title: Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database.
abstract: Recent advances in DNA sequencing have led to the discovery of thousands of single nucleotide polymorphisms (SNPs) in clinical isolates of Mycobacterium tuberculosis complex (MTBC). This genetic variation has changed our understanding of the differences and phylogenetic relationships between strains. Many of these mutations can serve as phylogenetic markers for strain classification, while others cause drug resistance. Moreover, SNPs can affect the bacterial phenotype in various ways, which may have an impact on the outcome of tuberculosis (TB) infection and disease. Despite the importance of SNPs for our understanding of the diversity of MTBC populations, the research community currently lacks a comprehensive, well-curated and user-friendly database dedicated to SNP data. First attempts to catalogue and annotate SNPs in MTBC have been made, but more work is needed. In this review, we discuss the biological and epidemiological relevance of SNPs in MTBC. We then review some of the analytical challenges involved in processing SNP data, and end with a list of features, which should be included in a new SNP database for MTBC.
authors.affiliation: Swiss Tropical and Public Health Institute, Basel, Switzerland.
authors.forename: David
authors.initials: D
authors.lastname: Stucki
authors.forename: Sebastien
authors.initials: S
authors.lastname: Gagneux
mesh_terms: D030541:Databases, Genetic; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D014376:Tuberculosis / Q000382:microbiology