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1. (WO2017138984) SYSTEMS, METHODS, AND MEDIA FOR DE NOVO ASSEMBLY OF WHOLE GENOME SEQUENCE DATA
Latest bibliographic data on file with the International Bureau

Pub. No.: WO/2017/138984 International Application No.: PCT/US2016/047899
Publication Date: 17.08.2017 International Filing Date: 19.08.2016
IPC:
C12Q 1/68 (2006.01) ,C12P 19/34 (2006.01) ,C04B 40/06 (2006.01) ,C40B 50/16 (2006.01) ,G01N 33/68 (2006.01)
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
C CHEMISTRY; METALLURGY
12
BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
P
FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
19
Preparation of compounds containing saccharide radicals
26
Preparation of nitrogen-containing carbohydrates
28
N-glycosides
30
Nucleotides
34
Polynucleotides, e.g. nucleic acids, oligoribonucleotides
C CHEMISTRY; METALLURGY
04
CEMENTS; CONCRETE; ARTIFICIAL STONE; CERAMICS; REFRACTORIES
B
LIME; MAGNESIA; SLAG; CEMENTS; COMPOSITIONS THEREOF, e.g. MORTARS, CONCRETE OR LIKE BUILDING MATERIALS; ARTIFICIAL STONE; CERAMICS; REFRACTORIES; TREATMENT OF NATURAL STONE
40
Processes, in general, for influencing or modifying the properties of mortars, concrete or artificial stone compositions, e.g. their setting or hardening ability
06
Inhibiting the setting, e.g. mortars of the deferred action type containing water in breakable containers
C CHEMISTRY; METALLURGY
40
COMBINATORIAL TECHNOLOGY
B
COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
50
Methods of creating libraries, e.g. combinatorial synthesis
14
Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
16
involving encoding steps
G PHYSICS
01
MEASURING; TESTING
N
INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
33
Investigating or analysing materials by specific methods not covered by groups G01N1/-G01N31/131
48
Biological material, e.g. blood, urine; Haemocytometers
50
Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
68
involving proteins, peptides or amino acids
Applicants:
10X GENOMICS, INC. [US/US]; 7068 Koll Center Parkway, Suite 401 Pleasanton, CA 94566, US
Inventors:
JAFFE, David; US
MARKS, Patrick; US
SCHNALL-LEVIN, Michael; US
WEISENFELD, Neil; US
Agent:
LAM, Amy; US
AGRAWAL, Trisha; US
ADVANI, Raj; US
ALEMOZAFAR, Ali; US
ANDERSON, Garrett; US
Priority Data:
62/294,18411.02.2016US
62/332,91406.05.2016US
Title (EN) SYSTEMS, METHODS, AND MEDIA FOR DE NOVO ASSEMBLY OF WHOLE GENOME SEQUENCE DATA
(FR) SYSTÈMES, PROCÉDÉS, ET MILIEUX DESTINÉS À L’ASSEMBLAGE DE NOVO DE DONNÉES DE SÉQUENCE DU GÉNOME ENTIER
Abstract:
(EN) Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.
(FR) La présente invention décrit des procédés informatisés, des systèmes, et des milieux pour ensemble diploïde en phase de novo de données de séquence d’acides nucléiques générées à partir d’un échantillon d’acide nucléique d’un individu utilisant des étiquettes d’acide nucléique pour conserver le contexte de séquence à long rayon d'action pour l’individu de sorte qu’un sous-ensemble de données de séquence de lecture courte dérivées d’une séquence de départ commune partage une étiquette commune. L’ensemble diploïde en phase est obtenu sans alignement sur une séquence de référence dérivée d'organismes autres que l’individu. Les procédés, les systèmes et les milieux décrits sont efficaces en termes de ressources informatiques, permettant la mise à l’échelle.
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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, 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:
SG11201806757XCN108779491EP3414341