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Open Access Highly Accessed Research article

Genetic diversity in black South Africans from Soweto

Andrew May12, Scott Hazelhurst3, Yali Li4, Shane A Norris5, Nimmisha Govind16, Mohammed Tikly6, Claudia Hon4, Keith J Johnson4, Nicole Hartmann7, Frank Staedtler7 and Michèle Ramsay128*

Author Affiliations

1 Division of Human Genetics, School of Pathology, University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa

2 Division of Human Genetics, National Health Laboratory Service, Johannesburg, South Africa

3 Wits Bioinformatics, University of the Witwatersrand, Johannesburg, South Africa

4 Novartis Institutes for Biomedical Research (NIBR), Human Genetics and Genomics, Cambridge, MA, USA

5 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

6 Division of Rheumatology, Chris Hani Baragwanath Hospital and the School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa

7 Novartis Institutes for Biomedical Research (NIBR), Human Genetics and Genomics, Basel, Switzerland

8 Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa

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BMC Genomics 2013, 14:644  doi:10.1186/1471-2164-14-644

Published: 23 September 2013

Abstract

Background

Due 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).

Results

Participants 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.

Conclusions

Sowetan 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.

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