CN104204220A - 一种遗传变异检测方法 - Google Patents

一种遗传变异检测方法 Download PDF

Info

Publication number
CN104204220A
CN104204220A CN201180076137.XA CN201180076137A CN104204220A CN 104204220 A CN104204220 A CN 104204220A CN 201180076137 A CN201180076137 A CN 201180076137A CN 104204220 A CN104204220 A CN 104204220A
Authority
CN
China
Prior art keywords
window
hereditary variation
statistic
sequencing
value
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.)
Granted
Application number
CN201180076137.XA
Other languages
English (en)
Other versions
CN104204220B (zh
Inventor
陈盛培
张春雷
陈芳
谢伟伟
潘小瑜
汪建
王俊
杨焕明
张秀清
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.)
Hainan Huada Gene Technology Co ltd
Original Assignee
BGI Shenzhen Co Ltd
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 BGI Shenzhen Co Ltd filed Critical BGI Shenzhen Co Ltd
Publication of CN104204220A publication Critical patent/CN104204220A/zh
Application granted granted Critical
Publication of CN104204220B publication Critical patent/CN104204220B/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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/18—Complex mathematical operations for evaluating statistical data, e.g. average values, frequency distributions, probability functions, regression analysis
    • 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

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • General Engineering & Computer Science (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Genetics & Genomics (AREA)
  • General Physics & Mathematics (AREA)
  • Data Mining & Analysis (AREA)
  • Mathematical Optimization (AREA)
  • Mathematical Analysis (AREA)
  • Computational Mathematics (AREA)
  • Pure & Applied Mathematics (AREA)
  • Mathematical Physics (AREA)
  • Operations Research (AREA)
  • Probability & Statistics with Applications (AREA)
  • Algebra (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

本发明公开了一种遗传变异检测方法，包括如下步骤：从测试样本获得测序序列；将所述测序序列与参考基因组序列进行比对；将所述参考基因组序列划分窗口，统计比对至各窗口的测序序列数目，基于所述测序序列数目得到各窗口的统计量；对于一段参考基因组序列，基于其上所有窗口的统计量在该段参考基因组序列上的变化，获得遗传变异位点。

Description

PCT国内申请，说明书已公开。

Claims (1)

  1. PCT国内申请，权利要求书已公开。
CN201180076137.XA 2011-12-31 2011-12-31 一种遗传变异检测方法 Active CN104204220B (zh)

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/CN2011/002244 WO2013097062A1 (zh) 2011-12-31 2011-12-31 一种遗传变异检测方法

Publications (2)

Publication Number Publication Date
CN104204220A true CN104204220A (zh) 2014-12-10
CN104204220B CN104204220B (zh) 2017-06-06

Family

ID=48696161

Family Applications (1)

Application Number Title Priority Date Filing Date
CN201180076137.XA Active CN104204220B (zh) 2011-12-31 2011-12-31 一种遗传变异检测方法

Country Status (9)

Country Link
US (1) US20140370504A1 (zh)
EP (1) EP2772549B8 (zh)
JP (1) JP5993029B2 (zh)
CN (1) CN104204220B (zh)
DK (1) DK2772549T3 (zh)
ES (1) ES2741966T3 (zh)
HU (1) HUE047193T2 (zh)
PL (1) PL2772549T3 (zh)
WO (1) WO2013097062A1 (zh)

Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105354443A (zh) * 2015-12-14 2016-02-24 孔祥军 无创产前基因检测分析软件
CN105734120A (zh) * 2014-12-11 2016-07-06 天津华大基因科技有限公司 检测性发育相关基因变异的方法和试剂盒
CN107480470A (zh) * 2016-06-08 2017-12-15 广州华大基因医学检验所有限公司 基于贝叶斯与泊松分布检验的已知变异检出方法和装置
WO2018214010A1 (zh) * 2017-05-23 2018-11-29 深圳华大基因研究院 一种基于测序数据的变异检测方法、装置和存储介质
CN109086571A (zh) * 2018-08-03 2018-12-25 国家卫生计生委科学技术研究所 一种单基因病遗传变异智能解读及报告的方法和系统
CN109097457A (zh) * 2017-06-20 2018-12-28 深圳华大智造科技有限公司 确定核酸样本中预定位点突变类型的方法
CN109920485A (zh) * 2018-12-29 2019-06-21 浙江安诺优达生物科技有限公司 对测序序列进行变异模拟的方法及其应用
CN111139303A (zh) * 2020-01-03 2020-05-12 西北农林科技大学 一种山羊cadm2基因cnv标记辅助检测生长性状的方法及其应用
CN111429966A (zh) * 2020-04-23 2020-07-17 长沙金域医学检验实验室有限公司 基于稳健线性回归的染色体拷贝数变异判别方法及装置
CN113299342A (zh) * 2021-06-17 2021-08-24 苏州贝康医疗器械有限公司 基于芯片数据的拷贝数变异检测方法及检测装置
CN113436683A (zh) * 2020-03-23 2021-09-24 北京合生基因科技有限公司 筛选候选插入片段的方法和系统

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
SG11201404079SA (en) * 2012-01-20 2014-10-30 Bgi Diagnosis Co Ltd Method and system for determining whether copy number variation exists in sample genome, and computer readable medium
US20160154931A1 (en) 2013-07-17 2016-06-02 Bgi Genomics Co., Limited Method and device for detecting chromosomal aneuploidy
KR102429186B1 (ko) 2013-10-21 2022-08-03 베리나타 헬스, 인코포레이티드 사본수 변동을 결정함에 있어서 검출의 감수성을 향상시키기 위한 방법
CN103993069B (zh) * 2014-03-21 2020-04-28 深圳华大基因科技服务有限公司 病毒整合位点捕获测序分析方法
CA2950596C (en) * 2014-05-30 2023-10-31 Verinata Health, Inc. Detecting fetal sub-chromosomal aneuploidies and copy number variations
EP3502273B1 (en) 2014-12-12 2020-07-08 Verinata Health, Inc. Cell-free dna fragment
CN105986008A (zh) * 2015-01-27 2016-10-05 深圳华大基因科技有限公司 Cnv检测方法和装置
US10095831B2 (en) 2016-02-03 2018-10-09 Verinata Health, Inc. Using cell-free DNA fragment size to determine copy number variations
CN106367512A (zh) * 2016-09-22 2017-02-01 上海序康医疗科技有限公司 一种鉴定样本中肿瘤负荷的方法和系统
US11342047B2 (en) 2017-04-21 2022-05-24 Illumina, Inc. Using cell-free DNA fragment size to detect tumor-associated variant
CN107312850A (zh) * 2017-07-19 2017-11-03 华东医药（杭州）基因科技有限公司 一种pcr无效扩增的检测方法
CN109979529B (zh) * 2017-12-28 2021-01-08 北京安诺优达医学检验实验室有限公司 Cnv检测装置
CN108410970A (zh) * 2018-03-12 2018-08-17 博奥生物集团有限公司 一种单细胞基因组拷贝数变异的检测方法及试剂盒

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN101555528A (zh) * 2008-09-28 2009-10-14 南京市妇幼保健院 一种染色体22q11.2区微缺失、微重复的测定方法
WO2010001419A2 (en) * 2008-07-04 2010-01-07 Decode Genetics Ehf Copy number variations predictive of risk of schizophrenia
WO2010075459A1 (en) * 2008-12-22 2010-07-01 Celula, Inc. Methods and genotyping panels for detecting alleles, genomes, and transcriptomes

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010042716A1 (en) * 2008-10-08 2010-04-15 The Children's Hospital Of Philadelphia Genetic alterations associated with type i diabetes and methods of use thereof for diagnosis and treatment
US8954337B2 (en) * 2008-11-10 2015-02-10 Signature Genomic Interactive genome browser
WO2010057132A1 (en) * 2008-11-14 2010-05-20 The Children's Hospital Of Philadelphia Genetic alterations associated with schizophrenia and methods of use thereof for the diagnosis and treatment of the same

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010001419A2 (en) * 2008-07-04 2010-01-07 Decode Genetics Ehf Copy number variations predictive of risk of schizophrenia
CN101555528A (zh) * 2008-09-28 2009-10-14 南京市妇幼保健院 一种染色体22q11.2区微缺失、微重复的测定方法
WO2010075459A1 (en) * 2008-12-22 2010-07-01 Celula, Inc. Methods and genotyping panels for detecting alleles, genomes, and transcriptomes

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
SEUNGTAI YOON ET AL.: ""Sensitive and accurate detection of copy number variants using read depth of coverage"", 《GENOME RESEARCH》 *

Cited By (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105734120A (zh) * 2014-12-11 2016-07-06 天津华大基因科技有限公司 检测性发育相关基因变异的方法和试剂盒
CN105354443A (zh) * 2015-12-14 2016-02-24 孔祥军 无创产前基因检测分析软件
CN107480470A (zh) * 2016-06-08 2017-12-15 广州华大基因医学检验所有限公司 基于贝叶斯与泊松分布检验的已知变异检出方法和装置
CN110462063A (zh) * 2017-05-23 2019-11-15 深圳华大生命科学研究院 一种基于测序数据的变异检测方法、装置和存储介质
WO2018214010A1 (zh) * 2017-05-23 2018-11-29 深圳华大基因研究院 一种基于测序数据的变异检测方法、装置和存储介质
CN109097457A (zh) * 2017-06-20 2018-12-28 深圳华大智造科技有限公司 确定核酸样本中预定位点突变类型的方法
CN109086571A (zh) * 2018-08-03 2018-12-25 国家卫生计生委科学技术研究所 一种单基因病遗传变异智能解读及报告的方法和系统
CN109086571B (zh) * 2018-08-03 2019-08-23 国家卫生健康委科学技术研究所 一种单基因病遗传变异智能解读及报告的方法和系统
CN109920485A (zh) * 2018-12-29 2019-06-21 浙江安诺优达生物科技有限公司 对测序序列进行变异模拟的方法及其应用
CN109920485B (zh) * 2018-12-29 2023-10-31 浙江安诺优达生物科技有限公司 对测序序列进行变异模拟的方法及其应用
CN111139303A (zh) * 2020-01-03 2020-05-12 西北农林科技大学 一种山羊cadm2基因cnv标记辅助检测生长性状的方法及其应用
CN113436683A (zh) * 2020-03-23 2021-09-24 北京合生基因科技有限公司 筛选候选插入片段的方法和系统
CN111429966A (zh) * 2020-04-23 2020-07-17 长沙金域医学检验实验室有限公司 基于稳健线性回归的染色体拷贝数变异判别方法及装置
CN113299342A (zh) * 2021-06-17 2021-08-24 苏州贝康医疗器械有限公司 基于芯片数据的拷贝数变异检测方法及检测装置
CN113299342B (zh) * 2021-06-17 2024-03-15 苏州贝康医疗器械有限公司 基于芯片数据的拷贝数变异检测方法及检测装置

Also Published As

Publication number Publication date
WO2013097062A1 (zh) 2013-07-04
DK2772549T3 (da) 2019-08-19
US20140370504A1 (en) 2014-12-18
PL2772549T3 (pl) 2019-12-31
EP2772549A1 (en) 2014-09-03
EP2772549B1 (en) 2019-07-31
HUE047193T2 (hu) 2020-04-28
EP2772549B8 (en) 2019-09-11
JP2015502749A (ja) 2015-01-29
EP2772549A4 (en) 2015-03-18
ES2741966T3 (es) 2020-02-12
CN104204220B (zh) 2017-06-06
JP5993029B2 (ja) 2016-09-14

Similar Documents

Publication Publication Date Title
CN104204220B (zh) 一种遗传变异检测方法
CN104221022B (zh) 一种拷贝数变异检测方法和系统
CN110313034B (zh) 对核酸分子进行测序的方法、机器可读介质和计算机系统
JP6521956B2 (ja) 性染色体におけるコピー数変異を判定するための方法
CN106544407B (zh) 确定受体cfDNA样本中供体来源cfDNA比例的方法
EP3656875B1 (en) Non-invasive prenatal diagnosis
CN105392894B (zh) 确定样本基因组中是否存在拷贝数变异的方法、系统和计算机可读介质
CN103608818B (zh) 非侵入性产前倍性识别装置
JP2020054400A (ja) 高度多重ｐｃｒ法および組成物
CN107077537B (zh) 用短读测序数据检测重复扩增
JP2021101742A (ja) 卵子提供による妊娠での胎児異数性の非侵襲的検出
CN109439729A (zh) 检测低频变异用的接头、接头混合物及相应方法
KR20180020137A (ko) 고유 분자 색인(umi)을 갖는 용장성 판독을 사용하는 서열분석된 dna 단편의 오류 억제
JP2022514879A (ja) 無細胞ｄｎａ末端特性
CN112126677B (zh) 耳聋单倍型基因突变无创检测方法
CN109971846A (zh) 使用双等位基因snp靶向下一代测序的非侵入性产前测定非整倍体的方法
CN105051208A (zh) 确定胚胎基因组中预定区域碱基信息的方法、系统和计算机可读介质
CN105555970A (zh) 同时进行单体型分析和染色体非整倍性检测的方法和系统
CN110373458B (zh) 一种地中海贫血检测的试剂盒及分析系统
CN110993025A (zh) 胎儿浓度定量的方法和装置及胎儿基因分型的方法和装置
CN112760365B (zh) 一种适用于产前无创的poag基因检测试剂盒及其检测方法
JP2014530629A (ja) 染色体の微細欠失及び微細重複を検出する方法
EP3596229A1 (en) Method and system for nucleic acid sequencing
CN108866197A (zh) Ptch2基因突变位点在判断年轻乳腺癌易感性中的应用
CN117925820A (zh) 一种用于胚胎植入前变异检测的方法

Legal Events

Date Code Title Description
C06 Publication
PB01 Publication
C10 Entry into substantive examination
SE01 Entry into force of request for substantive examination
CB02 Change of applicant information

Address after: Yantian District of Shenzhen City, Guangdong province 518083 Hongan street No. 21 China Comprehensive Park 7 Building 7 layer -14 layer

Applicant after: BGI SHENZHEN CO LTD

Address before: 2, 3 floor, Beishan Industrial Zone, 146 North Mountain Road, Yantian District, Shenzhen, Guangdong, China 11

Applicant before: Shenzhen BGI Medicine Co., Ltd.

COR Change of bibliographic data
GR01 Patent grant
GR01 Patent grant
TR01 Transfer of patent right
TR01 Transfer of patent right

Effective date of registration: 20220112

Address after: 570311 room 201-2, floor 2, building a, leading science and Technology Innovation Park, Haikou national high tech Zone, No. 6, Yaogu 1st Road, Xiuying District, Haikou City, Hainan Province

Patentee after: Hainan Huada Gene Technology Co.,Ltd.

Address before: 518083 Huada Complex Park, 21 Hongan Third Street, Yantian District, Shenzhen City, Guangdong Province, 7 buildings, 7 floors-14 floors

Patentee before: BGI SHENZHEN Co.,Ltd.