PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Issue Volume 51:Issue D1(2023) (16th October 2022)

• Record Type: Journal Article
• Authors: Wang, Yimin; Ling, Yunchao; Gong, Jiao; Zhao, Xiaohan; Zhou, Hanwen; Xie, Bo; Lou, Haiyi; Zhuang, Xinhao; Jin, Li; Fan, Shaohua; Zhang, Guoqing; Xu, Shuhua
• Is Part Of: Nucleic acids research. Volume 51:Issue D1(2023)
• Page Start: D1109
• Page End: D1116
• Publication Date: 2022-10-16
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac905
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: 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 .