Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology

被引：68

作者：

Chernyaeva, Ekaterina N. ^{[1
]}

Shulgina, Marina V. ^{[2
]}

Rotkevich, Mikhail S. ^{[1
]}

Dobrynin, Pavel V. ^{[1
]}

Simonov, Serguei A. ^{[1
]}

Shitikov, Egor A. ^{[3
]}

Ischenko, Dmitry S. ^{[3
,4
]}

Karpova, Irina Y. ^{[3
]}

Kostryukova, Elena S. ^{[3
]}

Ilina, Elena N. ^{[3
]}

Govorun, Vadim M. ^{[3
]}

Zhuravlev, Vyacheslav Y. ^{[2
]}

Manicheva, Olga A. ^{[2
]}

Yablonsky, Peter K. ^{[2
]}

Isaeva, Yulia D. ^{[5
]}

Nosova, Elena Y. ^{[5
]}

Mokrousov, Igor V. ^{[6
]}

Vyazovaya, Anna A. ^{[6
]}

Narvskaya, Olga V. ^{[6
]}

Lapidus, Alla L. ^{[1
,7
]}

O'Brien, Stephen J. ^{[1
]}

机构：

[1] St Petersburg State Univ, Theodosius Dobzhansky Ctr Genome Bioinformat, St Petersburg 199034, Russia

[2] St Petersburg Inst Phthisiopulmonol, St Petersburg, Russia

[3] Res Inst Phys Chem Med, Moscow, Russia

[4] Moscow Inst Phys & Technol, Dolgoprudnyi, Russia

[5] Moscow Sci Pract Ctr Treatment TB Moscow Healthca, Moscow, Russia

[6] St Petersburg Pasteur Inst, St Petersburg, Russia

[7] St Petersburg Acad Univ, St Petersburg, Russia

来源：

BMC GENOMICS | 2014年 / 15卷

关键词：

Mycobacterium tuberculosis; Genome variations; Mutation; Genetic diversity; Whole genome sequencing; Database; DRUG-RESISTANT TUBERCULOSIS; GENETIC DIVERSITY; RECOMMENDATIONS; POLYMORPHISM; POPULATION; EVOLUTION; JBROWSE; FORMAT; KEGG;

D O I：

10.1186/1471-2164-15-308

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：8

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