Early detection is at the core of good outcomes for several diseases — and is easier to achieve when a person’s risk of contracting a particular disease can be predicted. Some of the available methods of disease risk prediction rely on determining genetic makeup via a metric referred to as Genetic Risk Scores GRSs, which is already finding broad healthcare application in health systems around the world, including the United Kingdom’s NHS.
For Africa, due to the continent’s underrepresentation in the global genome data, there are several hurdles to scale and a very wide knowledge gap for African scientists.
However, according to Tinashe Chikowore at the Johannesburg-based University of the Witwatersrand, the continent can start benefiting from translational research on GRSs) within five years. Genetic risk score was a relatively new subject when he started his PhD, constructing a genetic risk score using some genetic mutations that had been identified among Europeans, to see how it worked on an African data set.
“So initially, there was this thought to say polygenic risk scores developed from European populations are 4.5 or less accurate in people of African ancestry,” he told Nature Africa. This then grew into questioning whether what is regarded as a polygenic condition elsewhere is the same in Africa. “We saw that it's not the same,” he said.
Recently, Chikowore and colleagues reported that while GRSs derived from data of African American people enhance polygenic prediction of lipid traits in Sub-Saharan Africa, compared to European and multi ancestry scores, GRS prediction varied greatly within Africa — specifically between the South African Zulu and Ugandan cohorts. This observation, Chikowore said, adds credibility to concerns regarding the interaction between GRSs and the environment.
“It might not only be genetic differences, but environmental ones, and this is something that cannot be picked up from Europe. In Europe, there is a lot of homogeneity in lifestyles, unlike here where there are wide differences between rural and urban communities. The type of diets that people eat when they're in a rural setting are different from that of urban ones,” he said.
With this trend, Chikowore noted that more evidence has been provided to justify the need for research to be conducted by people living in such settings instead of trying to adapt what is done abroad.
“I think there's a need to really consider these environmental differences if we want to translate polygenic risk scores to be usable in Africa,” he told Nature Africa.
The long road ahead
Chikowore and colleagues hope to optimize polygenic prediction in Africa, and to go into translation research in which insights from the findings will be used for potential trait differences between men and women in South Africa, and, between women. They would attempt to explain, for instance, why some benefit from the human papillomavirus vaccine while others don’t.
“We can get to the point where treatment can be personalized. We're not really there to pinpoint an individual, but we already have insights of GRSs’ potentials. So the more research we do, particularly in Africa, will make us really optimize this to the best and benefit the people in Africa,” he said.
The research element is just one aspect of what is needed for Africa to fully unlock disease prediction that could greatly improve prognoses by aiding prevention, management, and treatment. Equally critical, Chikowore noted, is expanding African genome data and taking a more continent-wide approach that commits to collaboratively unlock genomics’ full potential to benefit Africans.
“Africa is the home of the greatest diversity. Who knows? We might actually start to patent new therapeutics. Think of the PCSK9, an African story. It’s now being used as the American story, because it was only found in African Americans, and now it has been translated into PCSK9 inhibitor drug which lowers cholesterol. But you and I might be living with several of such mutations that might be due to peculiar environmental factors that only affect some Africans,” Chikowore said.