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1. (WO2017136059) USING CELL-FREE DNA FRAGMENT SIZE TO DETERMINE COPY NUMBER VARIATIONS
Latest bibliographic data on file with the International Bureau

Pub. No.: WO/2017/136059 International Application No.: PCT/US2016/067886
Publication Date: 10.08.2017 International Filing Date: 20.12.2016
IPC:
C12Q 1/68 (2006.01) ,G06F 19/24 (2011.01) ,G06F 19/18 (2011.01) ,G06F 19/22 (2011.01) ,G06F 19/00 (2011.01)
C CHEMISTRY; METALLURGY
12
BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
Q
MEASURING OR TESTING PROCESSES INVOLVING ENZYMES OR MICRO-ORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
1
Measuring or testing processes involving enzymes or micro-organisms; Compositions therefor; Processes of preparing such compositions
68
involving nucleic acids
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
10
Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
24
for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
10
Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
18
for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
10
Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
22
for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
G PHYSICS
06
COMPUTING; CALCULATING; COUNTING
F
ELECTRIC DIGITAL DATA PROCESSING
19
Digital computing or data processing equipment or methods, specially adapted for specific applications
Applicants:
VERINATA HEALTH, INC. [US/US]; 5200 Illumina Way San Diego, California 92122, US
Inventors:
DUENWALD, Sven; US
COMSTOCK, David A.; US
BARBACIORU, Catalin; US
CHUDOVA, Darya I.,; US
RAVA, Richard P.; US
JONES, Keith W.; US
CHEN, Gengxin; US
SKVORTSOV, Dimitri; US
Agent:
ZHOU, Feng; US
WEAVER, Jeffrey K; US
AUSTIN, James E.; US
VILLENEUVE, Joseph M.; US
SAMPSON, Roger S.; US
BERGIN, Denise S.; US
GRIFFITH, John F.; US
SCHOLZ, Christian D.; US
Priority Data:
15/382,50816.12.2016US
62/290,89103.02.2016US
Title (EN) USING CELL-FREE DNA FRAGMENT SIZE TO DETERMINE COPY NUMBER VARIATIONS
(FR) UTILISATION DE LA TAILLE DE FRAGMENTS D'ADN ACELLULAIRE POUR DÉTERMINER LES VARIATIONS DU NOMBRE DE COPIES
Abstract:
(EN) Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter. In some implementations, information from fragments of different sizes are used to evaluate copy number variations. In some implementations, one or more t-statistics obtained from coverage information of the sequence of interest is used to evaluate copy number variations. In some implementations, one or more fetal fraction estimates are combined with one or more t-statistics to determine copy number variations.
(FR) La présente invention concerne des procédés permettant de déterminer la variation du nombre de copies (VNC) que l'on sait ou que l'on soupçonne être associée à diverses affections médicales. Selon certains modes de réalisation, l'invention concerne des procédés destinés à la détermination de la variation du nombre de copies de fœtus au moyen d'échantillons maternels comprenant l'ADN acellulaire fœtal et maternel. Selon certains modes de réalisation, l'invention concerne des procédés permettant de déterminer des VNC que l'on sait ou que l'on soupçonne être associées à diverses affections médicales. Certains modes de réalisation de l'invention concernent des procédés permettant d'améliorer la sensibilité et/ou la spécificité de l'analyse de données de séquences en dérivant un paramètre de taille de fragments. Dans certaines mises en oeuvre, des informations de fragments de tailles différentes sont utilisées pour évaluer des variations du nombre de copies. Dans certaines mises en oeuvre, une ou plusieurs statistiques t obtenues à partir des informations de couverture de la séquence d'intérêt sont utilisées pour évaluer des variations du nombre de copies. Dans certaines mises en oeuvre, une ou plusieurs estimations de la fraction foetale sont combinées avec une ou plusieurs statistiques t pour déterminer des variations du nombre de copies.
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Designated States: AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW
African Regional Intellectual Property Organization (ARIPO) (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW)
Eurasian Patent Organization (AM, AZ, BY, KG, KZ, RU, TJ, TM)
European Patent Office (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR)
African Intellectual Property Organization (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG)
Publication Language: English (EN)
Filing Language: English (EN)
Also published as:
UAa201809058CA3013572AU2016391100SG11201806595UKR1020180123020CN108884491
IL260938IN201817032050EA201891580BR112018015913