CN104937598B - 靶向的测序读取值的准确且快速的定位 - Google Patents

靶向的测序读取值的准确且快速的定位 Download PDF

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CN104937598B
CN104937598B CN201380062074.1A CN201380062074A CN104937598B CN 104937598 B CN104937598 B CN 104937598B CN 201380062074 A CN201380062074 A CN 201380062074A CN 104937598 B CN104937598 B CN 104937598B
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interest
sequence reads
sequence
genome
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CN104937598A (zh
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X.陈
Y.李
W-m.刘
X.(M.).马
S-J.张
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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)
CN201380062074.1A 2012-11-29 2013-11-27 靶向的测序读取值的准确且快速的定位 Active CN104937598B (zh)

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
US13/689314 2012-11-29
PCT/EP2013/074799 WO2014083023A1 (en) 2012-11-29 2013-11-27 Accurate and fast mapping of targeted sequencing reads

Publications (2)

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CN104937598A CN104937598A (zh) 2015-09-23
CN104937598B true CN104937598B (zh) 2017-11-07

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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)

Families Citing this family (26)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3246416B1 (en) 2011-04-15 2024-06-05 The Johns Hopkins University Safe sequencing system
WO2014070462A1 (en) 2012-10-29 2014-05-08 The Johns Hopkins University Papanicolaou test for ovarian and endometrial cancers
US10216895B2 (en) * 2014-05-12 2019-02-26 Roche Molecular Systems, Inc. Rare variant calls in ultra-deep sequencing
ES2898435T3 (es) * 2014-09-03 2022-03-07 Otsuka Pharma Co Ltd Dispositivo de ayuda para la determinación de patología, método, programa y medio de almacenamiento
US20160125130A1 (en) * 2014-11-05 2016-05-05 Agilent Technologies, Inc. Method for assigning target-enriched sequence reads to a genomic location
US10429342B2 (en) 2014-12-18 2019-10-01 Edico Genome Corporation Chemically-sensitive field effect transistor
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
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
JP6765433B2 (ja) 2016-02-12 2020-10-07 リジェネロン・ファーマシューティカルズ・インコーポレイテッドＲｅｇｅｎｅｒｏｎ Ｐｈａｒｍａｃｅｕｔｉｃａｌｓ， Ｉｎｃ． 異常な核型の検出のための方法
WO2017201081A1 (en) 2016-05-16 2017-11-23 Agilome, Inc. Graphene fet devices, systems, and methods of using the same for sequencing nucleic acids
WO2018017832A1 (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
KR20250047324A (ko) 2017-08-07 2025-04-03 더 존스 홉킨스 유니버시티 암을 평가하고 치료하기 위한 방법 및 재료
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
US10854317B2 (en) * 2017-12-29 2020-12-01 Act Genomics Co., Ltd. Method and system for sequence alignment and variant calling
IL276891B2 (en) 2018-02-27 2025-05-01 Univ Cornell Highly sensitive detection of circulating DNA using genome-wide integration
WO2021163546A1 (en) 2020-02-14 2021-08-19 The Johns Hopkins University Methods and materials for assessing nucleic acids
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
WO2021226522A1 (en) * 2020-05-08 2021-11-11 Illumina, Inc. Genome sequencing and detection techniques

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN1207811A (zh) * 1995-12-06 1999-02-10 贝林格尔·英格海姆国际有限公司 诊断及治疗鳞状细胞癌的方法
US20030138778A1 (en) * 2001-11-30 2003-07-24 Garner Harold R. Prediction of disease-causing alleles from sequence context
CN1594564A (zh) * 2004-06-25 2005-03-16 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
CN101019019A (zh) * 2004-04-23 2007-08-15 奥克尼卡公司 表面强化的光谱学活性复合纳米颗粒

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7809509B2 (en) 2001-05-08 2010-10-05 Ip Genesis, Inc. Comparative mapping and assembly of nucleic acid sequences
WO2004104172A2 (en) 2003-05-15 2004-12-02 Bioarray Solutions, Ltd. Hybridization-mediated analysis of polymorphisms
US20140066317A1 (en) * 2012-09-04 2014-03-06 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
PL2893040T3 (pl) * 2012-09-04 2019-05-31 Guardant Health Inc Sposoby wykrywania rzadkich mutacji i wariantu liczby kopii

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN1207811A (zh) * 1995-12-06 1999-02-10 贝林格尔·英格海姆国际有限公司 诊断及治疗鳞状细胞癌的方法
US20030138778A1 (en) * 2001-11-30 2003-07-24 Garner Harold R. Prediction of disease-causing alleles from sequence context
CN101019019A (zh) * 2004-04-23 2007-08-15 奥克尼卡公司 表面强化的光谱学活性复合纳米颗粒
CN1594564A (zh) * 2004-06-25 2005-03-16 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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Publication number Publication date
US10127351B2 (en) 2018-11-13
EP2926288B1 (en) 2021-03-17
US20140149049A1 (en) 2014-05-29
US9218450B2 (en) 2015-12-22
JP2015536661A (ja) 2015-12-24
US20160092630A1 (en) 2016-03-31
WO2014083023A1 (en) 2014-06-05
EP2926288A1 (en) 2015-10-07
JP6240210B2 (ja) 2017-11-29
CN104937598A (zh) 2015-09-23
CA2891731C (en) 2017-09-12
CA2891731A1 (en) 2014-06-05
ES2869292T3 (es) 2021-10-25

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