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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JP2017520821A (ja
JP2017520821A5 (https=
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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)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Ecology (AREA)
  • Physiology (AREA)
  • Public Health (AREA)
  • Primary Health Care (AREA)
  • Epidemiology (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 (https=) 2018-06-21
JP6618929B2 true JP6618929B2 (ja) 2019-12-11

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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 (https=)
EP (1) EP3143537B1 (https=)
JP (1) JP6618929B2 (https=)
CN (1) CN106462670B (https=)
WO (1) WO2015173222A1 (https=)

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ES2790823T3 (es) * 2014-11-14 2020-10-29 Liquid Genomics Inc Uso de ARN sin células circulante para el diagnóstico y/o la monitorización de cáncer
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
US11286531B2 (en) 2015-08-11 2022-03-29 The Johns Hopkins University Assaying ovarian cyst fluid
EP3405573A4 (en) * 2016-01-22 2019-09-18 Grail, Inc. METHOD AND SYSTEMS FOR HIGH-FIDELITY SEQUENCING
CA3014292A1 (en) 2016-02-12 2017-08-17 Regeneron Pharmaceuticals, Inc. Methods and systems for detection of abnormal karyotypes
MX2018014856A (es) 2016-06-01 2019-03-07 Quantum Si Inc Llamador de pulso y llamador de base.
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
JP7113838B2 (ja) * 2016-11-16 2022-08-05 イルミナ インコーポレイテッド 配列バリアントコールのための有効化方法およびシステム
AU2017361069B2 (en) * 2016-11-16 2023-09-21 Illumina, Inc. Methods of sequencing data read realignment
WO2018144782A1 (en) * 2017-02-01 2018-08-09 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
IL319255A (en) 2017-08-07 2025-04-01 Univ Johns Hopkins Methods and materials for cancer assessment and treatment
KR102035615B1 (ko) * 2017-08-07 2019-10-23 연세대학교 산학협력단 유전자 패널에 기초한 염기서열의 변이 검출방법 및 이를 이용한 염기서열의 변이 검출 디바이스
CN111164701A (zh) * 2017-10-06 2020-05-15 格瑞尔公司 针对靶标定序的定点噪声模型
WO2019079182A1 (en) 2017-10-16 2019-04-25 Illumina, Inc. SEMI-SUPERVISED APPRENTICESHIP FOR THE LEARNING OF A SET OF NEURONAL NETWORKS WITH DEEP CONVOLUTION
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
AU2018375302A1 (en) * 2017-11-28 2020-06-11 Grail, Llc Models for targeted sequencing
JP7013490B2 (ja) 2017-11-30 2022-02-15 イルミナ インコーポレイテッド 配列バリアントコールのためのバリデーションの方法及びシステム
KR102369895B1 (ko) 2018-01-08 2022-03-03 일루미나, 인코포레이티드 칩-기반 서열분석기를 위한 고-처리율 염기 콜링
US11378544B2 (en) 2018-01-08 2022-07-05 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
IL283427B2 (en) * 2018-01-15 2023-10-01 Illumina Inc Identifying variants using Empiric ranking of variants
KR20200115590A (ko) 2018-01-26 2020-10-07 퀀텀-에스아이 인코포레이티드 서열화 디바이스들을 위한 머신 학습 가능형 펄스 및 염기 호출
WO2019161419A1 (en) * 2018-02-16 2019-08-22 Illumina, Inc. Systems and methods for correlated error event mitigation for variant calling
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
JP7166434B2 (ja) * 2018-08-13 2022-11-07 エフ．ホフマン－ラ ロシュ アーゲー 生殖細胞系列および体細胞変異の呼び出しのためにニューラルネットワークを使用するシステムおよび方法
US20210313011A1 (en) * 2018-10-17 2021-10-07 Quest Diagnostics Investments Llc Genomic sequencing selection system
WO2020078595A1 (en) * 2018-10-19 2020-04-23 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
JP2023513606A (ja) 2020-02-14 2023-03-31 ザ・ジョンズ・ホプキンス・ユニバーシティー 核酸を評価するための方法および材料
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

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CA2878246C (en) 2012-07-20 2022-01-11 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
JP2017520821A (ja) 2017-07-27
WO2015173222A1 (en) 2015-11-19
EP3143537B1 (en) 2023-03-01
EP3143537A1 (en) 2017-03-22
CN106462670B (zh) 2020-04-10
US20150324519A1 (en) 2015-11-12
CN106462670A (zh) 2017-02-22
US10216895B2 (en) 2019-02-26

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