PolyTB: a genomic variation map for Mycobacterium tuberculosis

9 Páginas, 5 figuras, 1 tabla

Detalles Bibliográficos
Autores: Coll, Francesc, Preston, Mark, Guerra-Assunção, José Afonso, Hill-Cawthorn, Grant, Harris, David, Perdigão, João, Viveiros, Miguel, Portugal, Isabel, Drobniewski, Francis, Gagneux, Sebastien, Glynn, Judith R., Pain, Arnab, Parkhill, Julian, McNerney, Ruth, Martin, Nigel, Clark, Taane G.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2014
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/346127
Acceso en línea:http://hdl.handle.net/10261/346127
Access Level:acceso abierto
Palabra clave:Database
Genomics
Molecular epidemiology
Mycobacterium tuberculosis
Software
Whole-genome sequencing
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spelling PolyTB: a genomic variation map for Mycobacterium tuberculosisColl, FrancescPreston, MarkGuerra-Assunção, José AfonsoHill-Cawthorn, GrantHarris, DavidPerdigão, JoãoViveiros, MiguelPortugal, IsabelDrobniewski, FrancisGagneux, SebastienGlynn, Judith R.Pain, ArnabParkhill, JulianMcNerney, RuthMartin, NigelClark, Taane G.DatabaseGenomicsMolecular epidemiologyMycobacterium tuberculosisSoftwareWhole-genome sequencing9 Páginas, 5 figuras, 1 tablaTuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second major cause of death from an infectious disease worldwide. Recent advances in DNA sequencing are leading to the ability to generate whole genome information in clinical isolates of M. tuberculosis complex (MTBC). The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies. Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies. Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800). We have developed the PolyTB web-based tool (http://pathogenseq.lshtm.ac.uk/polytb) to visualise the resulting variation and important meta-data (e.g. in silico inferred strain-types, location) within geographical map and phylogenetic views. This resource will allow researchers to identify polymorphisms within candidate genes of interest, as well as examine the genomic diversity and distribution of strains. PolyTB source code is freely available to researchers wishing to develop similar tools for their pathogen of interest.This work was supported by a Bloomsbury Research Fund PhD studentshipPeer reviewedElsevierBloomsbury Research FoundationColl, Francesc [0000-0002-7882-2325]202420242014info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/346127reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttps://dx.doi.org/10.1016/j.tube.2014.02.005Noinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3461272026-05-22T06:33:51Z
dc.title.none.fl_str_mv PolyTB: a genomic variation map for Mycobacterium tuberculosis
title PolyTB: a genomic variation map for Mycobacterium tuberculosis
spellingShingle PolyTB: a genomic variation map for Mycobacterium tuberculosis
Coll, Francesc
Database
Genomics
Molecular epidemiology
Mycobacterium tuberculosis
Software
Whole-genome sequencing
title_short PolyTB: a genomic variation map for Mycobacterium tuberculosis
title_full PolyTB: a genomic variation map for Mycobacterium tuberculosis
title_fullStr PolyTB: a genomic variation map for Mycobacterium tuberculosis
title_full_unstemmed PolyTB: a genomic variation map for Mycobacterium tuberculosis
title_sort PolyTB: a genomic variation map for Mycobacterium tuberculosis
dc.creator.none.fl_str_mv Coll, Francesc
Preston, Mark
Guerra-Assunção, José Afonso
Hill-Cawthorn, Grant
Harris, David
Perdigão, João
Viveiros, Miguel
Portugal, Isabel
Drobniewski, Francis
Gagneux, Sebastien
Glynn, Judith R.
Pain, Arnab
Parkhill, Julian
McNerney, Ruth
Martin, Nigel
Clark, Taane G.
author Coll, Francesc
author_facet Coll, Francesc
Preston, Mark
Guerra-Assunção, José Afonso
Hill-Cawthorn, Grant
Harris, David
Perdigão, João
Viveiros, Miguel
Portugal, Isabel
Drobniewski, Francis
Gagneux, Sebastien
Glynn, Judith R.
Pain, Arnab
Parkhill, Julian
McNerney, Ruth
Martin, Nigel
Clark, Taane G.
author_role author
author2 Preston, Mark
Guerra-Assunção, José Afonso
Hill-Cawthorn, Grant
Harris, David
Perdigão, João
Viveiros, Miguel
Portugal, Isabel
Drobniewski, Francis
Gagneux, Sebastien
Glynn, Judith R.
Pain, Arnab
Parkhill, Julian
McNerney, Ruth
Martin, Nigel
Clark, Taane G.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Bloomsbury Research Foundation
Coll, Francesc [0000-0002-7882-2325]
dc.subject.none.fl_str_mv Database
Genomics
Molecular epidemiology
Mycobacterium tuberculosis
Software
Whole-genome sequencing
topic Database
Genomics
Molecular epidemiology
Mycobacterium tuberculosis
Software
Whole-genome sequencing
description 9 Páginas, 5 figuras, 1 tabla
publishDate 2014
dc.date.none.fl_str_mv 2014
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/346127
url http://hdl.handle.net/10261/346127
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://dx.doi.org/10.1016/j.tube.2014.02.005
No
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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