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1. (WO2015048753) METHODS AND SYSTEM FOR DETECTING SEQUENCE VARIANTS
Latest bibliographic data on file with the International Bureau

Pub. No.: WO/2015/048753 International Application No.: PCT/US2014/058328
Publication Date: 02.04.2015 International Filing Date: 30.09.2014
IPC:
G06F 19/22 (2011.01) ,C12Q 1/68 (2006.01) ,C40B 40/06 (2006.01) ,C40B 60/12 (2006.01)
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
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
C CHEMISTRY; METALLURGY
40
COMBINATORIAL TECHNOLOGY
B
COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
40
Libraries per se, e.g. arrays, mixtures
04
Libraries containing only organic compounds
06
Libraries containing nucleotides or polynucleotides, or derivatives thereof
C CHEMISTRY; METALLURGY
40
COMBINATORIAL TECHNOLOGY
B
COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
60
Apparatus specially adapted for use in combinatorial chemistry or with libraries
12
for screening libraries
Applicants:
SEVEN BRIDGES GENOMICS INC. [US/US]; 1 Broadway 14th Floor Cambrige, MA, US
Inventors:
KURAL, Deniz; US
Agent:
MEYERS, Thomas C.; US
Priority Data:
14/041,85030.09.2013US
61/884,38030.09.2013US
Title (EN) METHODS AND SYSTEM FOR DETECTING SEQUENCE VARIANTS
(FR) PROCÉDÉS ET SYSTÈME DE DÉTECTION DE VARIANTES DE SÉQUENCES
Abstract:
(EN) The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.
(FR) L'invention concerne des procédés destinés à identifier des variantes rares à proximité d'une variation structurale dans une séquence génétique, par exemple dans un échantillon d'acide nucléique prélevé sur un sujet. L'invention comprend de plus des procédés destinés à aligner des relevés (par ex. des relevés d'acide nucléique) sur un constituant de séquence de référence prenant en compte la variation structurale, des procédés destinés à construire un constituant de séquence de référence prenant en compte la variation structurale ou la variation structurale et la variante rare, et des systèmes utilisant les procédés d'alignement pour identifier des variantes rares. Le procédé est extensible et peut être utilisé pour aligner des millions de relevés sur un constituant long de milliers de bases, voire plus long.
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, 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, KN, KP, KR, 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:
CA2925335SG11201602306SKR1020160062127CN105793859AU2014324438EP3053073
IN201637010582JP2016540275