PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis

Handle URI:
http://hdl.handle.net/10754/552987
Title:
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis
Authors:
Benavente, Ernest D; Coll, Francesc; Furnham, Nick; McNerney, Ruth; Glynn, Judith R; Campino, Susana; Pain, Arnab ( 0000-0002-1755-2819 ) ; Mohareb, Fady R; Clark, Taane G
Abstract:
Background Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting. Results We have developed a web-based tool called PhyTB (http://pathogenseq.lshtm.ac.uk/phytblive/index.php webcite) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates. Conclusion PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms (http://sourceforge.net/projects/phylotrack webcite).
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis 2015, 16 (1) BMC Bioinformatics
Publisher:
Springer Nature
Journal:
BMC Bioinformatics
Issue Date:
13-May-2015
DOI:
10.1186/s12859-015-0603-3
PubMed ID:
25968323
PubMed Central ID:
PMC4429496
Type:
Article
ISSN:
1471-2105
Additional Links:
http://www.biomedcentral.com/1471-2105/16/155
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorBenavente, Ernest Den
dc.contributor.authorColl, Francescen
dc.contributor.authorFurnham, Nicken
dc.contributor.authorMcNerney, Ruthen
dc.contributor.authorGlynn, Judith Ren
dc.contributor.authorCampino, Susanaen
dc.contributor.authorPain, Arnaben
dc.contributor.authorMohareb, Fady Ren
dc.contributor.authorClark, Taane Gen
dc.date.accessioned2015-05-17T20:39:34Zen
dc.date.available2015-05-17T20:39:34Zen
dc.date.issued2015-05-13en
dc.identifier.citationPhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis 2015, 16 (1) BMC Bioinformaticsen
dc.identifier.issn1471-2105en
dc.identifier.pmid25968323en
dc.identifier.doi10.1186/s12859-015-0603-3en
dc.identifier.urihttp://hdl.handle.net/10754/552987en
dc.description.abstractBackground Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting. Results We have developed a web-based tool called PhyTB (http://pathogenseq.lshtm.ac.uk/phytblive/index.php webcite) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates. Conclusion PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms (http://sourceforge.net/projects/phylotrack webcite).en
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.biomedcentral.com/1471-2105/16/155en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.subjectTuberculosisen
dc.subjectPhylogenyen
dc.subjectSequencingen
dc.titlePhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosisen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalBMC Bioinformaticsen
dc.identifier.pmcidPMC4429496en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionFaculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UKen
dc.contributor.institutionEngineering Sciences Division, School of Engineering, Cranfield University, Cranfield, UKen
dc.contributor.institutionFaculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel St, London, UKen
dc.contributor.institutionWellcome Trust Sanger Institute, Hinxton, Cambridge, UKen
kaust.authorPain, Arnaben

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