In 1987, 10-year-old Segun Fatumo was on the streets of Lagos, Nigeria, hawking palm oil, yams, and pepper each day after school to help put food on the table. In the evenings, he and his family crowded into a two-room dwelling without running water or electricity. He knew nothing of the plan being hatched by U.S. and U.K. geneticists to sequence the human genome.
Thirteen years later, when researchers completed the draft sequence of the human genome, Fatumo—then an undergraduate studying computer science—heard all about it. “I knew the project would change our world,” he recalls. What he didn’t realize at the time was how it would change his life.
Fast forward more than 2 decades. Fatumo is now a computational geneticist in Entebbe, Uganda, with the Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine. Genome data by the terabytes flow through his seven-person lab, which is working to pinpoint genes involved in heart, kidney, and other diseases. All members of his team are African, the data come from African donors, and the ultimate goal is to improve the health of the people of Africa.
Until recently, genetic research in Africa was scanty, and most was done by researchers swooping in from afar to gather samples, then leaving to do analyses in well-equipped labs in the United States or Europe. “African genomic study was characterized by ethical dumping, helicopter science, and exploitation,” Fatumo says. Researchers gathered samples with little regard for informed consent and without giving back to the communities they studied, he says.
Today, Fatumo and scores of other young Africans are doing a substantial and growing share of this research. “African genomics is a story that’s going to be told more and more by Africans,” says Charles Rotimi, a genetic epidemiologist at the U.S. National Human Genome Research Institute (NHGRI).
Bolstered by the internationally funded Human Heredity & Health in Africa (H3Africa) Initiative, which sponsored Fatumo as a postdoc, these researchers hope to one day use their data to bring genetically tailored medicine to people who in some places still struggle to get electricity and basic health care. The work is beginning to close a wide gap in who benefits from the human genome revolution. “There’s this genomics expansion across the world,” says Neil Hanchard, molecular geneticist at Baylor College of Medicine. “Why should Africa be left behind?”
Including African populations is also paving the way for a better understanding of the links between disease and genes in everyone, everywhere, because Africa holds more genomic diversity than any other continent. “The African genome should be used as the reference genome for the entire world,” says Tesfaye Mersha, a geneticist at the University of Cincinnati and Cincinnati Children's Hospital Medical Center.
But genomic research in Africa has a long way to go. Researchers have only studied between 5000 and 10,000 whole genomes from Africans, compared with as many as 1 million worldwide. Africa has received less than 1% of the global investment in genomics research and clinical studies, Mersha says.
What’s more, funding for all current projects in H3Africa, a $176 million program supported by the U.S. National Institutes of Health (NIH) and the Wellcome Trust that has jump-started African genomics, is set to end in 2022. Fatumo has corralled another prestigious fellowship, but researchers across the continent are scrambling to make sure the nascent genomics community can survive—and grow.
Fatumo decided he wanted to study genetics as a youngster, after a doctor explained sickle cell disease to him. His brother suffered weeklong bouts of pain from the condition. Fatumo learned that his brother had two copies of the responsible gene—and that he himself would be spared because he had just one copy. “The role genes play in disease got me thinking,” he recalls.
Sickle cell, which is now being treated through gene therapy, is a classic example of how genetic knowledge can inform medical practice. And it primarily affects people of African descent. Yet most sickle cell studies and medical advances have happened in rich countries. Fatumo wants more Africans doing such research in the future.
One of six children, whose father worked as an unskilled tailor and later as a subsistence farmer and bush hunter, Fatumo moved with his family to the outskirts of Lagos when he was 9 years old. He hiked 2 kilometers early every morning to retrieve water from a river, wielded hoe and cutlass to tend crops, trekked to Lagos for school, then topped off the day hawking.
He and his parents managed to pay the 105 Nigerian naira (about $1) per year for school, thanks, in part, to Fatumo’s hawking profits. Fatumo says poverty fueled in him a fierce determination to do better. “The story of my upbringing is the one that propels anger for success.”
Later, he earned a B.S. in computer science at the University of Science and Technology in Port-Harcourt, Nigeria. Because little genetics was being done at African universities, he pursued graduate degrees in computer science at Covenant University in Ota, Nigeria. “I was lucky to study at Covenant where they had some key resources and constant electricity,” he recalls. Even so, his bioinformatics analyses kept crashing the school’s computer system. He spent 1 year studying in Heidelberg, Germany, where “the same analysis was completed in less than 30 minutes” with high-performance computers.
But he was working his way through school at the right time, in the right place. In 2009, the founders of the 6-year-old African Society of Human Genetics met in Cameroon to discuss their vision for an African genome project. “It was a dream we had, but … we didn’t know where the funding would come from,” Rotimi says. Francis Collins, who had coordinated the Human Genome Project but was then between jobs, was invited to give the opening talk.
He and other participants knew how much genomics studies in Africa could contribute to research worldwide. Trace any human’s family tree back far enough and the roots wind up in Africa, where our species was born some 300,000 years ago. When some groups left the continent over the past 80,000 years or so and spread across the globe, they carried only a subset of human genomic diversity. As a result, the people of Africa today carry more genetic diversity than those of any other continent. “There are parts of our genome that we cannot study any place beside Africa,” says Rotimi, who directs NHGRI’s Center for Research on Genomics and Global Health.
Those at the 2009 meeting also recognized that Africans needed to lead the way. “The idea that people outside of Africa are going to be able to decide the priorities … just doesn’t work,” Collins says. Local investigators are more likely to understand the culture and constraints and to be trusted by the community, Mersha adds.
Some researchers were skeptical about funding African-based research. “People said the money would just disappear,” Collins recalls. But “I was pretty convinced we could step away from the colonial perspective where developed nations make the decisions.” Collins became NIH director in 2009 and helped launch H3Africa in 2011. NIH has committed $150 million to the initiative through 2022, and Wellcome, a U.K. biomedical philanthropy giant, has kicked in another $26 million.
The initiative aimed to set up a network of laboratories across the continent to explore the relative roles of environment and genes in diseases that plague Africans, such as HIV/AIDS, trypanosome infections, stroke, diabetes, and heart disease. It also established biorepository and bioinformatics networks. To ensure a lasting legacy, it supports training as well as research.
In 2013, with H3Africa funding, Fatumo traveled to the Wellcome Sanger Institute in Hinxton, U.K., and the University of Cambridge as a postdoc in genetic epidemiology. At Sanger, he took part in the largest African genomics project to date, a multimillion-dollar effort to analyze genomic data from 14,126 people from five African countries, including newly collected whole genomes from nearly 2000 Ugandans. The international team of researchers found 9.5 million gene variants not previously spotted, underscoring the diversity of African populations and laying the groundwork for future genomic studies.
The results, published in Cell in 2019, also included specific variants related to cardiovascular diseases in Africans, such as one previously linked to an inherited blood disorder called alpha thalassemia. That single variant could also shape the diagnosis of a third condition: It alters how sugars bind to red blood cells and so affects the results of the blood glucose test often used to track diabetes.
One year later, H3Africa’s milestone genome paper came out in Nature. Human geneticist Zané Lombard and bioinformaticist Ananyo Choudhury from the University of the Witwatersrand, along with other African and international colleagues, analyzed 426 genomes, many newly sampled, from 50 populations in 13 countries. They described more than 3 million new human DNA variants, most from previously unsampled populations. The analysis also confirmed the continent’s complex migration patterns, tracing the path of Bantu-speaking people as they expanded southward and eastward more than 3000 years ago. That was just one of nearly 300 papers published so far by H3Africa teams, describing results as well as providing curated data sets of African genomes.