TB-Lineage: an online tool for classification and analysis of strains of Mycobacterium tuberculosis complex
| Autor: | Cagri Ozcaglar, Scott Vandenberg, Nalin Rastogi, Kristin P. Bennett, Bülent Yener, Lauren S. Cowan, Amina Shabbeer |
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| Rok vydání: | 2011 |
| Předmět: |
Microbiology (medical)
DNA Bacterial Alias Genotype Locus (genetics) Computational biology Minisatellite Repeats Bioinformatics Microbiology Mycobacterium tuberculosis Naive Bayes classifier Genetics Humans Tuberculosis Molecular Biology Ecology Evolution Behavior and Systematics Phylogeny Genetic diversity Internet biology Molecular epidemiology Computational Biology biology.organism_classification Bacterial Typing Techniques Infectious Diseases Mycobacterium tuberculosis complex Software |
| Zdroj: | Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 12(4) |
| ISSN: | 1567-7257 |
| Popis: | This paper formulates a set of rules to classify genotypes of the Mycobacterium tuberculosis complex (MTBC) into major lineages using spoligotypes and MIRU-VNTR results. The rules synthesize prior literature that characterizes lineages by spacer deletions and variations in the number of repeats seen at locus MIRU24 (alias VNTR2687). A tool that efficiently and accurately implements this rule base is now freely available at http://tbinsight.cs.rpi.edu/run_tb_lineage.html. When MIRU24 data is not available, the system utilizes predictions made by a Naive Bayes classifier based on spoligotype data. This website also provides a tool to generate spoligoforests in order to visualize the genetic diversity and relatedness of genotypes and their associated lineages. A detailed analysis of the application of these tools on a dataset collected by the CDC consisting of 3198 distinct spoligotypes and 5430 distinct MIRU-VNTR types from 37,066 clinical isolates is presented. The tools were also tested on four other independent datasets. The accuracy of automated classification using both spoligotypes and MIRU24 is >99%, and using spoligotypes alone is >95%. This online rule-based classification technique in conjunction with genotype visualization provides a practical tool that supports surveillance of TB transmission trends and molecular epidemiological studies. |
| Databáze: | OpenAIRE |
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