CA3215514A1 - Voxelisation de proteine a canaux multiples pour predire une pathogenicite d'un variant a l'aide de reseaux neuronaux convolutifs profonds - Google Patents

Voxelisation de proteine a canaux multiples pour predire une pathogenicite d'un variant a l'aide de reseaux neuronaux convolutifs profonds Download PDF

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CA3215514A1
CA3215514A1 CA3215514A CA3215514A CA3215514A1 CA 3215514 A1 CA3215514 A1 CA 3215514A1 CA 3215514 A CA3215514 A CA 3215514A CA 3215514 A CA3215514 A CA 3215514A CA 3215514 A1 CA3215514 A1 CA 3215514A1
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amino acid
voxel
channels
atom
voxels
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CA3215514A
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Tobias HAMP
Hong Gao
Kai-How FARH
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Illumina Cambridge Ltd
Illumina Inc
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Illumina Cambridge Ltd
Illumina Inc
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Priority claimed from US17/703,935 external-priority patent/US12444482B2/en
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Publication of CA3215514A1 publication Critical patent/CA3215514A1/fr
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    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
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    • G06N3/02—Neural networks
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    • G06N3/044—Recurrent networks, e.g. Hopfield networks
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    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/08—Learning methods
    • G06N3/084—Backpropagation, e.g. using gradient descent

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Abstract

Un système comprend au moins un dispositif de voxelisation, un codeur d'allèle de substitution, un codeur de conservation évolutive et un réseau neuronal convolutif. Le dispositif de voxelisation accède à une structure tridimensionnelle d'une séquence d'acides aminés de référence d'une protéine et s'adapte à une grille tridimensionnelle de voxels sur des atomes dans la structure tridimensionnelle sur une base d'acides aminés en vue de générer des canaux de distance en acides aminés. Le codeur d'allèle de substitution code une séquence d'allèle de substitution pour chaque voxel dans la grille tridimensionnelle de voxels. Le codeur de conservation évolutive code une séquence de conservation évolutive pour chaque voxel dans la grille tridimensionnelle de voxels. Le réseau neuronal convolutif applique des convolutions tridimensionnelles à un tenseur qui comprend les canaux de distance en acides aminés codés avec la séquence d'allèle de substitution et des séquences de conservation évolutive respectives et détermine une pathogénicité d'un variant de nucléotide sur la base, au moins en partie, du tenseur.
CA3215514A 2021-04-15 2022-04-14 Voxelisation de proteine a canaux multiples pour predire une pathogenicite d'un variant a l'aide de reseaux neuronaux convolutifs profonds Pending CA3215514A1 (fr)

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US202163175495P 2021-04-15 2021-04-15
US63/175,495 2021-04-15
US202163175767P 2021-04-16 2021-04-16
US63/175,767 2021-04-16
US17/703,935 2022-03-24
US17/703,935 US12444482B2 (en) 2021-04-15 2022-03-24 Multi-channel protein voxelization to predict variant pathogenicity using deep convolutional neural networks
US17/703,958 US20220336057A1 (en) 2021-04-15 2022-03-24 Efficient voxelization for deep learning
US17/703,958 2022-03-24
PCT/US2022/024916 WO2022221591A1 (fr) 2021-04-15 2022-04-14 Voxelisation de protéine à canaux multiples pour prédire une pathogénicité d'un variant à l'aide de réseaux neuronaux convolutifs profonds

Publications (1)

Publication Number Publication Date
CA3215514A1 true CA3215514A1 (fr) 2022-10-20

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Family Applications (2)

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CA3215520A Pending CA3215520A1 (fr) 2021-04-15 2022-04-14 Voxelisation efficace pour apprentissage en profondeur
CA3215514A Pending CA3215514A1 (fr) 2021-04-15 2022-04-14 Voxelisation de proteine a canaux multiples pour predire une pathogenicite d'un variant a l'aide de reseaux neuronaux convolutifs profonds

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CA3215520A Pending CA3215520A1 (fr) 2021-04-15 2022-04-14 Voxelisation efficace pour apprentissage en profondeur

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EP (2) EP4323991A1 (fr)
JP (2) JP2024514894A (fr)
KR (2) KR20230170680A (fr)
AU (2) AU2022258691A1 (fr)
BR (2) BR112023021266A2 (fr)
CA (2) CA3215520A1 (fr)
IL (2) IL307661A (fr)
MX (2) MX2023012227A (fr)
WO (2) WO2022221593A1 (fr)
ZA (1) ZA202309343B (fr)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4323990A1 (fr) * 2021-04-15 2024-02-21 Illumina, Inc. Réseaux neuronaux convolutifs profonds pour prédire une pathogénicité d'un variant à l'aide de structures protéiques tridimensionnelles (3d)
CN117178327A (zh) * 2021-04-15 2023-12-05 因美纳有限公司 使用深度卷积神经网络来预测变体致病性的多通道蛋白质体素化
CN116153404B (zh) * 2023-02-28 2023-08-15 成都信息工程大学 一种单细胞ATAC-seq数据分析方法

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
WO2019084559A1 (fr) * 2017-10-27 2019-05-02 Apostle, Inc. Prédiction d'impact pathogène lié au cancer de mutations somatiques à l'aide de procédés basés sur un apprentissage profond
CN110245685B (zh) * 2019-05-15 2022-03-25 清华大学 基因组单位点变异致病性的预测方法、系统及存储介质

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Publication number Publication date
AU2022258691A1 (en) 2023-10-26
CA3215520A1 (fr) 2022-10-20
EP4323989A1 (fr) 2024-02-21
MX2023012227A (es) 2024-01-08
WO2022221593A1 (fr) 2022-10-20
KR20230170680A (ko) 2023-12-19
BR112023021266A2 (pt) 2023-12-12
EP4323991A1 (fr) 2024-02-21
MX2023012226A (es) 2024-01-08
BR112023021343A2 (pt) 2023-12-19
KR20230170679A (ko) 2023-12-19
JP2024514894A (ja) 2024-04-03
AU2022259667A1 (en) 2023-10-26
WO2022221591A1 (fr) 2022-10-20
IL307661A (en) 2023-12-01
ZA202309343B (en) 2025-07-30
JP2024513995A (ja) 2024-03-27
IL307667A (en) 2023-12-01

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