DK2623613T3 - Forøgelse af pålideligheden af allel-angivelser ved hjælp af molekylær tælling - Google Patents

Forøgelse af pålideligheden af allel-angivelser ved hjælp af molekylær tælling Download PDF

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DK2623613T3
DK2623613T3 DK13164430.4T DK13164430T DK2623613T3 DK 2623613 T3 DK2623613 T3 DK 2623613T3 DK 13164430 T DK13164430 T DK 13164430T DK 2623613 T3 DK2623613 T3 DK 2623613T3
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Denmark
Prior art keywords
dbr
polynucleotide
sample
polynucleotides
primer
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DK13164430.4T
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English (en)
Inventor
James Casbon
Sydney Brenner
Robert Osborne
Conrad Lichtenstein
Andreas Claas
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Population Genetics Tech Ltd
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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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
    • 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
    • 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
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10—Ploidy or copy number detection
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Claims (12)

1. Fremgangsmåde til bestemmelse af det minimale antal individuelle polynukleotid-molekyler, som stammer fra den samme genomiske region af den samme oprindelige prøve, som er blevet sekvenseret i en bestemt sekvensanalysekonfiguration eller -proces, omfattende: tilføjelse af en degenereret baseregion (DBR) til startpolynukleotidmolekyler; amplificering af de DBR-tilføjede startpolynukleotidmolekyler; sekvensering af de amplificerede polynukleotidmolekyler, hvor sekvensen af DBR såvel som en del af polynukleotidet opnås; bestemmelse af antallet af forskellige DBR'er hæftet til et polynukleotid af interesse; anvendelse af antallet af forskellige DBR-sekvenser, som foreligger i sekvenseringsforløbet for bestemmelse af det minimale antal individuelle polynukleotidmolekyler, som stammer fra den samme genomiske region af den samme oprindelige prøve, som er blevet sekvenseret i den bestemte sekvensanalysekonfiguration eller -proces; og bestemmelse af en statistisk værdi for en allelangivelse i et genotype-bestemmelsesassay, som ikke kan afledes af det aflæste antal alene.
2. Fremgangsmåde ifølge krav 1, hvor DBR'et tilføjes til startpolynukleotidet som en del af en adapter.
3. Fremgangsmåde ifølge krav 2, hvor DBR'et er en adapter, som også omfatter en sekvenseringsprimerposition.
4. Fremgangsmåde ifølge krav 1, hvor DBR'et har en længde fra 3 till0 baser.
5. Fremgangsmåde ifølge krav 1, hvor polynukleotiderne stammer fra genomisk DNA.
6. Fremgangsmåde ifølge krav 5, hvor polynukleotiderne i nukleinsyreprøven stammer fra et menneske.
7. Fremgangsmåde ifølge krav 2, hvor prøven er beriget for at reducere kompleksiteten af polynukleotiderfør adapter-ligation.
8. Fremgangsmåde ifølge krav 1, som omfatter berigelse af de DBR-tilføjede polynukleotider.
9. Fremgangsmåde ifølge krav 1, hvor DBR foreligger i forskellige lokationer på et polynukleotid.
10. Fremgangsmåde ifølge krav 1, hvor DBR foreligger i en nukleinsyresynteseprimer, således at DBR tilføres til et målpolynukleotid, når primeren anvendes i en polymeriseringsreaktion.
11. Fremgangsmåde ifølge krav 10, hvor nukleinsyresynteseprimeren er en PCR-primer.
12. Fremgangsmåde ifølge krav 11, som omfatter bestemmelse af antallet af startmolekyler som anvendes som template for en PCR-reaktion.
DK13164430.4T 2010-09-21 2011-09-20 Forøgelse af pålideligheden af allel-angivelser ved hjælp af molekylær tælling DK2623613T3 (da)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US38500110P 2010-09-21 2010-09-21
US201161432119P 2011-01-12 2011-01-12
EP11810645.9A EP2619327B1 (en) 2010-09-21 2011-09-20 Increasing confidence of allele calls with molecular counting

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DK2623613T3 true DK2623613T3 (da) 2016-10-03

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US (7) US8481292B2 (da)
EP (3) EP2623613B8 (da)
JP (2) JP5992911B2 (da)
CN (2) CN110878345A (da)
CA (1) CA2811185C (da)
DK (1) DK2623613T3 (da)
ES (3) ES2595433T3 (da)
PT (1) PT2623613T (da)
WO (1) WO2012038839A2 (da)

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