HRP20230134T1 - Analiza genoma fetusa iz biološkog uzorka majke - Google Patents

Analiza genoma fetusa iz biološkog uzorka majke Download PDF

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Publication number
HRP20230134T1
HRP20230134T1 HRP20230134TT HRP20230134T HRP20230134T1 HR P20230134 T1 HRP20230134 T1 HR P20230134T1 HR P20230134T T HRP20230134T T HR P20230134TT HR P20230134 T HRP20230134 T HR P20230134T HR P20230134 T1 HRP20230134 T1 HR P20230134T1
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Croatia
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nucleic acid
loci
genome
allele
acid molecules
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HRP20230134TT
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English (en)
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Yuk Ming Dennis Lo
Kwan Chee Chan
Wai Kwun Rossa Chiu
Charles Cantor
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The Chinese University Of Hong Kong
Sequenom, Inc.
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Publication of HRP20230134T1 publication Critical patent/HRP20230134T1/hr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10—Ploidy or copy number detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Claims (10)

1. Postupak za određivanje frakcijske koncentracije fetalne DNK u biološkom uzorku uzetom od trudnice sa fetusom, fetus ima oca i majku koja je trudna, majka ima majčin genom, fetus ima fetalni genom, pri čemu biološki uzorak sadrži smjesu majčine i fetalne nukleinske kiseline, postupak obuhvaća: analiziranje mnoštva molekula nukleinskih kiselina iz biološkog uzorka, gdje analiziranje molekula nukleinskih kiselina obuhvaća: identifikaciju lokacije molekula nukleinske kiseline u ljudskom genomu; i određivanje odgovarajućeg alela molekula nukleinske kiseline; određivanje jednog ili više prvih lokusa, gdje fetalni genom je heterozigotan u svakom prvom lokusu tako da fetalni genom ima odgovarajući prvi i drugi alel na prvim lokusima, i gdje je majčin genom homozigotan na prvim lokusima tako da majčini genom ima dva odgovarajuća druga alela na prvim lokusima, prvi alel je različit od drugog alela, pri čemu određivanje specifičnog lokusa da bude jedan od jednog ili više prvih lokusa uključuje: određivanje granične vrijednosti za broj predviđenog broja kopija odgovarajućeg prvog alela na specifičnom lokusu, granična vrijednost predviđa da li je majčin genom homozigotan i fetalni genom heterozigotan, gdje je granična vrijednost određena na osnovu statističke raspodjele brojeva broja kopija različitih kombinacija homozigotnosti i heterozigotnosti u specifičnom lokusu; na osnovu analize mnoštva molekula nukleinskih kiselina, otkrivanje odgovarajućih prvih alela i odgovarajućih drugih alela na specifičnom lokusu; određivanje broja stvarnog broja kopija odgovarajućeg prvog alela na osnovu analize mnoštva molekula nukleinske kiseline iz biološkog uzorka; i određivanje da je specifičnan lokus jedan od prvih lokusa kada broj stvarnog broja kopija je manji od granične vrijednosti; za bar jedan od prvih lokusa: određivanje prvog broja P broja kopija odgovarajućeg prvog alela i drugog broja Q broja kopija odgovarajućeg drugog alela; i izračunavanje frakcijske koncentracije zasnovane na prvim i drugom brojevima.
2. Postupak prema zahtjevu 1, gdje je frakcijska koncentracija određena kao 2xp/(p+q).
3. Postupak prema zahtjevu 1 ili 2, gdje su P i Q određeni za mnoštvo prvih lokusa, i gdje je frakcijska koncentracija f određena kao [image] 3. gdje pi je prvi broj za i-te prve lokuse i qi je drugi broj za i-te prve lokuse.
4. Postupak prema bilo kojem od prethodnih zahtjeva, gdje određivanje granične vrijednosti uključuje određivanje statističke raspodjele za maksimalnu i minimalnu frakcijsku koncentraciju.
5. Postupak prema bilo kojem od prethodnih zahtjeva, gdje analiziranje molekula nukleinske kiseline uključuje implementiranje na bar jedan dio molekula nukleinske kiseline bar jedne tehnike izabrane iz grupe koju čine masivno paralelno sekvenciranje, mikročipovi (eng.microarray), hibridizacija, PCR u realnom vremenu, digitalna PCR, i masena spektrometrija.
6. Postupak prema bilo kojem od prethodnih zahtjeva, gdje statistička raspodjela obuhvaća Poissonovu raspodjelu.
7. Postupak prema zahtjevu 6, koji još obuhvaća: obogaćivanje biološkog uzorka dobivenog od trudnice u molekulama nukleinske kiseline u ciljanom području; i sekvenciranje mnoštva molekula nukleinskih kiselina iz obogaćenog biološkog uzorka, sekvenciranje je specifično za ciljano područje, gdje identifikacija lokacije molekule nukleinske kiseline u ljudskom genomu uključuje upotrebu rezultata sekvenciranja kako bi se utvrdila lokacija molekula nukleinske kiseline u ciljnoj regiji ljudskog genoma.
8. Postupak prema zahtjevu 7, gdje obogaćivanje biološkog uzorka obuhvaća ciljano sekvenciranje hvatanjem faze rastvora, hvatanje mikročipova (eng. microarray capture), ili ciljana amplifikacija.
9. Postupak prema zahtjevu 7 ili 8, gdje otac ima genom oca, gdje određivanje jednog ili više lokusa obuhvaća : određivanje da je očev genom homozigotan za odgovarajući prvi alel na svakom lokusu prvih lokusa i određivanje da je majčin genom homozigotan za odgovarajući drugi alel na istom lokusu.
10. Računalni program koji obuhvaća kod softvera koji je u stanju izvršiti pomoću procesora računalnog sistema, a računalni program je konfiguriran za izvođenje, po izvršenju, postupka prema bilo kojem od prethodnih zahtjeva.
HRP20230134TT 2009-11-05 2010-11-05 Analiza genoma fetusa iz biološkog uzorka majke HRP20230134T1 (hr)

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US25856709P 2009-11-05 2009-11-05
US25907509P 2009-11-06 2009-11-06
US38185410P 2010-09-10 2010-09-10
EP20200970.0A EP3783110B1 (en) 2009-11-05 2010-11-05 Fetal genomic analysis from a maternal biological sample

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HRP20190601TT HRP20190601T1 (hr) 2009-11-05 2019-03-28 Genomska analiza fetusa iz majčinskog biološkog uzorka

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US (5) US8467976B2 (hr)
EP (5) EP3241914B1 (hr)
JP (3) JP5540105B2 (hr)
CN (2) CN102770558B (hr)
AU (1) AU2010315037B9 (hr)
BR (1) BR112012010694B8 (hr)
CA (1) CA2779695C (hr)
CY (1) CY1122003T1 (hr)
DK (3) DK3241914T3 (hr)
EA (1) EA033752B1 (hr)
ES (3) ES2934941T3 (hr)
FI (1) FI3783110T3 (hr)
HK (1) HK1222413A1 (hr)
HR (2) HRP20230134T1 (hr)
HU (3) HUE043574T2 (hr)
IL (3) IL219521A (hr)
LT (2) LT3783110T (hr)
MX (3) MX2012005214A (hr)
PL (3) PL3783110T3 (hr)
PT (3) PT3783110T (hr)
RS (2) RS63944B1 (hr)
SI (2) SI3241914T1 (hr)
TW (1) TWI458976B (hr)
WO (1) WO2011057094A1 (hr)

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