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    PolyTB: a genomic variation map for Mycobacterium tuberculosis

    Coll, F. and Preston, M. and Guerra-Assuncao, J. and Hill-Cawthorne, G. and Harris, D. and Perdigao, J. and Viveiros, M. and Portugal, I. and Drobniewski, F. and Gagneux, S. and Glynn, J. and Pain, A. and Parkhill, J. and McNerney, R. and Martin, Nigel and Clark, T. (2014) PolyTB: a genomic variation map for Mycobacterium tuberculosis. Tuberculosis 94 (3), pp. 346-354. ISSN 1472-9792.

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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.

    Metadata

    Item Type: Article
    Keyword(s) / Subject(s): Mycobacterium tuberculosis, Database, Genomics, Software, Molecular epidemiology, Whole-genome sequencing
    School: Birkbeck Schools and Departments > School of Business, Economics & Informatics > Computer Science and Information Systems
    Research Centre: Structural Molecular Biology, Institute of (ISMB), Birkbeck Knowledge Lab
    Depositing User: Nigel Martin
    Date Deposited: 26 Feb 2014 11:25
    Last Modified: 27 Jul 2019 00:09
    URI: http://eprints.bbk.ac.uk/id/eprint/9245

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