CA3184399A1 - Variant pathogenicity scoring and classification and uses thereof - Google Patents

Variant pathogenicity scoring and classification and uses thereof

Info

Publication number
CA3184399A1
CA3184399A1 CA3184399A CA3184399A CA3184399A1 CA 3184399 A1 CA3184399 A1 CA 3184399A1 CA 3184399 A CA3184399 A CA 3184399A CA 3184399 A CA3184399 A CA 3184399A CA 3184399 A1 CA3184399 A1 CA 3184399A1
Authority
CA
Canada
Prior art keywords
pathogenicity
gene
variant
variants
depletion
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
CA3184399A
Other languages
English (en)
French (fr)
Inventor
Hong Gao
Kai-How FARH
Jeremy Francis Mcrae
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Illumina Inc
Original Assignee
Illumina Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of CA3184399A1 publication Critical patent/CA3184399A1/en
Pending legal-status Critical Current

Links

Classifications

    • 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
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/28—Databases characterised by their database models, e.g. relational or object models
    • G06F16/284—Relational databases
    • G06F16/285—Clustering or classification
    • G—PHYSICS
    • 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
    • G—PHYSICS
    • 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
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/044—Recurrent networks, e.g. Hopfield networks
    • G—PHYSICS
    • 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
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/0464—Convolutional networks [CNN, ConvNet]
    • 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
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Biology (AREA)
  • Evolutionary Computation (AREA)
  • Software Systems (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Molecular Biology (AREA)
  • General Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Computational Linguistics (AREA)
  • Computing Systems (AREA)
  • Mathematical Physics (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Public Health (AREA)
  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Epidemiology (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Medical Treatment And Welfare Office Work (AREA)
CA3184399A 2020-07-23 2021-07-21 Variant pathogenicity scoring and classification and uses thereof Pending CA3184399A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202063055724P 2020-07-23 2020-07-23
US63/055,724 2020-07-23
PCT/US2021/042599 WO2022020487A1 (en) 2020-07-23 2021-07-21 Variant pathogenicity scoring and classification and uses thereof

Publications (1)

Publication Number Publication Date
CA3184399A1 true CA3184399A1 (en) 2022-01-27

Family

ID=77265352

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3184399A Pending CA3184399A1 (en) 2020-07-23 2021-07-21 Variant pathogenicity scoring and classification and uses thereof

Country Status (9)

Country Link
US (1) US20220027388A1 (https=)
EP (1) EP4186061A1 (https=)
JP (1) JP2023534616A (https=)
KR (1) KR20230043072A (https=)
CN (1) CN115715415A (https=)
AU (1) AU2021313211A1 (https=)
CA (1) CA3184399A1 (https=)
IL (1) IL299070A (https=)
WO (1) WO2022020487A1 (https=)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4036798A1 (de) * 2021-01-27 2022-08-03 Siemens Healthcare GmbH Computer-implementiertes verfahrens zur automatischen klassifikation von emitter-strukturen, vorrichtung zur durchführung des verfahrens, maschinenlesbarer programmcode und speichermedium
EP4612692A1 (en) * 2022-11-01 2025-09-10 Laboratory Corporation of America Holdings Population frequency modeling for quantitative variant pathogenicity estimation
EP4732284A1 (en) 2023-06-23 2026-04-29 Illumina, Inc. Method and system for estimating impact of mutations on fitness, lifespan, and fecundity

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20200097835A1 (en) * 2014-06-17 2020-03-26 Ancestry.Com Dna, Llc Device, system and method for assessing risk of variant-specific gene dysfunction
DE102016005947B3 (de) * 2016-05-16 2017-06-08 Dimo Dietrich Verfahren zur Abschätzung der Prognose und zur Prädiktion des Ansprechens auf eine Immuntherapie von Patienten mit malignen Erkrankungen
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

Also Published As

Publication number Publication date
CN115715415A (zh) 2023-02-24
US20220027388A1 (en) 2022-01-27
WO2022020487A1 (en) 2022-01-27
JP2023534616A (ja) 2023-08-10
EP4186061A1 (en) 2023-05-31
AU2021313211A1 (en) 2022-12-01
KR20230043072A (ko) 2023-03-30
IL299070A (en) 2023-02-01

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