Mapping the genetic architecture of Africa

Research by the African Genome Variation Project shows that cost-effective genetic research is possible in a genetically diverse continent. It will eventually produce a better understanding of how people with particular genes are susceptibility to specific diseases 

While identifying the genetic basis of human diseases in Europe has developed apace, the genetic diversity of populations in Africa has made such studies more difficult. But work and research released by the African Genome Variation Project has opened the door to understanding genetic variation in different regions and populations of Africa, and is giving us a window on the history of human beings as we moved across the continent of Africa thousands of years ago. 

Dr Deepti Gurdasani, a Postdoctoral Fellow at the Wellcome Trust Sanger Institute, explains the role of her speciality – genetic epidemiology – in the research, ‘genetic epidemiology is essentially trying to do large scale genetic studies and Africa is really interesting because it is largely understudied. More than 95% of the studies that are done in medical research are actually done in Europe – quite surprising given that Africa has a huge burden of communicable and non-communicable disease.’ The risk for disease, says Dr Gurdasani is very different because of Africa’s demographic history and different exposure to infectious disease. 

Genetic diversity

The project, which is part-funded by the Wellcome Trust, the Bill and Melinda Gates Foundation, the Foundation for the National Institutes of Health and the UK Medical Research Council, has taken around two and a half years to complete. They worked with doctors and researchers, across Africa – Ethiopia, the Gambia, Ghana, Kenya, Nigeria, South Africa and Uganda – and the samples were taken from 1,481 individuals from 18 ethno-linguistic groups from sub-Saharan Africa. 

Africa is meant to be the genetically oldest and most diverse populations in the world, explains Dr Gurdasani. The rest of the world is thought to be a subset of Africa. ‘About 80 to 100 thousand years ago, the European and Asian populations arose out of Africa in what was thought of as a bottleneck. Imagine you have a bowl of marbles, then one or two marbles are selected and they go out and populate the rest of the world. Those would naturally be less genetically diverse than the original bowl of marbles that they came from.’ 

Movements and migrations

While the population is very diverse, 70 percent of the population belong to a language group called the Bantu who were agriculturalists and pastoralists believed to have expanded across Africa around 5,000 years ago. The research begins to offer clues to the history of migrations. ‘There have been several events in Africa which have led to mixing and changed the genetic architecture of Africa quite a lot,’ says Dr Gurdasani. They also found a lot of mixing with indigenous hunter-gatherer populations which may have existed alongside a lot of these populations during the Bantu expansion. There were she says, ‘a lot of hunter-gatherer mixtures in sub-Saharan populations which indicate that this material may have been assimilated while they were spreading across the region.’ The research is providing rich information for further exploration. Evidence of European and Middle Eastern genetic ancestry among populations in West Africa dating back 9,000 years ago also suggests that there may have been migrations back to Africa. 

A primary aim of the project was to provide a framework for researchers to use to conduct medical genetic research. ‘One of the main findings of the study,’ says Dr Gurdasani, ‘is that large-scale cost-effective genetic research in Africa is possible and there are tools that we can develop for this based on the work we are doing now.’ It will feed into existing research networks such as the African Partnership for Chronic Disease Research. This group, explains Dr Gurdasani ‘are essentially setting up large scale medical and genetic studies across Africa and the findings from this will directly feed into the designs for these studies.’ It may be a few decades before we start seeing direct health effects but the investment in this research needs to start now. ‘When we start understanding the genetic basis for disease in Africa better,’ says Dr Gurdasani, ‘it could potentially lead to developing better therapeutic targets which are more specific to Africa.’