Putting Africa on the genomic map
In the ten years since the Human Genome Project was completed genomics has progressed in leaps and bounds, but surprisingly little has been about Africa or by African scientist.
The vast majority of genomic studies have been of American, Asian and European genomes, with just one genome-wide association study (looking at malaria) based on an African population – surprising considering that around one billion people live on the African continent.
That makes today’s announcement all the more exciting. A new partnership from the US National Institutes of Health (NIH) and the Wellcome Trust looks to fund population-based genetic studies in Africa. The $38 million Human Heredity and Health in Africa (H3 Africa) Project will also build capacity for African scientists to do genomic studies in their home countries.
Yesterday, I attended a press briefing for the launch of H3 Africa and heard how African populations are interesting, scientifically, for a number of reasons.
First, we know that African genomes contain more genetic variation than any other on Earth. African genomes are also much ‘older’ than European or Asian genomes. In practical terms, this means that it is easier to focus in on particular gene variants and work out their level of association with particular traits, say risk of high blood pressure, because the signal is clearer. The genetic variants in African genomes are more clearly associated with certain regions of the genome than in Asian and European genomes, which will make it easier to find those ‘ancient’ variants that are associated with disease risk and apply to everyone worldwide.
Some studies are easier to implement in Africa. Take a study of how salt in the diet affects hypertension, for example. Some African populations have only a handful of sources from which they get salt – in the US or Europe there are a plethora of foods containing varying levels of salt, making tracking and control difficult.
Then there are the studies you could only do in Africa, such as those on certain neglected diseases. Dr Charles Rotimi, President of the African Society for Human Genetics, cited an ongoing study into podoconiosis in Ethiopia. The disease is endemic in several African countries and has similar symptoms to elephantiasis but is caused by exposure of the feet to alkali clay soils rather than a parasite. As Rotimi described it, “you get it because you don’t wear shoes”. Researchers are conducting genome-wide association studies to try to understand the disease better and this is precisely the sort of gene-environment interaction you couldn’t study anywhere else.
The Project will fund research in both communicable and non-communicable diseases, the latter (including cancer, heart disease, diabetes) a rapidly growing cause of mortality in Africa. And researchers will use all the tools that modern genomic research has to offer, like high-tech sequencing and genome-wide association studies. As Dr Eric Green, Director of the NIH National Human Genome Research Institute, put it, the advances in sequencing, making it faster and – crucially – cheaper, are such that these technologies can now be brought to bear on projects that were previously neglected.
Of course, understanding the relevance of all of this won’t be easy, not least because gene–environment interactions are difficult to untangle. And though genome sequencing has progressed greatly in the ten years since the Human Genome Project, phenotyping – tracking which genes lead to which observable characteristics – remains difficult.
That will become easier with larger numbers of subjects, which makes it all the more important to get more studies started all over the world, particularly in the continent with the most genetic variation in the world.
Dr Francis Collins, Director of NIH, said, “the intention [of H3 Africa] is to empower scientists in Africa to take the lead”. In that respect, it builds on existing initiatives such as the Trust’s African Institutions Initiative and the NIH/PEPFAR Medical Education Partnership Initiative.
Collins hopes that H3 Africa will help to connect existing research in a useful way. The Project will assess what the current African infrastructure is like for population-based studies and genomics so that funding is distributed to where it might yield the most benefit.
With this, more training and improved infrastructure, hopefully more African scientists will be first authors on scientific papers. According to Professor Bongani Mayosi, Chief of Medicine at the University of Cape Town, African scientists produce just 50 of the thousands of genetics papers published each year.
At the briefing, he expressed disappointment that a lot of research in Africa is still done in a “colonial” way, with European or American researchers visiting to gather data and samples, before taking the analysis, and the subsequent kudos, elsewhere. The H3 Africa Project will hopefully change that and at last give African science a prominent place on the genomic map.