PolyTB: A genomic variation map for Mycobacterium tuberculosis.


Coll, F; Preston, M; Guerra-Assunção, JA; Hill-Cawthorn, G; Harris, D; Perdigão, J; Viveiros, M; Portugal, I; Drobniewski, F; Gagneux, S; Glynn, JR; Pain, A; Parkhill, J; McNerney, R; Martin, N; Clark, TG; (2014) PolyTB: A genomic variation map for Mycobacterium tuberculosis. Tuberculosis (Edinburgh, Scotland), 94 (3). pp. 346-54. ISSN 1472-9792 DOI: 10.1016/j.tube.2014.02.005

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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.<br/>

Item Type: Article
Faculty and Department: Faculty of Infectious and Tropical Diseases > Dept of Clinical Research
Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Faculty of Epidemiology and Population Health > Dept of Non-Communicable Disease Epidemiology
Research Centre: HIV Research Group
MEIRU
TB Centre
PubMed ID: 24637013
Web of Science ID: 335913700022
URI: http://researchonline.lshtm.ac.uk/id/eprint/1621582

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