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1. (WO2018068014) SYSTEM AND METHOD FOR SECONDARY ANALYSIS OF NUCLEOTIDE SEQUENCING DATA
Latest bibliographic data on file with the International BureauSubmit observation

Pub. No.: WO/2018/068014 International Application No.: PCT/US2017/055653
Publication Date: 12.04.2018 International Filing Date: 06.10.2017
IPC:
G06F 19/18 (2011.01) ,G06F 19/22 (2011.01)
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
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
Applicants:
ILLUMINA, INC. [US/US]; 5200 Illumina Way San Diego, CA 92122, US
Inventors:
GARCIA, Francisco, Jose; US
RACZY, Come; US
DAY, Aaron; US
CARNEY, Michael, J.; US
Agent:
FULLER, Michael, L.; US
Priority Data:
62/405,82407.10.2016US
Title (EN) SYSTEM AND METHOD FOR SECONDARY ANALYSIS OF NUCLEOTIDE SEQUENCING DATA
(FR) SYSTÈME ET PROCÉDÉ D'ANALYSE SECONDAIRE DE DONNÉES DE SÉQUENÇAGE DE NUCLÉOTIDES
Abstract:
(EN) Disclosed herein are systems and methods for performing secondary analyses of nucleotide sequencing data in a time-efficient manner. Some embodiments include performing a secondary analysis iteratively while sequence reads are generated by a sequencing system. Secondary analyses can encompass both alignment of sequence reads to a reference sequence (e.g., the human reference genome sequence) and utilization of this alignment to detect differences between a sample and the reference. Secondary analysis can enable detection of genetic differences, variant detection and genotyping, identification of single nucleotide polymorphisms (SNPs), small insertions and deletion (indels) and structural changes in the DNA, such as copy number variants (CNVs) and chromosomal rearrangements.
(FR) L'invention concerne des systèmes et des procédés permettant d'effectuer des analyses secondaires de données de séquençage de nucléotides d'une manière efficace et rapide. Certains modes de réalisation consistent à effectuer une analyse secondaire de manière itérative tandis que des lectures de séquence sont générées par un système de séquençage. Des analyses secondaires peuvent englober à la fois l'alignement de lectures de séquence avec une séquence de référence (par exemple, la séquence du génome de référence humain) et l'utilisation de cet alignement pour détecter des différences entre un échantillon et la référence. L'analyse secondaire peut permettre la détection de différences génétiques, la détection de variantes et le génotypage, l'identification de polymorphismes mononucléotidiques (SNP), des petites insertions et délétions (indels) et des modifications structurales dans l'ADN, telles que des variantes du nombre de copies (CNV) et des réarrangements chromosomiques.
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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, 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 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:
AU2017341069CA3027179SG11201810924WKR1020190017825CN109416927EP3458993
IN201917000806BR112018076983