Genome-wide association studies (GWAS) have revolutionised many aspects of clinical and biological research on common diseases in European populations. These advances are based on the accumulation of genome sequencing data on thousands of individuals, which have revealed common patterns of genetic variation in Europe and have enabled detailed statistical analyses of genetic factors that determine resistance and susceptibility to specific diseases.
There is a great need to apply similar approaches to major diseases that affect African populations, but currently we lack the necessary information about common patterns of genetic variation in Africa, where levels of genetic diversity are much higher than in other parts of the world.
Starting in 2009, the MRC Centre for Genomics and Global Health (CGGH) and the MRC Unit in the Gambia came together to develop a major project to establish a foundation for detailed genome-wide association studies in The Gambia and other parts of West Africa, by generating sequence data on 500 individuals drawn from each of The Gambia’s four ethnic groups.
The first phase of work was to establish a secure ethical foundation and to consult with key stakeholders in The Gambia including the Ministry of Health and Communities involved in this area of work, together with the process of sample collection, was led by Dr Muminatou Jallow, a paediatrician who has worked at the main government hospital in the Gambia for over 15 years and has led the clinical research team over that period.
“Sometimes individuals undertaking a GWAS analysis believe that the sample collection and data generation are the easy parts of a study. But good data do not just materialise. This project is about a long-term investment with people from many disciplines and institutions collaborating to build a resource for everyone’s benefit,” explains Dr Kirk Rockett, CGGH Scientific Research Manager, who has been part of the collaboration since it began.
The sequencing work for this project has been done at the Wellcome Trust Sanger Institute, and the next phase of work is to develop a detailed catalogue of variants and a reference panel of quality-controlled genotyping data that can be used for accurate imputation in genome-wide association studies of malaria and other diseases. The data will also be used to investigate the genetic diversity, demography and recent evolutionary history of The Gambian population.
The analysis, as with all aspects of this venture, is being undertaken collaboratively between the teams in Sanger, Oxford and The Gambia. The analysis group includes the data production team at Sanger led by Jim Stalker; Chris Spencer, Wellcome Trust Career Development fellow based at Oxford; and Alfred Amambua-Ngwa, MRC Career Development fellow based in The Gambia.
About MRC Unit, The Gambia
Established in The Gambia in 1947, the MRC Unit in The Gambia is the UK's single largest investment in medical research in a developing country. The Unit's research focuses on infectious diseases of immediate concern to The Gambia and the continent of Africa, with the aim of reducing the burden of illness and death in the country and the developing world as a whole.