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ArticleAuthors
Coll, Francesc
Preston, Mark
Guerra-Assunção, José Afonso
Hill-Cawthorne, Grant A.
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.

KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionBioscience Program
Pathogen Genomics Laboratory
Date
2014-02-15Online Publication Date
2014-02-15Print Publication Date
2014-05Permanent link to this record
http://hdl.handle.net/10754/334575
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Show full item recordAbstract
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.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 BVJournal
TuberculosisPubMed ID
24637013PubMed Central ID
PMC4066953ae974a485f413a2113503eed53cd6c53
10.1016/j.tube.2014.02.005
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Except where otherwise noted, this item's license is described as Open Access funded by Medical Research Council
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