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. 2025 Jan 6;53(D1):D1557-D1562.
doi: 10.1093/nar/gkae1015.

SV4GD: a comprehensive structural variation database specially for genetic diseases

Lei Shi  1 , Sainan Zhang  2 , Ying Li  1   3 , Hailong Li  2 , Xin Wang  1   4 , Meiyu Du  2 , Meiyi Zhang  2 , Liyan Ke  1   4 , Yueni Zhang  1   4 , Chao Xu  1   5 , Senwei Tan  2 , Zitong Zhang  1   4 , Duoyi Zhang  5 , Jiaping Wang  2 , Changlu Qi  2 , Xingwang Liu  2 , Xin Wang  6 , Kai Qian  2 , Liang Cheng  1   2 , Xue Zhang  1   3   7
Affiliations

SV4GD: a comprehensive structural variation database specially for genetic diseases

Lei Shi et al. Nucleic Acids Res. .

Abstract

Structural variations (SVs) contribute to a large extent to genomic diversity and are highly relevant for various human genetic diseases. The sensitivity and specificity of SV identification have significantly improved with the development and widespread application of high-throughput sequencing, making clinical diagnosis and treatment more accurate. Therefore, the SV4GD (Structural Variation for Genetic Diseases, https://bio-computing.hrbmu.edu.cn/SV4GD/), a manually curated database, was constructed to provide a comprehensive, standardized and user-friendly data resource for selective batch browsing, searching, downloading and comparing those genetic disease-relevant SVs. This database compiles 10 305 records of germline structural variants from 58 human neoplastic diseases and 232 non-neoplastic genetic diseases, including 2695 disease-related SVs, and other 7610 pending research SVs detected from patients. SV4GD provides a browser and search engine to query for the detailed information of SVs, human genetic diseases and the clinical information of patients, providing an easy-to-use online tool for clinical and molecular genetics research.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Overview of SV4GD. Relevant pieces of literature were searched based on keywords in the MEDLINE database. Literature information was extracted and sorted, and the data format was standardized. The database provides quick links to public disease (Disease Ontology and Online Mendelian Inheritance in Man) and variant (DGV and DECIPHER) databases and has different forms of search modules.
Figure 2.
Figure 2.
Statistics of the disease-related SVs in SV4GD. (A) Variant type. (B) Variant type per chromosome. (C) Parent of origin. (D) Inheritance pattern. The SVs with the X-linked origin were divided. (E) Pathogenic classification according to the ACMG guideline and the original publications. (F) Formation mechanism.
Figure 3.
Figure 3.
User interface of SV4GD. (A) The interface of the browse module with ‘Neoplastic disease’ page and ‘Non-neoplastic genetic disease’ page. (B) Global information visualization and detailed information table of SVs. (C) Search module and its submodules. (D) The detail content of SVs. (E) Download information for SVs.
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