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 samplesInfo
- 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
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.
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US08/862,905 | 1997-05-23 | ||
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 |
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)
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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 |
US6270973B1 (en) | 1998-03-13 | 2001-08-07 | Promega Corporation | Multiplex method for nucleic acid detection |
US6270974B1 (en) | 1998-03-13 | 2001-08-07 | Promega Corporation | Exogenous nucleic acid detection |
US6391551B1 (en) | 1998-03-13 | 2002-05-21 | Promega Corporation | Detection of nucleic acid hybrids |
US6277578B1 (en) | 1998-03-13 | 2001-08-21 | Promega Corporation | Deploymerization method for nucleic acid detection of an amplified nucleic acid target |
US6312902B1 (en) | 1998-03-13 | 2001-11-06 | Promega Corporation | Nucleic acid detection |
US7090975B2 (en) | 1998-03-13 | 2006-08-15 | Promega Corporation | Pyrophosphorolysis and incorporation of nucleotide method for nucleic acid detection |
US6703211B1 (en) | 1998-03-13 | 2004-03-09 | Promega Corporation | Cellular detection by providing high energy phosphate donor other than ADP to produce ATP |
US6235480B1 (en) * | 1998-03-13 | 2001-05-22 | Promega Corporation | Detection of nucleic acid hybrids |
US6268146B1 (en) | 1998-03-13 | 2001-07-31 | Promega Corporation | Analytical methods and materials 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 |
JP2003517309A (en) | 1999-12-02 | 2003-05-27 | ディーエヌエー サイエンシーズ インコーポレーテッド | Methods for determining single nucleotide mutations and genotyping |
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 |
AU2002351187A1 (en) | 2001-11-30 | 2003-06-17 | Fluidigm Corporation | Microfluidic device and methods of using same |
WO2004003136A2 (en) * | 2002-06-28 | 2004-01-08 | Sention, Inc. | 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 |
US7932060B2 (en) * | 2003-04-18 | 2011-04-26 | Becton, Dickinson And Company | Immuno-amplification |
US20050233314A1 (en) * | 2003-06-30 | 2005-10-20 | National Health Research Institutes | Sensitive and quantitative detection of pathogens by real-time nested PCR |
EP1732614B1 (en) * | 2004-04-08 | 2008-12-24 | Sangamo Biosciences Inc. | Compositions for treating neuropathic and neurodegenerative conditions |
AU2005233583B2 (en) * | 2004-04-08 | 2011-02-03 | Sangamo Therapeutics, Inc. | Methods and compositions for modulating cardiac contractility |
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) |
ATE553122T1 (en) * | 2005-02-28 | 2012-04-15 | Sangamo Biosciences Inc | ANTIANGIOGENIC METHODS AND COMPOSITIONS |
EP2518161A1 (en) | 2005-03-18 | 2012-10-31 | Fluidigm Corporation | Method for detection of mutant alleles |
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 |
DK2623605T3 (en) | 2007-04-09 | 2019-03-25 | Univ Florida | RAAV VECTOR COMPOSITIONS WITH TYROSIN MODIFIED CAPSIDE PROTEINS AND PROCEDURES FOR USE THEREOF |
ATE541946T1 (en) | 2007-09-07 | 2012-02-15 | Fluidigm Corp | METHOD AND SYSTEM FOR DETERMINING GENE COPY NUMBER VARIANTS |
JP2010538612A (en) * | 2007-09-07 | 2010-12-16 | サード ウェーブ テクノロジーズ,インコーポレーテッド | Methods and applications for target quantification |
WO2009098998A1 (en) * | 2008-02-05 | 2009-08-13 | Olympus Corporation | Nucleic acid detection method, and nucleic acid detection kit |
CA2722484A1 (en) * | 2008-04-24 | 2009-10-29 | Peter D. Ludowise | 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 |
CA2805033A1 (en) | 2009-07-14 | 2011-01-20 | Beth Israel Deaconess Medical Center, Inc. | Methods of increasing liver proliferation |
EP2659002B1 (en) | 2010-12-27 | 2017-02-01 | Abbott Molecular Inc. | Quantitating high titer samples by digital pcr |
US9222115B2 (en) | 2011-12-30 | 2015-12-29 | Abbott Molecular, Inc. | Channels with cross-sectional thermal gradients |
US9850515B2 (en) | 2013-02-08 | 2017-12-26 | Bio-Rad Laboratories, Inc. | Affinity-based partition assay for detection of target molecules |
EP2994559B1 (en) | 2013-05-09 | 2020-07-08 | Bio-rad Laboratories, Inc. | Magnetic immuno digital pcr assay |
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 |
EP3146076A4 (en) | 2014-05-22 | 2018-05-09 | 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 |
CN107209188A (en) | 2014-06-27 | 2017-09-26 | 雅培制药有限公司 | Composition and method for detecting people Pegivirus 2 (HPgV 2) |
EP3271849B1 (en) | 2015-03-17 | 2021-09-08 | Bio-Rad Laboratories, Inc. | Detection of genome editing |
US20240003918A1 (en) | 2020-11-30 | 2024-01-04 | Enigma Biointelligence, Inc. | Non-invasive assessment of alzheimer's disease |
CA3217862A1 (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)
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 |
DE69519783T2 (en) * | 1994-04-29 | 2001-06-07 | Perkin Elmer Corp | METHOD AND DEVICE FOR REAL-TIME DETECTION OF PRODUCTS OF NUCLEIC ACID AMPLIFICATION |
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 |
-
1997
- 1997-05-23 US US08/862,905 patent/US5863736A/en not_active Expired - Lifetime
-
1998
- 1998-04-27 CA CA002236067A patent/CA2236067C/en not_active Expired - Fee Related
- 1998-05-06 AU AU64749/98A patent/AU738398B2/en not_active Ceased
- 1998-05-22 EP EP98109364A patent/EP0915169B1/en not_active Expired - Lifetime
- 1998-05-22 ES ES98109364T patent/ES2251048T3/en not_active Expired - Lifetime
- 1998-05-22 AT AT98109364T patent/ATE307216T1/en not_active IP Right Cessation
- 1998-05-22 DE DE69831913T patent/DE69831913T2/en not_active Expired - Lifetime
- 1998-05-25 JP JP15989698A patent/JP3665477B2/en not_active Expired - Fee Related
Also Published As
Publication number | Publication date |
---|---|
EP0915169B1 (en) | 2005-10-19 |
JP3665477B2 (en) | 2005-06-29 |
US5863736A (en) | 1999-01-26 |
DE69831913D1 (en) | 2006-03-02 |
ATE307216T1 (en) | 2005-11-15 |
AU6474998A (en) | 1998-11-26 |
EP0915169A2 (en) | 1999-05-12 |
EP0915169A3 (en) | 2002-10-16 |
ES2251048T3 (en) | 2006-04-16 |
AU738398B2 (en) | 2001-09-20 |
CA2236067C (en) | 2003-08-05 |
DE69831913T2 (en) | 2006-07-13 |
JPH114688A (en) | 1999-01-12 |
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Legal Events
Date | Code | Title | Description |
---|---|---|---|
EEER | Examination request | ||
MKLA | Lapsed |
Effective date: 20130429 |
|
MKLA | Lapsed |
Effective date: 20130429 |