Biology Faculty Articles
Document Type
Article
Publication Date
4-25-2014
Publication Title
BMC Genomics
Keywords
Mycobacterium tuberculosis, Genome variations, Mutation, Genetic diversity, Whole genome sequencing, Database
ISSN
1471-2164
Volume
15
Issue/No.
308
First Page
1
Last Page
8
Abstract
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.
NSUWorks Citation
Chernyaeva, Ekaterina N.; Marina V. Shulgina; Mikhail Rotkevich; Pavel Dobrynin; Serguei Simonov; Egor A. Shitikov; Dmitry S. Ischenko; Irina Y. Karpova; Elena S. Kostryukova; Elena N. Ilina; Vadim M. Govorun; Vyacheslav Y. Zhuravlev; Olga A. Manicheva; Peter K. Yablonsky; Yulia D. Isaeva; Elena Y. Nosova; Igor V. Mokrousov; Anna A. Vyazovaya; Olga V. Narvskaya; Alla L. Lapidus; and Stephen J. O'Brien. 2014. "Genome-Wide Mycobacterium tuberculosis Variation (GMTV) Database: A New Tool for Integrating Sequence Variations and Epidemiology." BMC Genomics 15, (308): 1-8. https://nsuworks.nova.edu/cnso_bio_facarticles/727
Comments
© Chernyaeva et al.; licensee BioMed Central Ltd. 2014