CA2236067A1 - Methods, apparatus and computer program products for determining quantities of nucleic acid sequences in samples - Google Patents

Methods, apparatus and computer program products for determining quantities of nucleic acid sequences in samples

Info

Publication number
CA2236067A1
CA2236067A1 CA002236067A CA2236067A CA2236067A1 CA 2236067 A1 CA2236067 A1 CA 2236067A1 CA 002236067 A CA002236067 A CA 002236067A CA 2236067 A CA2236067 A CA 2236067A CA 2236067 A1 CA2236067 A1 CA 2236067A1
Authority
CA
Canada
Prior art keywords
nucleic acid
samples
acid sequence
time interval
quantities
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.)
Granted
Application number
CA002236067A
Other languages
French (fr)
Other versions
CA2236067C (en
Inventor
Perry D. Haaland
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.)
Becton Dickinson and Co
Original Assignee
Becton Dickinson and Co
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 Becton Dickinson and Co filed Critical Becton Dickinson and Co
Publication of CA2236067A1 publication Critical patent/CA2236067A1/en
Application granted granted Critical
Publication of CA2236067C publication Critical patent/CA2236067C/en
Anticipated expiration legal-status Critical
Expired - Fee Related legal-status Critical Current

Links

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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6851—Quantitative amplification

Abstract

Methods for determining quantities of nucleic acid sequences in samples include the steps of amplifying a plurality of known quantities of a nucleic acid sequence in respective calibration samples and an unknown quantity of a nucleic acid sequence in a test sample, in parallel, during a time interval. These samples may be amplified using an isothermal amplification method such as Strand Displacement Amplification (SDA), or a thermal cycling amplification method such as Polymerase Chain Reaction (PCR), for example. Indicia of the quantities of a nucleic acid sequence being amplified in the calibration and test samples are then measured using conventional techniques, at measurement points in the time interval. Steps are then performed to determine for a first potential cutoff level, a corresponding first set of time points in the time interval at which the indicia of the quantities of a nucleic acid sequence being amplified in each of the calibration samples equal the first cutoff level. This step is then repeated for each of a number of different potential cutoff levels so that respective sets of time points in the time interval can be obtained for each potential cutoff level. According to a preferred aspect of the present invention, a step is then performed to determine, relative to a statistical criterion, which of the sets of points in the time interval better satisfies the statistical criterion against the known quantities of a nucleic acid sequence in the calibration samples. A quantity of a nucleic acid sequence in the test sample is then determined based on the set of points determined to better or best satisfy the statistical criterion. The accuracy of the determination can also be improved using a relatively large number of potential cutoff levels.
CA002236067A 1997-05-23 1998-04-27 Methods, apparatus and computer program products for determining quantities of nucleic acid sequences in samples Expired - Fee Related CA2236067C (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US08/862,905 US5863736A (en) 1997-05-23 1997-05-23 Method, apparatus and computer program products for determining quantities of nucleic acid sequences in samples
US08/862,905 1997-05-23

Publications (2)

Publication Number Publication Date
CA2236067A1 true CA2236067A1 (en) 1998-11-23
CA2236067C CA2236067C (en) 2003-08-05

Family

ID=25339703

Family Applications (1)

Application Number Title Priority Date Filing Date
CA002236067A Expired - Fee Related CA2236067C (en) 1997-05-23 1998-04-27 Methods, apparatus and computer program products for determining quantities of nucleic acid sequences in samples

Country Status (8)

Country Link
US (1) US5863736A (en)
EP (1) EP0915169B1 (en)
JP (1) JP3665477B2 (en)
AT (1) ATE307216T1 (en)
AU (1) AU738398B2 (en)
CA (1) CA2236067C (en)
DE (1) DE69831913T2 (en)
ES (1) ES2251048T3 (en)

Families Citing this family (57)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
US6703211B1 (en) 1998-03-13 2004-03-09 Promega Corporation Cellular detection by providing high energy phosphate donor other than ADP to produce ATP
US6277578B1 (en) 1998-03-13 2001-08-21 Promega Corporation Deploymerization method for nucleic acid detection of an amplified nucleic acid target
US6235480B1 (en) * 1998-03-13 2001-05-22 Promega Corporation Detection of nucleic acid hybrids
US6391551B1 (en) 1998-03-13 2002-05-21 Promega Corporation Detection of nucleic acid hybrids
US7090975B2 (en) 1998-03-13 2006-08-15 Promega Corporation Pyrophosphorolysis and incorporation of nucleotide method for nucleic acid detection
US6270974B1 (en) 1998-03-13 2001-08-07 Promega Corporation Exogenous nucleic acid detection
US6268146B1 (en) 1998-03-13 2001-07-31 Promega Corporation Analytical methods and materials for nucleic acid detection
US6312902B1 (en) 1998-03-13 2001-11-06 Promega Corporation Nucleic acid detection
US6270973B1 (en) 1998-03-13 2001-08-07 Promega Corporation Multiplex method for nucleic acid detection
US6066458A (en) * 1998-05-18 2000-05-23 Becton, Dickinson And Company Methods, apparatus and computer program products for determining quantities of nucleic acid sequences in samples using standard curves and amplification ratio estimates
US6573047B1 (en) 1999-04-13 2003-06-03 Dna Sciences, Inc. Detection of nucleotide sequence variation through fluorescence resonance energy transfer label generation
US6180349B1 (en) 1999-05-18 2001-01-30 The Regents Of The University Of California Quantitative PCR method to enumerate DNA copy number
US6516276B1 (en) * 1999-06-18 2003-02-04 Eos Biotechnology, Inc. Method and apparatus for analysis of data from biomolecular arrays
WO2001013086A2 (en) * 1999-08-13 2001-02-22 Brandeis University Detection of nucleic acids
IL149676A0 (en) 1999-12-02 2002-11-10 Dna Sciences Inc Methods and kits for determining nucleotide variations
US6783934B1 (en) 2000-05-01 2004-08-31 Cepheid, Inc. Methods for quantitative analysis of nucleic acid amplification reaction
EP1158449A3 (en) * 2000-05-19 2004-12-15 Becton Dickinson and Company Computerized method and apparatus for analyzing readings of nucleic acid assays
US6355433B1 (en) 2000-06-02 2002-03-12 Dna Sciences, Inc. Determination of nucleotide sequence variations through limited primer extension
US7226732B2 (en) * 2001-07-16 2007-06-05 Cepheid Methods, apparatus, and computer programs for verifying the integrity of a probe
US7363168B2 (en) * 2001-10-02 2008-04-22 Stratagene California Adaptive baseline algorithm for quantitative PCR
ES2403560T3 (en) 2001-11-30 2013-05-20 Fluidigm Corporation Microfluidic device and procedures for its use
CN1665938B (en) * 2002-06-28 2012-10-10 普里梅拉蒂斯有限公司 Methods of detecting sequence differences
NL1021160C2 (en) * 2002-07-26 2004-01-27 Multigen Internat B V Method for determining the copy number of a nucleotide sequence.
US7666361B2 (en) 2003-04-03 2010-02-23 Fluidigm Corporation Microfluidic devices and methods of using same
WO2006102264A1 (en) 2005-03-18 2006-09-28 Fluidigm Corporation Thermal reaction device and method for using the same
JP5117719B2 (en) * 2003-04-18 2013-01-16 ベクトン・ディキンソン・アンド・カンパニー Immune amplification
US20050233314A1 (en) * 2003-06-30 2005-10-20 National Health Research Institutes Sensitive and quantitative detection of pathogens by real-time nested PCR
CA2561565C (en) * 2004-04-08 2013-11-26 Sangamo Biosciences, Inc. Methods for repression of phospholamban gene and modulating cardiac contractility
JP4903689B2 (en) * 2004-04-08 2012-03-28 サンガモ バイオサイエンシズ インコーポレイテッド Methods and compositions for treating neuropathy and neurodegenerative symptoms
US20050233332A1 (en) * 2004-04-14 2005-10-20 Collis Matthew P Multiple fluorophore detector system
US20060009916A1 (en) * 2004-07-06 2006-01-12 Xitong Li Quantitative PCR data analysis system (QDAS)
WO2006094106A2 (en) * 2005-02-28 2006-09-08 Sangamo Biosciences, Inc. Anti-angiogenic methods and compositions
WO2007019410A2 (en) * 2005-08-05 2007-02-15 The Board Of Trustees Of The Leland Stanford Junior University Mammalian obestatin receptors
WO2007044974A2 (en) * 2005-10-12 2007-04-19 The Research Foundation Of State University Of New York Absolute pcr quantification
HUE030719T2 (en) 2007-04-09 2017-05-29 Univ Florida Raav vector compositions having tyrosine-modified capsid proteins and methods for use
WO2009033156A2 (en) * 2007-09-07 2009-03-12 Third Wave Technologies, Inc. Methods and applications for target quantification
CA2698545C (en) 2007-09-07 2014-07-08 Fluidigm Corporation Copy number variation determination, methods and systems
JP5530185B2 (en) * 2008-02-05 2014-06-25 オリンパス株式会社 Nucleic acid detection method and nucleic acid detection kit
CN102046807B (en) * 2008-04-24 2014-11-26 3M创新有限公司 Analysis of nucleic acid amplification curves using wavelet transformation
WO2011006119A2 (en) 2009-07-09 2011-01-13 The Scripps Research Institute Gene expression profiles associated with chronic allograft nephropathy
CN102596188A (en) 2009-07-14 2012-07-18 贝思以色列女教会医学中心 Methods of increasing liver proliferation
WO2012092259A1 (en) 2010-12-27 2012-07-05 Ibis Biosciences, Inc. Quantitating high titer samples by digital pcr
CA2863121A1 (en) 2011-12-30 2013-07-04 Abbott Molecular Inc. Microorganism nucleic acid purification from host samples
CN105102696B (en) 2013-02-08 2017-08-15 生物辐射实验室股份有限公司 The experiment of the division based on affinity detected for target molecule
CN105431575B (en) 2013-05-09 2017-08-29 生物辐射实验室股份有限公司 Magnetic immuno digital pcr is tested
WO2015179773A1 (en) 2014-05-22 2015-11-26 The Scripps Research Institute Tissue molecular signatures of kidney transplant rejections
CN105531408B (en) 2014-02-13 2019-09-10 生物辐射实验室股份有限公司 Chromosomal conformation divides product capture
US10443100B2 (en) 2014-05-22 2019-10-15 The Scripps Research Institute Gene expression profiles associated with sub-clinical kidney transplant rejection
WO2015179777A2 (en) 2014-05-22 2015-11-26 The Scripps Research Institute Gene expression profiles associated with sub-clinical kidney transplant rejection
US11104951B2 (en) 2014-05-22 2021-08-31 The Scripps Research Institute Molecular signatures for distinguishing liver transplant rejections or injuries
GB2538006A (en) 2014-05-22 2016-11-02 Scripps Research Inst Gene expression profiles associated with sub-clinical kidney transplant rejection
ES2753573T3 (en) 2014-06-27 2020-04-13 Abbott Lab Compositions and methods for detecting human pegivirus 2 (HPGV-2)
US10066256B2 (en) 2015-03-17 2018-09-04 Bio-Rad Laboratories, Inc. Detection of genome editing
EP4252243A2 (en) 2020-11-30 2023-10-04 Enigma Biointelligence, Inc. Non-invasive assessment of alzheimer's disease
WO2022235929A1 (en) 2021-05-05 2022-11-10 Radius Pharmaceuticals, Inc. Animal model having homologous recombination of mouse pth1 receptor
WO2023006642A1 (en) 2021-07-26 2023-02-02 Glaxosmithkline Intellectual Property Development Limited Assay methods for titration of retrovirus and retroviral vectors

Family Cites Families (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5219727A (en) * 1989-08-21 1993-06-15 Hoffmann-Laroche Inc. Quantitation of nucleic acids using the polymerase chain reaction
US5455166A (en) * 1991-01-31 1995-10-03 Becton, Dickinson And Company Strand displacement amplification
US5994056A (en) * 1991-05-02 1999-11-30 Roche Molecular Systems, Inc. Homogeneous methods for nucleic acid amplification and detection
US5270184A (en) * 1991-11-19 1993-12-14 Becton, Dickinson And Company Nucleic acid target generation
US5650277A (en) * 1992-07-02 1997-07-22 Diagenetics Ltd. Method of determining the presence and quantifying the number of di- and trinucleotide repeats
CA2129787A1 (en) * 1993-08-27 1995-02-28 Russell G. Higuchi Monitoring multiple amplification reactions simultaneously and analyzing same
US5547861A (en) * 1994-04-18 1996-08-20 Becton, Dickinson And Company Detection of nucleic acid amplification
AU698953B2 (en) * 1994-04-29 1998-11-12 Applied Biosystems, Llc System for real time detection of nucleic acid amplification products
US5766889A (en) * 1994-06-08 1998-06-16 The Perkin-Elmer Corporation Method for determining the characteristics of the concentration growth of target nucleic acid molecules in polymerase chain reaction sample
US5550025A (en) * 1995-07-19 1996-08-27 Becton, Dickinson And Company Detection of hydrophobic amplification products by extraction into an organic phase
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

Also Published As

Publication number Publication date
ATE307216T1 (en) 2005-11-15
EP0915169B1 (en) 2005-10-19
JPH114688A (en) 1999-01-12
EP0915169A3 (en) 2002-10-16
AU6474998A (en) 1998-11-26
US5863736A (en) 1999-01-26
JP3665477B2 (en) 2005-06-29
EP0915169A2 (en) 1999-05-12
ES2251048T3 (en) 2006-04-16
DE69831913D1 (en) 2006-03-02
DE69831913T2 (en) 2006-07-13
AU738398B2 (en) 2001-09-20
CA2236067C (en) 2003-08-05

Similar Documents

Publication Publication Date Title
CA2236067A1 (en) Methods, apparatus and computer program products for determining quantities of nucleic acid sequences in samples
EP2850211B1 (en) Method for increasing accuracy in quantitative detection of polynucleotides
WO1996036736A3 (en) Wide dynamic range nucleic acid detection using an aggregate primer series
CA2497988A1 (en) Quantification of gene expression
CA2302881A1 (en) Method for quantification of an analyte
DK0395292T3 (en) Development of specific probes for target nucleotide sequences
WO1999057321A8 (en) Method of determining the nucleotide sequence of oligonucleotides and dna molecules
EP0379369A3 (en) Nucleic acid amplification using single primer
DK0862656T3 (en) Unimolecular segment amplification and detection
Wiseman State of the art and limitations of quantitative polymerase chain reaction
EP1542009A4 (en) Method of detecting nucleic acid by using dna microarrays and nucleic acid detection apparatus
ATE211771T1 (en) METHOD FOR DETECTING NUCLEIC ACID SEQUENCES USING COMPETITIVE AMPLIFICATION
DK0662156T3 (en) Improved method for quantifying nucleic acid
EP1909108A3 (en) Systems and methods to perform assays for detecting or quantifiying analytes
ATE131878T1 (en) METHOD FOR CHECKING CONTAMINATION OF OLIGONUCLEOTIDE DEPENDENT NUCLEIC ACID AMPLIFICATION REACTIONS
Birch et al. Evaluation of LabChipTM technology for GMO analysis in food
HK1068377A1 (en) Analytical method and kit
CN107164464B (en) Method and primer for detecting pollution of sequencing platform index sequence
Peccoud et al. Statistical estimations of PCR amplification rates
US20090246757A1 (en) Method, Program, and System for Normalizing Gene Expression Amounts
ATE412775T1 (en) METHOD FOR QUANTIFYING NUCLEIC ACIDS BY DETERMINING THE CELL NUMBER
EP1092782A3 (en) Genetic screening method and genetic screening apparatus
KR101919896B1 (en) Method for detecting multiple nucleic acid using a single fluorescence channel PCR machine
EP1323835A3 (en) Method for determining biospecies contained in test specimen and kit used for the same
HUT69947A (en) Detection of nucleotide sequences using simple sequence repeats and oligonucleotide ligation

Legal Events

Date Code Title Description
EEER Examination request
MKLA Lapsed

Effective date: 20130429

MKLA Lapsed

Effective date: 20130429