Publication:
Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis

dc.contributor.author Rosenberg, N en_US
dc.contributor.author Tsolaki, Anthony en_US
dc.contributor.author Tanaka, Mark en_US
dc.date.accessioned 2021-11-25T13:26:41Z
dc.date.available 2021-11-25T13:26:41Z
dc.date.issued 2003 en_US
dc.description.abstract In infectious disease epidemiology, it is useful to know how quickly genetic markers of pathogenic agents evolve while inside hosts. We propose a modular framework with which these genotype change rates can be estimated. The estimation scheme requires a model of the underlying process of genetic change, a detection scheme that filters this process into observable quantities, and a monitoring scheme that describes the timing of observations. We study a linear "birth-shift-death" model for change in transposable element genotypes, obtaining maximum-likelihood estimators for various detection and monitoring schemes. The method is applied to serial genotypes of the transposon IS6110 in Mycobacterium tuberculosis. The estimated birth rate of 0.0161 (events per copy of the transposon per year) and death rate of 0.0108 are both significantly larger than the estimated shift rate of 0.0018. The sum of these estimates, which corresponds to a "half-life" of 2.4 years for a typical strain that has 10 copies of the element, substantially exceeds a previous estimate of 0.0135 total changes per copy per year. We consider experimental design issues that enable the precision of estimates to be improved. We also discuss extensions to other markers and implications for molecular epidemiology. en_US
dc.identifier.issn 0040-5809 en_US
dc.identifier.uri http://hdl.handle.net/1959.4/39643
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 Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis 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/10.1016/S0040-5809(03)00010-8 en_US
unsw.relation.faculty Science
unsw.relation.ispartofjournal Theoretical Population Biology en_US
unsw.relation.ispartofpagefrompageto 347-363 en_US
unsw.relation.ispartofvolume 63 en_US
unsw.relation.originalPublicationAffiliation Rosenberg, N en_US
unsw.relation.originalPublicationAffiliation Tsolaki, Anthony en_US
unsw.relation.originalPublicationAffiliation Tanaka, Mark, Biotechnology & Biomolecular Sciences, Faculty of Science, UNSW en_US
unsw.relation.school School of Biotechnology & Biomolecular Sciences *
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