DK2516680T3 - Fremgangsmåde og kits til at identificere aneuploidi - Google Patents

Fremgangsmåde og kits til at identificere aneuploidi Download PDF

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DK2516680T3
DK2516680T3 DK10843520.7T DK10843520T DK2516680T3 DK 2516680 T3 DK2516680 T3 DK 2516680T3 DK 10843520 T DK10843520 T DK 10843520T DK 2516680 T3 DK2516680 T3 DK 2516680T3
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nucleic acid
nucleotide sequence
chromosome
species
amplified
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DK10843520.7T
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Mathias Ehrich
Cosmin Deciu
Guy Del Mistro
Yong Qing Chen
Ron Michael Mccullough
Roger Chan Tim
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Sequenom Inc
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    • G—PHYSICS
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    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
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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
    • C12Q1/6876—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
    • 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
    • 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
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • 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
    • C12Q2600/156—Polymorphic or mutational markers
    • 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
    • C12Q2600/16—Primer sets for multiplex assays

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
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  • Wood Science & Technology (AREA)
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Claims (15)

1. Fremgangsmåde til at identificere tilstedeværelsen eller fraværet af en aneuploidi for et målchromosom i et subjekt, som omfatter: a. fremstilling af adskillige sæt af amplificerede nukleinsyrearter ved at amplificere adskillige nukleotidsekvensartsæt fra ekstracellulær nukleinsyrematrix fra et subjekt, hvor: (i) den ekstracellulære nukleinsyrematrix omfatter føtal afledt og maternalt afledt nukleinsyre, (ii) nukleotidsekvensarten for et sæt placeres i et målchromosom og ét eller flere referencechromosomer, hvor et reference-chromosom er et chromosom, som ikke er knyttet til den aneuploidi, som skal identificeres, (iii) nukleotidsekvensarten i et sæt afviger med ét eller flere uoverensstemmende nukleotider; (iv) nukleotidsekvensarten for et sæt er reproducerbart amplificerede i forhold til hinanden, (v) primerhybridiserings-sekvenserne placerede i målnukleotidsekvensarten og i den ene eller flere referencenukleotidsekvensarter i et sæt deler en grad af sekvenslighed, som tillader et enkelt par af amplificeringsprimere at hybridisere til primer-hybridiseringssekvenserne således, at arterne af et sæt samamplificeres; og (vi) hver amplificeret nukleinsyreart i et sæt omfatter en nukleotidsekvens med det ene eller flere ikke overensstemmende nukleotider; b. bestemmelse af mængden af hver amplificeret nukleinsyreart i hvert sæt ved at detektere det ene eller flere ikke overensstemmende nukleotider i hver amplificeret nukleinsyreart; c. bestemmelse af et forhold imellem den relative mængde af (i) en amplificeret målnukleinsyreart og (ii) en amplificeret referencenukleinsyreart, i hvert sæt; og d. identifikation af tilstedeværelsen eller fraværet af en aneuploidi for et målchromosom, baseret på forholdene fra to eller flere sæt.
2. Fremgangsmåde ifølge krav 1, hvor den ekstracellulære nukleinsyre er fra blod, blodplasma eller blodserum fra et svangert kvindeligt subjekt.
3. Fremgangsmåde ifølge krav 2, hvor den ekstracellulære nukleinsyrematrix er fra et kvindeligt subjekt i det første trimester af svangerskab, andet trimester af svangerskab eller tredje trimester af svangerskab.
4. Fremgangsmåde ifølge ethvert af kravene 1 til 3, hvor den føtale nukleinsyre er 5% til 40% af den ekstracellulære nukleinsyre; eller antallet af føtale nukleinsyrekopier er 10 kopier til 2000 kopier af den totale ekstracellulære nukleinsyre.
5. Fremgangsmåde ifølge ethvert af kravene 1 til 4, som omfatter berigelse af den ekstracellulære nukleinsyre for føtal nukleinsyre.
6. Fremgangsmåde ifølge ethvert af kravene 1 til 5, som omfatter bestemmelse af den føtale nukleinsyrekoncentration i den ekstracellulære nukleinsyre.
7. Fremgangsmåde ifølge ethvert af kravene 1 til 6, hvor hver nukleotidsekvens i et sæt er i det væsentlige identisk med enhver anden nukleotidsekvens i sættet.
8. Fremgangsmåde ifølge ethvert af kravene 1 til 7, hvor den ene eller flere nukleotid-sekvensart vælges fra gruppen af nukleotidsekvensarter vist i tabel 4B.
9. Fremgangsmåde ifølge ethvert af kravene 1 til 8, hvor, i et sæt, nukleotidsekvens-arterne er på chromosom 21, chromosom 18 og chromosom 13.
10. Fremgangsmåde ifølge ethvert af kravene 1 til 8, hvor, i alle sæt, nukleotidsekvens-arterne foreligger på chromosom 21, chromosom 18 og chromosom 13.
11. Fremgangsmåde ifølge ethvert af kravene 1 til 10, hvor mængderne af de amplificerede nukleinsyrearter i hvert sæt varierer op til en værdi, som tillader detektion af aneuploidien for målchromosomet med en følsomhed på 90% eller mere, og en specificitet på 95% eller mere.
12. Fremgangsmåde ifølge ethvert af kravene 1 til 11, hvor de amplificerede nukleinsyrearter detekteres ved: at bringe de amplificerede nukleinsyrearter i kontakt med forlængelsesprimere, fremstilling af forlængede forlængelsesprimere, og bestemmelse af den relative mængde af den ene eller flere ikke overensstemmende nukleotider ved analyse af de forlængede forlængelsesprimere.
13. Fremgangsmåde ifølge ethvert af kravene 1 til 12, hvor mængderne af én eller flere amplificerede nukleinsyrearter vægtes forskelligt fra andre amplificerede nukleinsyre-arter, med henblik på at identificere tilstedeværelsen eller fraværet af aneuploidien for målchromosomet.
14. Fremgangsmåde ifølge ethvert af kravene 1 til 13, hvor der foreligger 10 til 70 sæt og 10 eller flere af sættene vælges fra tabel 14.
15. Fremgangsmåde ifølge krav 14, hvor der foreligger 56 sæt og hvor sættene er som angivet i tabel 14.
DK10843520.7T 2009-12-22 2010-12-20 Fremgangsmåde og kits til at identificere aneuploidi DK2516680T3 (da)

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