VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns

Integration of oncogenic DNA viruses into the human genome is a key step in most virus induced carcinogenesis. Here, we constructed a virus integration site (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein-Barr virus based on the next-generation sequencing (NGS) data, literature, and experimental data. There are 63,179 breakpoints and 47,411 junctional sequences with full annotations deposited in the VIS Atlas database, comprising 47 virus genotypes and 17 disease types. The VIS Atlas database provides (1) a genome browser for NGS breakpoint quality check, visualization of VISs, and the local genomic context; (2) a novel platform to discover integration patterns; and (3) a statistics interface for a comprehensive investigation of genotype specific integration features. Data collected in the VIS Atlas aid to provide insights into virus pathogenic mechanisms and the development of novel antitumor drugs. The VIS Atlas database is available at https://www.vis-atlas.tech/.

Automated summary

This study constructed a virus integration site (VIS) Atlas database, which collected integration breakpoints for three most prevalent oncoviruses. The database provides a genome browser, a platform to discover integration patterns, and a statistics interface for a comprehensive investigation of genotype specific integration features.