Genetic diversity in black South Africans from Soweto

BMC Genomics

Research Article

Andrew May¹  Michèle Ramsay²  Nimmisha Govind³  Mohammed Tikly⁴  Shane A Norris⁵  Nicole Hartmann⁶  Frank Staedtler⁶  Claudia Hon⁷  Keith J Johnson⁷  Yali Li⁷  Scott Hazelhurst⁸ 

[1] Division of Human Genetics, School of Pathology, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa;Division of Human Genetics, National Health Laboratory Service, Johannesburg, South Africa;Division of Human Genetics, School of Pathology, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa;Division of Human Genetics, National Health Laboratory Service, Johannesburg, South Africa;Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa;Division of Human Genetics, School of Pathology, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa;Division of Rheumatology, Chris Hani Baragwanath Hospital and the School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;Division of Rheumatology, Chris Hani Baragwanath Hospital and the School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa;Novartis Institutes for Biomedical Research (NIBR), Human Genetics and Genomics, Basel, Switzerland;Novartis Institutes for Biomedical Research (NIBR), Human Genetics and Genomics, Cambridge, MA, USA;Wits Bioinformatics, University of the Witwatersrand, Johannesburg, South Africa;

关键词: African population;    Soweto;    genetic diversity;    southeastern Bantu-speakers;    SNPs;    SAHGP;   

DOI  :  10.1186/1471-2164-14-644

 received in 2013-04-12, accepted in 2013-08-17,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundDue to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap and 1000 Genomes Projects. Notably excluded, however, is the southern Africa region, which is inhabited predominantly by southeastern Bantu-speakers, currently suffering under the dual burden of infectious and non-communicable diseases. Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure. Here, we present the most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg).ResultsParticipants were typed for ~4.3 million SNPs using the Illumina Omni5 beadchip. PCA and ADMIXTURE plots were used to compare the observed variation with that seen in selected populations worldwide. Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources. To assess the suitability of our sample as representative of Sowetans, we compared our results to participants in a larger rheumatoid arthritis case–control study. The control group showed good clustering with our sample, but among the cases were individuals who demonstrated notable admixture.ConclusionsSowetan population structure appears unique compared to other black Africans, and may have clinical implications. Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme.

【 授权许可】

Unknown   
© May et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.