PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform

doi:10.1093/nar/gkac905

	PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform
	Wang, Yimin 1,2; Ling, Yunchao 1,2; Gong, Jiao 3,4,5; Zhao, Xiaohan 3,4,5; Zhou, Hanwen 1,2; Xie, Bo 1,2; Lou, Haiyi 3; Zhuang, Xinhao 1,2; Jin, Li 3,4,5; Fan, Shaohua 3; Zhang, Guoqing 1,2; Xu, Shuhua3,4,5,6,7,8,9
	2022-10
发表期刊	NUCLEIC ACIDS RESEARCH (IF:16.6[JCR-2023],16.1[5-Year])
ISSN	0305-1048
EISSN	1362-4962
DOI	10.1093/nar/gkac905
摘要	Structural variations (SVs) play important roles in human evolution and diseases, but there is a lack of data resources concerning representative samples, especially for East Asians. Taking advantage of both next-generation sequencing and third-generation sequencing data at the whole-genome level, we developed the database PGG.SV to provide a practical platform for both regionally and globally representative structural variants. In its current version, PGG.SV archives 584 277 SVs obtained from whole-genome sequencing data of 6048 samples, including 1030 long-read sequencing genomes representing 177 global populations. PGG.SV provides (i) high-quality SVs with fine-scale and precise genomic locations in both GRCh37 and GRCh38, covering underrepresented SVs in existing sequencing and microarray data; (ii) hierarchical estimation of SV prevalence in geographical populations; (iii) informative annotations of SV-related genes, potential functions and clinical effects; (iv) an analysis platform to facilitate SV-based case-control association studies and (v) various visualization tools for understanding the SV structures in the human genome. Taken together, PGG. SV provides a user-friendly online interface, easy-to-use analysis tools and a detailed presentation of results. PGG. SV is freely accessible via https://www.biosino.org/pggsv.
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收录类别	SCIE ; SCOPUS
语种	英语
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000868391900001
出版者	OXFORD UNIV PRESS
原始文献类型	Article; Early Access
引用统计	被引频次：7[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/243242
专题	生命科学与技术学院_特聘教授组_徐书华组
通讯作者	Fan, Shaohua; Zhang, Guoqing; Xu, Shuhua
作者单位	1.Chinese Acad Sci, Univ Chinese Acad Sci, Natl Genom Data Ctr, Shanghai Inst Nutr & Hlth,Key Lab Computat Biol, Shanghai 200031, Peoples R China; 2.Chinese Acad Sci, Univ Chinese Acad Sci, Biomed Big Data Ctr, Shanghai 200031, Peoples R China; 3.Fudan Univ, Ctr Evolutionary Biol, Collaborat Innovat Ctr Genet & Dev, Sch Life Sci,State Key Lab Genet Engn, Shanghai 200438, Peoples R China; 4.Fudan Univ, Human Phenome Inst, Zhangjiang Fudan Int Innovat Ctr, Shanghai 201203, Peoples R China; 5.Fudan Univ, Minist Educ, Key Lab Contemporary Anthropol, Shanghai 201203, Peoples R China; 6.Fudan Univ, Zhongshan Hosp, Dept Liver Surg, Shanghai 200032, Peoples R China; 7.Fudan Univ, Zhongshan Hosp, Transplantat Liver Canc Inst, Shanghai 200032, Peoples R China; 8.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China; 9.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
通讯作者单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Wang, Yimin,Ling, Yunchao,Gong, Jiao,et al. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform[J]. NUCLEIC ACIDS RESEARCH,2022.
APA	Wang, Yimin.,Ling, Yunchao.,Gong, Jiao.,Zhao, Xiaohan.,Zhou, Hanwen.,...&Xu, Shuhua.(2022).PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform.NUCLEIC ACIDS RESEARCH.
MLA	Wang, Yimin,et al."PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform".NUCLEIC ACIDS RESEARCH (2022).