JP6618929B2 - ウルトラディープシークエンシングにおける希少バリアントコール - Google Patents

ウルトラディープシークエンシングにおける希少バリアントコール Download PDF

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Publication number
JP6618929B2
JP6618929B2 JP2016565058A JP2016565058A JP6618929B2 JP 6618929 B2 JP6618929 B2 JP 6618929B2 JP 2016565058 A JP2016565058 A JP 2016565058A JP 2016565058 A JP2016565058 A JP 2016565058A JP 6618929 B2 JP6618929 B2 JP 6618929B2
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variant
sample
allele
sequence
samples
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JP2017520821A5 (enExample
JP2017520821A (ja
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リウ ウエイ−ミン
リウ ウエイ−ミン
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F Hoffmann La Roche AG
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F Hoffmann La Roche AG
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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
    • 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
    • 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
    • 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
    • G16B20/40—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
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance

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  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Ecology (AREA)
  • Physiology (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Primary Health Care (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
JP2016565058A 2014-05-12 2015-05-12 ウルトラディープシークエンシングにおける希少バリアントコール Active JP6618929B2 (ja)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201461991820P 2014-05-12 2014-05-12
US61/991,820 2014-05-12
PCT/EP2015/060442 WO2015173222A1 (en) 2014-05-12 2015-05-12 Rare variant calls in ultra-deep sequencing

Publications (3)

Publication Number Publication Date
JP2017520821A JP2017520821A (ja) 2017-07-27
JP2017520821A5 JP2017520821A5 (enExample) 2018-06-21
JP6618929B2 true JP6618929B2 (ja) 2019-12-11

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Family Applications (1)

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JP2016565058A Active JP6618929B2 (ja) 2014-05-12 2015-05-12 ウルトラディープシークエンシングにおける希少バリアントコール

Country Status (5)

Country Link
US (1) US10216895B2 (enExample)
EP (1) EP3143537B1 (enExample)
JP (1) JP6618929B2 (enExample)
CN (1) CN106462670B (enExample)
WO (1) WO2015173222A1 (enExample)

Families Citing this family (37)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2012242847B2 (en) 2011-04-15 2017-01-19 The Johns Hopkins University Safe sequencing system
ES2701742T3 (es) 2012-10-29 2019-02-25 Univ Johns Hopkins Prueba de Papanicolaou para cánceres de ovario y de endometrio
WO2016077709A1 (en) * 2014-11-14 2016-05-19 Liquid Genomics, Inc. Use of circulating cell-free rna for diagnosis and/or monitoring cancer
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
WO2017027653A1 (en) 2015-08-11 2017-02-16 The Johns Hopkins University Assaying ovarian cyst fluid
CN108603229A (zh) * 2016-01-22 2018-09-28 格瑞尔公司 用于高保真测序的方法和系统
EP3414691A1 (en) 2016-02-12 2018-12-19 Regeneron Pharmaceuticals, Inc. Methods and systems for detection of abnormal karyotypes
EP4009330A1 (en) 2016-06-01 2022-06-08 Quantum-si Incorporated Pulse caller and base caller
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
BR112019009830A2 (pt) * 2016-11-16 2019-08-13 Illumina, Inc. métodos para realinhamento de leitura de dados de sequenciamento
WO2018093780A1 (en) * 2016-11-16 2018-05-24 Illumina, Inc. Validation methods and systems for sequence variant calls
US11978535B2 (en) * 2017-02-01 2024-05-07 The Translational Genomics Research Institute Methods of detecting somatic and germline variants in impure tumors
WO2018152267A1 (en) * 2017-02-14 2018-08-23 Bahram Ghaffarzadeh Kermani Reliable and secure detection techniques for processing genome data in next generation sequencing (ngs)
CN108660252B (zh) * 2017-04-01 2021-11-26 北京博尔晟科技发展有限公司 一种基于焦磷酸测序的人类免疫缺陷病毒耐药性分析方法
KR102035615B1 (ko) * 2017-08-07 2019-10-23 연세대학교 산학협력단 유전자 패널에 기초한 염기서열의 변이 검출방법 및 이를 이용한 염기서열의 변이 검출 디바이스
CN120400338A (zh) 2017-08-07 2025-08-01 约翰斯霍普金斯大学 用于评估和治疗癌症的方法和材料
WO2019071219A1 (en) * 2017-10-06 2019-04-11 Grail, Inc. SPECIFIC SITE NOISE MODEL FOR TARGETED SEQUENCING
NZ759818A (en) 2017-10-16 2022-04-29 Illumina Inc Semi-supervised learning for training an ensemble of deep convolutional neural networks
US11861491B2 (en) 2017-10-16 2024-01-02 Illumina, Inc. Deep learning-based pathogenicity classifier for promoter single nucleotide variants (pSNVs)
JP7067896B2 (ja) * 2017-10-27 2022-05-16 シスメックス株式会社 品質評価方法、品質評価装置、プログラム、および記録媒体
JP2021503922A (ja) * 2017-11-28 2021-02-15 グレイル， インコーポレイテッドＧｒａｉｌ， Ｉｎｃ． ターゲットシーケンシングのためのモデル
IL271235B2 (en) 2017-11-30 2024-12-01 Illumina Inc Validation methods and systems for detecting sequence variants
WO2019136376A1 (en) 2018-01-08 2019-07-11 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
CA3279137A1 (en) 2018-01-08 2025-10-30 Illumina, Inc. Systems and devices for high-throughput sequencing with semiconductor-based detection
EP3619653B1 (en) 2018-01-15 2021-05-19 Illumina Inc. Deep learning-based variant classifier
JP2021511829A (ja) 2018-01-26 2021-05-13 クアンタム−エスアイ インコーポレイテッドＱｕａｎｔｕｍ−Ｓｉ Ｉｎｃｏｒｐｏｒａｔｅｄ シークエンシングデバイスに関する機械学習可能なパルス決定および塩基決定
CN120015114A (zh) * 2018-02-16 2025-05-16 伊鲁米那股份有限公司 用于变体识别的相关错误事件缓解的系统和方法
SE541799C2 (en) * 2018-04-11 2019-12-17 David Yudovich Determination of frequency distribution of nucleotide sequence variants
JP2019191952A (ja) * 2018-04-25 2019-10-31 特定非営利活動法人Ｎｏｒｔｈ Ｅａｓｔ Ｊａｐａｎ Ｓｔｕｄｙ Ｇｒｏｕｐ プログラム、情報処理方法および情報処理装置
CN113168886B (zh) * 2018-08-13 2025-01-21 豪夫迈·罗氏有限公司 用于使用神经网络进行种系和体细胞变体调用的系统和方法
WO2020081648A1 (en) 2018-10-17 2020-04-23 Quest Diagnostics Investments Llc Genomic sequencing selection system
EP3867408A1 (en) * 2018-10-19 2021-08-25 F. Hoffmann-La Roche AG Electric field-assisted junctions for sequencing
CN111073961A (zh) * 2019-12-20 2020-04-28 苏州赛美科基因科技有限公司 一种基因稀有突变的高通量检测方法
IL295297A (en) 2020-02-14 2022-10-01 Univ Johns Hopkins Methods and materials for assessing nucleic acids
AU2021227920A1 (en) * 2020-02-28 2022-09-08 Grail, Llc Systems and methods for calling variants using methylation sequencing data
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

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014014497A1 (en) * 2012-07-20 2014-01-23 Verinata Health, Inc. Detecting and classifying copy number variation in a cancer genome
US20140066317A1 (en) * 2012-09-04 2014-03-06 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
US20140143188A1 (en) * 2012-11-16 2014-05-22 Genformatic, Llc Method of machine learning, employing bayesian latent class inference: combining multiple genomic feature detection algorithms to produce an integrated genomic feature set with specificity, sensitivity and accuracy
US9218450B2 (en) * 2012-11-29 2015-12-22 Roche Molecular Systems, Inc. Accurate and fast mapping of reads to genome

Also Published As

Publication number Publication date
CN106462670B (zh) 2020-04-10
US10216895B2 (en) 2019-02-26
CN106462670A (zh) 2017-02-22
EP3143537B1 (en) 2023-03-01
JP2017520821A (ja) 2017-07-27
WO2015173222A1 (en) 2015-11-19
EP3143537A1 (en) 2017-03-22
US20150324519A1 (en) 2015-11-12

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