DK2334812T3 - Ikke-invasiv diagnose af føtal aneuploidi ved sekvensering - Google Patents

Ikke-invasiv diagnose af føtal aneuploidi ved sekvensering Download PDF

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DK2334812T3
DK2334812T3 DK09815105.3T DK09815105T DK2334812T3 DK 2334812 T3 DK2334812 T3 DK 2334812T3 DK 09815105 T DK09815105 T DK 09815105T DK 2334812 T3 DK2334812 T3 DK 2334812T3
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chromosome
sequence
dna
fetal
sequencing
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DK09815105.3T
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Stephen R Quake
Hei-Mun Christina Fan
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Univ Leland Stanford Junior
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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
    • C12Q1/6876—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
    • C12Q1/6869—Methods for sequencing
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/38—Pediatrics
    • G01N2800/385—Congenital anomalies
    • G01N2800/387—Down syndrome; Trisomy 18; Trisomy 13

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
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  • Bioinformatics & Cheminformatics (AREA)
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  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Claims (12)

1. Fremgangsmåde til at teste for en abnorm fordeling af en specificeret kromosomdel i en blandet prøve af normalt og abnormt fordelte kromosomdele opnået fra et individ, hvor den abnorme fordeling er en føtal aneuploidi, og hvor prøven er en blanding af maternel og føtal DNA i en maternel plasmaprøve, omfattende: (a) at opnå sekvenser, ved massiv parallel sekvensering, fra multiple kromosomdele af den blandede prøve for at opnå et antal sekvens-tags med tilstrækkelig længde afen bestemt sekvens der skal tildeles en kromosomplacering i et genom og med et tilstrækkeligt antal til at afspejle abnorm fordeling af den specificerede kromosomdel; (b) at tildele sekvens-tags'ene til tilsvarende kromosomdele omfattende mindst den specificerede kromosomdel ved at sammenligne sekvens-tags'ene med en reference genomsekvens; (c) at bestemme værdier for et antal sekvens-tags der kortlægges til normalt og abnormt fordelte kromosomdele ved: (i) at tælle sekvens-tags i en række foruddefinerede vinduer med samme længde i mindst en normalt fordelt kromosomdel for at opnå en første værdi; og (ii) at tælle sekvens-tags i en række foruddefinerede vinduer med samme længde i den specificerede kromosomdel forat opnå en anden værdi; og (d) at anvende værdier fra trin (c) til at bestemme en forskel, mellem den første værdi og den anden værdi, der er bestemmende for overrepræsentationen eller under-repræsentationen af den specificerede kromosomdel i blandingen af maternel og føtal DNA.
2. Fremgangsmåde ifølge krav 1, hvor de foruddefinerede vinduer er 10 kb til 100 kb i længden.
3. Fremgangsmåde ifølge krav 1 hvor bestemmelsen af en forskel omfatter trinnet at sammenligne en normaliseret sekvens-tag densitet af den specificerede kromosomdel med en normaliseret sekvens-tag densitet af en anden kromosomdel i den blandede prøve, hvor alle autosomer anvendes til at beregne den normaliserede sekvens-tag densitet.
4. Fremgangsmåde ifølge krav 1, hvor: den abnorme fordeling er en aneuploidi af mindst et af kromosom 13, 18 og 21; eller den specificerede kromosomdel er en hvilken som helst af kromosomerne X, Y, 18, 21, 17 eller 13.
5. Fremgangsmåde ifølge krav 1 hvor trinnet at tildele sekvens-tags til tilsvarende kromosomdele tillader en fejlparring.
6. Fremgangsmåde ifølge krav 1 hvor sekvens-tags'ene erca. 25-100 bp i længden.
7. Fremgangsmåde ifølge krav 1 eller krav 6 hvor mindst 1 million sekvens-tags opnås.
8. Fremgangsmåde ifølge krav 6 endvidere omfattende trinnet at sammenligne en normaliseret sekvens-tag densitet af den specificerede kromosomdel med en normaliseret sekvens-tag densitet afen anden kromosomdel i den blandede prøve.
9. Fremgangsmåde ifølge krav 8 hvor trinnet at bestemme en forskel omfatter trinnet at sammenligne en normaliseret sekvens-tag densitet af den specificerede kromosomdel med en normaliseret sekvens-tag densitet af en anden kromosomdel i den blandede prøve, hvor alle autosomer anvendes til at beregne den normaliserede sekvens-tag densitet.
10. Fremgangsmåde ifølge krav 1 eller krav 9 yderligere omfattende trinnet at måle over- og under-repræsentation af et kromosom ved at bestemme en sekvens-tag densitet for hvert kromosom i prøven, nemlig kromosomer 1-22, X og også kromosom Y hvis det er til stede.
11. Fremgangsmåde ifølge krav 1 hvor: at bestemme en forskel omfatter et opnå en sekvens-tag densitet af det abnormt fordelte kromosom og sammenligne det med en værdi af et disomisk kromosom; og/eller vinduerne består af glidende ikke-overlappende vinduer af 10-100 kb der strækker sig i det væsentlige langs et helt kromosom; og/eller endvidere omfattende trinnet at måle et antal sekvens-tags inden for transkriptionelle startsteder.
12. Fremgangsmåde ifølge krav 1, omfattende: at bestemme antallet af sekvens-tags kortlagt til hvert vindue på mindst hvert autosom; at bestemme et gennemsnit af antallet af hvert autosom og et andet gennemsnit for mindst alle autosomer; at beregnet en normaliseret værdi fra alle autosomer, under anvendelse af det andet gennemsnit; og at sammenligne normaliserede værdier blandt autosomer til at bestemme en hvilken som helst interessant abnorm fordelt autosomal kromosomdel.
DK09815105.3T 2008-09-20 2009-09-16 Ikke-invasiv diagnose af føtal aneuploidi ved sekvensering DK2334812T3 (da)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US9875808P 2008-09-20 2008-09-20
PCT/US2009/057136 WO2010033578A2 (en) 2008-09-20 2009-09-16 Noninvasive diagnosis of fetal aneuploidy by sequencing

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DK12183946.8T DK2562268T3 (da) 2008-09-20 2009-09-16 Ikke-invasiv diagnose af føtal aneuploidi ved sekvensering

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US (9) US20100112575A1 (da)
EP (5) EP3378951B1 (da)
AU (1) AU2009293354B2 (da)
CA (4) CA3069081C (da)
CY (2) CY1118802T1 (da)
DK (2) DK2334812T3 (da)
ES (2) ES2620294T3 (da)
HK (1) HK1217354A1 (da)
HR (2) HRP20170437T1 (da)
HU (2) HUE031849T2 (da)
IL (2) IL211794A (da)
LT (2) LT2334812T (da)
PL (2) PL2334812T3 (da)
PT (2) PT2562268T (da)
SG (1) SG10201500567VA (da)
SI (2) SI2562268T1 (da)
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