HRP20220296T1 - Razrješavanje frakcija genoma pomoću brojanja polimorfizma - Google Patents

Razrješavanje frakcija genoma pomoću brojanja polimorfizma Download PDF

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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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polymorphism
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fetus
pregnant woman
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Richard P. Rava
Brian K. Rhees
John P. Burke
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Verinata Health, Inc.
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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.
HRP20220296TT 2011-04-12 2012-04-12 Razrješavanje frakcija genoma pomoću brojanja polimorfizma HRP20220296T1 (hr)

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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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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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