CA2891731C - Accurate and fast mapping of targeted sequencing reads - Google Patents

Accurate and fast mapping of targeted sequencing reads Download PDF

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Publication number
CA2891731C
CA2891731C CA2891731A CA2891731A CA2891731C CA 2891731 C CA2891731 C CA 2891731C CA 2891731 A CA2891731 A CA 2891731A CA 2891731 A CA2891731 A CA 2891731A CA 2891731 C CA2891731 C CA 2891731C
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target region
alternate
region
variations
genome
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CA2891731A
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English (en)
French (fr)
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CA2891731A1 (en
Inventor
Xiaoying Chen
Yan Li
Wei-Min Liu
Xiaoju MA (Max)
Sim-Jasmine TRUONG
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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
    • 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

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  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA2891731A 2012-11-29 2013-11-27 Accurate and fast mapping of targeted sequencing reads Active CA2891731C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US13/689,314 US9218450B2 (en) 2012-11-29 2012-11-29 Accurate and fast mapping of reads to genome
US13/689,314 2012-11-29
PCT/EP2013/074799 WO2014083023A1 (en) 2012-11-29 2013-11-27 Accurate and fast mapping of targeted sequencing reads

Publications (2)

Publication Number Publication Date
CA2891731A1 CA2891731A1 (en) 2014-06-05
CA2891731C true CA2891731C (en) 2017-09-12

Family

ID=49641777

Family Applications (1)

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CA2891731A Active CA2891731C (en) 2012-11-29 2013-11-27 Accurate and fast mapping of targeted sequencing reads

Country Status (7)

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US (2) US9218450B2 (enExample)
EP (1) EP2926288B1 (enExample)
JP (1) JP6240210B2 (enExample)
CN (1) CN104937598B (enExample)
CA (1) CA2891731C (enExample)
ES (1) ES2869292T3 (enExample)
WO (1) WO2014083023A1 (enExample)

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DK3246416T3 (da) 2011-04-15 2024-09-02 Univ Johns Hopkins Sikkert sekventeringssystem
ES2886507T5 (es) 2012-10-29 2024-11-15 Univ Johns Hopkins Prueba de Papanicolaou para cánceres de ovario y de endometrio
EP3143537B1 (en) * 2014-05-12 2023-03-01 Roche Diagnostics GmbH Rare variant calls in ultra-deep sequencing
US20180032673A1 (en) * 2014-09-03 2018-02-01 Otsuka Pharmaceutical Co., Ltd. Pathology determination assistance device, method and storage medium
US20160125130A1 (en) * 2014-11-05 2016-05-05 Agilent Technologies, Inc. Method for assigning target-enriched sequence reads to a genomic location
EP3235010A4 (en) 2014-12-18 2018-08-29 Agilome, Inc. Chemically-sensitive field effect transistor
US10020300B2 (en) 2014-12-18 2018-07-10 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US10006910B2 (en) 2014-12-18 2018-06-26 Agilome, Inc. Chemically-sensitive field effect transistors, systems, and methods for manufacturing and using the same
US9859394B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US9618474B2 (en) 2014-12-18 2017-04-11 Edico Genome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US9857328B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same
US20160300013A1 (en) * 2015-04-10 2016-10-13 Agilent Technologies, Inc. METHOD FOR SIMULTANEOUS DETECTION OF GENOME-WIDE COPY NUMBER CHANGES, cnLOH, INDELS, AND GENE MUTATIONS
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
JP6675164B2 (ja) * 2015-07-28 2020-04-01 株式会社理研ジェネシス 変異判定方法、変異判定プログラムおよび記録媒体
WO2017027653A1 (en) 2015-08-11 2017-02-16 The Johns Hopkins University Assaying ovarian cyst fluid
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
WO2017201081A1 (en) 2016-05-16 2017-11-23 Agilome, Inc. Graphene fet devices, systems, and methods of using the same for sequencing nucleic acids
US20180025365A1 (en) * 2016-07-21 2018-01-25 Wal-Mart Stores, Inc. Vector-based characterizations of products and individuals with respect to selecting items for store locations
CN111868260B (zh) 2017-08-07 2025-02-21 约翰斯霍普金斯大学 用于评估和治疗癌症的方法和材料
JP7320345B2 (ja) * 2017-10-27 2023-08-03 シスメックス株式会社 遺伝子解析方法、遺伝子解析装置、遺伝子解析システム、プログラム、および記録媒体
JP7054133B2 (ja) 2017-11-09 2022-04-13 国立研究開発法人国立がん研究センター 配列解析方法、配列解析装置、参照配列の生成方法、参照配列生成装置、プログラム、および記録媒体
JP6710427B2 (ja) * 2017-12-29 2020-06-17 アクト ゲノミクス （アイピー） カンパニー リミテッド 配列アライメントおよびバリアントコールのための方法およびシステム
CN115516108A (zh) 2020-02-14 2022-12-23 约翰斯霍普金斯大学 评估核酸的方法和材料
CN111477274B (zh) * 2020-04-02 2020-11-24 上海之江生物科技股份有限公司 微生物目标片段中特异性区域的识别方法、装置及应用
EP4147241A1 (en) * 2020-05-08 2023-03-15 Illumina, Inc. Genome sequencing and detection techniques

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UY24389A1 (es) * 1995-12-06 2001-10-25 Karlsruhe Forschzent Composición farmacéutica para el tratamiento de carcinoma de epitelio plano
US7809509B2 (en) 2001-05-08 2010-10-05 Ip Genesis, Inc. Comparative mapping and assembly of nucleic acid sequences
US20030138778A1 (en) * 2001-11-30 2003-07-24 Garner Harold R. Prediction of disease-causing alleles from sequence context
US20040229269A1 (en) 2003-05-15 2004-11-18 Ghazala Hashmi Hybridization-mediated analysis of polymorphisms
WO2006073439A2 (en) * 2004-04-23 2006-07-13 Oxonica, Inc. Surface enhanced spectroscpy-active composite nanop articles and their application in analysis and diagnosis
CN1277924C (zh) * 2004-06-25 2006-10-04 湖南西城杂交水稻基因科技有限公司 利用可转化大片段基因组文库发掘野生稻有利基因的方法
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KR102393608B1 (ko) * 2012-09-04 2022-05-03 가던트 헬쓰, 인크. 희귀 돌연변이 및 카피수 변이를 검출하기 위한 시스템 및 방법

Also Published As

Publication number Publication date
JP6240210B2 (ja) 2017-11-29
US20160092630A1 (en) 2016-03-31
CN104937598B (zh) 2017-11-07
CN104937598A (zh) 2015-09-23
US9218450B2 (en) 2015-12-22
CA2891731A1 (en) 2014-06-05
ES2869292T3 (es) 2021-10-25
JP2015536661A (ja) 2015-12-24
US20140149049A1 (en) 2014-05-29
EP2926288A1 (en) 2015-10-07
WO2014083023A1 (en) 2014-06-05
EP2926288B1 (en) 2021-03-17
US10127351B2 (en) 2018-11-13

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