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1. WO2010033578 - NONINVASIVE DIAGNOSIS OF FETAL ANEUPLOIDY BY SEQUENCING

Publication Number WO/2010/033578
Publication Date 25.03.2010
International Application No. PCT/US2009/057136
International Filing Date 16.09.2009
IPC
C12Q 1/68 2006.1
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING 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
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
G01N 33/48 2006.1
GPHYSICS
01MEASURING; TESTING
NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
33Investigating or analysing materials by specific methods not covered by groups G01N1/-G01N31/131
48Biological material, e.g. blood, urine; Haemocytometers
CPC
C12Q 1/6869
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms
68involving nucleic acids
6869Methods for sequencing
C12Q 1/6883
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms
68involving nucleic acids
6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
6883for diseases caused by alterations of genetic material
C12Q 2600/156
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
2600Oligonucleotides characterized by their use
156Polymorphic or mutational markers
G01N 2800/387
GPHYSICS
01MEASURING; TESTING
NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
2800Detection or diagnosis of diseases
38Pediatrics
385Congenital anomalies
387Down syndrome; Trisomy 18; Trisomy 13
G01N 33/48
GPHYSICS
01MEASURING; TESTING
NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
33Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
48Biological material, e.g. blood, urine
Applicants
  • THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY [US]/[US] (AllExceptUS)
  • FAN, Hei-Mun, Christina [CN]/[US] (UsOnly)
  • QUAKE, Stephen, R. [US]/[US] (UsOnly)
Inventors
  • FAN, Hei-Mun, Christina
  • QUAKE, Stephen, R.
Agents
  • ASTON, David, J.
Priority Data
61/098,75820.09.2008US
Publication Language English (en)
Filing Language English (EN)
Designated States
Title
(EN) NONINVASIVE DIAGNOSIS OF FETAL ANEUPLOIDY BY SEQUENCING
(FR) DIAGNOSTIC NON EFFRACTIF D'ANEUPLOÏDIE FOETALE PAR SEQUENÇAGE
Abstract
(EN) Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under- representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.
(FR) L'invention concerne une méthode permettant d'obtenir une quantification numérique d'ADN (par exemple de compter les différences entre des séquences identiques) par un séquençage à l'aveugle direct suivi d'une cartographie du chromosome d'origine et de l'énumération de fragments par chromosome. La méthode préférée selon l'invention met en oeuvre un séquençage massivement parallèle apte à produire des dizaines de millions d'étiquettes de séquences courtes dans un passage unique et à permettre d'obtenir un prélèvement pouvant être évalué statistiquement. Par comptage du nombre d'étiquettes de séquences cartographiées sur une fenêtre prédéfinie dans chaque chromosome, la sur-représentation ou la sous-représentation de n'importe quel chromosome dans l'ADN plasmatique maternel induite par un foetus aneuploïde peut être détectée. Cette méthode ne nécessite pas d'effectuer la différenciation de l'ADN foetal de l'ADN maternel. Le dénombrement médian de valeurs autosomiques sert de constante de normalisation pour représenter les différences dans le nombre total d'étiquettes de séquences et pour comparer des prélèvements et des chromosomes.
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