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Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology
BACKGROUND: Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehens...
Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234438/ https://www.ncbi.nlm.nih.gov/pubmed/24767249 http://dx.doi.org/10.1186/1471-2164-15-308 |
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author | Chernyaeva, Ekaterina N Shulgina, Marina V Rotkevich, Mikhail S Dobrynin, Pavel V Simonov, Serguei A Shitikov, Egor A Ischenko, Dmitry S Karpova, Irina Y Kostryukova, Elena S Ilina, Elena N Govorun, Vadim M Zhuravlev, Vyacheslav Y Manicheva, Olga A Yablonsky, Peter K Isaeva, Yulia D Nosova, Elena Y Mokrousov, Igor V Vyazovaya, Anna A Narvskaya, Olga V Lapidus, Alla L O’Brien, Stephen J |
author_facet | Chernyaeva, Ekaterina N Shulgina, Marina V Rotkevich, Mikhail S Dobrynin, Pavel V Simonov, Serguei A Shitikov, Egor A Ischenko, Dmitry S Karpova, Irina Y Kostryukova, Elena S Ilina, Elena N Govorun, Vadim M Zhuravlev, Vyacheslav Y Manicheva, Olga A Yablonsky, Peter K Isaeva, Yulia D Nosova, Elena Y Mokrousov, Igor V Vyazovaya, Anna A Narvskaya, Olga V Lapidus, Alla L O’Brien, Stephen J |
author_sort | Chernyaeva, Ekaterina N |
collection | PubMed |
description | BACKGROUND: Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. DESCRIPTION: Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. CONCLUSIONS: Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains. |
format | Online Article Text |
id | pubmed-4234438 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-42344382014-11-18 Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology Chernyaeva, Ekaterina N Shulgina, Marina V Rotkevich, Mikhail S Dobrynin, Pavel V Simonov, Serguei A Shitikov, Egor A Ischenko, Dmitry S Karpova, Irina Y Kostryukova, Elena S Ilina, Elena N Govorun, Vadim M Zhuravlev, Vyacheslav Y Manicheva, Olga A Yablonsky, Peter K Isaeva, Yulia D Nosova, Elena Y Mokrousov, Igor V Vyazovaya, Anna A Narvskaya, Olga V Lapidus, Alla L O’Brien, Stephen J BMC Genomics Database BACKGROUND: Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. DESCRIPTION: Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. CONCLUSIONS: Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains. BioMed Central 2014-04-25 /pmc/articles/PMC4234438/ /pubmed/24767249 http://dx.doi.org/10.1186/1471-2164-15-308 Text en Copyright © 2014 Chernyaeva et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Database Chernyaeva, Ekaterina N Shulgina, Marina V Rotkevich, Mikhail S Dobrynin, Pavel V Simonov, Serguei A Shitikov, Egor A Ischenko, Dmitry S Karpova, Irina Y Kostryukova, Elena S Ilina, Elena N Govorun, Vadim M Zhuravlev, Vyacheslav Y Manicheva, Olga A Yablonsky, Peter K Isaeva, Yulia D Nosova, Elena Y Mokrousov, Igor V Vyazovaya, Anna A Narvskaya, Olga V Lapidus, Alla L O’Brien, Stephen J Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology |
title | Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology |
title_full | Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology |
title_fullStr | Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology |
title_full_unstemmed | Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology |
title_short | Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology |
title_sort | genome-wide mycobacterium tuberculosis variation (gmtv) database: a new tool for integrating sequence variations and epidemiology |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234438/ https://www.ncbi.nlm.nih.gov/pubmed/24767249 http://dx.doi.org/10.1186/1471-2164-15-308 |
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