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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
immunology and microbiology
PolyTB: A genomic variation map for Mycobacterium tuberculosis
Tuberculosis, Volume 94, No. 3, Year 2014
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Description
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.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC4066953/bin/mmc1.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC4066953/bin/mmc2.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC4066953/bin/mmc3.docx
Authors & Co-Authors
Coll, Francesc
Unknown Affiliation
Preston, Mark D.
Unknown Affiliation
Guerra-Assunção, José Afonso
Unknown Affiliation
Hill-Cawthorne, Grant A.
Unknown Affiliation
Harris, David E.
Unknown Affiliation
Perdigão, João
Unknown Affiliation
Viveiros, Miguel
Unknown Affiliation
Portugal, Isabel
Unknown Affiliation
Drobniewski, Francis A.
Unknown Affiliation
Gagneux, Sébastien P.
Unknown Affiliation
Glynn, Judith R.
Unknown Affiliation
Pain, Arnab P.
Unknown Affiliation
Parkhill, Julian
Unknown Affiliation
McNerney, R.
Unknown Affiliation
Martin, Nigel
Unknown Affiliation
Clark, Taane Gregory
Unknown Affiliation
Statistics
Citations: 89
Authors: 16
Affiliations: 10
Identifiers
Doi:
10.1016/j.tube.2014.02.005
ISSN:
14729792
e-ISSN:
1873281X
Research Areas
Genetics And Genomics
Infectious Diseases