Last year we published the first findings from the African Genome Variation Project (AGVP) in the journal Nature. The primary aim of AGVP was to facilitate medical genetic research across Africa by characterizing the genetic variation across Africa and providing a framework for researchers undertaking medical genetic studies in the region.
Although many studies have explored genetic risk factors for diseases in European populations, there have been only a few such studies in African populations. The genetic contributors to disease risk in these populations are poorly understood. The high prevalence of infectious and non-communicable disease in the region further underlines the importance of focusing on genetic risk factors in the region.
Carrying out medical genetic studies in Africa can be challenging; this is the most genetically diverse region in the world. Characterising genetic diversity among populations in Africa would be key to developing a framework for large-scale medical genetics in the region. Towards this end, we worked in partnership with a range of African institutions, including field doctors, nurses and researchers, we collected genetic information from more than 1800 people from Ethiopia, the Gambia, Ghana, Kenya, Nigeria, South Africa and Uganda. We used this information to create a detailed genetic map of 18 ethnolinguistic groups in Africa. By sequencing the genomes of 320 individuals from east, west and southern Africa, we found 30 million genetic variants; a quarter of which have not previously been discovered in any population group.
AGVP also provided an important opportunity to improve our understanding of population history and migrations in Africa. We found evidence of widespread European or Middle Eastern genetic ancestry among several populations dating back up to 9,000 years, supporting the view that such populations have migrated back to Africa for thousands of years. In modern Africa, there are several populations that continue to lead a hunter-gatherer lifestyle and they represent some of the oldest populations in the continent. We found that many populations across Africa had some hunter-gatherer ancestry. We think this reflects aspects of a mass population migration from western central Africa to east Africa and Southern Africa, which is thought to have started around 5,000 years ago. Looking ahead, if we are to better understand the genetic landscape of ancient Africa, I believe we need to study DNA from both contemporary African populations, as well as DNA from ancient material, including from archeological studies.
This was a challenging but rewarding study to work on. Not only has it expanded our understanding of African genetic variation, it has also demonstrated that, notwithstanding the continent’s genetic diversity, it is possible to design methods and tools to help understand the genetic variation and identify genetic risk factors for disease. With the AGVP, we have developed a genetic resource to enable researchers in Africa to conduct such studies across the region. We aim to continue to support these efforts by building better tools and supporting scientists across the region to understand our human origins, history and evolutionary adaptation, and how this impacts on disease risk.
Funding for the AGVP was provided by the Wellcome Trust, the Bill and Melinda Gates Foundation, National Institutes of Health (NIH) and the UK Medical Research Council.