African genetic diversity to unlock disease susceptibility

Cape Town | The first government-funded human genomics research study performed on African soil, aimed at unlocking the unique genetic character of southern African populations, has revealed a high level of genetic diversity in individuals after a home grown team of researchers sequenced 24 South African individuals of different ethnolinguistic origins. 

“This study supports our understanding that African genomes are likely to yield many more unique genetic variants”, says Professor Michèle Ramsay from Human Genetics and the Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences at Wits University. “The next step of progress is to use this knowledge to decipher what potential impact the genetic variants can have on the health of individuals when we conduct health related research”, added Professor Michael Pepper Unit Director of the South African Medical Research Council’s (SAMRC) Stem Cell Research and Therapy Unit, Faculty of Health Sciences at the University of Pretoria.   

Funded by the National Department of Science & Technology (DST), the focus of the Southern African Human Genome Programme (SAHGP) was to capture a full spectrum of diversity in under-represented populations and therefore included ethnically self-identified individuals of different ancestries. Whole-genome sequencing was used to study the differences in some of the major ethnolinguistic groups in the country.  In this pilot project, eight admixed 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 constituted the sample group of the study.

Two study aims were to use novel whole-genome sequence data to (1) study possible correlations between language groups and genetic clustering, (2) investigate the ancestral compositions of these individuals, including maternal and paternal lineages.  The results indicate that despite a short period of geographic and cultural separation between the Nguni and Sotho-Tswana speakers there are measurable genetic differences between them.  These are in part the result of varying regional ancestral contributions, but also of a random process of genetic drift.

The paternal ancestry that was almost exclusively of African origin, while the 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 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 Coloureds compared to previous studies.

“We have a richer understanding of the past as the study confirms general historical accounts of African migration and admixture”, says Dr Ananyo Choudhury (PhD), Senior Scientist at the SBIMB at Wits University.

African populations harbor the greatest genetic diversity and have the highest per capita health burden yet they are rarely included in large genome studies of disease association. This diversity provides both a challenge and an opportunity for biomedical research and the hope that Africans will one day benefit from genomic medicine. The study highlights the potential implications for disease susceptibility in Africans.

“South Africa has cemented a critical stone in the foundation to advance precision medicine for its people”, concluded Glaudina Loots Director for Health Innovation at DST.

Study available on Nature Communications -

Note to the editor:

About Wits
The University of the Witwatersrand is a leading research-intensive University based in Johannesburg ranked in the top 1% in the world in several areas of study. Wits has a strong focus on trans-, cross- and interdisciplinary research which spans five faculties and hundreds of research areas, one of which is in precision medicine. Wits researchers produce world-class research that impacts locally and competes globally, and that ultimately benefits society and advances the public good. For more information on Wits University’s research, visit or watch some of Wits’ research videos

About the University of Pretoria
The University of Pretoria (UP) is situated in the heart of South Africa’s capital city. It is a diverse and dynamic leading research intensive university in South Africa. The university’s research is responsive to the needs of society by finding real solutions to real challenges. UP offers a wide range of undergraduate and postgraduate study options. In particular, the Faculty of Health Sciences at the University of Pretoria is recognized nationally and internationally as an outstanding institution in terms of its education of health professionals, its research and its clinical service. Visit for further information or to find out more about some of our research fields.

About the SAMRC
The scope of the SAMRC’s research includes basic laboratory investigations, clinical research and public health studies. Research at the SAMRC focuses on the following top 10 causes of death in South Africa ( ).  To assist with delivering on this vital mandate, the organisation is led by the National Department of Health, and works with other key stakeholders such as the Department of Science and Technology, South African and international science councils, medical schools, universities, research institutions and international collaborators.

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Release date: 
Tuesday, December 12, 2017 - 12:00
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