CA2453366C - Methods, apparatus, and computer programs for verifying the integrity of a probe - Google Patents

Methods, apparatus, and computer programs for verifying the integrity of a probe Download PDF

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Publication number
CA2453366C
CA2453366C CA2453366A CA2453366A CA2453366C CA 2453366 C CA2453366 C CA 2453366C CA 2453366 A CA2453366 A CA 2453366A CA 2453366 A CA2453366 A CA 2453366A CA 2453366 C CA2453366 C CA 2453366C
Authority
CA
Canada
Prior art keywords
probe
temperature
fluorescence
signal
target
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.)
Expired - Lifetime
Application number
CA2453366A
Other languages
English (en)
French (fr)
Other versions
CA2453366A1 (en
Inventor
Stanley H. Sakai
William Mcmillan
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.)
Cepheid
Original Assignee
Cepheid
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 Cepheid filed Critical Cepheid
Publication of CA2453366A1 publication Critical patent/CA2453366A1/en
Application granted granted Critical
Publication of CA2453366C publication Critical patent/CA2453366C/en
Anticipated expiration legal-status Critical
Expired - Lifetime legal-status Critical Current

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Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • YGENERAL 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
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/14Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333Saccharide [e.g., DNA, etc.]

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Physiology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Investigating Or Analysing Materials By The Use Of Chemical Reactions (AREA)
  • Investigating, Analyzing Materials By Fluorescence Or Luminescence (AREA)
  • Investigating Or Analyzing Materials By The Use Of Ultrasonic Waves (AREA)
  • Tests Of Electronic Circuits (AREA)
CA2453366A 2001-07-16 2002-07-16 Methods, apparatus, and computer programs for verifying the integrity of a probe Expired - Lifetime CA2453366C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US09/906,897 US7226732B2 (en) 2001-07-16 2001-07-16 Methods, apparatus, and computer programs for verifying the integrity of a probe
US09/906,897 2001-07-16
PCT/US2002/022728 WO2003009100A2 (en) 2001-07-16 2002-07-16 Methods, apparatuses, and computer programs for verifying the integrity of a probe

Publications (2)

Publication Number Publication Date
CA2453366A1 CA2453366A1 (en) 2003-01-30
CA2453366C true CA2453366C (en) 2013-04-16

Family

ID=25423168

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2453366A Expired - Lifetime CA2453366C (en) 2001-07-16 2002-07-16 Methods, apparatus, and computer programs for verifying the integrity of a probe

Country Status (9)

Country Link
US (3) US7226732B2 (OSRAM)
EP (1) EP1415152B1 (OSRAM)
JP (4) JP4392240B2 (OSRAM)
AT (1) ATE508360T1 (OSRAM)
AU (1) AU2002355109B2 (OSRAM)
CA (1) CA2453366C (OSRAM)
DE (1) DE60239940D1 (OSRAM)
ES (1) ES2365699T3 (OSRAM)
WO (1) WO2003009100A2 (OSRAM)

Families Citing this family (29)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7226732B2 (en) 2001-07-16 2007-06-05 Cepheid Methods, apparatus, and computer programs for verifying the integrity of a probe
WO2006039293A2 (en) * 2004-09-29 2006-04-13 University Of Virginia Patent Foundation Localized control of thermal properties on microdevices and applications thereof
US8056881B2 (en) 2004-10-13 2011-11-15 University Of Virginia Patent Foundation Electrostatic actuation for management of flow in micro-total analysis systems (μ-TAS) and related method thereof
US8084260B2 (en) * 2004-11-24 2011-12-27 Applied Biosystems, Llc Spectral calibration method and system for multiple instruments
JP4922185B2 (ja) * 2004-12-22 2012-04-25 ユニバーシティ・オブ・ヴァージニア・パテント・ファウンデーション マイクロデバイスまたはナノスケールデバイスにおける熱用途または非熱用途のためのマイクロ波の使用
US8343755B2 (en) * 2005-08-01 2013-01-01 University Of Virginia Patent Foundation Microdevices for chemical sensing and chemical actuation
EP1938425A4 (en) * 2005-08-23 2010-09-15 Univ Virginia PASSIVE COMPONENTS FOR MICROFLUIDIC FLOW PROFILE FORMATION AND METHOD THEREOF
WO2007041671A2 (en) * 2005-10-04 2007-04-12 University Of Virginia Patent Foundation Microchip-based acoustic trapping or capture of cells for forensic analysis and related method thereof
US8916375B2 (en) * 2005-10-12 2014-12-23 University Of Virginia Patent Foundation Integrated microfluidic analysis systems
US20070207490A1 (en) * 2006-03-06 2007-09-06 Applera Corporation Method and system for generating sample plate layout for validation
WO2007114338A1 (ja) 2006-03-31 2007-10-11 Takeda Pharmaceutical Company Limited 酸分泌抑制薬
JP2008180677A (ja) * 2007-01-26 2008-08-07 Konica Minolta Medical & Graphic Inc マイクロチップ検査システム、マイクロチップ検査装置及びプログラム
FR2922897B1 (fr) * 2007-10-25 2009-11-27 Bio Rad Pasteur Mesure d'une population d'acides nucleiques,en particulier par pcr en temps reel.
US10662474B2 (en) 2010-01-19 2020-05-26 Verinata Health, Inc. Identification of polymorphic sequences in mixtures of genomic DNA by whole genome sequencing
EP3006573B1 (en) 2010-01-19 2018-03-07 Verinata Health, Inc Methods for determining fraction of fetal nucleic acids in maternal samples
US9323888B2 (en) 2010-01-19 2016-04-26 Verinata Health, Inc. Detecting and classifying copy number variation
US8700341B2 (en) 2010-01-19 2014-04-15 Verinata Health, Inc. Partition defined detection methods
US9260745B2 (en) 2010-01-19 2016-02-16 Verinata Health, Inc. Detecting and classifying copy number variation
US20120100548A1 (en) * 2010-10-26 2012-04-26 Verinata Health, Inc. Method for determining copy number variations
WO2011090556A1 (en) 2010-01-19 2011-07-28 Verinata Health, Inc. Methods for determining fraction of fetal nucleic acid in maternal samples
US10388403B2 (en) 2010-01-19 2019-08-20 Verinata Health, Inc. Analyzing copy number variation in the detection of cancer
EP2588629B1 (en) 2010-06-30 2017-05-17 Gen-Probe Incorporated Method and apparatus for identifying analyte-containing samples using single-read determination of analyte and process control signals
DK2697392T3 (en) 2011-04-12 2016-03-29 Verinata Health Inc SOLUTION OF GENOME FRACTIONS USING Polymorphism COUNTS
US9411937B2 (en) 2011-04-15 2016-08-09 Verinata Health, Inc. Detecting and classifying copy number variation
US9987576B2 (en) 2012-12-10 2018-06-05 University Of Virginia Patent Foundation Frequency-based filtering of mechanical actuation using fluidic device
GB201403076D0 (en) * 2014-02-21 2014-04-09 ALERE TECHNOLOGIES GmbH Methods for detecting multiple nucleic acids in a sample
LT3204517T (lt) * 2014-10-10 2021-11-25 Rutgers, The State University Of New Jersey Polimerazės grandininės reakcijos pradmenys ir zondai, skirti mycobacterium tuberculosis
US20190093155A1 (en) * 2017-05-25 2019-03-28 Roche Molecular Systems, Inc. Multiplex Nucleic Acid Amplification Assay
US11667945B2 (en) 2017-08-28 2023-06-06 Shizuoka Prefecture Public University Corporation Detection method and detection probe for colibactin and colibactin-producing bacteria

Family Cites Families (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4683202A (en) 1985-03-28 1987-07-28 Cetus Corporation Process for amplifying nucleic acid sequences
US4683195A (en) 1986-01-30 1987-07-28 Cetus Corporation Process for amplifying, detecting, and/or-cloning nucleic acid sequences
AU653712B2 (en) * 1990-02-16 1994-10-13 F. Hoffmann-La Roche Ag Improvements in the specificity and convenience of the polymerase chain reaction
US5627032A (en) * 1990-12-24 1997-05-06 Ulanovsky; Levy Composite primers for nucleic acids
US5994056A (en) 1991-05-02 1999-11-30 Roche Molecular Systems, Inc. Homogeneous methods for nucleic acid amplification and detection
NZ333135A (en) 1996-06-04 2000-02-28 Univ Utah Res Found Systems and methods for monitoring for DNA amplification by fluorescence using acceptor fluorophore labeled nucleic acid probe and a donor fluorophore labeled nucleic acid probe which hybridise to adjacent regions of a target sequence
DK1179600T3 (da) 1996-06-04 2005-09-05 Univ Utah Res Found Overvågning af hybridisering under PCR
US5736333A (en) 1996-06-04 1998-04-07 The Perkin-Elmer Corporation Passive internal references for the detection of nucleic acid amplification products
US5866336A (en) * 1996-07-16 1999-02-02 Oncor, Inc. Nucleic acid amplification oligonucleotides with molecular energy transfer labels and methods based thereon
US5863736A (en) * 1997-05-23 1999-01-26 Becton, Dickinson And Company Method, apparatus and computer program products for determining quantities of nucleic acid sequences in samples
US5952202A (en) 1998-03-26 1999-09-14 The Perkin Elmer Corporation Methods using exogenous, internal controls and analogue blocks during nucleic acid amplification
US6312929B1 (en) 2000-12-22 2001-11-06 Cepheid Compositions and methods enabling a totally internally controlled amplification reaction
US7226732B2 (en) * 2001-07-16 2007-06-05 Cepheid Methods, apparatus, and computer programs for verifying the integrity of a probe

Also Published As

Publication number Publication date
US9206470B2 (en) 2015-12-08
US9464317B2 (en) 2016-10-11
JP2013188228A (ja) 2013-09-26
JP2009165475A (ja) 2009-07-30
JP5955274B2 (ja) 2016-07-20
ATE508360T1 (de) 2011-05-15
WO2003009100A3 (en) 2003-11-27
ES2365699T3 (es) 2011-10-10
JP5328412B2 (ja) 2013-10-30
AU2002355109B2 (en) 2007-05-31
EP1415152A4 (en) 2005-03-23
JP2005515404A (ja) 2005-05-26
US20030064368A1 (en) 2003-04-03
DE60239940D1 (de) 2011-06-16
EP1415152A2 (en) 2004-05-06
JP2016154550A (ja) 2016-09-01
JP4392240B2 (ja) 2009-12-24
US7226732B2 (en) 2007-06-05
US20070259362A1 (en) 2007-11-08
WO2003009100A2 (en) 2003-01-30
US20080227090A1 (en) 2008-09-18
EP1415152B1 (en) 2011-05-04
CA2453366A1 (en) 2003-01-30
JP6434930B2 (ja) 2018-12-05

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Effective date: 20220718