BIG-Annotator：基因组测序数据高效功能注释及其在遗传诊断中的应用

doi:10.16288/j.yczz.18-274

遗传 ›› 2018, Vol. 40 ›› Issue (11): 1015-1023.doi: 10.16288/j.yczz.18-274

BIG-Annotator：基因组测序数据高效功能注释及其在遗传诊断中的应用

黄莹^1,²,刘琪¹,池连江¹,石承民¹,吴祯¹,胡敏³,石宏⁴,陈华^1,²()

^1. 中国科学院北京基因组研究所,中国科学院精准基因组医学重点实验室,北京 100101
^2. 中国科学院大学未来技术学院,北京 100094
^3. 云南省骨代谢性疾病机理及药物干预重点实验室,昆明 650214
^4. 昆明理工大学灵长类转化医学研究中心,昆明 650500

收稿日期:2018-09-29 修回日期:2018-11-02 出版日期:2018-11-20 发布日期:2018-11-06
通讯作者: 陈华 E-mail:chenh@big.ac.cn
作者简介:黄莹,硕士研究生,专业方向：群体与计算遗传学。E-mail: huangying@big.ac.cn
基金资助:
国家自然科学基金项目(31571370);国家自然科学基金项目(91631106);中国科学院“百人计划”项目资助

Application of BIG-Annotator in the genome sequencing data functional annotation and genetic diagnosis

Ying Huang^1,²,Qi Liu¹,Lianjiang Chi¹,Chengmin Shi¹,Zhen Wu¹,Min Hu³,Hong Shi⁴,Hua Chen^1,²()

^1. CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
^2. School of Future Technology, University of Chinese Academy of Sciences, Beijing 100094, China
^3. Yunnan Key Laboratory of Basic Research on Bone and Joint Diseases, Kunming 650214, China
^4. Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China

Received:2018-09-29 Revised:2018-11-02 Online:2018-11-20 Published:2018-11-06
Contact: Chen Hua E-mail:chenh@big.ac.cn
Supported by:
Supported by the National Natural Science Foundation of China(31571370);Supported by the National Natural Science Foundation of China(91631106);the “Hundred Talents Program” of Chinese Academy of Sciences

摘要/Abstract

摘要：

近年来二代测序技术发展迅速,在精准医疗和遗传诊断上得到日益广泛的应用。对二代测序数据进行分析的一个核心环节是对遗传变异位点的识别和注释。基于此,本课题组开发了一个能高效对全基因组单核苷酸多态位点进行功能注释的软件——BIG-Annotator。该软件以JAVA语言编写,且提供多线程运行模式,运行更为高效,比现有的同类软件或流程提速10多倍,适用于人群队列研究、大样本全基因组关联分析等数据量庞大、时效性要求高的分析需求。同时,该软件还集成了目前常用的二代测序遗传变异注释数据库,以及临床数据解读与报告的标准指南(2015 ACMG-AMP《解读报告标准指南》),并且增加了针对肿瘤组织遗传变异注释的信息。最后,通过两个研究实例具体说明该软件在遗传诊断中的应用。

关键词: 二代测序, 遗传变异注释, 遗传诊断, 精准医学

Abstract:

The next generation sequencing (NGS) technology has been playing important roles in genetic diagnosis of diseases in recent years, and serving as a technological basis of precision medicine. In analyzing NGS data, the variant annotation is an important step. In this study, we developed a computationally efficient software (BIG-Annotator) to perform functional annotation for whole-genome single nucleotide polymorphisms. BIG-Annotator integrates the widely used databases and pipelines for variant annotation of genetic diseases and tumors, and follows the 2015 ACMG-AMP Standard Guide for Interpretation and Reporting of Clinical Variants. BIG-Annotator is ten times faster than the existing software, and suitable for annotating genomic sequencing data from large samples. Here we present two analysis cases of genetic diagnosis using BIG-Annotator to show its applications.

Key words: NGS, variant annotation, genetic diagnosis, precision medicine

黄莹,刘琪,池连江,石承民,吴祯,胡敏,石宏,陈华. BIG-Annotator：基因组测序数据高效功能注释及其在遗传诊断中的应用[J]. 遗传, 2018, 40(11): 1015-1023.

Ying Huang,Qi Liu,Lianjiang Chi,Chengmin Shi,Zhen Wu,Min Hu,Hong Shi,Hua Chen. Application of BIG-Annotator in the genome sequencing data functional annotation and genetic diagnosis[J]. Hereditas(Beijing), 2018, 40(11): 1015-1023.

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BIG-Annotator：基因组测序数据高效功能注释及其在遗传诊断中的应用

Application of BIG-Annotator in the genome sequencing data functional annotation and genetic diagnosis

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