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

Info

Publication number
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
Authority
CN
China
Prior art keywords
region
interest
sequence reads
sequence
genome
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Active
Application number
CN201380062074.1A
Other languages
English (en)
Chinese (zh)
Other versions
CN104937598A (zh
Inventor
X.陈
Y.李
W-m.刘
X.(M.).马
S-J.张
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
F Hoffmann La Roche AG
Original Assignee
F Hoffmann La Roche AG
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by F Hoffmann La Roche AG filed Critical F Hoffmann La Roche AG
Publication of CN104937598A publication Critical patent/CN104937598A/zh
Application granted granted Critical
Publication of CN104937598B publication Critical patent/CN104937598B/zh
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • 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

Landscapes

  • 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)

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

Family

ID=49641777

Family Applications (1)

Application Number Title Priority Date Filing Date
CN201380062074.1A Active CN104937598B (zh) 2012-11-29 2013-11-27 靶向的测序读取值的准确且快速的定位

Country Status (7)

Country Link
US (2) US9218450B2 (cg-RX-API-DMAC7.html)
EP (1) EP2926288B1 (cg-RX-API-DMAC7.html)
JP (1) JP6240210B2 (cg-RX-API-DMAC7.html)
CN (1) CN104937598B (cg-RX-API-DMAC7.html)
CA (1) CA2891731C (cg-RX-API-DMAC7.html)
ES (1) ES2869292T3 (cg-RX-API-DMAC7.html)
WO (1) WO2014083023A1 (cg-RX-API-DMAC7.html)

Families Citing this family (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2697397B1 (en) 2011-04-15 2017-04-05 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
US9857328B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same
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
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
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
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
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
US10854317B2 (en) * 2017-12-29 2020-12-01 Act Genomics Co., Ltd. Method and system for sequence alignment and variant calling
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
KR20230009877A (ko) * 2020-05-08 2023-01-17 일루미나, 인코포레이티드 게놈 서열분석 및 검출 기술

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
US20040229269A1 (en) 2003-05-15 2004-11-18 Ghazala Hashmi 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
KR102393608B1 (ko) * 2012-09-04 2022-05-03 가던트 헬쓰, 인크. 희귀 돌연변이 및 카피수 변이를 검출하기 위한 시스템 및 방법

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

Also Published As

Publication number Publication date
ES2869292T3 (es) 2021-10-25
CN104937598A (zh) 2015-09-23
EP2926288B1 (en) 2021-03-17
US20140149049A1 (en) 2014-05-29
JP2015536661A (ja) 2015-12-24
CA2891731A1 (en) 2014-06-05
US10127351B2 (en) 2018-11-13
CA2891731C (en) 2017-09-12
US9218450B2 (en) 2015-12-22
WO2014083023A1 (en) 2014-06-05
US20160092630A1 (en) 2016-03-31
JP6240210B2 (ja) 2017-11-29
EP2926288A1 (en) 2015-10-07

Similar Documents

Publication Publication Date Title
CN104937598B (zh) 靶向的测序读取值的准确且快速的定位
AU2023251452B2 (en) Validation methods and systems for sequence variant calls
CN106462670B (zh) 超深度测序中的罕见变体召集
CN113160882A (zh) 一种基于三代测序的病原微生物宏基因组检测方法
CN103975329B (zh) 一种基因分析方法及装置
JP2024056939A (ja) 生体試料のフィンガープリンティングのための方法
CN116189763A (zh) 一种基于二代测序的单样本拷贝数变异检测方法
CN115083521A (zh) 一种单细胞转录组测序数据中肿瘤细胞类群的鉴定方法及系统
CN115867665A (zh) 嵌合扩增子阵列测序
WO2019132010A1 (ja) 塩基配列における塩基種を推定する方法、装置及びプログラム
CN110475874A (zh) 脱靶序列在dna分析中的应用
KR20210040714A (ko) 핵산 서열 분석에서 위양성 변이를 검출하는 방법 및 장치
CN114974416A (zh) 一种检测相邻多核苷酸变异的方法及装置
HK40010599A (en) Validation methods and systems for sequence variant calls
HK40012524A (en) Validation methods and systems for sequence variant calls

Legal Events

Date Code Title Description
PB01 Publication
C10 Entry into substantive examination
SE01 Entry into force of request for substantive examination
GR01 Patent grant
GR01 Patent grant