CA2733186A1 - Detection algorithm for pcr assay - Google Patents
Detection algorithm for pcr assay Download PDFInfo
- Publication number
- CA2733186A1 CA2733186A1 CA2733186A CA2733186A CA2733186A1 CA 2733186 A1 CA2733186 A1 CA 2733186A1 CA 2733186 A CA2733186 A CA 2733186A CA 2733186 A CA2733186 A CA 2733186A CA 2733186 A1 CA2733186 A1 CA 2733186A1
- Authority
- CA
- Canada
- Prior art keywords
- nucleic acid
- target nucleic
- probe
- temperature
- slope
- 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.)
- Abandoned
Links
- 238000001514 detection method Methods 0.000 title abstract description 16
- 238000003556 assay Methods 0.000 title description 9
- 238000004422 calculation algorithm Methods 0.000 title description 2
- 150000007523 nucleic acids Chemical class 0.000 claims abstract description 95
- 108020004707 nucleic acids Proteins 0.000 claims abstract description 94
- 102000039446 nucleic acids Human genes 0.000 claims abstract description 94
- 239000000523 sample Substances 0.000 claims abstract description 80
- 238000000034 method Methods 0.000 claims abstract description 63
- 238000006243 chemical reaction Methods 0.000 claims abstract description 55
- 108020004711 Nucleic Acid Probes Proteins 0.000 claims abstract description 43
- 239000002853 nucleic acid probe Substances 0.000 claims abstract description 43
- 238000009396 hybridization Methods 0.000 claims abstract description 23
- 238000005259 measurement Methods 0.000 claims description 21
- 239000007850 fluorescent dye Substances 0.000 claims description 12
- 239000011541 reaction mixture Substances 0.000 claims description 9
- 230000003321 amplification Effects 0.000 claims description 8
- 238000000137 annealing Methods 0.000 claims description 8
- 238000003199 nucleic acid amplification method Methods 0.000 claims description 8
- 108090000790 Enzymes Proteins 0.000 claims description 5
- 102000004190 Enzymes Human genes 0.000 claims description 5
- 230000001351 cycling effect Effects 0.000 claims description 5
- 239000000758 substrate Substances 0.000 claims description 4
- 239000000872 buffer Substances 0.000 claims description 3
- 230000027455 binding Effects 0.000 abstract description 3
- 238000003752 polymerase chain reaction Methods 0.000 description 54
- 108020004414 DNA Proteins 0.000 description 16
- 230000000295 complement effect Effects 0.000 description 13
- 244000063299 Bacillus subtilis Species 0.000 description 11
- 235000014469 Bacillus subtilis Nutrition 0.000 description 11
- 241000193738 Bacillus anthracis Species 0.000 description 9
- 208000034784 Tularaemia Diseases 0.000 description 9
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 7
- ATJFFYVFTNAWJD-UHFFFAOYSA-N Tin Chemical compound [Sn] ATJFFYVFTNAWJD-UHFFFAOYSA-N 0.000 description 6
- 239000003153 chemical reaction reagent Substances 0.000 description 5
- 108091034117 Oligonucleotide Proteins 0.000 description 4
- BASFCYQUMIYNBI-UHFFFAOYSA-N platinum Chemical compound [Pt] BASFCYQUMIYNBI-UHFFFAOYSA-N 0.000 description 4
- 239000000843 powder Substances 0.000 description 4
- 108010014303 DNA-directed DNA polymerase Proteins 0.000 description 3
- 102000016928 DNA-directed DNA polymerase Human genes 0.000 description 3
- 238000002944 PCR assay Methods 0.000 description 3
- 238000004925 denaturation Methods 0.000 description 3
- 230000036425 denaturation Effects 0.000 description 3
- 238000002866 fluorescence resonance energy transfer Methods 0.000 description 3
- 244000052769 pathogen Species 0.000 description 3
- 108091033319 polynucleotide Proteins 0.000 description 3
- 102000040430 polynucleotide Human genes 0.000 description 3
- 239000002157 polynucleotide Substances 0.000 description 3
- 238000003753 real-time PCR Methods 0.000 description 3
- 230000035945 sensitivity Effects 0.000 description 3
- 239000000243 solution Substances 0.000 description 3
- 238000012360 testing method Methods 0.000 description 3
- 102000053602 DNA Human genes 0.000 description 2
- 206010035148 Plague Diseases 0.000 description 2
- 108010006785 Taq Polymerase Proteins 0.000 description 2
- 241000607479 Yersinia pestis Species 0.000 description 2
- 239000002253 acid Substances 0.000 description 2
- 150000007513 acids Chemical class 0.000 description 2
- 238000004364 calculation method Methods 0.000 description 2
- 238000003776 cleavage reaction Methods 0.000 description 2
- 238000003745 diagnosis Methods 0.000 description 2
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- 238000000338 in vitro Methods 0.000 description 2
- 238000009830 intercalation Methods 0.000 description 2
- 238000002372 labelling Methods 0.000 description 2
- 238000012417 linear regression Methods 0.000 description 2
- 239000000203 mixture Substances 0.000 description 2
- 239000013642 negative control Substances 0.000 description 2
- 229910052697 platinum Inorganic materials 0.000 description 2
- 230000007017 scission Effects 0.000 description 2
- WCKQPPQRFNHPRJ-UHFFFAOYSA-N 4-[[4-(dimethylamino)phenyl]diazenyl]benzoic acid Chemical compound C1=CC(N(C)C)=CC=C1N=NC1=CC=C(C(O)=O)C=C1 WCKQPPQRFNHPRJ-UHFFFAOYSA-N 0.000 description 1
- 238000012935 Averaging Methods 0.000 description 1
- 108020000946 Bacterial DNA Proteins 0.000 description 1
- 108020004513 Bacterial RNA Proteins 0.000 description 1
- 208000035143 Bacterial infection Diseases 0.000 description 1
- 238000012773 Laboratory assay Methods 0.000 description 1
- 101710163270 Nuclease Proteins 0.000 description 1
- 238000001190 Q-PCR Methods 0.000 description 1
- 108020004682 Single-Stranded DNA Proteins 0.000 description 1
- 108020004566 Transfer RNA Proteins 0.000 description 1
- 108020005202 Viral DNA Proteins 0.000 description 1
- 108020000999 Viral RNA Proteins 0.000 description 1
- 208000022362 bacterial infectious disease Diseases 0.000 description 1
- 239000012472 biological sample Substances 0.000 description 1
- 239000007853 buffer solution Substances 0.000 description 1
- 150000001768 cations Chemical class 0.000 description 1
- 239000003795 chemical substances by application Substances 0.000 description 1
- 238000004590 computer program Methods 0.000 description 1
- 238000001816 cooling Methods 0.000 description 1
- 230000007423 decrease Effects 0.000 description 1
- 230000003247 decreasing effect Effects 0.000 description 1
- 201000010099 disease Diseases 0.000 description 1
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 1
- 239000012153 distilled water Substances 0.000 description 1
- 230000009977 dual effect Effects 0.000 description 1
- 239000000975 dye Substances 0.000 description 1
- 230000000694 effects Effects 0.000 description 1
- 238000007848 endpoint PCR Methods 0.000 description 1
- 230000002255 enzymatic effect Effects 0.000 description 1
- 235000013305 food Nutrition 0.000 description 1
- 238000012252 genetic analysis Methods 0.000 description 1
- 238000010438 heat treatment Methods 0.000 description 1
- 230000003993 interaction Effects 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 238000012067 mathematical method Methods 0.000 description 1
- 238000002844 melting Methods 0.000 description 1
- 230000008018 melting Effects 0.000 description 1
- 108020004999 messenger RNA Proteins 0.000 description 1
- 239000003068 molecular probe Substances 0.000 description 1
- 239000002777 nucleoside Substances 0.000 description 1
- 125000003835 nucleoside group Chemical group 0.000 description 1
- 238000005457 optimization Methods 0.000 description 1
- 230000001717 pathogenic effect Effects 0.000 description 1
- 238000006116 polymerization reaction Methods 0.000 description 1
- 238000012545 processing Methods 0.000 description 1
- 108090000623 proteins and genes Proteins 0.000 description 1
- 238000010791 quenching Methods 0.000 description 1
- 230000000171 quenching effect Effects 0.000 description 1
- -1 rRNA Proteins 0.000 description 1
- 239000011535 reaction buffer Substances 0.000 description 1
- 230000003252 repetitive effect Effects 0.000 description 1
- 238000005070 sampling Methods 0.000 description 1
- 230000009870 specific binding Effects 0.000 description 1
- 238000011895 specific detection Methods 0.000 description 1
- 238000012549 training Methods 0.000 description 1
- 239000001226 triphosphate Substances 0.000 description 1
- 235000011178 triphosphate Nutrition 0.000 description 1
- 125000002264 triphosphate group Chemical class [H]OP(=O)(O[H])OP(=O)(O[H])OP(=O)(O[H])O* 0.000 description 1
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Chemical compound O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 1
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
- C12Q1/6813—Hybridisation assays
-
- 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
-
- 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
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
-
- 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
- C12Q2527/00—Reactions demanding special reaction conditions
- C12Q2527/107—Temperature of melting, i.e. Tm
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Analytical Chemistry (AREA)
- Biophysics (AREA)
- Biochemistry (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Physics & Mathematics (AREA)
- Genetics & Genomics (AREA)
- Immunology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Investigating Or Analysing Materials By The Use Of Chemical Reactions (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US13604008P | 2008-08-08 | 2008-08-08 | |
| US61/136,040 | 2008-08-08 | ||
| PCT/US2009/053253 WO2010017543A1 (en) | 2008-08-08 | 2009-08-10 | Detection algorithm for pcr assay |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA2733186A1 true CA2733186A1 (en) | 2010-02-11 |
Family
ID=41259286
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA2733186A Abandoned CA2733186A1 (en) | 2008-08-08 | 2009-08-10 | Detection algorithm for pcr assay |
Country Status (10)
| Country | Link |
|---|---|
| US (1) | US20110151461A1 (cg-RX-API-DMAC7.html) |
| EP (1) | EP2315844A1 (cg-RX-API-DMAC7.html) |
| JP (1) | JP2011530296A (cg-RX-API-DMAC7.html) |
| KR (1) | KR20110052681A (cg-RX-API-DMAC7.html) |
| CN (1) | CN102112632A (cg-RX-API-DMAC7.html) |
| AU (1) | AU2009279457A1 (cg-RX-API-DMAC7.html) |
| BR (1) | BRPI0917434A2 (cg-RX-API-DMAC7.html) |
| CA (1) | CA2733186A1 (cg-RX-API-DMAC7.html) |
| RU (1) | RU2011107993A (cg-RX-API-DMAC7.html) |
| WO (1) | WO2010017543A1 (cg-RX-API-DMAC7.html) |
Families Citing this family (12)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| AU2009324806A1 (en) * | 2008-12-10 | 2011-07-07 | Smiths Detection Inc. | Identification and differentiation of nucleic acid sequence using temperature-dependent hybridization |
| US20130203057A1 (en) * | 2012-01-20 | 2013-08-08 | Biohelix Corporation | Step-wise detection of multiple target sequences in isothermal nucleic acid amplification reactions |
| CN107326085B (zh) | 2012-02-03 | 2022-05-03 | 加州理工学院 | 多路生化测定中信号的编码和解码 |
| EP2880184B1 (en) * | 2012-08-03 | 2021-03-31 | California Institute of Technology | Multiplexing and quantification in pcr with reduced hardware and requirements |
| WO2015147370A1 (en) * | 2014-03-28 | 2015-10-01 | Seegene, Inc. | Detection of target nucleic acid sequences using different detection temperatures |
| KR102016747B1 (ko) * | 2014-12-09 | 2019-09-02 | 주식회사 씨젠 | 상이한 검출 온도 및 기준값을 사용한 타겟 핵산 서열의 검출 |
| CN107208139B (zh) | 2014-12-09 | 2020-11-10 | Seegene株式会社 | 与靶核酸序列有关的信号的分辨 |
| KR102110999B1 (ko) * | 2016-01-26 | 2020-05-14 | 주식회사 씨젠 | 타겟 핵산 서열에 대한 시그널을 제공하는 방법 |
| AU2019209444A1 (en) | 2018-01-22 | 2020-07-30 | Luminex Corporation | Methods and compositions for discrete melt analysis |
| CN112424377A (zh) | 2018-04-17 | 2021-02-26 | 克罗玛科德公司 | 用于多重分析的方法和系统 |
| US12203129B2 (en) | 2018-07-03 | 2025-01-21 | ChromaCode, Inc. | Formulations and signal encoding and decoding methods for massively multiplexed biochemical assays |
| KR20240093623A (ko) * | 2021-10-21 | 2024-06-24 | 주식회사 씨젠 | 시료 내 표적 분석물질에 대한 양음성 판독 장치 및 방법 |
Family Cites Families (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US4683202A (en) * | 1985-03-28 | 1987-07-28 | Cetus Corporation | Process for amplifying nucleic acid sequences |
| US5475098A (en) * | 1994-06-14 | 1995-12-12 | The United States Of America As Represented By The Department Of Health And Human Services | Distinctive DNA sequence of E. coli 0157:H7 and its use for the rapid, sensitive and specific detection of 0157:H7 and other enterohemorrhagic E. coli |
| ATE440963T1 (de) * | 1998-07-02 | 2009-09-15 | Gen Probe Inc | Molekulare fackeln |
| US8900811B2 (en) * | 2000-11-16 | 2014-12-02 | Caliper Life Sciences, Inc. | Method and apparatus for generating thermal melting curves in a microfluidic device |
| US20050202470A1 (en) * | 2000-11-16 | 2005-09-15 | Caliper Life Sciences, Inc. | Binding assays using molecular melt curves |
| AU2002359329A1 (en) * | 2001-10-30 | 2003-05-12 | The Texas A And M University System | Method and apparatus for temperature gradient microfluidics |
| AU2006315489B2 (en) * | 2005-11-14 | 2012-09-06 | Gen-Probe Incorporated | Parametric calibration method |
-
2009
- 2009-08-10 CN CN2009801308017A patent/CN102112632A/zh active Pending
- 2009-08-10 JP JP2011522302A patent/JP2011530296A/ja active Pending
- 2009-08-10 AU AU2009279457A patent/AU2009279457A1/en not_active Abandoned
- 2009-08-10 KR KR1020117005036A patent/KR20110052681A/ko not_active Withdrawn
- 2009-08-10 EP EP09791325A patent/EP2315844A1/en not_active Withdrawn
- 2009-08-10 BR BRPI0917434A patent/BRPI0917434A2/pt not_active Application Discontinuation
- 2009-08-10 WO PCT/US2009/053253 patent/WO2010017543A1/en not_active Ceased
- 2009-08-10 CA CA2733186A patent/CA2733186A1/en not_active Abandoned
- 2009-08-10 RU RU2011107993/10A patent/RU2011107993A/ru not_active Application Discontinuation
- 2009-08-10 US US13/057,735 patent/US20110151461A1/en not_active Abandoned
Also Published As
| Publication number | Publication date |
|---|---|
| AU2009279457A1 (en) | 2010-02-11 |
| KR20110052681A (ko) | 2011-05-18 |
| RU2011107993A (ru) | 2012-09-20 |
| CN102112632A (zh) | 2011-06-29 |
| US20110151461A1 (en) | 2011-06-23 |
| EP2315844A1 (en) | 2011-05-04 |
| JP2011530296A (ja) | 2011-12-22 |
| BRPI0917434A2 (pt) | 2015-12-01 |
| WO2010017543A1 (en) | 2010-02-11 |
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Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| FZDE | Discontinued |
Effective date: 20130812 |