DK3077539T3 - Fremgangsmåde til evaluering af minoritetsvariationer i en prøve - Google Patents
Fremgangsmåde til evaluering af minoritetsvariationer i en prøve Download PDFInfo
- Publication number
- 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
- Authority
- DK
- Denmark
- Prior art keywords
- sequence
- sample
- fragments
- sequences
- previous
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Classifications
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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
-
- 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
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) |
Families Citing this family (38)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| 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 |
| US11111543B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
| US10081839B2 (en) | 2005-07-29 | 2018-09-25 | Natera, Inc | System and method for cleaning noisy genetic data and determining chromosome copy number |
| US10083273B2 (en) | 2005-07-29 | 2018-09-25 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
| US11111544B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
| EP2473638B1 (en) | 2009-09-30 | 2017-08-09 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US11408031B2 (en) | 2010-05-18 | 2022-08-09 | Natera, Inc. | Methods for non-invasive prenatal paternity testing |
| US11326208B2 (en) | 2010-05-18 | 2022-05-10 | Natera, Inc. | Methods for nested PCR amplification of cell-free DNA |
| US11332793B2 (en) | 2010-05-18 | 2022-05-17 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US11339429B2 (en) | 2010-05-18 | 2022-05-24 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US11322224B2 (en) | 2010-05-18 | 2022-05-03 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US20190010543A1 (en) | 2010-05-18 | 2019-01-10 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US11939634B2 (en) | 2010-05-18 | 2024-03-26 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| WO2011146632A1 (en) | 2010-05-18 | 2011-11-24 | Gene Security Network Inc. | Methods for non-invasive prenatal ploidy calling |
| US10316362B2 (en) | 2010-05-18 | 2019-06-11 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US11332785B2 (en) | 2010-05-18 | 2022-05-17 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US9677118B2 (en) | 2014-04-21 | 2017-06-13 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| JP6328934B2 (ja) | 2010-12-22 | 2018-05-23 | ナテラ， インコーポレイテッド | 非侵襲性出生前親子鑑定法 |
| AU2011358564B9 (en) | 2011-02-09 | 2017-07-13 | Natera, Inc | Methods for non-invasive prenatal ploidy calling |
| US10577655B2 (en) | 2013-09-27 | 2020-03-03 | Natera, Inc. | Cell free DNA diagnostic testing standards |
| US10262755B2 (en) | 2014-04-21 | 2019-04-16 | Natera, Inc. | Detecting cancer mutations and aneuploidy in chromosomal segments |
| CN113774132A (zh) | 2014-04-21 | 2021-12-10 | 纳特拉公司 | 检测染色体片段中的突变和倍性 |
| WO2016114009A1 (ja) * | 2015-01-16 | 2016-07-21 | 国立研究開発法人国立がん研究センター | 融合遺伝子解析装置、融合遺伝子解析方法、及びプログラム |
| US11479812B2 (en) | 2015-05-11 | 2022-10-25 | Natera, Inc. | Methods and compositions for determining ploidy |
| GB2541904B (en) * | 2015-09-02 | 2020-09-02 | Oxford Nanopore Tech Ltd | Method of identifying sequence variants using concatenation |
| GB201515557D0 (en) * | 2015-09-02 | 2015-10-14 | 14M Genomics Ltd | Method of sequencing |
| CN108603229A (zh) * | 2016-01-22 | 2018-09-28 | 格瑞尔公司 | 用于高保真测序的方法和系统 |
| WO2018067517A1 (en) | 2016-10-04 | 2018-04-12 | Natera, Inc. | Methods for characterizing copy number variation using proximity-litigation sequencing |
| US10011870B2 (en) | 2016-12-07 | 2018-07-03 | Natera, Inc. | Compositions and methods for identifying nucleic acid molecules |
| CA3049682C (en) | 2017-01-20 | 2023-06-27 | Sequenom, Inc. | Methods for non-invasive assessment of genetic alterations |
| CA3049139A1 (en) | 2017-02-21 | 2018-08-30 | Natera, Inc. | Compositions, methods, and kits for isolating nucleic acids |
| WO2018211497A1 (en) * | 2017-05-14 | 2018-11-22 | Foresee Genomic Ltd | Dna construct for sequencing and method for preparing the same |
| WO2018213235A1 (en) * | 2017-05-16 | 2018-11-22 | Life Technologies Corporation | Methods for compression of molecular tagged nucleic acid sequence data |
| WO2019169117A1 (en) * | 2018-02-28 | 2019-09-06 | Cornell University | Detecting variant alleles in complex, repetitive sequences within whole genome sequencing data sets |
| GB201804641D0 (en) * | 2018-03-22 | 2018-05-09 | Inivata Ltd | Methods of sequencing nucleic acids and error correction of sequence reads |
| US11525159B2 (en) | 2018-07-03 | 2022-12-13 | Natera, Inc. | Methods for detection of donor-derived cell-free DNA |
| WO2021195594A1 (en) * | 2020-03-26 | 2021-09-30 | San Diego State University (SDSU) Foundation, dba San Diego State University Research Foundation | Compositions and methods for treating or ameliorating infections |
| MX2022014017A (es) * | 2020-05-08 | 2022-11-30 | Illumina Inc | Secuenciacion de genoma y tecnicas de deteccion. |
Family Cites Families (28)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US4965188A (en) | 1986-08-22 | 1990-10-23 | Cetus Corporation | Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme |
| US4683195A (en) | 1986-01-30 | 1987-07-28 | Cetus Corporation | Process for amplifying, detecting, and/or-cloning nucleic acid sequences |
| US4800159A (en) | 1986-02-07 | 1989-01-24 | Cetus Corporation | Process for amplifying, detecting, and/or cloning nucleic acid sequences |
| CA2020958C (en) | 1989-07-11 | 2005-01-11 | Daniel L. Kacian | Nucleic acid sequence amplification methods |
| US5210015A (en) | 1990-08-06 | 1993-05-11 | Hoffman-La Roche Inc. | Homogeneous assay system using the nuclease activity of a nucleic acid polymerase |
| JP3080178B2 (ja) | 1991-02-18 | 2000-08-21 | 東洋紡績株式会社 | 核酸配列の増幅方法およびそのための試薬キット |
| US5854033A (en) | 1995-11-21 | 1998-12-29 | Yale University | Rolling circle replication reporter systems |
| ATE428801T1 (de) | 1996-06-04 | 2009-05-15 | Univ Utah Res Found | Überwachung der hybridisierung während pcr |
| US7393665B2 (en) | 2005-02-10 | 2008-07-01 | Population Genetics Technologies Ltd | Methods and compositions for tagging and identifying polynucleotides |
| US7452671B2 (en) * | 2005-04-29 | 2008-11-18 | Affymetrix, Inc. | Methods for genotyping with selective adaptor ligation |
| CA2910861C (en) | 2005-09-29 | 2018-08-07 | Michael Josephus Theresia Van Eijk | High throughput screening of mutagenized populations |
| EP3404114B1 (en) * | 2005-12-22 | 2021-05-05 | Keygene N.V. | Method for high-throughput aflp-based polymorphism detection |
| WO2008150432A1 (en) | 2007-06-01 | 2008-12-11 | 454 Life Sciences Corporation | System and meth0d for identification of individual samples from a multiplex mixture |
| WO2009133466A2 (en) | 2008-04-30 | 2009-11-05 | Population Genetics Technologies Ltd. | Asymmetric adapter library construction |
| DE102008025656B4 (de) | 2008-05-28 | 2016-07-28 | Genxpro Gmbh | Verfahren zur quantitativen Analyse von Nukleinsäuren, Marker dafür und deren Verwendung |
| US8383345B2 (en) | 2008-09-12 | 2013-02-26 | University Of Washington | Sequence tag directed subassembly of short sequencing reads into long sequencing reads |
| US20100323348A1 (en) | 2009-01-31 | 2010-12-23 | The Regents Of The University Of Colorado, A Body Corporate | Methods and Compositions for Using Error-Detecting and/or Error-Correcting Barcodes in Nucleic Acid Amplification Process |
| ES2595055T3 (es) | 2009-08-25 | 2016-12-27 | Illumina, Inc. | Métodos para seleccionar y amplificar polinucleótidos |
| US8835358B2 (en) | 2009-12-15 | 2014-09-16 | Cellular Research, Inc. | Digital counting of individual molecules by stochastic attachment of diverse labels |
| US9165109B2 (en) | 2010-02-24 | 2015-10-20 | Pacific Biosciences Of California, Inc. | Sequence assembly and consensus sequence determination |
| DK2623613T3 (da) | 2010-09-21 | 2016-10-03 | Population Genetics Tech Ltd | Forøgelse af pålideligheden af allel-angivelser ved hjælp af molekylær tælling |
| WO2012129363A2 (en) | 2011-03-24 | 2012-09-27 | President And Fellows Of Harvard College | Single cell nucleic acid detection and analysis |
| EP3246416A1 (en) * | 2011-04-15 | 2017-11-22 | The Johns Hopkins University | Safe sequencing system |
| HRP20211595T1 (hr) * | 2011-05-24 | 2022-01-21 | BioNTech SE | Individualizirana cjepiva protiv raka |
| DE202011102934U1 (de) | 2011-06-28 | 2012-10-10 | Pipe-Systems Gmbh | Ventileinheit zur Belüftungs- oder Rückstromsteuerung |
| DK3363901T3 (da) * | 2012-02-17 | 2021-02-22 | Hutchinson Fred Cancer Res | Sammensætninger og fremgangsmåder til præcis identificering af mutationer |
| ES2776673T3 (es) * | 2012-02-27 | 2020-07-31 | Univ North Carolina Chapel Hill | Métodos y usos para etiquetas moleculares |
| WO2013128281A1 (en) | 2012-02-28 | 2013-09-06 | Population Genetics Technologies Ltd | Method for attaching a counter sequence to a nucleic acid sample |
-
2014
- 2014-11-26 US US15/037,663 patent/US10927408B2/en active Active
- 2014-11-26 ES ES14841366.9T patent/ES2693217T3/es active Active
- 2014-11-26 EP EP14841366.9A patent/EP3077539B8/en active Active
- 2014-11-26 DK DK14841366.9T patent/DK3077539T3/da active
- 2014-11-26 WO PCT/IB2014/003082 patent/WO2015083004A1/en active Application Filing
Also Published As
| Publication number | Publication date |
|---|---|
| EP3077539B8 (en) | 2018-10-10 |
| ES2693217T3 (es) | 2018-12-10 |
| US20160289753A1 (en) | 2016-10-06 |
| US10927408B2 (en) | 2021-02-23 |
| EP3077539A1 (en) | 2016-10-12 |
| EP3077539B1 (en) | 2018-07-25 |
| WO2015083004A1 (en) | 2015-06-11 |
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