Correction: This story previously said the chronic kidney disease rate was 40%, it is in fact 14%.
A chip containing millions of genetic variations that are common in Africa could help scientists bring the benefits of precision medicine to the continent.
The chip could lead to new insights into human health as well as new treatments that work better on Africans. Its developers say it will be ready to use in early 2017.
“This will be the first chip that has been created to specifically target genetic variation in African populations and people of African descent,” says Nicola Mulder, a bio-informatician at the University of Cape Town in South Africa who led the work on the chip.
Precision medicine—the practice of scanning patients’ genes to devise tailor-made treatment programs—is already routine in rich countries for some diseases. Oncologists in the US and Europe use genetic tests to determine which treatments will work best for their patients’ cancers.
But Africans and people of African descent, such as African Americans, have been left behind in this medical revolution. Out of the more than 35 million participants that have participated in genetic screening studies to date, 81% were of European ancestry. Of the rest, three-quarters were Asians. Only 3% were of African origin.
This is a problem because Africans are the most genetically varied on Earth. Two Ugandans living in the same city can have greater genetic variation than, say, a Spaniard and a Belgian. And Africans have many genetic variations that do not appear at all in Caucasian populations. This means that precision medicine tools based on Caucasians could be less effective, or even potentially harmful, in African populations.
Scientists hope that Africa’s as-yet uncharted genetic variations can help explain why people on the continent are more susceptible to certain conditions. For example, Africans develop chronic kidney disease about twenty years earlier than Europeans. “It’s a complete nightmare illness,” says Adu Dwomoa, a Ghana-based researcher in charge of a multi-country study looking for genetic clues as to why the disease hits Africans so young. The disease affects up to 14% of sub-Saharan African adults, he says. Few have access to expensive dialysis treatment, and so they die. Dwomoa hopes his research will lead to new treatments that work in Africa.
But so far African scientists have had limited ability to carry out studies to pinpoint genetic causes for disease. In order to link a gene to a disease trait, scientists need to screen thousands of people’s genetic sequences against a reference library of genetic markers—specific variations in the genetic code—and see if they can pick up any patterns. These markers are stored on chips manufactured for researchers by biotech companies. But chips on the market currently cover little of Africa’s genetic wealth.
Enter the new chip, which will contain 2.5 million different markers hand-picked for their African relevance. It’s been produced by the Human Heredity and Health in Africa (H3Africa) initiative, a program to boost genetic research in Africa funded by the UK and the US. The program has collected tens of thousands of samples from Africans to study genetic links for diseases like diabetes, sleeping sickness, rheumatic heart disease and tuberculosis. This information has fed the chip with data from dozens of African population groups, from the Khoi-San in the south to the Yoruba in the West and Masaai in the East.
Because African countries don’t yet have the machinery to sequence entire human genomes quickly, that part of the work was done at Baylor College of Medicine in the US. The resulting data—all 144 terabytes of it—took weeks, if not months, to transfer back to Africa via high-speed networks, where it was analyzed. The samples will be returned to Africa after sequencing to be stored in biological sample banks on the continent.
The project has been an Africa-led effort from the start, says UCT’s Mulder. But the benefits should be felt beyond the continent, she adds. Since humankind originated in Africa, its genetics charts the history of all of humanity, says Charles Rotimi, a Nigerian geneticist who works for the US National Institutes of Health based in Bethesda, Maryland. “Understanding the genetics of African people is imperative. Without it you can’t tell the story of the rest of the world,” he says.