A team of South African researchers which includes researchers from the University of Pretoria (UP) recently completed a study aimed at unlocking the unique genetic character of southern African populations. The study involved the genetic sequencing of 24 South African individuals of different ethnolinguistic origins, the results of which revealed a high level of genetic diversity and highlights the potential implications for disease susceptibility in Africans. The study was the first government-funded human genomics research study to be performed on African soil.

Funded by the National Department of Science and Technology (DST), the focus of the Southern African Human Genome Programme was to capture a full spectrum of diversity in populations that are under-represented from the genomic perspective. To achieve this, the sample group for the study was compiled to include ethnically self-identified individuals of different ancestries, after which whole-genome sequencing was used to study the differences in some of the major ethnolinguistic groups in the country. The sample group consisted of eight mixed-race or coloured individuals from the Western Cape, seven Sotho speakers from the Free State, eight Xhosa speakers from the Eastern Cape and one Zulu speaker from Gauteng.

The study aimed to explore the ancestral compositions of these individuals, including maternal and paternal lineages, using novel whole-genome sequence data. The results indicate that despite a short period of geographic and cultural separation between Nguni and Sotho-Tswana speakers, there are measurable genetic differences between them.

The team explains that these are in part the result of varying regional ancestral contributions, but also of a random process of genetic drift. Paternal ancestry was almost exclusively of African origin, while maternal ancestry was often of Khoesan origin, which is consistent with previous studies showing cross-cultural assimilation of female hunter gatherers into Nguni and Sotho-Tswana speaking farming communities. Coloured individuals in turn, showed varying proportions of admixture with Khoesan, African and European populations, as well as populations from the Indian sub-continent. After the inclusion of additional representative populations in the analysis, the study revealed a much stronger South Asian ancestry in the coloured individuals than indicated by previous studies.

Although African populations are known to harbour the greatest genetic diversity and have the highest per capita health burden, they are rarely included in large genome studies of disease association. The team says that this diversity provides both a challenge and an opportunity for biomedical research and the hope that Africans will one day benefit from genomic medicine.

Professor Michael Pepper, Director of the Institute for Cellular and Molecular Medicine, and a professor in the Department of Immunology in the Faculty of Health Sciences at UP, who is also the Unit Director of the South African Medical Research Council’s (SAMRC) Stem Cell Research and Therapy Unit, adds that the next step will be to use the knowledge gained through the team’s research to determine the potential impact the genetic variants could have on the health of individuals when health-related research is conducted. 

The results of this study were published in Nature Communications on Tuesday, 12 December 2017.