PolyTB: A genomic variation map for Mycobacterium tuberculosis

Francesc Coll, Mark Preston, José Afonso Guerra-Assunção, Grant A. Hill-Cawthorne, David Harris, João Perdigão, Miguel Viveiros, Isabel Portugal, Francis Drobniewski, Sebastien Gagneux, Judith R. Glynn, Arnab Pain, Julian Parkhill, Ruth McNerney, Nigel Martin, Taane G. Clark

Research output: Contribution to journalArticlepeer-review

68 Scopus citations


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.
Original languageEnglish (US)
Pages (from-to)346-354
Number of pages9
Issue number3
StatePublished - Feb 15 2014

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01

ASJC Scopus subject areas

  • Infectious Diseases
  • Immunology
  • Microbiology
  • Microbiology (medical)


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