Publication:
Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes

dc.contributor.author Reyes, Josephine F en_US
dc.contributor.author Francis, Andrew R. en_US
dc.contributor.author Tanaka, Mark M en_US
dc.date.accessioned 2021-11-25T13:26:10Z
dc.date.available 2021-11-25T13:26:10Z
dc.date.issued 2008 en_US
dc.description.abstract Background: Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing such data is to construct graphs, including phylogenies. Inferences from graph representations of data assist in understanding the patterns of transmission of bacterial pathogens, and basing these graph constructs on biological models of evolution of the molecular marker helps make these inferences. Spoligotyping is a widely used method for genotyping isolates of Mycobacterium tuberculosis that exploits polymorphism in the direct repeat region. Our goal was to examine a range of models describing the evolution of spoligotypes in order to develop a visualization method to represent likely relationships among M. tuberculosis isolates. Results: We found that inferred mutations of spoligotypes frequently involve the loss of a single or very few adjacent spacers. Using a second-order variant of Akaike's Information Criterion, we selected the Zipf model as the basis for resolving ambiguities in the ancestry of spoligotypes. We developed a method to construct graphs of spoligotypes (which we call spoligoforests). To demonstrate this method, we applied it to a tuberculosis data set from Cuba and compared the method to some existing methods. Conclusion: We propose a new approach in analyzing relationships of M. tuberculosis isolates using spoligotypes. The spoligoforest recovers a plausible history of transmission and mutation events based on the selected deletion model. The method may be suitable to study markers based on loci of similar structure from other bacteria. The groupings and relationships in the spoligoforest can be analyzed along with the clinical features of strains to provide an understanding of the evolution of spoligotypes. en_US
dc.identifier.uri http://hdl.handle.net/1959.4/39631
dc.language English
dc.language.iso EN en_US
dc.rights CC BY-NC-ND 3.0 en_US
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/3.0/au/ en_US
dc.source Legacy MARC en_US
dc.title Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes en_US
dc.type Journal Article en
dcterms.accessRights metadata only access
dspace.entity.type Publication en_US
unsw.accessRights.uri http://purl.org/coar/access_right/c_14cb
unsw.identifier.doiPublisher http://dx.doi.org/10.1186/1471-2105-9-496 en_US
unsw.relation.faculty Science
unsw.relation.ispartofjournal BMC Bioinformatics en_US
unsw.relation.ispartofpagefrompageto 496 en_US
unsw.relation.ispartofvolume 9 en_US
unsw.relation.originalPublicationAffiliation Reyes, Josephine F, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW en_US
unsw.relation.originalPublicationAffiliation Francis, Andrew R. en_US
unsw.relation.originalPublicationAffiliation Tanaka, Mark M, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW en_US
unsw.relation.school School of Biotechnology & Biomolecular Sciences *
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