en
Anticipated expiration legal-status Critical
Publication of WO2002016648A3 publication Critical patent/WO2002016648A3/en
Ceased legal-status Critical Current

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    • 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
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • Y10S435/00—Chemistry: molecular biology and microbiology
    • Y10S435/81—Packaged device or kit

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Immunology (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)
  • Saccharide Compounds (AREA)

Abstract

Methods of nucleic acid amplification with external controls are provided that verify the absence or presence of specific target sequences, and correct primers and probes. A single-stranded, external control polynucleotide is amplified with primers of the same sequence as target primers. Probes with detectable labels and sequences specific for target and external control polynucleotides allow for detection and measurement. The primers and the detectable probe are adjacent or substantially adjacent when hybridization of a self-quenching probe complementary to both target and external control polynucleotides. A kit of PCR reagents can be dispensed into vessels for rapid and accurate nucleic acid amplification assay, with real-time or end-point measurements. The amplification control reagents, kits, and methods of the present invention provide positive and negative control tests which can be conducted concurrently with target amplification. Allelic differences at genetic loci can be detected, including single nucleotide polymorphisms (SNP).
PCT/US2001/026499 2000-08-24 2001-08-23 Methods for external controls for nucleic acid amplification Ceased WO2002016648A2 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
EP01964412A EP1339870B1 (en) 2000-08-24 2001-08-23 Methods for external controls for nucleic acid amplification
AU85267/01A AU8526701A (en) 2000-08-24 2001-08-23 Methods for external controls for nucleic acid amplification
AT01964412T ATE288964T1 (en) 2000-08-24 2001-08-23 METHODS FOR EXTERNAL CONTROLS ON NUCLEIC ACID AMPLIFICATION
DE60108897T DE60108897T2 (en) 2000-08-24 2001-08-23 METHODS FOR EXTERNAL CONTROLS FOR NUCLEIC ACID AMPLIFICATION
CA002386913A CA2386913A1 (en) 2000-08-24 2001-08-23 Methods for external controls for nucleic acid amplification
JP2002522318A JP2004507248A (en) 2000-08-24 2001-08-23 Methods for external control over nucleic acid amplification

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US09/645,959 US6358679B1 (en) 2000-08-24 2000-08-24 Methods for external controls for nucleic acid amplification
US09/645,959 2000-08-24

Publications (2)

Publication Number Publication Date
WO2002016648A2 WO2002016648A2 (en) 2002-02-28
WO2002016648A3 true WO2002016648A3 (en) 2003-06-19

Family

ID=24591151

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/026499 Ceased WO2002016648A2 (en) 2000-08-24 2001-08-23 Methods for external controls for nucleic acid amplification

Country Status (8)

Country Link
US (2) US6358679B1 (en)
EP (1) EP1339870B1 (en)
JP (1) JP2004507248A (en)
AT (1) ATE288964T1 (en)
AU (1) AU8526701A (en)
CA (1) CA2386913A1 (en)
DE (1) DE60108897T2 (en)
WO (1) WO2002016648A2 (en)

Families Citing this family (41)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002083952A1 (en) * 2001-04-12 2002-10-24 Caliper Technologies Corp. Systems and methods for high throughput genetic analysis
GB0119274D0 (en) * 2001-08-08 2001-10-03 Univ Durham Fusion proteins for insect control
US6544746B2 (en) * 2001-08-13 2003-04-08 St. Louis University Rapid and sensitive proximity-based assay for the detection and quantification of DNA binding proteins
US7172865B2 (en) 2001-08-13 2007-02-06 Saint Louis University Rapid and sensitive assay for the detection and quantification of coregulators of nucleic acid binding factors
US20030082606A1 (en) * 2001-09-04 2003-05-01 Lebo Roger V. Optimizing genome-wide mutation analysis of chromosomes and genes
DE60334132D1 (en) * 2002-05-31 2010-10-21 Nat Inst Of Advanced Ind Scien NEW METHOD FOR TESTING NUCLEIC ACID USING MARKED NUCLEOTIDE
EP1540009B1 (en) * 2002-08-05 2011-09-28 Quanta Biosciences, Inc. Improved compositions for in vitro amplification of nucleic acids
US20070065830A1 (en) * 2002-09-04 2007-03-22 Children's Hospital Medical Center Of Akron, Inc. Cloning multiple control sequences into chromosomes or into artificial centromeres
US20040138821A1 (en) * 2002-09-06 2004-07-15 Affymetrix, Inc. A Corporation Organized Under The Laws Of Delaware System, method, and computer software product for analysis and display of genotyping, annotation, and related information
WO2004055709A2 (en) * 2002-12-13 2004-07-01 Applera Corporation Methods for identifying, viewing, and analyzing syntenic and orthologous genomic regions between two or more species
EP2390352A1 (en) 2003-03-18 2011-11-30 Quantum Genetics Ireland Limited Systems and methods for improving protein and milk production of dairy herds
US20050038776A1 (en) * 2003-08-15 2005-02-17 Ramin Cyrus Information system for biological and life sciences research
US20060024690A1 (en) * 2003-09-19 2006-02-02 Kao H P Normalization of data using controls
US20050221357A1 (en) * 2003-09-19 2005-10-06 Mark Shannon Normalization of gene expression data
WO2005029041A2 (en) * 2003-09-19 2005-03-31 Applera Corporation High density sequence detection methods and apparatus
US7332280B2 (en) * 2003-10-14 2008-02-19 Ronald Levy Classification of patients having diffuse large B-cell lymphoma based upon gene expression
EP1718770B1 (en) 2004-02-19 2011-05-25 The Governors of the University of Alberta Leptin promoter polymorphisms and uses thereof
US20050244837A1 (en) * 2004-04-28 2005-11-03 Cepheid Method and device for sample preparation control
US20050255485A1 (en) * 2004-05-14 2005-11-17 Livak Kenneth J Detection of gene duplications
US7575863B2 (en) 2004-05-28 2009-08-18 Applied Biosystems, Llc Methods, compositions, and kits comprising linker probes for quantifying polynucleotides
US20060003337A1 (en) * 2004-06-30 2006-01-05 John Brandis Detection of small RNAS
EP1791982B1 (en) * 2004-09-21 2011-01-05 Life Technologies Corporation TWO-COLOR REAL-TIME/END-POINT QUANTITATION OF MICRORNAS (MIRNAs)
US7405044B2 (en) * 2004-10-08 2008-07-29 Reliagene Technologies Inc. Multiplex PCR for simultaneous quantitation of human nuclear, mitochondrial, and male Y-chromosome DNA
US20060111915A1 (en) * 2004-11-23 2006-05-25 Applera Corporation Hypothesis generation
US8084260B2 (en) * 2004-11-24 2011-12-27 Applied Biosystems, Llc Spectral calibration method and system for multiple instruments
US7892737B2 (en) * 2005-06-30 2011-02-22 Life Technologies Corporation Compositions, kits and methods pertaining to stability modulation of PNA oligomer/nucleic acid complexes
GB0612342D0 (en) * 2006-06-21 2006-08-02 Glaxosmithkline Biolog Sa Method
EP2484781B1 (en) 2006-08-01 2017-08-23 Applied Biosystems, LLC Detection of analytes and nucleic acids
EP2429704A2 (en) * 2009-05-14 2012-03-21 Streck Inc. Sample processing cassette, system, and method
WO2012142003A2 (en) 2011-04-15 2012-10-18 Life Technologies Corporation Chemical ligation
JP5920763B2 (en) * 2011-10-05 2016-05-18 国立大学法人名古屋大学 Fluorescently labeled oligonucleotide derivatives and uses thereof
EP2660332B1 (en) * 2012-05-01 2017-02-22 F. Hoffmann-La Roche AG Positive control concept
US9540699B2 (en) 2013-03-13 2017-01-10 William Beaumont Hospital Methods of diagnosing increased risk of developing MRSA
KR102207922B1 (en) 2014-03-06 2021-01-26 삼성전자주식회사 Primer set specific for a vancomycin resistant Enterococcus, composition comprising the same and method for detecting a vancomycin resistant Enterococcus in a sample
GB2525024A (en) * 2014-04-10 2015-10-14 Vela Operations Pte Ltd Universal controls for sequencing assays
US20180087106A1 (en) * 2014-10-17 2018-03-29 National University Corporation Tokyo Medical And Dental University Method for detecting and quantifying target nucleic acid in test sample using novel positive control nucleic acid
KR102287811B1 (en) 2014-10-31 2021-08-09 삼성전자주식회사 Method of bonding two surfaces and construct therefrom and microfluidic device containing the construct
CA3023256A1 (en) * 2016-05-18 2017-11-23 Integrated Nano-Technologies, Inc. Method for detection of a pcr product
CN118207299A (en) * 2016-08-26 2024-06-18 生命技术公司 Nucleic acid extraction and amplification controls and methods of use thereof
IT201900008781A1 (en) * 2019-06-12 2020-12-12 AB Analitica S R L METHOD OF AMPLIFICATION OF NUCLEIC ACIDS
JP7272202B2 (en) 2019-09-20 2023-05-12 株式会社島津製作所 Method and apparatus for testing target nucleic acid

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5538848A (en) * 1994-11-16 1996-07-23 Applied Biosystems Division, Perkin-Elmer Corp. Method for detecting nucleic acid amplification using self-quenching fluorescence probe
US5952202A (en) * 1998-03-26 1999-09-14 The Perkin Elmer Corporation Methods using exogenous, internal controls and analogue blocks during nucleic acid amplification

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5210015A (en) 1990-08-06 1993-05-11 Hoffman-La Roche Inc. Homogeneous assay system using the nuclease activity of a nucleic acid polymerase
JP2660661B2 (en) * 1994-05-11 1997-10-08 株式会社バイオセンサー研究所 Gene quantification method
US5801155A (en) * 1995-04-03 1998-09-01 Epoch Pharmaceuticals, Inc. Covalently linked oligonucleotide minor grove binder conjugates
FR2740782B1 (en) * 1995-11-06 1998-10-16 Microdiag METHOD AND KIT FOR QUANTIFICATION AND DETECTION OF MICROORGANISMS
JP4638043B2 (en) * 1998-12-14 2011-02-23 パシフィック バイオサイエンシーズ オブ カリフォルニア， インコーポレイテッド Systems and methods for sequencing single molecule nucleic acids by polymerase synthesis

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5538848A (en) * 1994-11-16 1996-07-23 Applied Biosystems Division, Perkin-Elmer Corp. Method for detecting nucleic acid amplification using self-quenching fluorescence probe
EP0972848A2 (en) * 1994-11-16 2000-01-19 Perkin-Elmer Corporation Self-quenching fluorescence probe and method
US5952202A (en) * 1998-03-26 1999-09-14 The Perkin Elmer Corporation Methods using exogenous, internal controls and analogue blocks during nucleic acid amplification

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
AFONINA ET AL: "Efficient priming of PCR with short oligonucleotides conjugated to a minor groove binder", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 25, no. 13, 1997, pages 2657 - 2660, XP002111427, ISSN: 0305-1048 *
COREY E. ET AL: "improved reverse transcriptase-polymerase chain reaction protocol with exogenous internal competitive control for prostate-specific antigen mRNA in blood and bone marrow", CLINICAL CHEMISTRY, vol. 43, 1997, pages 443 - 452, XP001122181 *
DUMOULIN F L ET AL: "Semi-quantification of human C-C chemokine mRNAs with reverse transcription/real-time PCR using multi-specific standards", JOURNAL OF IMMUNOLOGICAL METHODS, ELSEVIER SCIENCE PUBLISHERS B.V.,AMSTERDAM, NL, vol. 241, no. 1-2, 31 July 2000 (2000-07-31), pages 109 - 119, XP004213715, ISSN: 0022-1759 *
REISCHL U ET AL: "QUANTITATIVE PCR A SURVEY OF THE PRESENT TECHNOLOGY", MOLECULAR BIOTECHNOLOGY, TOTOWA, NJ, US, vol. 3, 1995, pages 55 - 71, XP000600241, ISSN: 1073-6085 *

Also Published As

Publication number Publication date
AU8526701A (en) 2002-03-04
US20030027179A1 (en) 2003-02-06
JP2004507248A (en) 2004-03-11
ATE288964T1 (en) 2005-02-15
US6890718B2 (en) 2005-05-10
EP1339870A2 (en) 2003-09-03
CA2386913A1 (en) 2002-02-28
EP1339870B1 (en) 2005-02-09
US6358679B1 (en) 2002-03-19
WO2002016648A2 (en) 2002-02-28
DE60108897T2 (en) 2006-03-02
DE60108897D1 (en) 2005-03-17

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