Oct 1, 2019 7:00 AM

The Massive, Overlooked Potential of African DNA

Genetic studies rely almost entirely on DNA from people of European descent. A startup called 54gene wants to fix that, and fast.

Illustration: Ariel Davis

When evening falls on a solar-panel-clad building outside the Nigerian city of Lagos, its generators roar to life. The electrical grid here is unpredictable, and the company that works out of the building, 54gene, isn’t taking any chances. Losing power, even for a few hours, isn’t an option when you’re housing thousands of tubes of blood and spit at a stable –80 degrees Celsius.

Around the world, tissue and blood banks have sprung up to catalog human DNA’s many mysteries. But not in Africa. About 80 percent of the human DNA used in genetic studies comes from people of European descent. When researchers survey vast numbers of genomes to unearth a disease’s genetic causes, they use almost no African data. Pharmaceutical companies, too, develop new drugs based overwhelmingly on the genomes of white people. That’s why 54gene has been amassing DNA samples in its industrial-grade freezers. The genomic revolution has left Africa behind.

“Currently, there’s this huge gap in genetic information,” says Abasi Ene-Obong, who studied cancer biology at the University of London before founding 54gene in January. After completing stints at Y Combinator and Google Launchpad Africa, the company secured $4.5 million in seed funding this summer to start filling that gap, the biggest seed round ever for a Nigerian health tech startup. Ene-Obong says they’re on track to collect 40,000 samples by the end of this year, and 200,000 samples by the end of 2020. If it reaches that number, 54gene would be competitive with some of the biggest biobanks in the world. “We want to make African genomics available to the world to power drug discoveries that can treat people of all races,” Ene-Obong says.

To get its DNA samples, 54gene is working with 17 hospitals across Nigeria, targeting patients with cancer, cardiovascular disease, metabolic conditions, neurodegenerative disorders, and sickle cell disease. The company piggybacks onto ongoing studies at those institutions, working with research assistants to recruit volunteers, obtain their consent, and collect samples—blood, tumor tissue, saliva. When 54gene starts processing its samples next year, researchers at those hospitals will get to see their patients’ genetic data, and in turn, 54gene will get access to those individuals’ health records.

The strategy is a bit of a pivot from 54gene’s initial plans to stockpile DNA by going straight to consumers. The company briefly dabbled in selling spit kits that delivered insights into health and ancestry, like the ones made by 23andMe. But after just a few months, 54gene dropped the test. Launching a consumer health product in Africa—where e-commerce is limited and customers are hard to reach—can be exceedingly difficult. But Ene-Obong says it wasn’t just distribution challenges that forced the change. “We decided ultimately that we didn’t want to use consumer DNA tests as a Trojan horse to get people’s data,” he says.

Instead, the company is being transparent about banking on the pharmaceutical industry’s willingness to shell out big sums for its information. Earlier this month, four of the world’s largest drug companies agreed to pay around $120 million for access to new data from the UK Biobank, one of the DNA databases from which 54gene draws inspiration, and which also links to electronic health records. Seth Bannon, a founding partner at the San Francisco–based venture fund Fifty Years, which invested in 54gene, lauds the shift to hospital partnerships. “54gene has found the ability to collect quality samples way faster than we thought possible.”

The company’s growing collection could potentially prove even more valuable than existing biobanks. Because humans have lived there longer than anywhere else, African populations are known to harbor the greatest genetic diversity in the world. Nigeria alone boasts 500 unique ethnic groups whose genetics have been conserved over millennia.

“African ancestry populations have a unique history that makes them incredibly useful for pinpointing the variants that are driving disease,” says Alicia Martin, a geneticist at the Broad Institute, Harvard Medical School, and Massachusetts General Hospital. She points to a class of newly approved cholesterol-lowering drugs that came out of the discovery, a decade ago, of a woman of African descent who had two mutant copies of a gene involved in lipid metabolism. “When the entire continent of Africa has been left out of genetic studies, it’s everyone that loses out.”

But it’s people of African ancestry, says Martin, who suffer the most. Scientists know comparatively little, for example, about the more complex genetic risks that individuals of non-European descent may face. If you know you’re at high risk of, say, breast cancer, prostate cancer, or cardiovascular disease, you can take preventive steps—like getting screened more often or going on cholesterol-reducing drugs. “It’s a basic function of population history. The farther away you get from the population that’s well studied, you’re doing a worse job understanding which variants are contributing,” says Martin. She documented these biases in a Nature Genetics perspective earlier this year, warning that without major attempts to diversify global genetic databases, advances in disease prediction will only benefit white populations.

Some efforts to diversify the world’s genetic data are already underway, including the National Institute of Health’s All of Us program in the US, which aims to sequence one million Americans, mostly from underrepresented populations. As of July, 175,000 participants had donated their specimens. Last week, the NIH launched an initiative to update the human reference genome (about 70 percent of which belongs to one white man from Buffalo, New York) to more fully represent the genetic diversity of the human species.

The most notable investment on the continent is the Human Heredity and Health in Africa Initiative, or H3Africa. Since 2012, the NIH and the UK’s Wellcome Trust have been funding this $216 million push for genetics research led by African investigators. H3Africa’s three biobanks are currently supporting more than 50 projects that will eventually generate genetic data on 50,000 individuals. (When asked, H3Africa administrators did not know how many samples are currently housed in its biorepositories.)

For now, 54gene is only collecting samples in Nigeria, but it says it is in talks with three other African countries to set up additional biobanks. As it expands, 54gene will have to grapple with Africa’s long, uncomfortable history of biomedical colonialism, in which foreign entities have plundered the continent for its biological resources without recompense. There’s no guarantee that this time the discoveries enabled by African blood will come back to the people there as life-saving medications.

Ene-Obong, who was born in Nigeria, acknowledges the challenges of that dark legacy. “But you need to be at the table,” he says. “The more valuable our dataset becomes, the more influence we’ll have.” The company could set strict terms, for example, on how its information gets used. “We’re still young. But soon we’ll begin to have more of a voice.”

Updated 10-01-19 8pm ET: The story was corrected to clarify that Lagos is not the capital of Nigeria. The capital is Abuja.