DK2697392T3 - Opløsning af genomfraktioner under anvendelse af polymorfisme-tællinger - Google Patents
Opløsning af genomfraktioner under anvendelse af polymorfisme-tællinger Download PDFInfo
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- DK2697392T3 DK2697392T3 DK12716939.9T DK12716939T DK2697392T3 DK 2697392 T3 DK2697392 T3 DK 2697392T3 DK 12716939 T DK12716939 T DK 12716939T DK 2697392 T3 DK2697392 T3 DK 2697392T3
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- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/10—Ploidy or copy number detection
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- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
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- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
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Claims (14)
1. Fremgangsmåde til at beregne fraktionen af føtalt DNA i DNA opnået fra en legemsvæske fra et gravidt individ, hvilken fremgangsmåde omfatter: (a) modtage en prøve af legemsvæsken; (b) ekstrahere DNA fra prøven under betingelser der ekstraherer DNA fra både et modergenom og et fostergonom der er til stede i legemsvæsken; (c) sekventering af det ekstraherede DNA med en nukleinsyresequencer under betingelser der producerer DNA-segmentsekvenser indeholdende én eller flere polymorfismer; (d) afbilde DNA-segmentsekvenserne afledt fra sekventering af DNA'et i legemsvæsken til én eller flere designerede polymorfismer på en referencesekvens, hvor afbildningen udføres under anvendelse af et dataapparat programmeret til at afbilde nukleinsyresekvenser til den ene eller flere designerede polymorfismer; (e) bestemme allel-frekvenser af de afbildede DNA-segmentsekvenser for mindst én af de designerede polymorfismer; (f) klassificeringen af den mindst ene designerede polymorfisme baseret på en kombination af zygositeten af det gravide individ og zygositeten af fosteret; og (g) beregne fraktionen af føtalt DNA i DNA'et opnået fra det gravide individ under anvendelse af allel-frekvenser bestemt i (e) i sammenhæng med klassifikationen af zygositeter fra (f), hvor (e)-(g) udføres på én eller flere processorer der kører under programinstruktionerne til bestemmelsen, klassificering og estimering, hvor sekventeringen i trin (c) producerer DNA-segmentsekvenser indeholdende en flerhed af polymorfismer og trinnene (d)-(f) udføres baseret på flerheden af polymorfismer; og hvor klassificeringen i (f) klassificerer hver af flerheden af polymorfismer ind i en af de følgende kombinationer: (i) det gravide individ er homozygotisk og fosteret er homozygotisk, (ii) det gravide individ er homozygotisk og fosteret er homozygotisk, (iii) det gravide individ er homozygotisk og fosteret er homozygotisk, and (iv) det gravide individ er homozygotisk og fosteret er homozygotisk.
2. Fremgangsmåden ifølge krav 1, hvor klassificeringen af flerheden af polymorfismer omfatter anvendelse af allel-sekvensdata fra (e), opnået for flerheden af polymorfismer, til en blandingsmodel.
3. Fremgangsmåden ifølge krav 2, yderligere omfatter løsning af serier af ligninger for faktorielle momenter af allel-frekvensdata for hver af flerheden af polymorfismesekvenser, hvor serien af ligninger er:
hvor Fj er det jth faktorielle moment, ai er den underordnede allelfrekvens af ith polymorfisme-sitet, di er dækningen af ith polymorfisme-sitet, og n er antallet af polymorfisme-sites.
4. Fremgangsmåden ifølge krav 2 eller 3, yderligere omfatter at relatere faktorielle momenter til {σ/,ρ/> ved
hvor Oi er delen af flerheden af polymorfisme-sekvenser i zygositetstilfælde i, pi er den binomiale sandsynlighed af den underordnede allel i zygositet tilfælde i, m i antallet af zygositet tilfælde, og g i antallet af beregnede faktorielle momenter.
5. Fremgangsmåden ifølge krav 3 eller 4, yderligere omfattende, før løsning af serien af ligninger for faktorielle momenter, datamæssigt fjernelse af allel-frekvenser for polymorfismer identificeret som værende: (A) homozygotisk i både fosteret og det gravide individ; (B) homozygous i både fosteret og det gravide individ; eller (C) homozygotisk i det gravide individ.
6. Fremgangsmåden ifølge et hvilket som helst af kravene 2-5, hvor blandingsmodellen forklarer sekventeringsfejl.
7. Fremgangsmåden ifølge krav 1, yderligere omfattende fjernelse fra betragtning enhver polymorfisme klassificeret i kombination (i) eller kombination (iv).
8. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, hvor klassificeringen af flerheden af polymorfismer omfatter anvendelse af en tærskelværdi til allel-frekvensen bestemt i (e).
9. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, yderligere omfattende filtrering af flerheden af polymorfismer for at fjerne fra betragtning enhver polymorfisme blandt flerheden af polymorfismer med en underordnet allel-frekvens på større eller mindre end en defineret tærskelværdi.
10. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, hvor afbildningen i (d) omfatter identificere en flerhed af bi-allelle polymorfismesekvenser.
11. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, hvor beregningen af fraktionen afføtalt DNA i DNA'et i (g) omfatter at transformere data fra tilfælde (iii) til data fra tilfælde (ii).
12. Fremgangsmåden ifølge krav 11, hvor: (a) transformering af data fra tilfælde (iii) til data fra tilfælde (ii) omfatter transformering af data (D, A) til (Dl, Al) som: Al = 0.5 D — A D1 = D hvor D er dækningen af polymorfismen og A er den underordnede allel-tælling af polymorfismen; (b) transformering af data fra tilfælde (iii) til data fra tilfælde (ii) omfatter trigonometrisk transformation eller anvendelse af rotationsmatricer; eller (c) fraktionen af føtalt DNA estimeres som 2 A/D for tilfælde (ii) og som 1 -2 A/D for tilfælde (iii), hvor A er den underordnede allel-frekvens og D er dækningen for de pågældende polymorfismer.
13. Fremgangsmåden ifølge krav 11 or 12, yderligere omfatter anvendelse af regressionsteknikker til data fra tilfælde (ii) og det transformerede data fra tilfælde (iii), hvor fraktionen af føtalt DNA estimeres som to gange hældningen af regressionslinjen fra en lineær regressionsmodel.
14. Fremgangsmåden ifølge et hvilket som helst af de foregående krav, hvor: (a) DNA'et opnået fra en legemsvæske fra et gravidt individ er celle-frit DNA opnået fra en plasma fra det gravide individ; eller (b) sekventeringen ufføres uden selektiv amplificering af hvilke som helst af den ene eller flere designerede polymorfismer.
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201161474362P | 2011-04-12 | 2011-04-12 | |
PCT/US2012/033391 WO2012142334A2 (en) | 2011-04-12 | 2012-04-12 | Resolving genome fractions using polymorphism counts |
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Publication Number | Publication Date |
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DK2697392T3 true DK2697392T3 (da) | 2016-03-29 |
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Family Applications (4)
Application Number | Title | Priority Date | Filing Date |
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DK12716939.9T DK2697392T3 (da) | 2011-04-12 | 2012-04-12 | Opløsning af genomfraktioner under anvendelse af polymorfisme-tællinger |
DK16158103.8T DK3078752T3 (da) | 2011-04-12 | 2012-04-12 | Løsning af genomfraktioner under anvendelse af polymorfismetællinger |
DK19178858.7T DK3567124T3 (da) | 2011-04-12 | 2012-04-12 | Opløsning af genomfraktioner ved anvendelse af polymorfisme-optællinger |
DK18186518.9T DK3456844T3 (da) | 2011-04-12 | 2012-04-12 | Bestemmelse af genomfraktioner under anvendelse af polymorfisme-tællinger |
Family Applications After (3)
Application Number | Title | Priority Date | Filing Date |
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DK16158103.8T DK3078752T3 (da) | 2011-04-12 | 2012-04-12 | Løsning af genomfraktioner under anvendelse af polymorfismetællinger |
DK19178858.7T DK3567124T3 (da) | 2011-04-12 | 2012-04-12 | Opløsning af genomfraktioner ved anvendelse af polymorfisme-optællinger |
DK18186518.9T DK3456844T3 (da) | 2011-04-12 | 2012-04-12 | Bestemmelse af genomfraktioner under anvendelse af polymorfisme-tællinger |
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Country | Link |
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US (3) | US9447453B2 (da) |
EP (5) | EP3456844B1 (da) |
JP (3) | JP5863946B2 (da) |
CN (2) | CN103797129B (da) |
AU (1) | AU2012242698C1 (da) |
CA (1) | CA2832468C (da) |
CY (4) | CY1117574T1 (da) |
DK (4) | DK2697392T3 (da) |
ES (4) | ES2806728T3 (da) |
HK (1) | HK1195103A1 (da) |
HR (3) | HRP20220296T1 (da) |
HU (3) | HUE041411T2 (da) |
IL (1) | IL228843A (da) |
LT (3) | LT3078752T (da) |
PL (4) | PL3567124T3 (da) |
PT (3) | PT3456844T (da) |
RS (3) | RS57837B1 (da) |
SI (3) | SI3567124T1 (da) |
TR (1) | TR201816062T4 (da) |
WO (1) | WO2012142334A2 (da) |
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- 2013-10-13 IL IL228843A patent/IL228843A/en active IP Right Grant
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2014
- 2014-08-18 HK HK14108407.4A patent/HK1195103A1/zh unknown
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2015
- 2015-12-22 JP JP2015249239A patent/JP6268153B2/ja active Active
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2016
- 2016-05-30 CY CY20161100473T patent/CY1117574T1/el unknown
- 2016-08-11 US US15/234,966 patent/US10658070B2/en active Active
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2017
- 2017-12-25 JP JP2017247208A patent/JP6760917B2/ja active Active
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2018
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2020
- 2020-04-20 US US16/853,347 patent/US20200251180A1/en active Pending
- 2020-08-10 HR HRP20201249TT patent/HRP20201249T1/hr unknown
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2022
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