A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing

Here we describe a virus discovery protocol for a range of different virus genera, that can be applied to biopsy-sized tissue samples. Our viral enrichment procedure, validated using canine and human liver samples, significantly improves viral read copy number and increases the length of viral conti...

Descripción completa

Detalles Bibliográficos
Autores principales: Daly, Gordon M., Bexfield, Nick, Heaney, Judith, Stubbs, Sam, Mayer, Antonia P., Palser, Anne, Kellam, Paul, Drou, Nizar, Caccamo, Mario, Tiley, Laurence, Alexander, Graeme J. M., Bernal, William, Heeney, Jonathan L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244418/
https://www.ncbi.nlm.nih.gov/pubmed/22216131
http://dx.doi.org/10.1371/journal.pone.0028879
_version_ 1782219727606644736
author Daly, Gordon M.
Bexfield, Nick
Heaney, Judith
Stubbs, Sam
Mayer, Antonia P.
Palser, Anne
Kellam, Paul
Drou, Nizar
Caccamo, Mario
Tiley, Laurence
Alexander, Graeme J. M.
Bernal, William
Heeney, Jonathan L.
author_facet Daly, Gordon M.
Bexfield, Nick
Heaney, Judith
Stubbs, Sam
Mayer, Antonia P.
Palser, Anne
Kellam, Paul
Drou, Nizar
Caccamo, Mario
Tiley, Laurence
Alexander, Graeme J. M.
Bernal, William
Heeney, Jonathan L.
author_sort Daly, Gordon M.
collection PubMed
description Here we describe a virus discovery protocol for a range of different virus genera, that can be applied to biopsy-sized tissue samples. Our viral enrichment procedure, validated using canine and human liver samples, significantly improves viral read copy number and increases the length of viral contigs that can be generated by de novo assembly. This in turn enables the Illumina next generation sequencing (NGS) platform to be used as an effective tool for viral discovery from tissue samples.
format Online
Article
Text
id pubmed-3244418
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-32444182012-01-03 A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing Daly, Gordon M. Bexfield, Nick Heaney, Judith Stubbs, Sam Mayer, Antonia P. Palser, Anne Kellam, Paul Drou, Nizar Caccamo, Mario Tiley, Laurence Alexander, Graeme J. M. Bernal, William Heeney, Jonathan L. PLoS One Research Article Here we describe a virus discovery protocol for a range of different virus genera, that can be applied to biopsy-sized tissue samples. Our viral enrichment procedure, validated using canine and human liver samples, significantly improves viral read copy number and increases the length of viral contigs that can be generated by de novo assembly. This in turn enables the Illumina next generation sequencing (NGS) platform to be used as an effective tool for viral discovery from tissue samples. Public Library of Science 2011-12-21 /pmc/articles/PMC3244418/ /pubmed/22216131 http://dx.doi.org/10.1371/journal.pone.0028879 Text en Daly et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Daly, Gordon M.
Bexfield, Nick
Heaney, Judith
Stubbs, Sam
Mayer, Antonia P.
Palser, Anne
Kellam, Paul
Drou, Nizar
Caccamo, Mario
Tiley, Laurence
Alexander, Graeme J. M.
Bernal, William
Heeney, Jonathan L.
A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing
title A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing
title_full A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing
title_fullStr A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing
title_full_unstemmed A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing
title_short A Viral Discovery Methodology for Clinical Biopsy Samples Utilising Massively Parallel Next Generation Sequencing
title_sort viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244418/
https://www.ncbi.nlm.nih.gov/pubmed/22216131
http://dx.doi.org/10.1371/journal.pone.0028879
work_keys_str_mv AT dalygordonm aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT bexfieldnick aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT heaneyjudith aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT stubbssam aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT mayerantoniap aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT palseranne aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT kellampaul aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT drounizar aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT caccamomario aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT tileylaurence aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT alexandergraemejm aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT bernalwilliam aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT heeneyjonathanl aviraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT dalygordonm viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT bexfieldnick viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT heaneyjudith viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT stubbssam viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT mayerantoniap viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT palseranne viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT kellampaul viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT drounizar viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT caccamomario viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT tileylaurence viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT alexandergraemejm viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT bernalwilliam viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing
AT heeneyjonathanl viraldiscoverymethodologyforclinicalbiopsysamplesutilisingmassivelyparallelnextgenerationsequencing

Ejemplares similares