DK2766496T3 - Fremgangsmåder og processer for ikke-invasiv vurdering af genetiske variationer - Google Patents

Fremgangsmåder og processer for ikke-invasiv vurdering af genetiske variationer Download PDF

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DK2766496T3
DK2766496T3 DK12778005.4T DK12778005T DK2766496T3 DK 2766496 T3 DK2766496 T3 DK 2766496T3 DK 12778005 T DK12778005 T DK 12778005T DK 2766496 T3 DK2766496 T3 DK 2766496T3
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chromosome
nucleic acid
counts
sequence reads
mapped
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DK12778005.4T
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Zeljko Dzakula
Cosmin Deciu
Amin Mazloom
Huiquan Wang
Lin Tang
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Sequenom Inc
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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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • C12Q1/6879—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for sex determination

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  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
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  • Proteomics, Peptides & Aminoacids (AREA)
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  • General Health & Medical Sciences (AREA)
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  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Claims (14)

1. Fremgangsmåde til at bestemme fosterkøn, omfattende: (a) at opnå tællinger af nukleotidsekvenslæsninger kortlagt til et delområde af genomiske afsnit beliggende mellem basekoordinater 1 til 28.000.000 i et Y-kromosom af et referencegenom, hvilke sekvenslæsninger er læsninger af cirkulerende cellefri nukleinsyre fra en testprøve fra en gravid hun bærende på et foster; (b) at summere tællingerne kortlagt til delområdet af genomiske afsnit og sammenligne de summerede tællinger med en mediantælling for genomiske afsnit i Y-kromosomet for prøven, for derved at generere en sammenligning; og (c) at bestemme fosterkøn i henhold til sammenligningen.
2. System til at bestemme fosterkøn omfattende en eller flere processorer og hukommelse, hvilken hukommelse omfatter instruktioner der kan udføres af den ene eller flere processorer og hvilken hukommelse omfatter tællinger af nukleotidsekvenslæsninger kortlagt til et delområde af genomiske afsnit beliggende mellem basekoordinater 1 til 28.000.000 i et Y-kromosom af et referencegenom, hvilke sekvenslæsninger er læsninger af cirkulerende cellefri nukleinsyre fra en testprøve fra en gravid hun bærende på et foster; og hvilke instruktioner der kan udføres af den ene eller flere processorer er konfigureret til: (a) at summere tællingerne kortlagt til delområdet af genomiske afsnit og sammenligne de summerede tællinger med en mediantælling for genomiske afsnit i Y-kromosomet for prøven, for derved at generere en sammenligning; og (b) at bestemme fosterkøn i henhold til sammenligningen.
3. Fremgangsmåden ifølge krav 1 eller systemet ifølge krav 2, hvor delområdet af genomiske afsnit omfatter: a) genomiske afsnit med et konsistent antal af positive tællinger for kortlagte sekvenslæsninger fra prøver fra gravide hunner bærende hankønsfostre; b) genomiske afsnit med et konsistent antal af tællinger for kortlagte sekvenslæsninger fra prøver fra gravide hunner bærende hunkønsfostre; og c) genomiske afsnit med en signifikant og konsistent forskel af kortlagte sekvenslæsningstællinger mellem prøver fra gravide hunner bærende hankønsfostre og prøver fra gravide hunner bærende hunkønsfostre.
4. Fremgangsmåden ifølge krav 1 eller 3 eller systemet ifølge krav 2 eller 3, hvor delområdet af genomiske afsnit i Y-kromosomet ikke inkluderer udvalgte genomiske afsnit i Y-kromosomet, hvilke udvalgte genomiske afsnit i Y-kromosomet, når fjernet fra delområdet, resulterer i en forøgelse i et separationsmellemrum mellem hankøns- og hunkønsfostre større end eller lige med værdien ε = 1 %.
5. Fremgangsmåden ifølge krav 1, 3 eller 4 eller systemet ifølge et hvilket som helst af kravene 2 til 4, hvor antallet af sekvenslæsninger kortlagt til hver af de genomiske afsnit i delområdet er signifikant og konsistent højere for prøver fra gravide hunner bærende hankønsfostre versus prøver fra gravide hunner bærende hunkønsfostre.
6. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 3 til 5 eller systemet ifølge et hvilket som helst af kravene 2 til 5, hvor sekvenslæsningerne kortlagt til delområdet af genomiske afsnit er unikt kortlagte sekvenslæsninger.
7. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 3 til 6 eller systemet ifølge et hvilket som helst af kravene 2 til 6, hvor mediantællingen for genomiske afsnit i Y-kromosomet er lig med medianen af positiv værdi råsekvenslæsningstællinger i Y-kromosomet.
8. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 3 til 7 eller systemet ifølge et hvilket som helst af kravene 2 til 7, omfattende at bestemme en hankøn separatorområdescore (MSRscore) for antallet af nukleotidsekvenslæsninger kortlagt til hver af de genomiske afsnit i delområdet i henhold til Ligning A:
Li g n i ng A hvor S er en prøve, MSR er hankøn separatorområde, RAW er råsekvenslæsningstællinger, bm er et genomisk afsnit i MSR, og M er mediansekvenslæsningstælling.
9. Fremgangsmåden eller systemet ifølge krav 8, hvor mediansekvenslæsningstællingen (M) er en median af positiv værdi råsekvenslæsningstællinger for genomiske afsnit af Y-kromosom.
10. Fremgangsmåden eller systemet ifølge krav 8 eller 9, hvor fosterkønnet bestemmes som hankøn, når MSRscoren er 6,5 eller mere eller fosterkønnet bestemmes som hunkøn, når MSRscoren er mindre end 6,5.
11. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 3 til 10 eller systemet ifølge et hvilket som helst af kravene 2 til 10, hvor sammenligningen korreleres til fosterkvantifikationsresultater.
12. Fremgangsmåden eller systemet ifølge krav 11, hvor fosterkvantifikationsresultaterne er SRY-baserede kvantifikationsresultater.
13. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 3 til 12 eller systemet ifølge et hvilket som helst af kravene 2 til 12, hvor fosterkønnet bestemmes med en nøjagtighed på omkring 0,9938 eller større med et 95 % konfidensinterval, og fortrinsvis med en nøjagtighed på omkring 0,994 eller større med et 95 % konfidensinterval.
14. Fremgangsmåden ifølge et hvilket som helst af kravene 1 og 3 til 13 eller systemet ifølge et hvilket som helst af kravene 2 til 13, hvor prøven er blod, serum eller plasma.
DK12778005.4T 2011-10-11 2012-10-10 Fremgangsmåder og processer for ikke-invasiv vurdering af genetiske variationer DK2766496T3 (da)

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US201161545977P 2011-10-11 2011-10-11
US201261663477P 2012-06-22 2012-06-22
US201261663361P 2012-06-22 2012-06-22
PCT/US2012/059592 WO2013055817A1 (en) 2011-10-11 2012-10-10 Methods and processes for non-invasive assessment of genetic variations

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EP3243908A1 (en) 2017-11-15
WO2013055817A1 (en) 2013-04-18
EP3243908B1 (en) 2019-01-02
HK1200875A1 (en) 2015-08-14
CA2851537C (en) 2020-12-29
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ES2624686T3 (es) 2017-07-17
CA2851537A1 (en) 2013-04-18
EP2766496A1 (en) 2014-08-20

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