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DK2630263T3 - Varital tælling af nucleinsyrer for at opnå information om antal genomiske kopier - Google Patents

Varital tælling af nucleinsyrer for at opnå information om antal genomiske kopier Download PDF

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DK2630263T3
DK2630263T3 DK11835243.4T DK11835243T DK2630263T3 DK 2630263 T3 DK2630263 T3 DK 2630263T3 DK 11835243 T DK11835243 T DK 11835243T DK 2630263 T3 DK2630263 T3 DK 2630263T3
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acid molecules
genome
labeled nucleic
genomic
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DK2630263T4 (da
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James Hicks
Nicholas Navin
Jennifer Troge
Zihua Wang
Michael Wigler
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Cold Spring Harbor Laboratory
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    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
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Claims (16)

1. Fremgangsmåde til opnåelse af information om antallet af genomiske kopier der ikke er påvirket af forvrængninger af amplifikation, i et genomisk materiale, hvilken fremgangsmåde omfatter: a) at opnå segmenter af det genomiske materiale; b) at mærke segmenterne med nucleinsyremarkører for at danne unikt mærkerede nucleinsyremolekyler, således at hvert af de unikt mærkede nucleinsyremolekyler omfatter et segment af det genomiske materiale ifølge trin (a) og en markør; c) at udsætte de mærkede nucleinsyremolekyler for en amplifikation ved polymerasekædereaktion (PCR); d) at generere markør-associerede sekvensreads ved at sekventere produktet ifølge trin (c); e) at tildele hvert mærket nucleinsyremolekyle et sted på et genom der er forbundet med det genomiske materiale, ved at kortlægge undersekvensen af hvert markør-associeret sekvensread, der svarer til et segment af det genomiske materiale på et sted på genomet; og f) at tælle antallet af mærkede nucleinsyremolekyler der omfatter en anden markør, som er blevet tildelt det samme sted på genomet, for derved at opnå information om antallet af genomiske kopier der ikke er påvirket af forvrængninger af amplifikation.
2. Fremgangsmåden ifølge krav 1, der yderligere omfatter at estimere et antal genomiske kopier i et område af genomet, der omfatter mere end et sted på genomet, ved at tildele antallet af kopier for området det højeste antal der er opnået ifølge trin (f) for stederne inden for området.
3. Fremgangsmåden ifølge krav 1 der yderligere omfatter at sammenligne en tælling som er opnået ifølge trin (f) for et sted på genomet, med en tælling for det samme sted der er opnået fra en referenceprøve, for derved at estimere et relativt antal genomisk kopier for stedet.
4. Fremgangsmåden ifølge krav 1, der yderligere omfatter g) at summere de opnåede tællinger ifølge trin (f) for steder på genomet, som omfatter et første område af genomet, hvor det første område omfatter mere end et sted; h) at summere de opnåede tællinger ifølge trin (f) for steder på genomet, som omfatter et andet område af genomet, hvilket andet område består af et antal steder, som kan sammenlignes med antallet af steder i det første område; i) at sammenligne værdien der er opnået ifølge trin (g) med værdien, der er opnået ifølge trin (h), for derved at estimere det relative antal genomiske kopier af det første område af genomet i forhold til antallet af genomiske kopier af det andet område af genomet.
5. Fremgangsmåden ifølge krav 4, hvor trin (h) yderligere omfatter: j) at summere de opnåede tællinger ifølge trin (f) for steder på genomet, som omfatter et tredje område af genomet, hvor det tredje område består af et antal steder, der kan sammenlignes med antallet af steder i det første område; og k) at opnå et gennemsnit af summen af de opnåede tællinger ifølge trin (f) for steder, der omfatter det andet område, og summen af de opnåede tællinger ifølge trin (f) for steder, der omfatter det tredje område.
6. Fremgangsmåden ifølge krav 4, hvor det andet område af genomet omfatter et centromer.
7. Fremgangsmåden ifølge krav 1, der yderligere omfatter at summere de opnåede tællinger ifølge trin (f) for steder, som omfatter et område af genomet, og at sammenligne summen med en sum der er opnået fra en referenceprøve for det samme område af genomet, for derved at estimere et relativt antal genomiske kopier for området af genomet.
8. Fremgangsmåde til opnåelse af information om antallet af mRNA-kopier fra mRNA-transkripter der ikke er påvirket af forvrængninger af amplifikation, hvilken fremgangsmåde omfatter: a) at generere unikt mærkede nucleinsyremolekyler, der omfatter: i) at udsætte mRNA-transkripter for en polymerasekædereaktion under betingelser, der fremmer dannelsen af kun ét komplement, hvorved der genereres derivatstrenge af første orden; ii) at tilsætte en polynukleotid-ende til derivatstrengene af første orden; og iii) at udsætte derivatstrengene af første orden for en polymerasereakti-on i nærvær af primere, der er i stand til at hybridisere til polynukleotid-enden der er tilsat ifølge trin (ii) under betingelser, som fremmer dannelsen af kun ét komplement, for derved at generere derivatstrenge af anden orden, hvor primerne ifølge mindst et af trin (i) og (iii) omfatter nucleinsyremarkører, således at hvert mærket nucleinsyremolekyle er unikt, for derved at danne unikt mærkede nucleinsyremolekyler; b) at udsætte de mærkede nucleinsyremolekyler for polymerasekædereaktion (PCR) amplifikation; c) at generere markør-associerede sekvensreads ved at sekventere produktet ifølge trin (b); d) at tildele hvert mærket nucleinsyremolekyler et sted på et cDNA-bibliotek der er associeret med mRNA-transkripterne, ved at kortlægge undersekvensen af hver markør-associeret sekvensread, der svarer til et mRNA-transkript et sted på cDNA-biblioteket; og e) at tælle antallet af mærkede nucleinsyremolekyler med en anden markør, der er blevet tildelt samme sted på cDNA-biblioteket, for derved at opnå information om antallet af mRNA-kopier der ikke er påvirket af forvrængninger af amplifikation.
9. Fremgangsmåde ifølge et hvilket som helst af kravene 1-7, hvor mærkning af segmenterne for at danne mærkede nucleinsyremolekyler omfatter: (i) at tilsætte en polynukleotid-ende til enderne af segmenterne af det genomiske materiale for at danne derivatstrenge af nulte orden; (ii) at udsætte derivatstrengene af nulte orden ifølge trin (i) for en poly-merasereaktion i nærvær af primere, der er i stand til at hybridisere til polynukleotid-enden af strengene af nulte orden under betingelser, som fremmer dannelsen af kun ét komplement, for derved at generere derivatstrenge af første orden; (iii) at tilsætte en polynukleotid-ende til derivatstrengene af første orden; (iv) at udsætte derivatstrengene af første orden for en polymerasereak-tion i nærvær af primere, der er i stand til at hybridisere til polynukleotid-enden af derivatstrengene af første orden under betingelser, der fremmer dannelsen af kun ét komplement, hvorved der genereres derivatstrenge af anden orden, hvor primerne ifølge mindst et af trin (ii) og (iv) omfatter nucleinsyremarkører, således at hvert mærket nucleinsyremolekyle er unikt, for derved at danne unikt mærkede nucleinsyremolekyler.
10. Fremgangsmåde ifølge et hvilket som helst af kravene 1-7, hvor mærkning af segmenterne for at danne mærkede nucleinsyremolekyler omfatter: i) at tilsætte en polynukleotid-ende til enderne af segmenterne af geno-misk materiale for at danne derivatstrenge af nulte orden, ii) at udsætte derivatstrengene af nulte orden ifølge trin (i) for en ligationsreaktion i nærvær af primere, der er i stand til at hybridisere til polynukleotid-enden af derivatstrengene af nulte orden der er tilsat ifølge trin (i) under betingelser, der fremmer ligationen af en primer til 5'-enderne af derivatstrengene af nulte orden, iii) at udsætte produktet ifølge trin (ii) for en polymerasereaktion i nærvær af primere der er i stand til at hybridisere til polynukleotid-enden, som er tilsat ifølge trin (i) under betingelser, der fremmer dannelsen af kun ét komplement, hvor primerne ifølge trin (iii) har forskellige nuc-leotidsekvenser end primerne ifølge trin (ii), og hvor polymerasen har 3'-5'-korrekturlæsningsaktivitet, hvor primerne ifølge mindst et af trin (ii) og (iii) omfatter nucleinsyremarkører, således at hvert mærket nucleinsyremolekyle er unikt, for derved at generere unikt mærkede nucleinsyremolekyler.
11. Fremgangsmåden ifølge krav 10, hvor tilsætning af en polynukleotid-ende omfatter anvendelsen af en terminal transferase.
12. Fremgangsmåde ifølge et hvilket som helst af kravene 1-11, hvor de mærkede nucleinsyremolekyler er udsat for en hybrid-capture- fremgangsmåde forud for PCR eller forud for sekventering, hvor de mærkede nucleinsyremolekyler er dannet fra en enkelt art, hvor de mærkede nucleinsyremolekyler er dannet fra en enkelt celle, hvor de mærkede nucleinsyremolekyler er dannet fra to eller flere organismer, eller hvor de mærkede nucleinsyremolekyler er dannet af to eller flere arter, hvor de mærkede nucleinsyremolekyler er dannet ud fra en population af mikrober, og hvor information om antallet af genomiske kopier der er opnået for forskellige arter af populationen sammenlignes for at bestemme det relative antal af de forskellige arter i populationen.
13. Fremgangsmåde ifølge et hvilket som helst af kravene 1-12, hvor markørsekvenserne yderligere omfatter en prøve-markør.
14. Fremgangsmåden ifølge krav 13, hvor de mærkede nucleinsyremolekyler er samlet med et antal mærkede nucleinsyremolekyler der har en forskellig prøvemarkør forud for PCR-amplifikation eller forud for sekventering.
15. Fremgangsmåden ifølge krav 14, der yderligere omfatter dekonvolutering af de markør-associerede sekvensreads ved at gruppere de markør-associerede sekvensreads ifølge prøve-markør.
16. Fremgangsmåden ifølge krav 1, hvor stedet på et genom der er associeret med det genomiske materiale er identisk med undersekvensen af en markørassocieret sekvensread der svarer til en art af nucleinsyremolekyle.
DK11835243.4T 2010-10-22 2011-10-21 Varital tælling af nucleinsyrer for at opnå information om antal genomiske kopier DK2630263T4 (da)

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US40606710P 2010-10-22 2010-10-22
US201161510579P 2011-07-22 2011-07-22
PCT/US2011/057350 WO2012054873A2 (en) 2010-10-22 2011-10-21 Varietal counting of nucleic acids for obtaining genomic copy number information
US13/278,333 US9404156B2 (en) 2010-10-22 2011-10-21 Varietal counting of nucleic acids for obtaining genomic copy number information

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EP (4) EP4328321A3 (da)
AU (1) AU2011316807C1 (da)
CA (4) CA2815076C (da)
DK (1) DK2630263T4 (da)
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