VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing |
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| Authors: | Jonah D. Hocum Logan R. Battrell Ryan Maynard Jennifer E. Adair Brian C. Beard David J. Rawlings Hans-Peter Kiem Daniel G. Miller Grant D. Trobridge |
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| Affiliation: | .Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210 USA ;.Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 USA ;.Department of Pediatrics, University of Washington, Seattle, WA 98195 USA ;.School of Molecular Biosciences, Washington State University, Pullman, WA 99164 USA |
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| 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. |
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| Keywords: | Bioinformatics Gene therapy Retroviral vectors Next-generation sequencing Retroviral mutagenesis |
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