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1. (WO2016057902) METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR CALCULATING CORRECTED AMPLICON COVERAGES
Latest bibliographic data on file with the International Bureau   

Pub. No.: WO/2016/057902 International Application No.: PCT/US2015/054910
Publication Date: 14.04.2016 International Filing Date: 09.10.2015
IPC:
G06F 19/18 (2011.01) ,G06F 19/20 (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
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
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: LIFE TECHNOLOGIES CORPORATION[US/US]; 5791 Van Allen Way Carlsbad, CA 92008, US
Inventors: VEITCH, James; US
ZHAN, Yiping; US
Priority Data:
62/062,31210.10.2014US
Title (EN) METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR CALCULATING CORRECTED AMPLICON COVERAGES
(FR) PROCÉDÉS, SYSTÈMES ET SUPPORTS LISIBLES PAR ORDINATEUR POUR CALCULER DES COUVERTURES D'AMPLICON CORRIGÉES
Abstract:
(EN) Methods, systems, and computer-readable media are disclosed for calculating corrected amplicon coverages. One method includes: mapping a plurality of reads of a plurality of amplicons based on amplified target regions of a sample suspected of having one or more genetic abnormalities to a reference sequence that includes one or more nucleic acid sequences corresponding to the amplified target regions; calculating amplicon coverages and total reads, wherein amplicon coverages is a number of reads mapped to an amplicon, and total reads is a number of mapped reads; and calculating corrected amplicon coverages based on the calculated amplicon coverages and calculated total reads by applying a batch effect correction.
(FR) L'invention concerne des procédés, des systèmes et des supports lisibles par ordinateur pour calculer des couvertures d'amplicon corrigées. Un procédé consiste à : mapper une pluralité de lectures d'une pluralité d'amplicons sur la base de régions cibles amplifiées d'un échantillon suspecté d'avoir une ou plusieurs anomalies génétiques sur une séquence de référence qui comprend une ou plusieurs séquences d'acides nucléiques correspondant aux régions cibles amplifiées; calculer des couvertures d'amplicon et des lectures totales, les couvertures d'amplicon constituant un nombre de lectures mappées sur un amplicon, et les lectures totales étant un nombre de lectures mappées; et calculer des couvertures d'amplicon corrigées sur la base des couvertures d'amplicon calculées et des lectures totales calculées par application d'une correction d'effet discontinu.
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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 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)