African genetic diversity could hold answer to unlocking disease susceptibility

A team of South African researchers which includes researchers from the University of Pretoria (UP) from the Department of Immunology in the Faculty of Health Sciences at 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.

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

Researchers

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  Professor Michael Pepper

  Professor Michael S Pepper is Director of the Institute for Cellular and Molecular Medicine at the University of Pretoria (UP) and Director of the South African Medical Research Council’s Extramural Unit for Stem Cell Research and Therapy.
  
  His research goal is to understand disease pathogenesis and to develop cell and gene therapies for selected diseases. Prof Pepper has been conducting research at UP since 2005, and through his work, aims to improve the quality of life of South Africans and reduce the heavy disease burden in the country.
  
  The professor’s research group has identified key areas that contribute to the burden of disease in South Africa, including communicable diseases such as HIV and COVID-19, non-communicable diseases like obesity or cancer, and maternal and child health issues such as birth asphyxia.
  
  The group’s birth asphyxia project recently received funding from the Bill & Melinda Gates Foundation, and focuses on the identification of biomarkers (molecular and imaging) for the condition. This is important in understanding disease pathogenesis and for the design of an interventional clinical trial aimed at assessing the efficacy of one or more neuroprotective agents.
  
  Over the past 18 months, Prof Pepper’s research group has also started two new COVID-19 projects: genetic determinants of susceptibility and severity as well as novel therapies for acute respiratory distress syndrome.
  
  Prof Pepper is working with Prof Fourie Joubert of the University’s Faculty of Natural and Agricultural Sciences and Prof Pieter de Villiers of the Faculty of Engineering, Built Environment and Information Technology in transdisciplinary cross-faculty research. Prof Pepper says the work they are doing is inspired by a need to address the needs of South Africans and to ensure that taxpayers’ money is being spent responsibly. Significant advances are being made, and medical research in selected fields in South Africa is being conducted at the highest level globally.
  
  Prof Pepper’s advice to prospective and undergraduate students who are interested in his field is to find their passion and not to be driven by a desire for fame or material possessions. They should be prepared to work hard and be ready to adapt to the rapidly changing environment in which we live.
  
  He enjoys the theatre and horse riding.
  

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  African genetic diversity could hold answer to unlocking disease susceptibility