Swiss Tropical and Public Health Institute, Basel, Switzerland.
Tuberculosis (Edinb). 2013 Jan;93(1):30-9. doi: 10.1016/j.tube.2012.11.002. Epub 2012 Dec 21.
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.
近年来，DNA 测序技术的进步使得人们在结核分枝杆菌复合群（Mycobacterium tuberculosis complex，MTBC）的临床分离株中发现了数千个单核苷酸多态性（single nucleotide polymorphisms，SNPs）。这种遗传变异改变了我们对菌株间差异和系统发育关系的理解。许多这些突变可以作为菌株分类的系统发育标记，而其他突变则导致药物耐药性。此外，SNP 可以通过多种方式影响细菌表型，这可能会影响结核病（tuberculosis，TB）感染和疾病的结果。尽管 SNPs 对我们了解 MTBC 种群的多样性非常重要，但研究界目前缺乏一个全面、精心维护且用户友好的 SNP 数据库。人们已经首次尝试对 MTBC 中的 SNPs 进行编目和注释，但还需要做更多的工作。在这篇综述中，我们讨论了 MTBC 中 SNPs 的生物学和流行病学相关性。然后，我们回顾了处理 SNP 数据所涉及的一些分析挑战，并列出了一个新的 MTBC SNP 数据库应具备的特征。
