Genetic variation in TLR genes in Ugandan and South African populations and comparison with HapMap data

 

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dc.contributor.author Baker, Allison R en_ZA
dc.contributor.author Qiu, Feiyou en_ZA
dc.contributor.author Randhawa, April Kaur en_ZA
dc.contributor.author Horne, David J en_ZA
dc.contributor.author Adams, Mark D en_ZA
dc.contributor.author Shey, Muki en_ZA
dc.contributor.author Barnholtz-Sloan, Jill en_ZA
dc.contributor.author Mayanja-Kizza, Harriet en_ZA
dc.contributor.author Kaplan, Gilla en_ZA
dc.contributor.author Hanekom, Willem A en_ZA
dc.contributor.author Boom, W Henry en_ZA
dc.contributor.author Hawn, Thomas R en_ZA
dc.contributor.author Stein, Catherine M en_ZA
dc.date.accessioned 2016-01-11T06:52:14Z
dc.date.available 2016-01-11T06:52:14Z
dc.date.issued 2012 en_ZA
dc.identifier.citation Baker, A. R., Qiu, F., Randhawa, A. K., Horne, D. J., Adams, M. D., Shey, M., ... & Boom, W. H. (2011). Genetic variation in TLR genes in Ugandan and South African populations and comparison with HapMap data. PloS one, 7(10), e47597. doi:10.1371/journal.pone.0047597 en_ZA
dc.identifier.uri http://hdl.handle.net/11427/16260
dc.identifier.uri http://dx.doi.org/10.1371/journal.pone.0047597
dc.description.abstract Genetic epidemiological studies of complex diseases often rely on data from the International HapMap Consortium for identification of single nucleotide polymorphisms (SNPs), particularly those that tag haplotypes. However, little is known about the relevance of the African populations used to collect HapMap data for study populations conducted elsewhere in Africa. Toll-like receptor (TLR) genes play a key role in susceptibility to various infectious diseases, including tuberculosis. We conducted full-exon sequencing in samples obtained from Uganda (n = 48) and South Africa (n = 48), in four genes in the TLR pathway: TLR2, TLR4, TLR6, and TIRAP. We identified one novel TIRAP SNP (with minor allele frequency [MAF] 3.2%) and a novel TLR6 SNP (MAF 8%) in the Ugandan population, and a TLR6 SNP that is unique to the South African population (MAF 14%). These SNPs were also not present in the 1000 Genomes data. Genotype and haplotype frequencies and linkage disequilibrium patterns in Uganda and South Africa were similar to African populations in the HapMap datasets. Multidimensional scaling analysis of polymorphisms in all four genes suggested broad overlap of all of the examined African populations. Based on these data, we propose that there is enough similarity among African populations represented in the HapMap database to justify initial SNP selection for genetic epidemiological studies in Uganda and South Africa. We also discovered three novel polymorphisms that appear to be population-specific and would only be detected by sequencing efforts. en_ZA
dc.language.iso eng en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. en_ZA
dc.rights.uri http://creativecommons.org/licenses/by/4.0 en_ZA
dc.source PLoS One en_ZA
dc.source.uri http://journals.plos.org/plosone en_ZA
dc.subject.other Haplotypes en_ZA
dc.subject.other Population genetics en_ZA
dc.subject.other Toll-like receptors en_ZA
dc.subject.other Africans en_ZA
dc.subject.other Tuberculosis en_ZA
dc.subject.other Genetic epidemiology en_ZA
dc.subject.other Sequence databases en_ZA
dc.subject.other Genetics of disease en_ZA
dc.title Genetic variation in TLR genes in Ugandan and South African populations and comparison with HapMap data en_ZA
dc.type Journal Article en_ZA
dc.rights.holder © 2012 Baker et al en_ZA
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department South African Tuberculosis Vaccine Initiative (SATVI) en_ZA
uct.type.filetype Text
uct.type.filetype Image


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This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Except where otherwise noted, this item's license is described as This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.