Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis.

Autor: Reyes JF; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia., Chan CH, Tanaka MM
Jazyk: angličtina
Zdroj: Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [Infect Genet Evol] 2012 Jun; Vol. 12 (4), pp. 811-8. Date of Electronic Publication: 2011 May 30.
DOI: 10.1016/j.meegid.2011.05.018
Abstrakt: Homoplasy is the occurrence of genotypes that are identical by state but not by descent. It arises through a number of means including convergent and reverse evolution, and horizontal gene transfer. When using molecular markers that are based on sequences possessing a finite number of character states, such as VNTR or spoligotypes, this is an unavoidable phenomenon. Here we discuss the extent of homoplasy and its impact on inferences drawn from spoligotypes and VNTR in epidemiological studies of tuberculosis. To further explore this problem, we developed a computer simulation model combining the processes of mutation and transmission. Our results show that while the extent of homoplasy is not negligible, its effect on the proportion of isolates clustered ("n-1 method") is likely to be relatively low for spoligotyping. For VNTR-typing, homoplasy occurs at a low rate provided the number of loci used is high and the mutation rate is relatively high. However, deep phylogenetic inferences using spoligotypes or VNTRs with a small number of loci are likely to be unreliable.
(Copyright © 2011 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
Externí odkaz: