CN107076729A - 变异体调用器 - Google Patents

变异体调用器 Download PDF

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Publication number
CN107076729A
CN107076729A CN201580055934.8A CN201580055934A CN107076729A CN 107076729 A CN107076729 A CN 107076729A CN 201580055934 A CN201580055934 A CN 201580055934A CN 107076729 A CN107076729 A CN 107076729A
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China
Prior art keywords
error table
reads
generating
sites
scoring
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CN201580055934.8A
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English (en)
Chinese (zh)
Inventor
A·L·吉比安斯盖
I·S·哈克
J·R·马奎尔
A·D·J·罗伯逊
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Counsyl Inc
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Counsyl Inc
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Publication of CN107076729A publication Critical patent/CN107076729A/zh
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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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • G16B30/10—Sequence alignment; Homology search

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  • 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)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Physiology (AREA)
  • General Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Software Systems (AREA)
  • Mathematical Physics (AREA)
  • Evolutionary Computation (AREA)
  • Data Mining & Analysis (AREA)
  • Artificial Intelligence (AREA)
  • Computing Systems (AREA)
  • Ecology (AREA)
  • Computational Linguistics (AREA)
  • Biomedical Technology (AREA)
  • Computational Mathematics (AREA)
  • Probability & Statistics with Applications (AREA)
  • Algebra (AREA)
  • Pure & Applied Mathematics (AREA)
  • Mathematical Analysis (AREA)
  • Mathematical Optimization (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CN201580055934.8A 2014-10-16 2015-10-15 变异体调用器 Pending CN107076729A (zh)

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
CN107076729A true CN107076729A (zh) 2017-08-18

Family

ID=55747365

Family Applications (1)

Application Number Title Priority Date Filing Date
CN201580055934.8A Pending CN107076729A (zh) 2014-10-16 2015-10-15 变异体调用器

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)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN109949866A (zh) * 2018-06-22 2019-06-28 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

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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
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

Citations (6)

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WO2001080156A1 (en) * 2000-04-18 2001-10-25 Genaissance Pharmaceuticals, Inc. 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)
US20050214811A1 (en) * 2003-12-12 2005-09-29 Margulies David M Processing and managing genetic information
US20130054508A1 (en) * 2011-08-25 2013-02-28 Complete Genomics, Inc. Analyzing genome sequencing information to determine likelihood of co-segregating alleles on haplotypes
CN103930439A (zh) * 2011-05-09 2014-07-16 米纳瓦生物技术公司 基因工程生长因子变异体
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

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US20030211501A1 (en) * 2001-04-18 2003-11-13 Stephens J. Claiborne Method and system for determining haplotypes from a collection of polymorphisms
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

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001080156A1 (en) * 2000-04-18 2001-10-25 Genaissance Pharmaceuticals, Inc. 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)
US20050214811A1 (en) * 2003-12-12 2005-09-29 Margulies David M Processing and managing genetic information
CN103930439A (zh) * 2011-05-09 2014-07-16 米纳瓦生物技术公司 基因工程生长因子变异体
US20130054508A1 (en) * 2011-08-25 2013-02-28 Complete Genomics, Inc. Analyzing genome sequencing information to determine likelihood of co-segregating alleles on 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

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN109949866A (zh) * 2018-06-22 2019-06-28 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
WO2019242445A1 (zh) * 2018-06-22 2019-12-26 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

Also Published As

Publication number Publication date
US20160140289A1 (en) 2016-05-19
EP3207369A1 (en) 2017-08-23
IL251742A0 (en) 2017-06-29
CA2963425A1 (en) 2016-04-21
JP2018501539A (ja) 2018-01-18
WO2016061396A1 (en) 2016-04-21
EP3207369A4 (en) 2018-06-13
AU2015332389A1 (en) 2017-04-20

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