HRP20210716T1 - Neinvazivno određivanje metiloma tumora iz plazme - Google Patents

Neinvazivno određivanje metiloma tumora iz plazme Download PDF

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Publication number
HRP20210716T1
HRP20210716T1 HRP20210716TT HRP20210716T HRP20210716T1 HR P20210716 T1 HRP20210716 T1 HR P20210716T1 HR P20210716T T HRP20210716T T HR P20210716TT HR P20210716 T HRP20210716 T HR P20210716T HR P20210716 T1 HRP20210716 T1 HR P20210716T1
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Croatia
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cancer
methylation
determining
sequence reads
cell
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HRP20210716TT
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English (en)
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Rossa Wai Kwun Chiu
Kwan Chee Chan
Yuk-Ming Dennis Lo
Miu Fan Lun
Peiyong Jiang
Wai Man Chan
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The Chinese University Of Hong Kong
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Priority claimed from US13/842,209 external-priority patent/US9732390B2/en
Application filed by The Chinese University Of Hong Kong filed Critical The Chinese University Of Hong Kong
Publication of HRP20210716T1 publication Critical patent/HRP20210716T1/hr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • 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
    • C12Q2523/00—Reactions characterised by treatment of reaction samples
    • C12Q2523/10—Characterised by chemical treatment
    • C12Q2523/125—Bisulfite(s)
    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
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    • 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

Claims (17)

1. Postupak određivanja tipa raka analiziranjem DNK molekula bez stanica iz biološkog uzorka organizma, a postupak obuhvaća: (a) dobivanje, računalnim sustavom, očitavanja sekvence iz molekula DNK bez stanica iz biološkog uzorka, gdje očitavanja sekvence obuhvaćaju status metilacije DNK molekula bez stanica; (b) analiziranje, računalnim sustavom, očitavanja sekvence da se odrede, pri rezoluciji jednog nukleotida, statusi metilacije za više mjesta u DNK molekulama bez stanica; (c) određivanje, računalnim sustavom, profila metilacije uzorka iz statusa metilacije za više mjesta; i (d) određivanje da organizam ima prvi tip raka na osnovu bar dijelom uspoređivanja profila metilacije uzorka sa referentnim profilima metilacije određenim iz statusa metilacije drugih organizama istog tipa, gdje su bar dva od drugih organizama identificirani da imaju različite tipove raka, uključujući prvi tip raka.
2. Postupak prema zahtjevu 1, gdje je biološki uzorak izabran iz grupe koju čine krv, plazma, serum, urin, vaginalna tekućina, tekućina ispiranja maternice ili vagine, pluralna tekućina, ascitna tekućina, cerebrospinalna tekućina, pljuvačka, znoj, suze, sputum, tekućina bronhoalveolarnog ispiranja, i stolica.
3. Postupak prema zahtjevu 1 ili 2, gdje određivanje da organizam ima prvi tip raka obuhvaća određivanje porijekla raka i gdje je porijeklo izabrano iz grupe koju čine mozak, kost, pluća, srce, bubreg, jetra, grudi, debelo crijevo, prostata, nazofarinks, želudac, testisi, koža, jajnici, gušterača, maternica, i limfni čvor.
4. Postupak prema bilo kojem od prethodnih zahtjeva, gdje je prvi tip raka izabran iz grupe koju čine rak pluća, rak grudi, kolorektalni rak, rak prostate, rak nazofarinksa, rak želuca, rak testisa, rak kože, rak koji pogađa živčani sustav, rak kostiju, rak jajnika, rak jetre, hematološki maligniteti, rak gušterače, karcinom endometrija, i rak bubrega.
5. Postupak prema bilo kojem od prethodnih zahtjeva, gdje više mjesta obuhvaća CpG mjesta koja su organizirana u više CpG otoka.
6. Postupak prema zahtjevu 5, gdje određivanje profila metilacije uzorka za više mjesta obuhvaća, za svaki CpG otok iz više CpG otoka, određivanje broja očitavanja sekvence koji pokazuje metilaciju na CpG mjestima u CpG otoku.
7. Postupak prema bilo kojem od prethodnih zahtjeva, gdje određivanje profila metilacije uzorka za više mjesta čini, za svako mjesto iz više mjesta, određivanje broja očitavanja sekvence pokazivanjem metilacije na mjestu i određivanja ukupnog broja očitavanja sekvence na više mjesta.
8. Postupak prema bilo kojem od prethodnih zahtjeva, gdje analiziranje dalje obuhvaća određivanje lokacija DNK molekula bez stanica u genomu.
9. Postupak prema zahtjevu 8, gdje određivanje profila metilacije uzorka obuhvaća određivanje broja očitavanja sekvence DNK molekula bez stanica pokazujući metilaciju na mjestima u području genoma.
10. Postupak prema bilo kojem od prethodnih zahtjeva, gdje drugi organizmi, iz kojih su određeni referentni profili metilacije, obuhvaćaju zdrave subjekte.
11. Postupak prema bilo kojem od prethodnih zahtjeva, što dalje obuhvaća određivanje razine metilacije u jednom ili više mjesta genoma u DNK molekuli bez stanica.
12. Postupak prema bilo kojem od prethodnih zahtjeva, gdje određivanje profila metilacije obuhvaća određivanje razine metilacije za jedan ili više CpG otoka.
13. Postupak prema bilo kojem od prethodnih zahtjeva, gdje je organizam čovjek i ostali organizmi istog tipa su drugi ljudi.
14. Postupak prema bilo kojem od prethodnih zahtjeva, gdje očitavanja sekvence su dobivena korištenjem sekvencioniranja koje uzima u obzir metilaciju, i gdje sekvencioniranje koje uzima u obzir metilaciju obuhvaća sekvencioniranje bisulfita.
15. Postupak prema zahtjevu 14, gdje sekvencioniranje bisulfita čini sekvencioniranje bisulfita širom genoma.
16. Postupak prema zahtjevu 14 ili 15, što dalje obuhvaća obogaćivanje molekula DNK bez stanica prije sekvencioniranja, i što obogaćivanje obuhvaća upotrebu hibridizacijskih sondi, pojačavanje polimeraznom lančanom reakcijom , ili hibridizaciju u čvrstom stanju.
17. Računalni program koji obuhvaća više uputa koje je u stanju izvršiti računalni sustav, da tako izvršeni upravljaju računalnim sustavom koji izvodi postupak prema bilo kojem od zahtjeva 1 do 13.
HRP20210716TT 2012-09-20 2021-05-07 Neinvazivno određivanje metiloma tumora iz plazme HRP20210716T1 (hr)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201261703512P 2012-09-20 2012-09-20
US13/842,209 US9732390B2 (en) 2012-09-20 2013-03-15 Non-invasive determination of methylome of fetus or tumor from plasma
US201361830571P 2013-06-03 2013-06-03
EP17202149.5A EP3354747B1 (en) 2012-09-20 2013-09-20 Non-invasive determination of methylome of tumor from plasma

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HRP20210716T1 true HRP20210716T1 (hr) 2021-06-11

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HRP20240210TT HRP20240210T1 (hr) 2012-09-20 2013-09-20 Neinvazivno određivanje metiloma tumora iz plazme
HRP20210716TT HRP20210716T1 (hr) 2012-09-20 2021-05-07 Neinvazivno određivanje metiloma tumora iz plazme

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EP (6) EP2898100B9 (hr)
JP (5) JP6317354B2 (hr)
KR (5) KR20230145530A (hr)
CN (2) CN104781422B (hr)
AU (4) AU2013317708C1 (hr)
BR (3) BR122021021823B1 (hr)
CA (2) CA3122779A1 (hr)
CY (1) CY1124139T1 (hr)
DK (3) DK2898100T4 (hr)
EA (1) EA201500327A1 (hr)
ES (2) ES2862726T3 (hr)
FI (1) FI3536807T3 (hr)
HK (3) HK1206797A1 (hr)
HR (2) HRP20240210T1 (hr)
HU (1) HUE053822T2 (hr)
IL (3) IL299444A (hr)
LT (1) LT3354747T (hr)
MX (1) MX360034B (hr)
MY (2) MY173356A (hr)
NZ (2) NZ706269A (hr)
PH (1) PH12015500547A1 (hr)
PL (2) PL3354747T3 (hr)
PT (3) PT3354747T (hr)
SG (2) SG11201501927VA (hr)
TW (5) TWI784258B (hr)
WO (1) WO2014043763A1 (hr)
ZA (1) ZA201501772B (hr)

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