DK3077539T3 - Fremgangsmåde til evaluering af minoritetsvariationer i en prøve - Google Patents
Fremgangsmåde til evaluering af minoritetsvariationer i en prøve Download PDFInfo
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- DK3077539T3 DK3077539T3 DK14841366.9T DK14841366T DK3077539T3 DK 3077539 T3 DK3077539 T3 DK 3077539T3 DK 14841366 T DK14841366 T DK 14841366T DK 3077539 T3 DK3077539 T3 DK 3077539T3
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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
- C12Q1/6869—Methods for sequencing
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B30/10—Sequence alignment; Homology search
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B30/20—Sequence assembly
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- Medical Informatics (AREA)
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- General Engineering & Computer Science (AREA)
- Genetics & Genomics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Chemical Kinetics & Catalysis (AREA)
Claims (16)
1. En metode til evaluering af en sekvensvariation i en prøve, som omfatter: a) amplifikation af et nukleinsyreprodukt fra en initialprøve; b) fragmentering af en mængde af nukleinsyreproduktet produceret ved trin a) til at producere fragmenter; c) vedhæftning af en adapter til hver ende af fragmenterne skabt på trin b) til at producere fragmenter fæstnet til adapteren; d) prøveudtagning af ikke mere end 10 % af produktet i trin c) og amplifikation af de fragmenter fæstnet til adapteren der er indeholdt i det prøveudtagne produkt ved at bruge en eller flere primere, der krydser til adapteren til at producere kopier af fragmenterne; e) sekventering af mindst nogle af kopierne af fragmenterne produceret i d) til at producere en flerhed af sekvensaflæsninger; f) datamatisk gruppering af sekvensaflæsninger for kopier af fragmenter, der har samme fragmentations-breakpoint og væsentligt identiske sekvenser til at producere aflæsningsgrupper; g) udledning af en konsensus-sekvens for hver af aflæsningsgrupperne; h) opstilling af konsensus-sekvenserne på linje med en referencesekvens; og i) identifikation af en position i opstillingen på linje, som udgør en sekvensvariation.
2. Metoden i krav 1, som yderligere omfatter estimering af rigeligheden af sekvensvariationen i prøven.
3. Metoden i ethvert tidligere krav, hvor metoden yderligere omfatter: på en position svarende til en sekvensvariation, der tæller: i. antallet af konsensussekvenser, som sekvensvariationen omfatter; og ii. antallet af konsensussekvenser, som ikke omfatter sekvensvariationen eller det samlede antal konsensussekvenser.
4. Metoden i krav 3, som yderligere omfatter: fastsættelse af hvorvidt sekvensvariationen er til stede i prøven og/eller estimering af rigeligheden af sekvensvariationen i prøven ved brug af det talte antal i i, og ii; fastsættelse af hvorvidt omtalte sekvensvariant er i prøven, hvor et større antal af konsensussekvenser for sekvensvarianten i forhold til antallet af konsensussekvenser som ikke omfatter sekvensvariationen eller det samlede antal konsensussekvenser, som omfatter positionen af sekvensvariationen, øger tilliden til fastsættelsen; eller estimering af mængden af sekvensvarianten i prøven, hvor et større antal konsensussekvenser til sekvensvarianten i forhold til antallet af konsensussekvenser,som ikke omfatter sekvensvariationen, eller det samlede antal konsensussekvenser, som omfatter positionen af sekvensvariationen, samkører med rigeligheden af sekvensvarianten i prøven.
5. Metoden i ethvert tidligere krav, hvor amplimeren produceret i trin a), har en længde i området 100 bp til 50 kb.
6. Metoden i ethvert tidligere krav, hvor nukleinsyreproduktet, der er forstærket fra initialprøven i a), omfatter et segment af et viralt eller bakterielt genom, eller hvor nukleinsyreproduktet forstærket fra initialprøven a) omfatter et segment af et pattedyr- eller mitokondrie-genom.
7. Metoden i ethvert tidligere krav, hvor sekvensvariationen er til stede i et antal kopier på mindre end 1 ud af 20, i forhold til andre molekyler, som ikke indeholder sekvensvariationen, i produktet produceret af trin a).
8. Metoden i ethvert tidligere krav, hvor amplifikation af trin a) er foretaget af PCR eller RT-PCR.
9. Metoden i ethvert tidligere krav, hvor fragmenteringen trin b) er foretaget ved hjælp af fysiske, kemiske eller enzymatiske midler eller ved anvendelse af transposoner.
10. Metoden i ethvert tidligere krav, hvor den gennemsnitlige størrelse af fragmenterne har en længde i området 100-700 nukleotider.
11. Metoden i ethvert tidligere krav, hvor det forstærkende trin d) omfatter 5-40 PCR- cyklusser.
12. Metoden i ethvert tidligere krav, hvor det forstærkende trin d) resulterer i amplifikation af mindre end 1 ud af 1.000 af fragmenterne produceret i trin b).
13. Metoden i ethvert tidligere krav, hvor metoden omfatter tilføjelse af en molekyleidentifikationssekvens til fragmenterne forud for eller i det første trin af amplifikationstrin c), og hver grupperingstrinnet f) foretages ved at identificere hvilken sekvenslæsning, der har den samme slutsekvens og den samme molekyleidentifikationssekvens.
14. Metoden i ethvert tidligere krav, hvor initialprøven indeholder et ukendt antal initialskabelonmolekyler.
15. Metoden i ethvert tidligere krav, hvor aflæsningsgrupperne er definerede af parrede-ende-af læsninger.
16. Metoden i ethvert tidligere krav, hvor amplifikationen af trin d) omfatter tilføjelse af en prøveidentificeringssekvens til de forstærkede fragmenter.
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201361910890P | 2013-12-02 | 2013-12-02 | |
| PCT/IB2014/003082 WO2015083004A1 (en) | 2013-12-02 | 2014-11-26 | Method for evaluating minority variants in a sample |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| DK3077539T3 true DK3077539T3 (da) | 2018-11-19 |
Family
ID=52596523
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| DK14841366.9T DK3077539T3 (da) | 2013-12-02 | 2014-11-26 | Fremgangsmåde til evaluering af minoritetsvariationer i en prøve |
Country Status (5)
| Country | Link |
|---|---|
| US (1) | US10927408B2 (da) |
| EP (1) | EP3077539B8 (da) |
| DK (1) | DK3077539T3 (da) |
| ES (1) | ES2693217T3 (da) |
| WO (1) | WO2015083004A1 (da) |
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| US11111544B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
| US9424392B2 (en) | 2005-11-26 | 2016-08-23 | Natera, Inc. | System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals |
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2014
- 2014-11-26 DK DK14841366.9T patent/DK3077539T3/da active
- 2014-11-26 ES ES14841366.9T patent/ES2693217T3/es active Active
- 2014-11-26 US US15/037,663 patent/US10927408B2/en active Active
- 2014-11-26 WO PCT/IB2014/003082 patent/WO2015083004A1/en active Application Filing
- 2014-11-26 EP EP14841366.9A patent/EP3077539B8/en active Active
Also Published As
| Publication number | Publication date |
|---|---|
| US20160289753A1 (en) | 2016-10-06 |
| EP3077539B1 (en) | 2018-07-25 |
| US10927408B2 (en) | 2021-02-23 |
| EP3077539B8 (en) | 2018-10-10 |
| WO2015083004A1 (en) | 2015-06-11 |
| ES2693217T3 (es) | 2018-12-10 |
| EP3077539A1 (en) | 2016-10-12 |
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