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PolyTB: A genomic variation map for Mycobacterium tuberculosis

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 identifi...

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Autores principales: Coll, Francesc, Preston, Mark, Guerra-Assunção, José Afonso, Hill-Cawthorn, Grant, 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Churchill Livingstone 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066953/
https://www.ncbi.nlm.nih.gov/pubmed/24637013
http://dx.doi.org/10.1016/j.tube.2014.02.005
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author Coll, Francesc
Preston, Mark
Guerra-Assunção, José Afonso
Hill-Cawthorn, Grant
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.
author_facet Coll, Francesc
Preston, Mark
Guerra-Assunção, José Afonso
Hill-Cawthorn, Grant
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.
author_sort Coll, Francesc
collection PubMed
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.
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spelling pubmed-40669532014-06-25 PolyTB: A genomic variation map for Mycobacterium tuberculosis Coll, Francesc Preston, Mark Guerra-Assunção, José Afonso Hill-Cawthorn, Grant 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. Tuberculosis (Edinb) Article 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. Churchill Livingstone 2014-05 /pmc/articles/PMC4066953/ /pubmed/24637013 http://dx.doi.org/10.1016/j.tube.2014.02.005 Text en © 2014 The Authors https://creativecommons.org/licenses/by/3.0/This work is licensed under a Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/) .
spellingShingle Article
Coll, Francesc
Preston, Mark
Guerra-Assunção, José Afonso
Hill-Cawthorn, Grant
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.
PolyTB: A genomic variation map for Mycobacterium tuberculosis
title PolyTB: A genomic variation map for Mycobacterium tuberculosis
title_full PolyTB: A genomic variation map for Mycobacterium tuberculosis
title_fullStr PolyTB: A genomic variation map for Mycobacterium tuberculosis
title_full_unstemmed PolyTB: A genomic variation map for Mycobacterium tuberculosis
title_short PolyTB: A genomic variation map for Mycobacterium tuberculosis
title_sort polytb: a genomic variation map for mycobacterium tuberculosis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066953/
https://www.ncbi.nlm.nih.gov/pubmed/24637013
http://dx.doi.org/10.1016/j.tube.2014.02.005
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