CA2894317C - Systemes et methodes de classement, priorisation et interpretation de variants genetiques et therapies employant un reseau neuronal profond - Google Patents

Systemes et methodes de classement, priorisation et interpretation de variants genetiques et therapies employant un reseau neuronal profond Download PDF

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CA2894317C
CA2894317C CA2894317A CA2894317A CA2894317C CA 2894317 C CA2894317 C CA 2894317C CA 2894317 A CA2894317 A CA 2894317A CA 2894317 A CA2894317 A CA 2894317A CA 2894317 C CA2894317 C CA 2894317C
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Brendan Frey
Michael K.K. Leung
Andrew Thomas Delong
Hui Yuan XIONG
Babak Alipanahi
Leo J. Lee
Hannes Bretschneider
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    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
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    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/20—Probabilistic models

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Abstract

Il est décrit des systèmes et procédés qui reçoivent, comme entrée, une séquence dacide désoxyribonucléique (ADN) ou dacide ribonucléique, extraient des caractéristiques, et appliquent des couches dunités de traitement afin de calculer au moins une variable de cellule propre à une condition, correspondant à des quantités cellulaires mesurées dans différentes conditions. Le système pourrait sappliquer à une séquence contenant une variante génétique, ainsi quà une séquence de référence correspondante, afin de déterminer jusquà quel point les variables de cellule propres à une condition changent en raison de la variante. Le changement dans les variables de cellule propres à une condition est utilisé pour calculer un score représentant jusquà quel point la variante est nuisible, pour classer le niveau de caractère nuisible dune variante, pour établir des variantes aux fins de traitement subséquent, et pour comparer une variante de test à des variantes délétères connues. En modifiant la variante ou les caractéristiques extraites pour intégrer les effets de modification dADN, de thérapie doligonucléotide, de thérapie de liaison de protéine dADN ou dacide ribonucléique, ou dautres thérapies, le système peut être utilisé pour déterminer sil est possible de réduire les effets nuisibles de la variante originale.
CA2894317A 2015-06-15 2015-06-15 Systemes et methodes de classement, priorisation et interpretation de variants genetiques et therapies employant un reseau neuronal profond Active CA2894317C (fr)

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Families Citing this family (37)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
BR112019009949A2 (pt) 2016-11-16 2019-08-20 Illumina, Inc. método implantado por computador para validar chamadas de variante e sistema para validar chamadas de variante
CN108229523B (zh) * 2017-04-13 2021-04-06 深圳市商汤科技有限公司 图像检测、神经网络训练方法、装置和电子设备
US12165065B2 (en) * 2017-08-18 2024-12-10 Intel Corporation Efficient neural networks with elaborate matrix structures in machine learning environments
CN110832596B (zh) * 2017-10-16 2021-03-26 因美纳有限公司 基于深度学习的深度卷积神经网络训练方法
WO2019079202A1 (fr) 2017-10-16 2019-04-25 Illumina, Inc. Détection de raccordement aberrant à l'aide de réseaux neuronaux à convolution (cnn)
US11861491B2 (en) 2017-10-16 2024-01-02 Illumina, Inc. Deep learning-based pathogenicity classifier for promoter single nucleotide variants (pSNVs)
US11378544B2 (en) 2018-01-08 2022-07-05 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
KR102239487B1 (ko) 2018-01-08 2021-04-14 일루미나, 인코포레이티드 반도체-기반 검출을 사용한 고-처리율 서열분석
CA3065939A1 (fr) * 2018-01-15 2019-07-18 Illumina, Inc. Classificateur de variants base sur un apprentissage profond
CN108680861B (zh) * 2018-03-05 2021-01-01 北京航空航天大学 锂电池剩余循环寿命预测模型的构建方法及装置
CN110362807A (zh) * 2018-03-26 2019-10-22 中国科学院信息工程研究所 基于自编码器的变体词识别方法及系统
NL2020861B1 (en) * 2018-04-12 2019-10-22 Illumina Inc Variant classifier based on deep neural networks
US20190318806A1 (en) * 2018-04-12 2019-10-17 Illumina, Inc. Variant Classifier Based on Deep Neural Networks
WO2019222120A1 (fr) * 2018-05-14 2019-11-21 Quantum-Si Incorporated Ensemble polymère biologique activé par apprentissage automatique
US11482305B2 (en) 2018-08-18 2022-10-25 Synkrino Biotherapeutics, Inc. Artificial intelligence analysis of RNA transcriptome for drug discovery
US11443832B2 (en) * 2019-03-07 2022-09-13 Nvidia Corporation Genetic mutation detection using deep learning
US11842794B2 (en) 2019-03-19 2023-12-12 The University Of Hong Kong Variant calling in single molecule sequencing using a convolutional neural network
US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
US11783917B2 (en) 2019-03-21 2023-10-10 Illumina, Inc. Artificial intelligence-based base calling
US11423306B2 (en) 2019-05-16 2022-08-23 Illumina, Inc. Systems and devices for characterization and performance analysis of pixel-based sequencing
US11593649B2 (en) 2019-05-16 2023-02-28 Illumina, Inc. Base calling using convolutions
CN121034400A (zh) 2020-02-20 2025-11-28 因美纳有限公司 基于人工智能的多对多碱基判读
US12592298B2 (en) 2020-02-20 2026-03-31 Illumina, Inc. Hardware execution and acceleration of artificial intelligence-based base caller
US12354008B2 (en) 2020-02-20 2025-07-08 Illumina, Inc. Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
US12591780B2 (en) 2020-02-20 2026-03-31 Illumina, Inc. Data compression for artificial intelligence-based base calling
US11830606B2 (en) * 2020-04-28 2023-11-28 Siemens Healthcare Gmbh Risk prediction for COVID-19 patient management
CN113810335B (zh) * 2020-06-12 2023-08-22 武汉斗鱼鱼乐网络科技有限公司 一种识别目标ip的方法及系统、存储介质、设备
CN112017771B (zh) * 2020-08-31 2024-02-27 吾征智能技术(北京)有限公司 一种基于精液常规检查数据的疾病预测模型的构建方法及系统
US12525320B2 (en) 2021-03-16 2026-01-13 Illumina, Inc. Neural network parameter quantization for base calling
US12217829B2 (en) 2021-04-15 2025-02-04 Illumina, Inc. Artificial intelligence-based analysis of protein three-dimensional (3D) structures
US12444482B2 (en) 2021-04-15 2025-10-14 Illumina, Inc. Multi-channel protein voxelization to predict variant pathogenicity using deep convolutional neural networks
US12100486B2 (en) * 2021-05-14 2024-09-24 International Business Machines Corporation Identification of unknown genomes and closest known genomes
US12530882B2 (en) 2021-07-01 2026-01-20 Illumina, Inc. Efficient artificial intelligence-based base calling of index sequences
CN114360652B (zh) * 2022-01-28 2023-04-28 深圳太力生物技术有限责任公司 细胞株相似性评价方法及相似细胞株培养基配方推荐方法
CN116798521B (zh) * 2023-07-19 2024-02-23 广东美赛尔细胞生物科技有限公司 免疫细胞培养控制系统的异常监测方法及系统
CN119719955B (zh) * 2024-12-17 2025-09-05 四川大学华西医院 一种基于贝叶斯模型的证据优化方法、装置、计算机设备及存储介质
CN120809106B (zh) * 2025-09-16 2025-12-02 成都市第三人民医院 一种全膝关节置换术需求预测方法及系统

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