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VCAT: an integrated variant function annotation tools.

Bi Huang^1,2, Cong Fan^1,2, Ken Chen³

¹Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China.

|August 27, 2024

Summary

This summary is machine-generated.

VCAT is a novel webserver that annotates human genomic variants, linking them to functions via epigenome, protein, drug, and RNA data. This tool aids in understanding genotype-phenotype relationships and disease diagnosis by consolidating information from multiple databases.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Advancements in sequencing technology have led to the discovery of numerous human genome variants.
Identifying the functional impact of these variants is crucial for linking genotype to phenotype and diagnosing diseases.
Current variant annotation processes often require researchers to access multiple disparate databases.

Purpose of the Study:

To introduce VCAT (Variant function annotation tools), a comprehensive one-stop webserver for human genomic variant function annotation.
To establish the first platform connecting variants to functional information through epigenome, protein, drug, and RNA data.
To provide interactive visualizations of variant annotations, including charts and molecular structures.

Main Methods:

Development of a user-friendly webserver (VCAT) accessible at https://biomed.nscc-gz.cn/zhaolab/VCAT/.
Integration of data from major genomic variant repositories: dbSNP, 1000 Genomes, gnomAD, ICGC, TCGA, and HPRC Pangenome.
Implementation of data upload in VCF format and results download via URL.
Annotation of over 1.2 billion genomic variants.

Main Results:

VCAT successfully annotated 1,262,041,068 variants from diverse genomic projects.
The webserver provides functional annotations linked to epigenome, protein, drug, and RNA data.
All annotations are presented through interactive visualizations, including charts and molecular structures.
Users can search for variant functions, associated diseases, and potential drug targets.

Conclusions:

VCAT serves as a centralized platform for exploring the functional significance of human genomic variants.
The tool facilitates the investigation of variant-disease and variant-drug relationships.
VCAT enhances the process of genotype-phenotype correlation and disease diagnostics through integrated and visualized variant annotation.