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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.

journal_name

Genome Med

journal_title

Genome medicine

authors

Calabria A,Leo S,Benedicenti F,Cesana D,Spinozzi G,Orsini M,Merella S,Stupka E,Zanetti G,Montini E

doi

10.1186/s13073-014-0067-5

subject

Has Abstract

pub_date

2014-09-03 00:00:00

pages

67

issue

9

issn

1756-994X

pii

67

journal_volume

6

pub_type

杂志文章

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