dc.contributor.author	Daya, Michelle	en_ZA
dc.contributor.author	Van der Merwe, Lize	en_ZA
dc.contributor.author	Gignoux, Christopher R.	en_ZA
dc.contributor.author	Van Helden, Paul D.	en_ZA
dc.contributor.author	Moller, Marlo	en_ZA
dc.contributor.author	Hoal, Eileen G.	en_ZA
dc.date.accessioned	2015-07-24T06:58:13Z
dc.date.available	2015-07-24T06:58:13Z
dc.date.issued	2014-11
dc.date.updated	2014-12-02T12:04:24Z
dc.description	Please cite as follows: Daya, M. et al. 2014. Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population. BMC Genomics, 15(1):1021, doi:10.1186/1471-2164-15-1021.	en_ZA
dc.description	The original publication is available at http://www.biomedcentral.com/1471-2164/15/1021	en_ZA
dc.description	Publication of this article was funded by the Stellenbosch University Open Access Fund.
dc.description.abstract	Background: The admixed South African Coloured population is ideally suited to the discovery of tuberculosis susceptibility genetic variants and their probable ethnic origins, but previous attempts at finding such variants using genome-wide admixture mapping were hampered by the inaccuracy of local ancestry inference. In this study, we infer local ancestry using the novel algorithm implemented in RFMix, with the emphasis on identifying regions of excess San or Bantu ancestry, which we hypothesize may harbour TB susceptibility genes. Results Using simulated data, we demonstrate reasonable accuracy of local ancestry inference by RFMix, with a tendency towards miss-calling San ancestry as Bantu. Regions with either excess San ancestry or excess African (San or Bantu) ancestry are less likely to be affected by this bias, and we therefore proceeded to identify such regions, found in cases but not in controls (642 cases and 91 controls). A number of promising regions were found (overall p-values of 7.19×10-5 for San ancestry and <2.00×10-16 for African ancestry), including chromosomes 15q15 and 17q22, which are close to genomic regions previously implicated in TB. Promising immune-related susceptibility genes such as the GADD45A, OSM and B7-H5 genes are also harboured in the identified regions. Conclusion Admixture mapping is feasible in the South African Coloured population and a number of novel TB susceptibility genomic regions were uncovered.	en_ZA
dc.description.version	Publishers' version	en_ZA
dc.identifier.citation	Daya, M. et al. 2014. Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population. BMC Genomics, 15(1):1021, doi:10.1186/1471-2164-15-1021.	en_ZA
dc.identifier.issn	1471-2164 (online)	en_ZA
dc.identifier.other	doi:10.1186/1471-2164-15-1021	en_ZA
dc.identifier.uri	http://hdl.handle.net/10019.1/97259
dc.language.iso	en_ZA	en_ZA
dc.publisher	BioMed Central	en_ZA
dc.rights.holder	Michelle Daya et al.; licensee BioMed Central Ltd.	en_ZA
dc.subject	Tuberculosis -- Susceptibility	en_ZA
dc.subject	Tuberculosis -- Genetic aspects	en_ZA
dc.title	Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population	en_ZA
dc.type	Article	en_ZA

Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population

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