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1. WO2020035446 - SYSTEMS AND METHODS FOR USING NEURAL NETWORKS FOR GERMLINE AND SOMATIC VARIANT CALLING

Publication Number WO/2020/035446
Publication Date 20.02.2020
International Application No. PCT/EP2019/071580
International Filing Date 12.08.2019
IPC
G16B 20/20 2019.1
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
20Allele or variant detection, e.g. single nucleotide polymorphism detection
G16B 40/20 2019.1
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
20Supervised data analysis
G16B 30/10 2019.1
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
10Sequence alignment; Homology search
CPC
G06N 3/08
GPHYSICS
06COMPUTING; CALCULATING; COUNTING
NCOMPUTER SYSTEMS BASED ON SPECIFIC COMPUTATIONAL MODELS
3Computer systems based on biological models
02using neural network models
08Learning methods
G16B 20/20
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16B 30/10
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
10Sequence alignment; Homology search
G16B 40/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G16B 40/20
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
20Supervised data analysis
Applicants
  • F. HOFFMANN-LA ROCHE AG [CH]/[CH] (AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BE, BF, BG, BH, BJ, BN, BR, BW, BY, BZ, CA, CF, CG, CH, CI, CL, CM, CN, CO, CR, CU, CY, CZ, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, FR, GA, GB, GD, GE, GH, GM, GN, GQ, GR, GT, GW, HN, HR, HU, ID, IE, IL, IN, IR, IS, IT, JO, JP, KE, KG, KH, KM, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LT, LU, LV, LY, MA, MC, MD, ME, MG, MK, ML, MN, MR, MT, MW, MX, MY, MZ, NA, NE, NG, NI, NL, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SI, SK, SL, SM, SN, ST, SV, SY, SZ, TD, TG, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, UZ, VC, VN, ZA, ZM, ZW)
  • ROCHE DIAGNOSTICS GMBH [DE]/[DE] (DE)
  • ROCHE SEQUENCING SOLUTIONS, INC. [US]/[US] (US)
Inventors
  • LAM, Hugo Y. K.
  • MOHIYUDDIN, Marghoob
  • SAHRAEIAN, Mohammad
Agents
  • FINALE, Christian Thierry
Priority Data
62/718,33813.08.2018US
62/855,54131.05.2019US
Publication Language English (en)
Filing Language English (EN)
Designated States
Title
(EN) SYSTEMS AND METHODS FOR USING NEURAL NETWORKS FOR GERMLINE AND SOMATIC VARIANT CALLING
(FR) SYSTÈMES ET PROCÉDÉS D'UTILISATION DE RÉSEAUX NEURONAUX POUR L'APPEL DE VARIANTS DE LIGNÉE GERMINALE ET SOMATIQUES
Abstract
(EN) The present disclosure provides systems and methods that utilize neural networks such as convolutional neural networks to analyze genomic sequence data generated by a sequencer and generate accurate prediction data identifying and describing germline and/or somatic variants within the sequence data.
(FR) La présente invention concerne des systèmes et des procédés qui utilisent des réseaux neuronaux tels que des réseaux neuronaux convolutionnels pour analyser des données de séquence génomique générées par un séquenceur et générer des données de prédiction précises identifiant et décrivant des variantes de lignée germinale et/ou somatiques dans les données de séquence.
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