Africa is the geographic origin of modern human populations and their migration across the world. Populations in Africa harbor more genetic diversity compared to non-African populations, and yet individuals of African descent are poorly represented in most genetic studies. Examining the breadth and depth of genetic diversity across African populations is important for a more complete understanding of the human genome, human migration, and helping to identify individuals and populations at risk for developing specific diseases. The Common Fund’s Human Heredity and Health in Africa (H3Africa) program (link is external) is generating unique data to help fill significant gaps in knowledge of the diversity within human genomes.

A study published in Nature, and conducted through the H3Africa consortium, features sequenced DNA samples from 426 individuals that represent 50 distinct groups of people from 13 African countries, including previously unstudied populations. The researchers uncovered over three million novel genetic variants (very small changes in DNA sequence) adding to a greater understanding of the breadth of genetic diversity in Africa. Studying these new variants may help to explain differences in disease prevalence associated with specific populations and may eventually guide targeted treatments.

This research has also shed light on human migration by examining the timing of the Bantu migration to southern Africa. The routes and events of this migration have been debated in both the fields of genetics and linguistics. Data from this study provided evidence to support that Bantu populations from Central West Africa likely migrated into modern Zambia before migrating to East and South Africa. This finding supports a theory that Bantu populations migrated into Central Africa at a later point in time (~2,000 years ago) than previously thought. Understanding the Bantu migration and other migrations can help define the demographic event of African genetic diversity. 

In terms of clinically important variants, the team studied HLA-B*570, a variant associated with an allergic reaction to the antiretroviral drug Abacavir. This variant was previously only found in North East African and Kenyan populations, as well as people of European and Asian Ancestry. Here, new data showed HLA-B*570 was present in other African populations such as Bantu populations from Zambia, Ugandan Nilo-Saharan, and Xhosa populations. The data are relevant to HIV patients of African descent who are at risk of an adverse reaction to Abacavir and may help inform better treatment options. 

This work also showcases infrastructure developed through the H3Africa program to enhance genomics research in African institutions. Large genomics studies like this require huge computing capacity, and initiatives such as H3Africa provide both infrastructure and skill development of local researchers to help support large-scale genomics on the continent. The H3Africa consortium will continue to use this infrastructure for further studies of human genetic variation and capitalize on the promise of genomics for better understanding health and disease. 

Watch a video on H3Africa researchers explaining findings for this study: https://www.youtube.com/watch?v=YU8ZoNp3rlc&feature=emb_title (link is external).
  
Read news articles about this work at: NIH Director’s Blog, Nature (link is external), The Scientist (link is external).
 

Reference: 
High-depth African genomes inform human migration and health. Choudhury, Ananyo,Aron, Shaun,Botigué, Laura R,Sengupta, Dhriti,Botha, Gerrit,Bensellak, Taoufik,Wells, Gordon,Kumuthini, Judit,Shriner, Daniel,Fakim, Yasmina J,Ghoorah, Anisah W,Dareng, Eileen,Odia, Trust,Falola, Oluwadamilare,Adebiyi, Ezekiel,Hazelhurst, Scott,Mazandu, Gaston,Nyangiri, Oscar A,Mbiyavanga, Mamana,Benkahla. Nature.2020 Oct;586(7831):741-748