CN110462063A - 一种基于测序数据的变异检测方法、装置和存储介质 - Google Patents

一种基于测序数据的变异检测方法、装置和存储介质 Download PDF

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CN110462063A
CN110462063A CN201780089042.9A CN201780089042A CN110462063A CN 110462063 A CN110462063 A CN 110462063A CN 201780089042 A CN201780089042 A CN 201780089042A CN 110462063 A CN110462063 A CN 110462063A
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CN110462063B (zh
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莫晓东
杨焕杰
张涛
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BGI Shenzhen Co Ltd
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Abstract

一种基于测序数据的变异检测方法、装置和存储介质，该方法包括：将来源于同一群体的多个个体的测序数据比对到参考基因组并进行变异检测，得到读长的比对位置和变异信息；针对各个变异位点，将群体中所有个体的变异位点总深度、变异碱基型深度分别加和，然后计算各个变异位点在群体中的次等位基因频率和/或哈迪温伯格平衡；绘制变异位点总深度和/或变异碱基型深度与dbSNP%关系图，并对变异位点总深度和/或变异碱基型深度以及次等位基因频率和/或哈迪温伯格平衡进行过滤；对每个个体的变异信息进行过滤，得到每个个体的最终变异信息。本发明的方法能够利用群体的低深度测序数据进行精准的变异检测，提高数据利用率。

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PCT国内申请，说明书已公开。

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  1. PCT国内申请，权利要求书已公开。
CN201780089042.9A 2017-05-23 2017-05-23 一种基于测序数据的变异检测方法、装置和存储介质 Active CN110462063B (zh)

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CN111292803B (zh) * 2020-02-10 2024-04-26 广州金域医学检验集团股份有限公司 基因组断裂点识别方法及应用
CN113517022A (zh) * 2021-06-10 2021-10-19 阿里巴巴新加坡控股有限公司 基因检测方法、特征提取方法、装置、设备及系统

Citations (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN102952854A (zh) * 2011-08-25 2013-03-06 深圳华大基因科技有限公司 单细胞分类和筛选方法及其装置
CN103080333A (zh) * 2010-09-14 2013-05-01 深圳华大基因科技有限公司 一种基因组结构性变异检测方法和系统
CN103525899A (zh) * 2012-07-02 2014-01-22 中国科学院上海生命科学研究院 2型糖尿病易感基因位点及检测方法和试剂盒
CN103617256A (zh) * 2013-11-29 2014-03-05 北京诺禾致源生物信息科技有限公司 待变异检测文件的处理方法及装置
CN104204220A (zh) * 2011-12-31 2014-12-10 深圳华大基因医学有限公司 一种遗传变异检测方法
WO2016000267A1 (zh) * 2014-07-04 2016-01-07 深圳华大基因股份有限公司 确定探针序列的方法和基因组结构变异的检测方法
CN105512514A (zh) * 2014-09-23 2016-04-20 深圳华大基因股份有限公司 一种mhc补全数据库、其构建方法和应用
CN106156538A (zh) * 2016-06-29 2016-11-23 天津诺禾医学检验所有限公司 一种全基因组变异数据的注释方法和注释系统
JP2017016665A (ja) * 2015-07-03 2017-01-19 国立大学法人東北大学 配列のデータからの変異情報の選択方法、システム、及び、コンピュータプログラム

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105441432B (zh) * 2014-09-05 2019-05-28 天津华大基因科技有限公司 组合物及其在序列测定和变异检测中的用途
WO2016049878A1 (zh) * 2014-09-30 2016-04-07 深圳华大基因科技有限公司 一种基于snp分型的亲子鉴定方法及应用
CN105989246B (zh) * 2015-01-28 2018-10-26 深圳华大智造科技有限公司 一种基于基因组组装的变异检测方法和装置
CN105760712B (zh) * 2016-03-01 2019-03-26 西安电子科技大学 一种基于新一代测序的拷贝数变异检测方法
CN105925685A (zh) * 2016-05-13 2016-09-07 万康源(天津)基因科技有限公司 一种基于家系的外显子组潜在致病变异检测方法
CN106520940A (zh) * 2016-11-04 2017-03-22 深圳华大基因研究院 一种染色体非整倍体和拷贝数变异检测方法及其应用

Patent Citations (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN103080333A (zh) * 2010-09-14 2013-05-01 深圳华大基因科技有限公司 一种基因组结构性变异检测方法和系统
CN102952854A (zh) * 2011-08-25 2013-03-06 深圳华大基因科技有限公司 单细胞分类和筛选方法及其装置
CN104204220A (zh) * 2011-12-31 2014-12-10 深圳华大基因医学有限公司 一种遗传变异检测方法
CN103525899A (zh) * 2012-07-02 2014-01-22 中国科学院上海生命科学研究院 2型糖尿病易感基因位点及检测方法和试剂盒
CN103617256A (zh) * 2013-11-29 2014-03-05 北京诺禾致源生物信息科技有限公司 待变异检测文件的处理方法及装置
WO2016000267A1 (zh) * 2014-07-04 2016-01-07 深圳华大基因股份有限公司 确定探针序列的方法和基因组结构变异的检测方法
CN105512514A (zh) * 2014-09-23 2016-04-20 深圳华大基因股份有限公司 一种mhc补全数据库、其构建方法和应用
JP2017016665A (ja) * 2015-07-03 2017-01-19 国立大学法人東北大学 配列のデータからの変異情報の選択方法、システム、及び、コンピュータプログラム
CN106156538A (zh) * 2016-06-29 2016-11-23 天津诺禾医学检验所有限公司 一种全基因组变异数据的注释方法和注释系统

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
ANDRÉ ALTMANN ET AL.: "A beginners guide to SNP calling from high-throughput DNA-sequencing data", 《HUM GENET》 *
ANDRÉ ALTMANN ET AL.: "A beginners guide to SNP calling from high-throughput DNA-sequencing data", 《HUM GENET》, vol. 131, no. 10, 30 October 2012 (2012-10-30), pages 1541 - 1554, XP035106208, DOI: 10.1007/s00439-012-1213-z *
李燕 等: "新一代测序的拷贝数变异检测算法研究与设计", 《生物信息学》 *
李燕 等: "新一代测序的拷贝数变异检测算法研究与设计", 《生物信息学》, vol. 13, no. 3, 15 September 2015 (2015-09-15), pages 186 - 191 *

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