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

BMC Bioinformatics

Software

Joaquín Dopazo¹  Asunción Gallego²  Joaquín Tárraga³  José M. Juanes⁴  Vicente Arnau⁵  Felipe J. Chaves⁶  Pablo Marín-Garcia⁷  Ignacio Medina⁸ 

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

关键词: Gene therapy;    Viral insertion;    Viral integration;    Sequence mapping;    Genome viewer;   

DOI  :  10.1186/s12859-017-1837-z

 received in 2017-02-13, accepted in 2017-09-12,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere 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.ConclusionsBecause 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.

【 授权许可】

CC BY   
© The Author(s). 2017