title: VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing.
abstract: BACKGROUND
  Analyzing 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.
  
  
  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 then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads.
  
  
  CONCLUSIONS
  VISA 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.
authors.affiliation: Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. jhocum@wsu.edu.
authors.forename: Jonah D
authors.initials: JD
authors.lastname: Hocum
authors.affiliation: Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. logan_battrell@wsu.edu.
authors.forename: Logan R
authors.initials: LR
authors.lastname: Battrell
authors.affiliation: Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. ryan.maynard@wsu.edu.
authors.forename: Ryan
authors.initials: R
authors.lastname: Maynard
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. jadair@fhcrc.org.
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Adair
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. bbeard@fhcrc.org.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Beard
authors.affiliation: Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA. drawling@uw.edu.
authors.forename: David J
authors.initials: DJ
authors.lastname: Rawlings
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. hkiem@fhcrc.org.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Kiem
authors.affiliation: Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA. dgmiller@uw.edu.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Miller
authors.affiliation: Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. grant.trobridge@wsu.edu.|School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA. grant.trobridge@wsu.edu.
authors.forename: Grant D
authors.initials: GD
authors.lastname: Trobridge
mesh_terms: D005822:Genetic Vectors; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020407:Internet; D012190:Retroviridae / Q000235:genetics*; D012984:Software; D016662:Virus Integration / Q000235:genetics*