DK2376661T3 - Simultan bestemmelse af aneuploidi og føtal fraktion - Google Patents

Simultan bestemmelse af aneuploidi og føtal fraktion Download PDF

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DK2376661T3
DK2376661T3 DK10830939.4T DK10830939T DK2376661T3 DK 2376661 T3 DK2376661 T3 DK 2376661T3 DK 10830939 T DK10830939 T DK 10830939T DK 2376661 T3 DK2376661 T3 DK 2376661T3
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chromosome
sequence
sequencing
fetal
nucleic acids
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Richard P Rava
Gabrielle Heilek
Stephen Quake
David A Comstock
Manjula Chinnappa
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Verinata Health Inc
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Claims (18)

1. Fremgangsmåde til simultan bestemmelse af aneuploidi og føtal fraktion i maternel blod, plasma- eller serumprøve omfattende en blanding af føtale og materneile nukleinsyremolekyler, hvor blandingen af føtale og materneile nukleinsyremolekyler er celle-fri DNA (cfDNA)-molekyler og den føtale fraktion er fraktionen af nukleinsyremolekylerne fra et føtus til blandingen af føtale og materneile nukleinsyremolekyler, hvilken fremgangsmåde omfatter: (a) berige blandingen med en flerhed af polymorfe target-nukleinsyrer, hvor hver af target-nukleinsyrerne er kendt for at omfatte mindst ét polymorft sted, og hvor berigelsen omfatter: (i) specifikt amplificere flerheden af target-nukleinsyrer i en del af blandingen under anvendelse af primerpar hver i stand til at amplificere en target-nukleinsyresekvens omfattende et polymorft sted i en multipleks-PCR-omsætning for at generere et panel af amplificerede polymorfe steder der indeholder et tilstrækkeligt antal polymorfe steder således at mindst to er informative polymorfe steder; og (ii) kombinere mindst en del eller alle de amplificerede produkter med mindst en del af de resterende ikke-amplificerede prøver fra hvilke delen var fjernet; (b) sekventering af mindst en del af den berigede blanding opnået i trin (a), hvor sekventeringen omfatter at tilvejebringe en flerhed af læsesekvenser der er kortlagt til et genom til at identificere en flerhed af kortlagte sekvens-tagstags; og (c) anvende flerheden af kortlagt sekvens-tagstags, simultan bestemmelse af den føtale fraktion og aneuploidien, hvor: (i) bestemmelse af den føtale fraktion omfatter: (1) anvende de kortlagte sekvens-tags for at identificere mindst to informative polymorfe steder i panelet af opformerede polymorfe steder, hvor de informative polymorfe steder identificeres ved forskellen i allel-sekvenserne og antallet af sekvens-tags kortlagt til hver af de mulige alleller ved hvert polymorft sted; og (2) at beregne den føtale fraktion baseret på totalt antal sekvens-tags der afbilder til en første allel og det totale antal af sekvens-tags der afbilder til en anden allel ved hvert af de informative polymorfe steder; og (ii) bestemme aneuploidi'en omfattende kvantificering af antallet af sekvens-tags der aligner til et kromosom af interesse, og sammenligne opnåede resultater for kromosomet af interesse til en tærskelværdi, hvor tærskelværdien er et antal der tjener som en diagnosegrænse for en aneuploidi og hvor tilstedeværelsen af en aneuploidi for kromosomet af interesse identificeres hvis tærskelværdien overstiges af resultaterne opnået for kromosomet af interesse.
2. Fremgangsmåden ifølge krav 1, hvor berigelsestrin (a) omfatter: (i) amplificere en flerhed af polymorfe target-nukleinsyrer for at generere et panel of polymorfe steder der indeholder et tilstrækkeligt antal polymorfe steder således at mindst tre er informative polymorfe steder; (ii) amplificere en flerhed af polymorfe target-nukleinsyrer for at generere et panel of polymorfe steder der indeholder et tilstrækkeligt antal polymorfe steder således at mindst fire er informative polymorfe steder; eller (iii) amplificere en flerhed af polymorfe target-nukleinsyrer for at generere et panel of polymorfe steder der indeholder et tilstrækkeligt antal polymorfe steder således at mindst fem er informative polymorfe steder.
3. Fremgangsmåden ifølge krav 1 eller krav 2, hvor bestemmelse af den føtale fraktion i trin (c) omfatter at beregne den føtale fraktion baseret på: (i) det totale antal sekvens-tags der afbilder til en første allel og det totale antal sekvens-tags der afbilder til en anden allel for hver af de mindst tre informative alleller; (ii) det totale antal sekvens-tags der afbilder til en første allel og det totale antal af sekvens-tags der afbilder til en anden allel for hver af de mindst fire informative alleller; eller (iii) det totale antal sekvens-tags der afbilder til en første allel og det totale antal af sekvens-tags der afbilder til en anden allel for hver af mindst fem informative alleller.
4. Fremgangsmåden ifølge et hvilket som helst af kravene 1-3, hvor berigelsestrin (a) omfatter at amplificere en flerhed af polymorfe target-nukleinsyrer i en del af en oprenset blanding af føtale og materneile nukleinsyrer.
5. Fremgangsmåden ifølge et hvilket som helst af kravene 1-3, hvor berigelsen omfatter: (i) fremstille et første sekventeringsbibliotek fra blandingen af føtale og materneile nukleinsyremolekyler; (ii) fremstille et andet sekventeringsbibliotek af de opformerede polymorfe target-nukleinsyrer; og (iii) kombinere mindst en del fra det første sekventeringsbibliotek med mindst en del af det andet sekventeringsbibliotek.
6. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, hvor de polymorfe target-nukleinsyrer er lokaliseret på det samme kromosom.
7. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, hvor de polymorfe target-nukleinsyrer er lokaliseret på forskellige kromosomer.
8. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, hvor hver af flerheden af polymorfe target-nukleinsyrer omfatter mindst en enkelt nukleotid-polymorfisme (SNP).
9. Fremgangsmåden ifølge krav 8, hvor SNP'en er en enkelt SNP.
10. Fremgangsmåden ifølge krav 9, hvor den mindst ene SNP er en enkelt SNP valgt fra hver af flerheden af polymorfe target-nukleinsyrer der omfatter en SNP valgt fra rs560681, rsll09037, rs9866013, rsl3182883, rsl3218440, rs7041158, rs740598, rsl0773760, rs4530059, rs7205345, rs8078417, rs576261, rs2567608, rs430046, rs9951171, rs338882, rsl0776839, rs9905977, rsl277284, rs258684, rsl347696, rs508485, rs9788670, rs8137254, rs3143, rs2182957, rs3739005, og rs530022.
11. Fremgangsmåden ifølge krav 8, hvor SNP'en er en tandem-SNP.
12. Fremgangsmåden ifølge krav 11, hvor den mindst ene SNP er en tandem-SNP valgt fra sæt af tandem SNP'er rs7277033-rs2110153; rs2822654-rsl882882; rs368657-rs376635; rs2822731-rs2822732; rsl475881-rs7275487; rsl735976-rs2827016; rs447340-rs2824097; rs418989-rsl3047336; rs987980- rs987981; rs4143392- rs4143391; rsl691324- rsl3050434; rsll909758-rs9980111; rs2826842-rs232414; rsl980969-rsl980970; rs9978999-rs9979175; rsl034346-rsl2481852; rs7509629-rs2828358; rs4817013-rs7277036; rs9981121-rs2829696; rs455921-rs2898102; rs2898102-rs458848; rs961301-rs2830208; rs2174536-rs458076; rsll088023-rsll088024; rsl011734-rsl011733; rs2831244-rs9789838; rs8132769-rs2831440; rs8134080-rs2831524; rs4817219-rs4817220; rs2250911-rs2250997; rs2831899-rs2831900; rs2831902-rs2831903; rsll088086-rs2251447; rs2832040-rsll088088; rs2832141-rs2246777; rs2832959-rs9980934; rs2833734-rs2833735; rs933121-rs933122; rs2834140-rsl2626953; rs2834485-rs3453; rs9974986-rs2834703; rs2776266-rs2835001; rsl984014-rsl984015; rs7281674-rs2835316; rsl3047304-rsl3047322; rs2835545-rs4816551; rs2835735-rs2835736; rsl3047608-rs2835826; rs2836550-rs2212596; rs2836660-rs2836661; rs465612-rs8131220; rs9980072-rs8130031; rs418359-rs2836926; rs7278447-rs7278858; rs385787-rs367001; rs367001-rs386095; rs2837296-rs2837297; og rs2837381-rs4816672.
13. Fremgangsmåden ifølge et hvilket som helst af kravene 1-7, hvor hver af flerheden af polymorfe target-nukleinsyrer omfatter mindst én kort tandem-repeat (STR).
14. Fremgangsmåden ifølge krav 13, hvor hver af flerheden af polymorfe target-nukleinsyrer er en STR valgt fra CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D2S1338, Penta D, Penta E, D22S1045, D20S1082, D20S482, D18S853, D17S1301, D17S974, D14S1434, D12ATA63, D11S4463, D10S1435, D10S1248, D9S2157, D9S1122, D8S1115, D6S1017, D6S474, D5S2500, D4S2408, D4S2364, D3S4529, D3S3053, D2S1776, D2S441, D1S1677, D1S1627 og D1GATA113.
15. Fremgangsmåden ifølge krav 13, hvor den mindst ene STR er mindre end ca. 300 basepar.
16. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, hvor sekventeringen: (i) er næste generations-sekventering (NGS); (ii) er massiv parallel-sekventering under anvendelse af sekventering-ved-syntese med reversible farveterminatorer; (iii) er sekventering-ved-ligering; (iv) omfatter en amplifikation; eller (v) er enkelt-molekyle-sekventering.
17. Fremgangsmåden ifølge et hvilket som helst af kravene 1-16, hvor aneuploidien er en fuldstændig kromosomal aneuploidi; fortrinsvis en kromosomal aneuploidi valgt fra trisomi 8, trisomi 13, trisomi 15, trisomi 16, trisomi 18, trisomi 21, trisomi 22, monosomi X, XXX, XXY og XYY.
18. Fremgangsmåden ifølge et hvilket som helst af kravene 1-16, hvor aneuploidien er en delvis kromosomal aneuploidi.
DK10830939.4T 2010-01-19 2010-12-01 Simultan bestemmelse af aneuploidi og føtal fraktion DK2376661T3 (da)

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US29635810P 2010-01-19 2010-01-19
US36083710P 2010-07-01 2010-07-01
US40701710P 2010-10-26 2010-10-26
US45584910P 2010-10-26 2010-10-26
PCT/US2010/058612 WO2011090558A1 (en) 2010-01-19 2010-12-01 Simultaneous determination of aneuploidy and fetal fraction

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DK18160303.6T DK3382037T3 (da) 2010-01-19 2010-12-01 Fremgangsmåder til bestemmelse af fraktionen af føtale nukleinsyrer i maternelle prøver
DK10844163.5T DK2513339T3 (da) 2010-01-19 2010-12-01 Fremgangsmåde til bestemmelse af fraktion af føtal nukleinsyre i maternel-prøver
DK18201917.4T DK3492601T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekvenseringsbiblioteker
DK17180803.3T DK3260555T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekventeringsbiblioteker
DK10830939.4T DK2376661T3 (da) 2010-01-19 2010-12-01 Simultan bestemmelse af aneuploidi og føtal fraktion
DK10830938.6T DK2366031T3 (da) 2010-01-19 2010-12-01 Fremgangsmåder til sekventering i prænatale diagnoser

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DK18201917.4T DK3492601T3 (da) 2010-01-19 2010-12-01 Hidtil ukendt protokol til fremstilling af sekvenseringsbiblioteker
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