Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology.
| Autor: | Chernyaeva EN; St, Petersburg State University, Theodosius Dobzhansky Center for Genome Bioinformatics, 41 Sredniy prospect, St, Petersburg, Russia. echernya@gmail.com., Shulgina MV, Rotkevich MS, Dobrynin PV, Simonov SA, Shitikov EA, Ischenko DS, Karpova IY, Kostryukova ES, Ilina EN, Govorun VM, Zhuravlev VY, Manicheva OA, Yablonsky PK, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Lapidus AL, O'Brien SJ |
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| Jazyk: | angličtina |
| Zdroj: | BMC genomics [BMC Genomics] 2014 Apr 25; Vol. 15, pp. 308. Date of Electronic Publication: 2014 Apr 25. |
| DOI: | 10.1186/1471-2164-15-308 |
| Abstrakt: | 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. |
| Databáze: | MEDLINE |
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