VISPA: A computational pipeline for the identification and analysis of genomic vector integration sites

Andrea Calabria, Simone Leo, Fabrizio Benedicenti, Daniela Cesana, Giulio Spinozzi, Massimilano Orsini, Stefania Merella, Elia Stupka, Gianluigi Zanetti, Eugenio Montini

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number67
JournalGenome Medicine
Volume6
Issue number9
DOIs
Publication statusPublished - Sep 3 2014

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Hematopoietic Stem Cells
Computational Biology
Genetic Therapy
Galaxies
Safety
Hematopoiesis
Cell- and Tissue-Based Therapy
Cell Biology
Stem Cells
Clinical Trials

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics
  • Molecular Biology
  • Molecular Medicine

Cite this

VISPA : A computational pipeline for the identification and analysis of genomic vector integration sites. / Calabria, Andrea; Leo, Simone; Benedicenti, Fabrizio; Cesana, Daniela; Spinozzi, Giulio; Orsini, Massimilano; Merella, Stefania; Stupka, Elia; Zanetti, Gianluigi; Montini, Eugenio.

In: Genome Medicine, Vol. 6, No. 9, 67, 03.09.2014.

Research output: Contribution to journalArticle

Calabria, A, Leo, S, Benedicenti, F, Cesana, D, Spinozzi, G, Orsini, M, Merella, S, Stupka, E, Zanetti, G & Montini, E 2014, 'VISPA: A computational pipeline for the identification and analysis of genomic vector integration sites', Genome Medicine, vol. 6, no. 9, 67. https://doi.org/10.1186/s13073-014-0067-5
Calabria, Andrea ; Leo, Simone ; Benedicenti, Fabrizio ; Cesana, Daniela ; Spinozzi, Giulio ; Orsini, Massimilano ; Merella, Stefania ; Stupka, Elia ; Zanetti, Gianluigi ; Montini, Eugenio. / VISPA : A computational pipeline for the identification and analysis of genomic vector integration sites. In: Genome Medicine. 2014 ; Vol. 6, No. 9.
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