Important new study reveals the complexity and great diversity of Africa’s genetic variation

Africa is the cradle of mankind. All people are descendants of this common pool of ancestors. Africa and its multitude of ethnolinguistic groups are therefore important in learning more about mankind and our origins.

A human genome refers to the complete set of genetic information found in a human cell. We inherit our genomes from our parents. Studying the variations in different people’s genomes provides important clues as to how genetic information affects people’s appearance and health. It can also tell us about our ancestry. To date, very few individuals in Africa have been included in studies examining genetic variation. Studying African genomes not only fills a gap in the current understanding of human genetic variation, but also reveals new insights into the history of African populations.

Me and my colleagues, who are all members of the Human inheritance and health (H3Africa) consortium, contributed to a study point on genetic genetics. This study focused on 426 individuals from 13 African countries. More than 50 different ethnolinguistic groups were represented in the study – one of the most diverse groups of Africans ever included in such a study. We made the entire genome of each of these individuals sequentially – that means we can read each part of the genome to look for variation.

This study contributes an important, new source of African genomic data, showcasing the complex and vast diversity of African genetic variation. And it will support research for decades to come.

Our findings are of great importance, from more information on African history and migration, to clinical research on the impact of specific variants on health outcomes.

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One of the most important outcomes was the discovery of more than three million new genetic variants. This is important as we learn more about human genetic diversity in general and discover more differences related to diseases or traits in the future.

This study also adds details known about the migration and expansion of groups across the continent. We were able to show that Zambia was probably an interim place on the probable migration route from West Africa to East and South Africa. Evidence supporting the movement from East Africa to Central Nigeria between 1500 and 2000 years ago has also been revealed by identifying a significant amount of East African descent in a central Nigerian ethnolinguistic group, the Berom.

The study also enabled us to reclassify certain variants that previously presumably caused disease. Variants that cause serious genetic diseases are often rare in the general population, mostly because their effect is so severe that a person with such a variant often does not reach adulthood. However, we observed many of these variants at common levels in the populations studied. One would not expect this type of disease-causing variant to be so common in healthy adults. This finding helps to classify these variants for clinical interpretation.

Finally, we found a surprising number of regions with signatures of natural selection that have not been reported before. Selection means that when individuals are exposed to environmental factors such as a viral infection, or a drastic new dietary component, some gene variants may offer an extra adaptive benefit to the people they carry in their genome.

Our best interpretation of these findings is that, since humans across Africa were exposed to different environments – sometimes due to migration – these variants were probably important to survive in those new conditions. It left a ‘imprint’ on the genome and contributes to genomic diversity across the continent.

Our data showed that we have not yet found all the variation in the human genome. There is more to learn by adding new, uneducated population groups. We know it less than a quarter participants in genomics research are of non-European descent. Most available genetic data comes from just three countries – the United Kingdom (40%), the USA (19%) and Iceland (12%).

It is essential to continue to add more genomic data from all world populations – including Africa. This will ensure that everyone can benefit from the advances in health that precision medicine presentations. Precision medicine refers to the adaptation of health care that suits the individual. The inclusion of personal genetic information can drastically change the nature and scope of healthcare options that will work best for that individual.

Next steps

The Human Genetics and Health Consortium is now in its eighth year of existence and supports more than 51 diverse projects. These include studies focusing on diseases such as diabetes, HIV and tuberculosis. The reference data generated by our study are already used by many of the consortium studies.

Next, we plan to examine the data even more deeply to better understand what other types of genetic variation exist. We also hope to add further unstudied populations to grow and enrich this dataset.

Building capacity for genomics research on the African continent is an important goal of human heredity and health. An important aspect of this study is that it was driven and conducted by researchers and scientists from the African continent. Researchers from 24 institutions across Africa participated and led this investigation. This study demonstrates the availability of both infrastructure and skills for large-scale genomics research on the continent. It also highlights the prospect of future world-class research on Africa on this topic.

Zané Lombard, Chief Medical Scientist, Associate Professor, University of the Witwatersrand


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