HRP20220296T1 - Razrješavanje frakcija genoma pomoću brojanja polimorfizma - Google Patents
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- HRP20220296T1 HRP20220296T1 HRP20220296TT HRP20220296T HRP20220296T1 HR P20220296 T1 HRP20220296 T1 HR P20220296T1 HR P20220296T T HRP20220296T T HR P20220296TT HR P20220296 T HRP20220296 T HR P20220296T HR P20220296 T1 HRP20220296 T1 HR P20220296T1
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- 108020004414 DNA Proteins 0.000 claims 25
- 102000054765 polymorphisms of proteins Human genes 0.000 claims 15
- 108700028369 Alleles Proteins 0.000 claims 13
- 210000003754 fetus Anatomy 0.000 claims 12
- 230000001605 fetal effect Effects 0.000 claims 11
- 238000000034 method Methods 0.000 claims 11
- 239000000523 sample Substances 0.000 claims 10
- 210000001124 body fluid Anatomy 0.000 claims 7
- 108091028043 Nucleic acid sequence Proteins 0.000 claims 6
- 239000010839 body fluid Substances 0.000 claims 6
- 238000013507 mapping Methods 0.000 claims 5
- 230000008774 maternal effect Effects 0.000 claims 4
- 108091033319 polynucleotide Proteins 0.000 claims 4
- 102000040430 polynucleotide Human genes 0.000 claims 4
- 239000002157 polynucleotide Substances 0.000 claims 4
- 238000012163 sequencing technique Methods 0.000 claims 4
- 238000001712 DNA sequencing Methods 0.000 claims 3
- 238000009396 hybridization Methods 0.000 claims 3
- 150000007523 nucleic acids Chemical group 0.000 claims 3
- 239000008280 blood Substances 0.000 claims 2
- 210000004369 blood Anatomy 0.000 claims 2
- 238000001914 filtration Methods 0.000 claims 2
- 239000000758 substrate Substances 0.000 claims 2
- 238000007400 DNA extraction Methods 0.000 claims 1
- 230000003321 amplification Effects 0.000 claims 1
- 230000015572 biosynthetic process Effects 0.000 claims 1
- 238000000605 extraction Methods 0.000 claims 1
- 230000000977 initiatory effect Effects 0.000 claims 1
- 238000012423 maintenance Methods 0.000 claims 1
- 238000003199 nucleic acid amplification method Methods 0.000 claims 1
- 108020004707 nucleic acids Proteins 0.000 claims 1
- 102000039446 nucleic acids Human genes 0.000 claims 1
- 230000008520 organization Effects 0.000 claims 1
- 238000003786 synthesis reaction Methods 0.000 claims 1
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Claims (12)
1. Postupak procjene udjela fetalne DNK u DNK dobivenoj iz tjelesne tekućine trudnice, te postupak uključuje:
(a) poravnavanje ili mapiranje na drugi način segmenata sekvenci DNK izvedenih sekvenciranjem DNK u tjelesnoj tekućini na jedan ili više označenih polimorfizama na referentnoj sekvenci, pri čemu se poravnavanje ili mapiranje na drugi način izvodi pomoću računalnog uređaja programiranog za mapiranje sekvenci nukleinskih kiselina na jedan ili više označenih polimorfizama;
(b) određivanje frekvencija alela mapiranih segmenata sekvenci DNK za najmanje jedan od naznačenih polimorfizama;
(c) razvrstavanje najmanje jednog označenog polimorfizma na temelju kombinacije zigotnosti trudnice i zigotnosti fetusa; i
(d) procjenjivanje udjela fetalne DNK u DNK dobivenoj od trudne jedinke korištenjem frekvencija alela određenih u (b) u vezi s klasifikacijom zigoziteta iz (c),
pri čemu se koraci (b)-(d) izvode na jednom ili više procesora koji rade prema programskim uputama radi određivanja, klasifikacije i procjene; i
pri čemu klasifikacija u (c) klasificira najmanje jedan naznačeni polimorfizam u jednu od sljedećih kombinacija: (i) trudnica je homozigotna i fetus je homozigotan, (ii) trudnica je homozigotna, a fetus je heterozigotan, (iii) trudnica je heterozigotna i fetus je homozigotan, i (iv) trudnica je heterozigotna i fetus je heterozigotan.
2. Postupak prema patentnom zahtjevu 1 naznačen time što:
(a) dalje uključuje uklanjanje iz razmatranja bilo kojeg polimorfizma klasificiranog u kombinaciju (i) ili kombinaciju (iv);
(b) dalje obuhvaća filtriranje najmanje jednog označenog polimorfizma kako bi se uklonio iz razmatranja bilo koji polimorfizam koji ima frekvenciju sporednog alela veću od definiranog praga;
(c) dalje uključuje filtriranje najmanje jednog označenog polimorfizma kako bi se uklonio iz razmatranja bilo koji polimorfizam koji ima frekvenciju sporednog alela manju od definiranog praga;
(d) pri čemu klasificiranje najmanje jednog označenog polimorfizma uključuje primjenu praga na frekvenciju alela utvrđenu u (b);
(e) pri čemu klasificiranje najmanje jednog označenog polimorfizma uključuje primjenu podataka o frekvenciji alela iz (b), dobivenih za mnoštvo polimorfizama, na mješoviti model, po izboru pri čemu mješoviti model koristi faktorske momente;
(f) pri čemu DNK dobivena iz tjelesne tekućine trudne osobe je DNK bez stanica dobivena iz plazme trudne osobe;
(g) pri čemu mapiranje segmenata DNK dobivenih iz krvi osobe koja nosi fetus obuhvaća računalno mapiranje navedenih segmenata u bazu podataka polimorfizama;
(h) naznačen time što dalje sadrži izvršavanje programskih instrukcija na jednom ili više procesora za automatsko bilježenje udjela fetalne DNK kako je procijenjeno u (d) u medicinskom zapisu pacijenta, pohranjenom na računalno čitljivom mediju, za trudnu osobu;
(i) pri čemu nadalje obuhvaća, na temelju procjene udjela fetalne DNK, propisivanje, započinjanje i/ili mijenjanje liječenja ljudskog subjekta od kojeg je uzet majčin testni uzorak; ili
(j) pri čemu nadalje obuhvaća, na temelju procjene udjela fetalne DNK, naručivanje i/ili provođenje jednog ili više dodatnih testova.
3. Postupak prema patentnom zahtjevu 1 naznačen time što dalje sadrži, prije koraka (a), sekvenciranje DNK sekvencerom nukleinske kiseline pod uvjetima koji proizvode segmente sekvence DNK koji sadrže jedan ili više polimorfizama, izborno pri čemu se sekvenciranje provodi bez selektivnog pojačavanja bilo kojeg od ili više označenih polimorfizama.
4. Postupak prema patentnom zahtjevu 3, naznačen time što dalje sadrži, prije sekvenciranja DNK, ekstrakciju DNK iz uzorka pod uvjetima koji ekstrahiraju DNK i majčinog genoma i fetalnog genoma koji je prisutan u tjelesnoj tekućini.
5. Postupak prema patentnom zahtjevu 4, naznačen time što dalje sadrži, prije ekstrakcije DNK iz uzorka, primanje uzorka tjelesne tekućine.
6. Postupak prema bilo kojem od patentnih zahtjeva 3-5, naznačen time što obuhvaća sekvenciranje sintezom.
7. Postupak prema bilo kojem od patentnih zahtjeva 3-5, naznačen time što obuhvaća sekvenciranje hibridizacijom.
8. Postupak prema patentnom zahtjevu 7, naznačen time što hibridizacija uključuje dovođenje u kontakt više polinukleotidnih sekvenci s mnoštvom polinukleotidnih sondi, pri čemu je svaka od mnoštva polinukleotidnih sondi vezana za supstrat, pri čemu je supstrat ravna površina koja sadrži niz poznatih nukleotidnih sekvenci.
9. Postupak prema patentnom zahtjevu 8, naznačen time što se uzorak hibridizacije na niz koristi za određivanje polinukleotidnih sekvenci prisutnih u uzorku.
10. Postupak prema bilo kojem od patentnih zahtjeva 1-9, naznačen time što je referentna sekvenca pohranjena lista ili druga organizirana zbirka podataka o referentnim polimorfizmima za trudnicu, izborno pri čemu je referentna sekvenca baza podataka sekvenci, na primjer baza podataka sekvenci alela.
11. Uređaj za procjenu udjela fetalne DNK u DNK dobivenoj iz tjelesne tekućine trudne osobe, te uređaj sadrži:
(a) sekvencer konfiguriran za (i) primanje DNK ekstrahirane iz uzorka tjelesne tekućine koja sadrži DNK genoma majke i genoma fetusa, i (ii) sekvenciranje ekstrahirane DNK pod uvjetima koji proizvode segmente sekvence DNK koje sadrže jedan ili više označenih polimorfizama; i
(b) računalni uređaj konfiguriran da daje upute jednom ili više procesora za poravnavanje ili na drugi način mapiranje sekvenci nukleinske kiseline na jedan ili više označenih polimorfizama na referentnoj sekvenci,
određivanje frekvencije alela mapiranih segmenata sekvenci DNK za najmanje jedan od označenih polimorfizama,
klasificiranje najmanje jednog označenog polimorfizma na temelju kombinacije zigotnosti trudnice i zigotnosti fetusa, i
procjenjivanje udjela fetalne DNK u DNK dobivenoj od trudnice koristeći frekvencije alela u vezi s klasifikacijom zigotnosti; i
pri čemu je računski uređaj nadalje konfiguriran da uputi jednom ili više procesora da klasificiraju najmanje jedan naznačeni polimorfizam u jednu od sljedećih kombinacija: (i) trudnica je homozigotna i fetus je homozigotan, (ii) trudnica je homozigotna i fetus je heterozigotan, (iii) trudnica je heterozigotna i fetus je homozigotan, i (iv) trudnica je heterozigotna i fetus je heterozigotan.
12. Uređaj prema patentnom zahtjevu 11 naznačen time što
(a) dalje sadrži alat za ekstrakciju DNK iz uzorka pod uvjetima koji ekstrahiraju DNK iz genoma majke i genoma fetusa;
(b) pri čemu je računski uređaj dalje konfiguriran da daje upute jednom ili više procesora da uklone iz razmatranja bilo koji polimorfizam klasificiran u kombinaciji (i) ili kombinaciji (iv);
(c) pri čemu je računski uređaj dalje konfiguriran da daje upute jednom ili više procesora da uklone iz razmatranja bilo koji polimorfizam koji ima frekvenciju sporednog alela veću od definiranog praga;
(d) pri čemu je računski uređaj dalje konfiguriran da daje upute jednom ili više procesora da filtriraju jedan ili više označenih polimorfizama kako bi se uklonio iz razmatranja bilo koji polimorfizam koji ima frekvenciju sporednog alela manju od definiranog praga;
(e) pri čemu je računski uređaj konfiguriran da daje upute jednom ili više procesora da klasificiraju najmanje jedan označeni polimorfizam primjenom praga na frekvenciju alela;
(f) pri čemu je računski uređaj dalje konfiguriran da daje upute jednom ili više procesora da klasificiraju najmanje jedan označeni polimorfizam primjenom podataka o frekvenciji alela, dobivenih za mnoštvo polimorfizama, na mješoviti model, po izboru pri čemu miješani mješoviti model koristi faktorske momente;
(g) pri čemu dalje sadrži uređaj za ekstrakciju DNK bez stanica dobivene iz plazme trudnice za sekvenciranje u sekvenceru;
(h) pri čemu dalje sadrži bazu podataka polimorfizama, pri čemu je računski uređaj dalje konfiguriran da daje upute jednom ili više procesora da mapiraju segmente DNK dobivene iz krvi pojedinca koji nosi fetus računalnim mapiranjem navedenih segmenata u bazu podataka polimorfizama; ili
(i) pri čemu je računski uređaj nadalje konfiguriran da daje upute jednom ili više procesora da automatski zabilježe udio fetalne DNK u medicinskom zapisu pacijenta, pohranjenom na računalno čitljivom mediju, za trudnu osobu, po izboru pri čemu navedeni medicinski zapis pacijenta održavaju laboratorij, liječnički ured, bolnica, organizacija za održavanje zdravlja, osiguravajuće društvo, ili web-mjesto osobnog medicinskog zapisa.
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Application Number | Priority Date | Filing Date | Title |
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US201161474362P | 2011-04-12 | 2011-04-12 | |
EP19178858.7A EP3567124B1 (en) | 2011-04-12 | 2012-04-12 | Resolving genome fractions using polymorphism counts |
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HRP20220296T1 true HRP20220296T1 (hr) | 2022-05-13 |
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HRP20220296TT HRP20220296T1 (hr) | 2011-04-12 | 2012-04-12 | Razrješavanje frakcija genoma pomoću brojanja polimorfizma |
HRP20181770TT HRP20181770T1 (hr) | 2011-04-12 | 2018-10-26 | Rješavanje genomskih frakcija upotrebom broja kopija polimorfizama |
HRP20201249TT HRP20201249T1 (hr) | 2011-04-12 | 2020-08-10 | Razrješavanje genomskih frakcija upotrebom broja kopija polimorfizama |
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HRP20181770TT HRP20181770T1 (hr) | 2011-04-12 | 2018-10-26 | Rješavanje genomskih frakcija upotrebom broja kopija polimorfizama |
HRP20201249TT HRP20201249T1 (hr) | 2011-04-12 | 2020-08-10 | Razrješavanje genomskih frakcija upotrebom broja kopija polimorfizama |
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US (3) | US9447453B2 (hr) |
EP (5) | EP3078752B1 (hr) |
JP (3) | JP5863946B2 (hr) |
CN (2) | CN106319047B (hr) |
AU (1) | AU2012242698C1 (hr) |
CA (1) | CA2832468C (hr) |
CY (4) | CY1117574T1 (hr) |
DK (4) | DK3078752T3 (hr) |
ES (4) | ES2692333T3 (hr) |
HK (1) | HK1195103A1 (hr) |
HR (3) | HRP20220296T1 (hr) |
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LT (3) | LT3078752T (hr) |
PL (4) | PL2697392T3 (hr) |
PT (3) | PT3078752T (hr) |
RS (3) | RS57837B1 (hr) |
SI (3) | SI3456844T1 (hr) |
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US11111544B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
US11111543B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
US10083273B2 (en) | 2005-07-29 | 2018-09-25 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
US10081839B2 (en) | 2005-07-29 | 2018-09-25 | Natera, Inc | System and method for cleaning noisy genetic data and determining chromosome copy number |
US9424392B2 (en) | 2005-11-26 | 2016-08-23 | Natera, Inc. | System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals |
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