VCAT: an integrated variant function annotation tools.

IF 3.8 2区生物学 Q2 GENETICS & HEREDITY Human Genetics Pub Date : 2024-11-01 Epub Date: 2024-08-27 DOI:10.1007/s00439-024-02699-6

Bi Huang, Cong Fan, Ken Chen, Jiahua Rao, Peihua Ou, Chong Tian, Yuedong Yang, David N Cooper, Huiying Zhao

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Abstract

The development of sequencing technology has promoted discovery of variants in the human genome. Identifying functions of these variants is important for us to link genotype to phenotype, and to diagnose diseases. However, it usually requires researchers to visit multiple databases. Here, we presented a one-stop webserver for variant function annotation tools (VCAT, https://biomed.nscc-gz.cn/zhaolab/VCAT/ ) that is the first one connecting variant to functions via the epigenome, protein, drug and RNA. VCAT is also the first one to make all annotations visualized in interactive charts or molecular structures. VCAT allows users to upload data in VCF format, and download results via a URL. Moreover, VCAT has annotated a huge number (1,262,041,068) of variants collected from dbSNP, 1000 Genomes projects, gnomAD, ICGC, TCGA, and HPRC Pangenome project. For these variants, users are able to searcher their functions, related diseases and drugs from VCAT. In summary, VCAT provides a one-stop webserver to explore the potential functions of human genomic variants including their relationship with diseases and drugs.

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VCAT：综合变异功能注释工具。

测序技术的发展促进了人类基因组变异的发现。确定这些变异的功能对于我们将基因型与表型联系起来以及诊断疾病非常重要。然而，这通常需要研究人员访问多个数据库。在这里，我们展示了变异功能注释工具的一站式网络服务器（VCAT, https://biomed.nscc-gz.cn/zhaolab/VCAT/），它是第一个通过表观基因组、蛋白质、药物和 RNA 将变异与功能联系起来的工具。VCAT 也是第一个将所有注释可视化为交互式图表或分子结构的工具。VCAT 允许用户以 VCF 格式上传数据，并通过 URL 下载结果。此外，VCAT 还注释了从 dbSNP、1000 基因组项目、gnomAD、ICGC、TCGA 和 HPRC Pangenome 项目中收集的大量变异（1,262,041,068 个）。对于这些变异，用户可以从 VCAT 中搜索其功能、相关疾病和药物。总之，VCAT 提供了一个一站式网络服务器来探索人类基因组变异的潜在功能，包括它们与疾病和药物的关系。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Human Genetics 生物-遗传学

CiteScore

10.80

自引率

3.80%

发文量

审稿时长

1 months

期刊介绍： Human Genetics is a monthly journal publishing original and timely articles on all aspects of human genetics. The Journal particularly welcomes articles in the areas of Behavioral genetics, Bioinformatics, Cancer genetics and genomics, Cytogenetics, Developmental genetics, Disease association studies, Dysmorphology, ELSI (ethical, legal and social issues), Evolutionary genetics, Gene expression, Gene structure and organization, Genetics of complex diseases and epistatic interactions, Genetic epidemiology, Genome biology, Genome structure and organization, Genotype-phenotype relationships, Human Genomics, Immunogenetics and genomics, Linkage analysis and genetic mapping, Methods in Statistical Genetics, Molecular diagnostics, Mutation detection and analysis, Neurogenetics, Physical mapping and Population Genetics. Articles reporting animal models relevant to human biology or disease are also welcome. Preference will be given to those articles which address clinically relevant questions or which provide new insights into human biology. Unless reporting entirely novel and unusual aspects of a topic, clinical case reports, cytogenetic case reports, papers on descriptive population genetics, articles dealing with the frequency of polymorphisms or additional mutations within genes in which numerous lesions have already been described, and papers that report meta-analyses of previously published datasets will normally not be accepted. The Journal typically will not consider for publication manuscripts that report merely the isolation, map position, structure, and tissue expression profile of a gene of unknown function unless the gene is of particular interest or is a candidate gene involved in a human trait or disorder.