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BMC Bioinformatics. 2017 Sep 20;18(1):421. doi: 10.1186/s12859-017-1837-z.

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.

Author information

1
Departamento de Informática, Escuela Técnica Superior de Ingeniería (ETSE), Universidad de Valencia, 46100, Valencia, Burjassot, Spain.
2
Computational Genomics Department, Prince Felipe Research Center, 46012, Valencia, Spain.
3
Clinical Bioinformatics Research Area, Fundación Progreso y Salud, Hospital Virgen del Rocío, 41013, Sevilla, Spain.
4
Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Hospital Virgen del Rocío, 41013, Sevilla, Spain.
5
HPC Service, University Information Services, University of Cambridge, Cambridge, UK.
6
Genotyping and Genetic Diagnosis Unit, Health Research Institute, INCLIVA, Valencia, Spain.
7
CIBERDem, Health Institute Carlos III, Madrid, Spain.
8
Institute for Integrative Systems Biology (I2SysBio), Universidad de Valencia-CSIC, 46980, Valencia, Paterna, Spain.
9
Clinical Bioinformatics Research Area, Fundación Progreso y Salud, Hospital Virgen del Rocío, 41013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es.
10
Bioinformatics and Data Analysis Unit, Genomic Medicine Institute Imegen, Valencia, Spain. joaquin.dopazo@juntadeandalucia.es.
11
Functional Genomics Node, INB-ELIXIR-es, Hospital Virgen del Rocío, 42013, Sevilla, Spain. joaquin.dopazo@juntadeandalucia.es.

Abstract

BACKGROUND:

The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use.

RESULTS:

Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites. VISMapper can be found at: http://vismapper.babelomics.org .

CONCLUSIONS:

Because it uses novel mapping algorithms VISMapper is remarkably faster than previous available programs. It also provides a useful graphical interface to analyze the integration sites found in the genomic context.

KEYWORDS:

Gene therapy; Genome viewer; Sequence mapping; Viral insertion; Viral integration

PMID:
28931371
PMCID:
PMC5607581
DOI:
10.1186/s12859-017-1837-z
[Indexed for MEDLINE]
Free PMC Article

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