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 2012-11-29
US13/689,314 US9218450B2 (en) 2012-11-29 2012-11-29 Accurate and fast mapping of reads to genome
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)

Application Number Title Priority Date Filing Date
CA2891731A Active CA2891731C (en) 2012-11-29 2013-11-27 Accurate and fast mapping of targeted sequencing reads

Country Status (7)

Country Link
US (2) US9218450B2 (https=)
EP (1) EP2926288B1 (https=)
JP (1) JP6240210B2 (https=)
CN (1) CN104937598B (https=)
CA (1) CA2891731C (https=)
ES (1) ES2869292T3 (https=)
WO (1) WO2014083023A1 (https=)

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ES2625288T3 (es) 2011-04-15 2017-07-19 The Johns Hopkins University Sistema de secuenciación segura
AU2013338393C1 (en) 2012-10-29 2024-07-25 The Johns Hopkins University Papanicolaou test for ovarian and endometrial cancers
JP6618929B2 (ja) * 2014-05-12 2019-12-11 エフ．ホフマン−ラ ロシュ アーゲーＦ． Ｈｏｆｆｍａｎｎ−Ｌａ Ｒｏｃｈｅ Ａｋｔｉｅｎｇｅｓｅｌｌｓｃｈａｆｔ 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
CA2974182A1 (en) * 2014-09-03 2016-03-10 Otsuka Pharmaceutical Co., Ltd. Pathology determination assistance device, method, program 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
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
US9859394B2 (en) 2014-12-18 2018-01-02 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
US9857328B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same
US10020300B2 (en) 2014-12-18 2018-07-10 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US10429342B2 (en) 2014-12-18 2019-10-01 Edico Genome Corporation Chemically-sensitive field effect transistor
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
US11286531B2 (en) 2015-08-11 2022-03-29 The Johns Hopkins University Assaying ovarian cyst fluid
CA3014292A1 (en) 2016-02-12 2017-08-17 Regeneron Pharmaceuticals, Inc. Methods and systems for detection of abnormal karyotypes
WO2017201081A1 (en) 2016-05-16 2017-11-23 Agilome, Inc. Graphene fet devices, systems, and methods of using the same for sequencing nucleic acids
MX2019000762A (es) * 2016-07-21 2019-10-30 Walmart Apollo Llc Caracterizaciones basadas en vectores de productos e individuos con respecto a la seleccion de articulos para ubicaciones de tiendas.
IL319255A (en) 2017-08-07 2025-04-01 Univ Johns Hopkins Methods and materials for cancer assessment and treatment
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
SG11201907280QA (en) * 2017-12-29 2019-09-27 Act Genomics Co Ltd Method and system for sequence alignment and variant calling
CN112601826B (zh) 2018-02-27 2025-03-11 康奈尔大学 通过全基因组整合进行循环肿瘤dna的超灵敏检测
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
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
US20210350873A1 (en) * 2020-05-08 2021-11-11 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
DK1749122T3 (da) * 2004-04-23 2019-11-11 Becton Dickinson Co Overfladeforbedrede spektroskopi-aktive kompositnanopartikler
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
US20140066317A1 (en) * 2012-09-04 2014-03-06 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
GB2533006B (en) * 2012-09-04 2017-06-07 Guardant Health Inc Systems and methods to detect copy number variation

Also Published As

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

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