PolyTB: A genomic variation map for Mycobacterium tuberculosis

Handle URI:
http://hdl.handle.net/10754/334575
Title:
PolyTB: A genomic variation map for Mycobacterium tuberculosis
Authors:
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 ( 0000-0002-1755-2819 ) ; Parkhill, Julian; McNerney, Ruth; Martin, Nigel; Clark, Taane G.
Abstract:
Tuberculosis (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. 2014 Elsevier Ltd. All rights reserved.
KAUST Department:
Pathogen Genomics Laboratory
Citation:
Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, et al. (2014) PolyTB: A genomic variation map for Mycobacterium tuberculosis. Tuberculosis 94: 346-354. doi:10.1016/j.tube.2014.02.005.
Publisher:
Elsevier BV
Journal:
Tuberculosis
Issue Date:
15-Feb-2014
DOI:
10.1016/j.tube.2014.02.005
PubMed ID:
24637013
PubMed Central ID:
PMC4066953
Type:
Article
ISSN:
14729792
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorColl, Francescen
dc.contributor.authorPreston, Marken
dc.contributor.authorGuerra-Assunção, José Afonsoen
dc.contributor.authorHill-Cawthorn, Granten
dc.contributor.authorHarris, Daviden
dc.contributor.authorPerdigão, Joãoen
dc.contributor.authorViveiros, Miguelen
dc.contributor.authorPortugal, Isabelen
dc.contributor.authorDrobniewski, Francisen
dc.contributor.authorGagneux, Sebastienen
dc.contributor.authorGlynn, Judith R.en
dc.contributor.authorPain, Arnaben
dc.contributor.authorParkhill, Julianen
dc.contributor.authorMcNerney, Ruthen
dc.contributor.authorMartin, Nigelen
dc.contributor.authorClark, Taane G.en
dc.date.accessioned2014-11-11T14:30:19Z-
dc.date.available2014-11-11T14:30:19Z-
dc.date.issued2014-02-15en
dc.identifier.citationColl F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, et al. (2014) PolyTB: A genomic variation map for Mycobacterium tuberculosis. Tuberculosis 94: 346-354. doi:10.1016/j.tube.2014.02.005.en
dc.identifier.issn14729792en
dc.identifier.pmid24637013en
dc.identifier.doi10.1016/j.tube.2014.02.005en
dc.identifier.urihttp://hdl.handle.net/10754/334575en
dc.description.abstractTuberculosis (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. 2014 Elsevier Ltd. All rights reserved.en
dc.language.isoenen
dc.publisherElsevier BVen
dc.rightsOpen Access funded by Medical Research Councilen
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/en
dc.subjectDatabaseen
dc.subjectGenomicsen
dc.subjectMolecular epidemiologyen
dc.subjectMycobacterium tuberculosisen
dc.subjectSoftwareen
dc.subjectWhole-genome sequencingen
dc.subjectrifampicinen
dc.subjectbacterium isolateen
dc.subjectcomputer modelen
dc.subjectcontrolled studyen
dc.subjectgene frequencyen
dc.subjectgenetic codeen
dc.subjectgenetic variabilityen
dc.subjectindel mutationen
dc.subjectmultigene familyen
dc.subjectnucleotide sequenceen
dc.subjectpoint mutationen
dc.subjectpriority journalen
dc.subjectsingle nucleotide polymorphismen
dc.subjecttuberculosisen
dc.titlePolyTB: A genomic variation map for Mycobacterium tuberculosisen
dc.typeArticleen
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.identifier.journalTuberculosisen
dc.identifier.pmcidPMC4066953en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdomen
dc.contributor.institutionFaculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, WC1E 7HT London, United Kingdomen
dc.contributor.institutionSydney Emerging Infections and Biosecurity Institute, School of Public Health, Sydney, NSW 2006, Australiaen
dc.contributor.institutionPathogen Genomics Faculty, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA Cambridge, United Kingdomen
dc.contributor.institutionCentro de Patognese Molecular, Faculdade de Farmcia, Universidade de Lisboa, 1649-003 Lisboa, Portugalen
dc.contributor.institutionGrupo de Micobactrias, Unidade de Microbiologia Mdica, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugalen
dc.contributor.institutionCentre for Immunology and Infectious Disease, Queen Mary University of London, E1 2AT London, United Kingdomen
dc.contributor.institutionSwiss Tropical and Public Health Institute, 4002 Basel, Switzerlanden
dc.contributor.institutionSchool of Computer Science and Information Systems, Birkbeck College, WC1E 7HX London, United Kingdomen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorHill-Cawthorne, Grant A.en
kaust.authorPain, Arnaben

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