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1. (WO2019047181) METHOD FOR GENOTYPING ON THE BASIS OF LOW-DEPTH GENOME SEQUENCING, DEVICE AND USE
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Pub. No.: WO/2019/047181 International Application No.: PCT/CN2017/101128
Publication Date: 14.03.2019 International Filing Date: 08.09.2017
IPC:
C12Q 1/68 (2018.01) ,G06F 19/20 (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
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:
深圳华大生命科学研究院 BGI SHENZHEN [CN/CN]; 中国广东省深圳市 盐田区北山工业区综合楼 Mainbuilding, Beishan Industrial Zone, Yantian District Shenzhen, Guangdong 518083, CN
Inventors:
郭瑞东 GUO, Ruidong; CN
贾超 JIA, Chao; CN
Agent:
北京清亦华知识产权代理事务所(普通合伙) TSINGYIHUA INTELLECTUAL PROPERTY LLC; 中国北京市 海淀区清华园清华大学照澜院商业楼301室 Room 301 Trade Building Zhaolanyuan, Tsinghua University Qinghuayuan, Haidian District Beijing 100084, CN
Priority Data:
Title (EN) METHOD FOR GENOTYPING ON THE BASIS OF LOW-DEPTH GENOME SEQUENCING, DEVICE AND USE
(FR) PROCÉDÉ DE GÉNOTYPAGE SUR LA BASE DE SÉQUENÇAGE DE GÉNOME À FAIBLE PROFONDEUR, DISPOSITIF ET UTILISATION
(ZH) 基于低深度基因组测序进行基因分型的方法、装置及其用途
Abstract:
(EN) Provided is a method for genotyping on the basis of low-depth genome sequencing. The method comprises: (a) performing low-depth genome sequencing on the whole genome of a sample to be tested in order to obtain a sequencing result consisting of a plurality of sequencing data; (b) for at least one known variant site, constructing a reference sequence set of the known variant site, the reference sequence set comprising the variant type of the known variant site, and upstream and downstream sequences of the variant site; (c) comparing the sequencing result obtained in step (a) with the reference sequence set so as to determine a comparison result for each known variant site, the comparison result comprising a matching variant type of the sequencing result and the number of matches of the matching variant type; and (d) determining a high-probability variant type of the known variation site on the basis of the comparison result.
(FR) La présente invention concerne le génotypage sur la base du séquençage de génome à faible profondeur. Le procédé comprend : (a) l’exécution du séquençage de génome à faible profondeur sur le génome entier d’un échantillon à tester afin d’obtenir un résultat de séquençage constitué d’une pluralité de données de séquençage ; (b) pour au moins un site variant connu, la construction d’un ensemble de séquences de référence du site variant connu, l’ensemble de séquences de référence comprenant le type variant du site variant connu, et les séquences en amont et en aval du site variant ; (c) la comparaison du résultat de séquençage obtenu dans l’étape (a) à l’ensemble de séquences de référence afin de déterminer un résultat de comparaison pour chaque site variant connu, le résultat de comparaison comprenant un type variant correspondant du résultat de séquençage et le nombre de correspondances du type variant correspondant ; et (d) la détermination d’un type variant de probabilité élevée du site de variation connu sur la base du résultat de comparaison.
(ZH) 提供了一种基于低深度基因组测序进行基因分型的方法。其中,该方法包括:(a)对待测样本全基因组进行低深度基因组测序,以便获得由多个测序数据构成的测序结果;(b)针对至少一个已知变异位点,构建所述已知变异位点的参考序列集,所述参考序列集含有所述已知变异位点的变异类型以及所述变异位点的上下游序列;(c)将步骤(a)中所得到的所述测序结果与所述参考序列集进行比对,以便确定各已知变异位点的比对结果,所述比对结果包括测序结果的匹配变异类型以及所述匹配变异类型的匹配次数;以及(d)基于所述比对结果,确定所述已知变异位点的高概率变异类型。
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, JO, 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: Chinese (ZH)
Filing Language: Chinese (ZH)