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1. (WO2017147702) SYSTEM AND PROCESS FOR DATA-DRIVEN DESIGN, SYNTHESIS, AND APPLICATION OF MOLECULAR PROBES
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Pub. No.: WO/2017/147702 International Application No.: PCT/CA2017/050273
Publication Date: 08.09.2017 International Filing Date: 01.03.2017
IPC:
C07H 21/00 (2006.01) ,C07H 21/04 (2006.01) ,C12N 15/10 (2006.01) ,C12Q 1/68 (2006.01) ,C40B 30/04 (2006.01) ,G06F 19/10 (2011.01) ,G06F 19/20 (2011.01)
C CHEMISTRY; METALLURGY
07
ORGANIC CHEMISTRY
H
SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
21
Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
C CHEMISTRY; METALLURGY
07
ORGANIC CHEMISTRY
H
SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
21
Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
04
with deoxyribosyl as saccharide radical
C CHEMISTRY; METALLURGY
12
BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
N
MICRO-ORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICRO-ORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
15
Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
09
Recombinant DNA-technology
10
Processes for the isolation, preparation or purification of DNA or RNA
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
30
Methods of screening libraries
04
by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
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
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
20
for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
Applicants:
FUSION GENOMICS CORPORATION; Discovery 1, 1450 Simon Fraser University 8888 University Drive Burnaby, British Columbia V5A 1S6, CA
Inventors:
ZHAN, Shing H.; CA
KWOK, Brian S.; CA
QADIR, Mohammad A.; CA
Agent:
VANGUARD IP LLP; 101-1001 West Broadway Suite 674 Vancouver, British Columbia, V6H 4E4, CA
Priority Data:
62/302,07801.03.2016US
Title (EN) SYSTEM AND PROCESS FOR DATA-DRIVEN DESIGN, SYNTHESIS, AND APPLICATION OF MOLECULAR PROBES
(FR) SYSTÈME ET PROCÉDÉ POUR UNE CONCEPTION ET UNE SYNTHÈSE GUIDÉES PAR LES DONNÉES ET APPLICATION DE SONDES MOLÉCULAIRES
Abstract:
(EN) The disclosure provides methods and systems for designing and synthesizing probes to capture a representative sample of genomic variants of a target genome from a sample. The methods include providing a multiple sequence alignment (MSA), designing a plurality of representative subsequences, and optionally synthesizing a nucleic acid probe. The designing step can comprise designating a plurality of intervals in the MSA, shifting start positions for each MSA subset, clustering the aligned subsequences within each adjusted subset, and determining a representative sequence for each reduced MSA subset. The disclosure also encompasses methods of isolating a plurality of nucleic acid variants of a targeted genomic subregion from a sample using the disclosed probe design, as well as the probe compositions themselves.
(FR) L'invention concerne des procédés et des systèmes pour concevoir et synthétiser des sondes pour capturer un échantillon représentatif de variants génomiques d'un génome cible à partir d'un échantillon. Les procédés comprennent l'utilisation d'un alignement de séquences multiples (ASM), la conception d'une pluralité de sous-séquences représentatives et, éventuellement, la synthèse d'une sonde d'acide nucléique. L'étape de conception peut comprendre la conception d'une pluralité d'intervalles dans l'ASM, le décalage des positions de départ pour chaque sous-ensemble d'ASM, le groupement des sous-séquences alignées dans chaque sous-ensemble ajusté et la détermination d'une séquence représentative pour chaque sous-ensemble d'ASM réduit. L'invention concerne également des procédés pour isoler une pluralité de variants d'acide nucléique d'une sous-région génomique ciblée à partir d'un échantillon à l'aide de la conception de sonde divulguée ainsi que les compositions de sondes elles-mêmes.
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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 Office (AM, AZ, BY, KG, KZ, RU, TJ, TM)
European Patent Office (EPO) (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)