title: VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites.
abstract: The analysis of the genomic distribution of viral vector genomic integration sites is a key step in hematopoietic stem cell-based gene therapy applications, allowing to assess both the safety and the efficacy of the treatment and to study the basic aspects of hematopoiesis and stem cell biology. Identifying vector integration sites requires ad-hoc bioinformatics tools with stringent requirements in terms of computational efficiency, flexibility, and usability. We developed VISPA (Vector Integration Site Parallel Analysis), a pipeline for automated integration site identification and annotation based on a distributed environment with a simple Galaxy web interface. VISPA was successfully used for the bioinformatics analysis of the follow-up of two lentiviral vector-based hematopoietic stem-cell gene therapy clinical trials. Our pipeline provides a reliable and efficient tool to assess the safety and efficacy of integrating vectors in clinical settings.
authors.affiliation: San Raffaele Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, 20132 Milano, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Calabria
authors.affiliation: Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09010 Pula, CA Italy ; Università degli Studi di Cagliari, 09124 Cagliari, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Leo
authors.affiliation: San Raffaele Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, 20132 Milano, Italy.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Benedicenti
authors.affiliation: San Raffaele Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, 20132 Milano, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Cesana
authors.affiliation: San Raffaele Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, 20132 Milano, Italy ; Department of Informatics, Systems and Communication (DISCo) - University of Milano-Bicocca, Milano, Italy.
authors.forename: Giulio
authors.initials: G
authors.lastname: Spinozzi
authors.affiliation: Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09010 Pula, CA Italy.
authors.forename: Massimilano
authors.initials: M
authors.lastname: Orsini
authors.affiliation: Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Merella
authors.affiliation: Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy.
authors.forename: Elia
authors.initials: E
authors.lastname: Stupka
authors.affiliation: Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09010 Pula, CA Italy.
authors.forename: Gianluigi
authors.initials: G
authors.lastname: Zanetti
authors.affiliation: San Raffaele Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, 20132 Milano, Italy.
authors.forename: Eugenio
authors.initials: E
authors.lastname: Montini