VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy
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. Therefo...
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| Format: | Article |
| Language: | English |
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BMC
2017-09-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-017-1837-z |
| _version_ | 1818571030868787200 |
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| author | José M. Juanes Asunción Gallego Joaquín Tárraga Felipe J. Chaves Pablo Marín-Garcia Ignacio Medina Vicente Arnau Joaquín Dopazo |
| author_facet | José M. Juanes Asunción Gallego Joaquín Tárraga Felipe J. Chaves Pablo Marín-Garcia Ignacio Medina Vicente Arnau Joaquín Dopazo |
| author_sort | José M. Juanes |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T13:50:09Z |
| format | Article |
| id | doaj.art-657e533142b04fec94d76a62bf742616 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-14T13:50:09Z |
| publishDate | 2017-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-657e533142b04fec94d76a62bf7426162022-12-21T22:59:08ZengBMCBMC Bioinformatics1471-21052017-09-011811510.1186/s12859-017-1837-zVISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapyJosé M. Juanes0Asunción Gallego1Joaquín Tárraga2Felipe J. Chaves3Pablo Marín-Garcia4Ignacio Medina5Vicente Arnau6Joaquín Dopazo7Departamento de Informática, Escuela Técnica Superior de Ingeniería (ETSE), Universidad de ValenciaClinical Bioinformatics Research Area, Fundación Progreso y Salud, Hospital Virgen del RocíoComputational Genomics Department, Prince Felipe Research CenterGenotyping and Genetic Diagnosis Unit, Health Research Institute, INCLIVAGenotyping and Genetic Diagnosis Unit, Health Research Institute, INCLIVAHPC Service, University Information Services, University of CambridgeDepartamento de Informática, Escuela Técnica Superior de Ingeniería (ETSE), Universidad de ValenciaClinical Bioinformatics Research Area, Fundación Progreso y Salud, Hospital Virgen del RocíoAbstract 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.http://link.springer.com/article/10.1186/s12859-017-1837-zGene therapyViral insertionViral integrationSequence mappingGenome viewer |
| spellingShingle | José M. Juanes Asunción Gallego Joaquín Tárraga Felipe J. Chaves Pablo Marín-Garcia Ignacio Medina Vicente Arnau Joaquín Dopazo VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy BMC Bioinformatics Gene therapy Viral insertion Viral integration Sequence mapping Genome viewer |
| title | VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy |
| title_full | VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy |
| title_fullStr | VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy |
| title_full_unstemmed | VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy |
| title_short | VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy |
| title_sort | vismapper ultra fast exhaustive cartography of viral insertion sites for gene therapy |
| topic | Gene therapy Viral insertion Viral integration Sequence mapping Genome viewer |
| url | http://link.springer.com/article/10.1186/s12859-017-1837-z |
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