VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.

Jonah D Hocum,Grant D Trobridge,Ryan Maynard,Brian C Beard,Logan R Battrell,Daniel G Miller,David J Rawlings,Jennifer E Adair,Hans-Peter Kiem

doi:10.1186/s12859-015-0653-6

Abstract

BackgroundAnalyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens.ResultsWe developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads.ConclusionsVISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0653-6) contains supplementary material, which is available to authorized users.

Highlights

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use
We present a Vector Integration Site Analysis (VISA) server, a tool that allows investigators with limited bioinformatics experience to rapidly analyze large next generation sequencing (NGS) datasets for Retroviral vector integration site (RIS)
Memory efficiency is largely accomplished by employing a MySQL database for the initial alignment filtering

Summary

Results

We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads

Conclusions

Background

Results and discussion