CA2963425A1 - Variant caller - Google Patents

Variant caller Download PDF

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Publication number
CA2963425A1
CA2963425A1 CA2963425A CA2963425A CA2963425A1 CA 2963425 A1 CA2963425 A1 CA 2963425A1 CA 2963425 A CA2963425 A CA 2963425A CA 2963425 A CA2963425 A CA 2963425A CA 2963425 A1 CA2963425 A1 CA 2963425A1
Authority
CA
Canada
Prior art keywords
error table
generating
graph
diplotypes
reads
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.)
Abandoned
Application number
CA2963425A
Other languages
English (en)
French (fr)
Inventor
Andrew Leonidovich Gibiansky
Imran Saeedul Haque
Jared Robert Maguire
Alexander De Jong Robertson
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.)
Myriad Womens Health Inc
Original Assignee
Counsyl 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 Counsyl Inc filed Critical Counsyl Inc
Publication of CA2963425A1 publication Critical patent/CA2963425A1/en
Abandoned legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/12—Computing arrangements based on biological models using genetic models
    • G06N3/126—Evolutionary algorithms, e.g. genetic algorithms or genetic programming
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N7/00—Computing arrangements based on specific mathematical models
    • G06N7/01—Probabilistic graphical models, e.g. probabilistic networks
    • 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
    • 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
    • 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
    • G16B20/40—Population genetics; Linkage disequilibrium
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Medical Informatics (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Physiology (AREA)
  • General Physics & Mathematics (AREA)
  • Artificial Intelligence (AREA)
  • Mathematical Physics (AREA)
  • Evolutionary Computation (AREA)
  • Data Mining & Analysis (AREA)
  • Computing Systems (AREA)
  • General Engineering & Computer Science (AREA)
  • Software Systems (AREA)
  • Ecology (AREA)
  • Computational Linguistics (AREA)
  • Biomedical Technology (AREA)
  • Probability & Statistics with Applications (AREA)
  • Computational Mathematics (AREA)
  • Mathematical Analysis (AREA)
  • Mathematical Optimization (AREA)
  • Pure & Applied Mathematics (AREA)
  • Algebra (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA2963425A 2014-10-16 2015-10-15 Variant caller Abandoned CA2963425A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201462064717P 2014-10-16 2014-10-16
US62/064,717 2014-10-16
PCT/US2015/055807 WO2016061396A1 (en) 2014-10-16 2015-10-15 Variant caller

Publications (1)

Publication Number Publication Date
CA2963425A1 true CA2963425A1 (en) 2016-04-21

Family

ID=55747365

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2963425A Abandoned CA2963425A1 (en) 2014-10-16 2015-10-15 Variant caller

Country Status (8)

Country Link
US (1) US20160140289A1 (enExample)
EP (1) EP3207369A4 (enExample)
JP (1) JP2018501539A (enExample)
CN (1) CN107076729A (enExample)
AU (1) AU2015332389A1 (enExample)
CA (1) CA2963425A1 (enExample)
IL (1) IL251742A0 (enExample)
WO (1) WO2016061396A1 (enExample)

Families Citing this family (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
US20170270245A1 (en) 2016-01-11 2017-09-21 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing
CN109074426B (zh) 2016-02-12 2022-07-26 瑞泽恩制药公司 用于检测异常核型的方法和系统
EP4362030A3 (en) * 2016-06-07 2024-07-17 Illumina, Inc. Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing
US10600499B2 (en) 2016-07-13 2020-03-24 Seven Bridges Genomics Inc. Systems and methods for reconciling variants in sequence data relative to reference sequence data
CA3044231A1 (en) * 2016-11-16 2018-05-24 Illumina, Inc. Validation methods and systems for sequence variant calls
US11821027B2 (en) 2017-01-10 2023-11-21 Juno Therapeutics, Inc. Epigenetic analysis of cell therapy and related methods
US20190024161A1 (en) * 2017-07-21 2019-01-24 Helix OpCo, LLC Genomic services platform supporting multiple application providers
US11861491B2 (en) 2017-10-16 2024-01-02 Illumina, Inc. Deep learning-based pathogenicity classifier for promoter single nucleotide variants (pSNVs)
MX2019014690A (es) 2017-10-16 2020-02-07 Illumina Inc Tecnicas basadas en aprendizaje profundo para el entrenamiento de redes neuronales convolucionales profundas.
AU2019205496B2 (en) 2018-01-08 2021-08-19 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
WO2019136376A1 (en) 2018-01-08 2019-07-11 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
CN109949866B (zh) * 2018-06-22 2021-02-02 深圳市达仁基因科技有限公司 病原体操作组的检测方法、装置、计算机设备和存储介质
US11361194B2 (en) 2020-10-27 2022-06-14 Illumina, Inc. Systems and methods for per-cluster intensity correction and base calling
US11538555B1 (en) 2021-10-06 2022-12-27 Illumina, Inc. Protein structure-based protein language models
US12431218B2 (en) 2022-03-08 2025-09-30 Illumina, Inc. Multi-pass software-accelerated genomic read mapping engine

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2001253720A1 (en) * 2000-04-18 2001-10-30 Genaissance Pharmaceuticals, Inc. Method and system for determining haplotypes from a collection of polymorphisms
US20030211501A1 (en) * 2001-04-18 2003-11-13 Stephens J. Claiborne Method and system for determining haplotypes from a collection of polymorphisms
US20040265816A1 (en) * 2001-07-05 2004-12-30 Eiichi Tanaka Method of judging risk of side effects of remedys for rheumatoid arthritis (ra)
US20050209787A1 (en) * 2003-12-12 2005-09-22 Waggener Thomas B Sequencing data analysis
DK2511843T3 (en) * 2009-04-29 2017-03-27 Complete Genomics Inc METHOD AND SYSTEM FOR DETERMINING VARIATIONS IN A SAMPLE POLYNUCLEOTIDE SEQUENCE IN TERMS OF A REFERENCE POLYNUCLEOTIDE SEQUENCE
WO2011139797A2 (en) * 2010-04-27 2011-11-10 Spiral Genetics Inc. Method and system for analysis and error correction of biological sequences and inference of relationship for multiple samples
CA2835453A1 (en) * 2011-05-09 2012-11-15 Minerva Biotechnologies Corporation Genetically engineered growth factor variants
WO2013028739A1 (en) * 2011-08-25 2013-02-28 Complete Genomics Phasing of heterozygous loci to determine genomic haplotypes
CN103955629A (zh) * 2014-02-18 2014-07-30 吉林大学 基于模糊k均值的宏基因组片段聚类方法

Also Published As

Publication number Publication date
US20160140289A1 (en) 2016-05-19
EP3207369A1 (en) 2017-08-23
IL251742A0 (en) 2017-06-29
CN107076729A (zh) 2017-08-18
JP2018501539A (ja) 2018-01-18
WO2016061396A1 (en) 2016-04-21
EP3207369A4 (en) 2018-06-13
AU2015332389A1 (en) 2017-04-20

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Legal Events

Date Code Title Description
FZDE Discontinued

Effective date: 20201015