Building a Precision Medicine Ecosystem in Africa

African populations are not well represented in genomic research, despite the enormous amount of genetic variation present in African populations. This gap makes it harder to develop fair and effective precision medicine programs that work for everyone.

Lack of funding and infrastructure in the region has made it hard to establish local programs in Africa in the past, but things are changing. Genomics and the early stages of precision medicine are now being set up in a number of countries on the continent.

The idea of precision medicine, or tailoring treatment to a patient’s individual characteristics, is not a new one. The so-called “Father of Western Medicine,” Hippocrates, who practiced medicine over 2,000 years ago, wrote about the importance of tailoring a patient’s treatment based on factors like age, physique, and constitution.

However, tailoring therapy requires as much information as possible. The completion of the Human Genome Project and rapid improvements in genetic technology over the last 20 years have made it increasingly possible to make precision medicine a reality.

Resource-rich developed countries such as the U.S. and U.K. have benefitted the most from advances in precision medicine. For example, while it is yet to be applied in all areas of medicine, it is now common for patients in these regions to undergo genetic diagnostic testing to assess cancer types and progression risks, and receive appropriately tailored treatments as a result.

Human genomic databases and research are the backbone of modern precision medicine. To build a polygenic risk score that can predict risk for a specific disease, researchers first need to carry out large-scale genome wide association studies (GWAS). To date, the majority of these studies have been carried out almost exclusively on people of European ancestry.

A website built by researchers at the University of Oxford, the GWAS Diversity Monitor, has been tracking the diversity of participants in published GWAS studies in real time since 2005. The percentage of African or African American/Afro-Caribbean people included in this kind of research remains depressingly low at 0.19% and 0.46%, respectively, compared with 94.53% people of European ancestry (as measured on Nov 2, 2024).

“If we continue this way, we are not going to get to a point of having precision medicine in Africa,” emphasized Segun Fatumo, PhD, a professor at Queen Mary University of London who focuses on genomic diversity research. He is from Nigeria and also holds a position as the head of NCD Genomics at the Medical Research Council/Uganda Virus Research Institute. “We are still far, far behind in terms of precision medicine. We need to improve our representation of African genomics first.”

Fatumo went on to add that it is important for genomic research to be carried out on as large a scale as possible in different populations in African countries, as opposed to just in people of African ancestry who live in Western countries.

“You cannot just focus on the Africans in diaspora, because they don’t fully represent the diversity in Africa. In Africa there are more than 3,000 ethnic groups, and they speak more than 2,100 languages. The African ancestry individuals in the U.K. and the U.S. represent a very tiny proportion of what you see in the African population, so you cannot just take those individuals in diaspora and say, ‘This is Africa.’”

Although there is a long way to go before many people in Africa can truly have access to precision medicine, there are signs that things are moving in the right direction. This is particularly evident in countries like South Africa, which has built up substantial genomic and genetic resources over the last two decades.

“Genomics is where we need to focus. Embedding it within public health, with governmental and regional governmental support, is the way for us to be able to provide these services not only to our own South African population, but to our neighbors and to the region,” said Shahida Moosa, MBChB, PhD, a professor of medical genetics at Stellenbosch University and head of medical genetics at Tygerberg Hospital in Cape Town, South Africa.

Early foundations for precision medicine in Africa

The Uganda General Population Cohort (GPC) was set up in 1989 as a joint project between the Medical Research Council in the U.K. and the Uganda Virus Research Institute to study HIV prevalence, incidence, and factors affecting viral spread. It includes around 22,000 people from 25 villages in southwestern Uganda.

The GPC has had in-depth community engagement and consultation built into the program from the start. In 2011, during round 22 of the study, a new group of participants was recruited from the original cohort to take part in a spin-off project called the Uganda Genome Resource, led by Fatumo. This group includes 6,500 participants with genotype data, and around 2,000 who have had their genomes sequenced.

A cardiometabolic GWAS was carried out using the Uganda Genome Resource cohort data, as well as other African and European genomic data for comparison purposes. Published in Cell in 2019, the paper showed significant differences between the African and European samples in terms of genetic variation. Many new genetic variants linked to blood, lipid, and glycemic traits were found in the African samples, including 9.5 million genetic variants only found in the Ugandan samples.

“We are currently expanding the Ugandan genome resource,” said Fatumo. “The phenotyping and the study we did previously was focusing on cardiometabolic traits, but now we are expanding much more than that and looking at psychiatric traits like depression and PTSD.”

The African Society of Human Genetics was founded in 2003 and has been a key player in driving the development of human genetics and genomics in the region. In a meeting in 2007, members agreed to start an African genome project, which became Human Heredity and Health in Africa (H3Africa). The goal was to “empower African researchers to be competitive in genomic sciences, establish and nurture effective collaborations among African researchers on the African continent, and generate unique data that could be used to improve both African and global health.”

H3Africa was funded over a ten-year period between 2011 and 2021 and received funding from the National Institutes of Health (NIH), the Wellcome Trust, and the African Academy of Sciences (AAS). The project achieved many things, like raising the profile of African genomics and improving training in the region, but its key achievements were the establishment of three African biorepositories in Nigeria, Uganda, and South Africa, and the creation of H3ABioNet, a pan-African bioinformatics network across 17 countries (16 in Africa). Overall, 51 projects led by African scientists resulted in the genotyping of 50,000 human samples during the project and whole-genome sequencing of samples from 426 people from 50 ethnolinguistic groups.

“I think H3Africa has been perhaps the best example of how to really bring genomics to the continent,” said Ananyo Choudhury, PhD, a reader and senior researcher at the University of the Witwatersrand in Johannesburg. “For the last ten years, I have gotten a lot of resources and training from H3Africa and have been very involved in that project.”

Oncology has been a poster child for precision medicine in the West, but targeted therapies can only be effectively used when healthcare providers have enough clinical and genetic data about their patients.

Yvonne Joko Walburga, MD, PhD, a clinician and researcher from Cameroon, is currently a research associate at the University of Cambridge who studies cancer epidemiology in the U.K. and Africa.

She has worked with the African Cancer Registry Network, which was founded in 2012 and includes 34 registries in countries across the continent. The network was set up to improve knowledge of patients with cancer in Africa and to promote research and access to better treatments and diagnostics. The registries record data such as the date of diagnosis, place of residence, profession, exact tumor type, and sometimes, stage at diagnosis of cancer patients attending hospitals in the region. The registries do not currently include genetic data.

“It’s a great network because it brings together the different registries. It helps us increase the quality of the data and help it to be used for international studies and comparisons,” said Joko Walburga.

“It also does a lot of training and capacity building for the staff, so it’s not just about data which is being taken away and published in big papers, but it’s also about ensuring capacity building across Africa.”

Expanding knowledge and investing in infrastructure

While the H3Africa project has ended, its legacy continues. Many new projects have been founded to continue or expand on the work it started.

A key barrier to rolling out genomic and precision medicine in the African region is a lack of infrastructure, access to relevant data, and expertise. For example, a lack of suitable labs, equipment, and people qualified to analyze the data.

A dearth of genetic testing or sequencing facilities means that African researchers or clinicians are often faced with higher costs than their counterparts in the West, mostly due to the need to ship samples to a suitable facility in a different country.

“We don’t have enough sequencers or skilled people. We don’t have logistics chains to organize this even if we get enough money,” explained Choudhury.

“If you go to an African service provider and say, ‘We need 500 sequences in six months,’ they will say, ‘Oh, we can’t do it.’ So that’s the problem. I think there are a select few places here that can do anything at scale and others are really not equipped to do those things.”

One way to build capacity and knowledge in genomics is through the initiation of sequencing projects in the region. For example, a large-scale genome project is underway in South Africa.

“On a day-to-day basis, if I do a clinical test like a clinical exome or a clinical genome, it’s very difficult for me to interpret those results because I have to compare them to a reference sequence, and the reference is not based on the population that we’re serving here,” explained Moosa.

“A positive step in that direction is the South African 110,000 Genomes Project. I think they’re going to start with a pilot project of 10,000, and then it’s going to be 100,000 after that from different populations around the country.”

Earlier work carried out by Fatumo and colleagues using data from the Uganda Genome Resource shows just how varied genetic diversity is in Africa. For example, a genetic risk score linked to lipid levels performed significantly better in a South African Zulu cohort versus a Ugandan one. This finding, among others, illustrates the need for more diverse data on genetic variation in African populations.

The Assessing Genomic Diversity in Africa study is seeking to change this by sequencing genomes from around 1,100 people from African groups and countries which have historically had limited or no access to genetic resources or projects.

Choudhury is working on this ongoing project along with other African colleagues such as Ezekiel Adebiyi, PhD, a professor at Covenant University in Nigeria and at the German Center of Cancer Research in Heidelberg.

“Our aim was to include under-studied geographic regions as well as ethnolinguistic divisions,” explained Adebiyi.

“This project was very difficult to implement, because for four of these countries this was their first major genomic project, but we managed to do it,” added Choudhury. “It’s not a big dataset, but it’s really diverse, because it’s filling 11 different blocks in the African map.”

Moosa is helping to build genetics knowledge in two ways. First, by improving medical training and second, by compiling a rare disease genetic database to help diagnose children and adults with these conditions in her clinics.

“Most people here have never done genetics in their undergrad medical training. That’s something that I changed when I came back to South Africa five years ago and I joined Tygerberg Hospital and the University. We completely revamped the undergrad genetics and genomics curriculum,” she explained.

Moosa works to help children and adults with rare diseases achieve a diagnosis and treatment. As with patients in Western medical systems, the diagnostic odyssey can be long and arduous. “I started the Undiagnosed Disease Program, which is the first in the region, just under four years ago. We started with exome sequencing. And within the first year, the diagnostic rate was around 50%, which was phenomenal because most of those individuals were getting diagnoses and being the first in Africa with that diagnosis.” The cohort Moosa is building is still small, but having a local database to draw on seems to be effective in many cases, despite its size.

Access to sequencing facilities in Africa is getting better, particularly in richer countries such as South Africa, but analyzing genomic sequences and big datasets needed to implement precision medicine remains difficult.

This is something Adebiyi and fellow bioinformatician Daudi Jjingo, PhD, a senior researcher at Makerere University in Uganda, have been working to improve for the last few years with two H3Africa spinout projects: Nurturing Genomics and Bioinformatics Research Capacity in Africa (BRECA) and the West African Sustainable Leadership and Innovation Training in Bioinformatics Research (WASLITBRe). These are just two of several similar projects designed to increase bioinformatics capacity across Africa.

“Our emphasis for the first three to four years was actually training students at a graduate level. That means having them trained, not just for a week or a single day workshop, but having them trained in depth, so that they can be able to really competently handle this,” explained Jjingo.

“We’re still very much doing work on that, but now that most of these trainees are beginning to come of age in terms of their skills and exposure, we are now beginning to try and bring these tools and skills to bear on abiding problems in our ecosystem.”

Breaking down barriers

Building up infrastructure and a good knowledge base are essential tools to enable genomic and precision medicine, but other challenges to broader rollout exist in Africa.

A key problem in Africa, both in academia and medicine, is the “brain drain” phenomenon. “In the last five years, all the registrars that we’ve trained have moved either into private practice or moved overseas,” said Moosa. “And by overseas, I mean Canada, Australia, or similar. They’ve been trained as the new generation of geneticists and it’s a real loss for our country and for the region.”

Joko Walburga believes thought needs to be put into how to retain good people or encourage them to come back to their home countries. “When it comes to training and capacity building, it’s always about making it easier for researchers trained elsewhere to go back home. You can get all the training, but sometimes you really want to give back. You really want to be able to do what you’re doing in the West back home, but you may not have the right infrastructure in place.”

Moosa acknowledges that South African hospitals and research institutes are better equipped than those in many other countries in the region, but says there is still much more that needs to be done to bring precision medicine to Africa.

“We have many more resources available to us, we’ve got the machines that are necessary to bring precision medicine into the mainstream, into public health. We are training the people necessary to do the human work that goes into it, but there hasn’t been that much buy in from our really key stakeholders. I’m talking about the national government. I’m talking about the Department of Health,” she emphasized.

Choudhury agreed: “So many of our local governments don’t want to bother about this. They have many other challenges, and this is not on their priority list.”

Simply getting access to necessary genetic testing and a healthcare professional who can explain the results can be very difficult. “When I compare us and our situation in South Africa to other parts of sub-Saharan Africa, you won’t find genetic services until you reach the Democratic Republic of Congo, and there it’s done mainly on a research basis,” said Moosa.

“There’s no genetic counseling other than in South Africa. There’s a new program in Ghana, and I think they’ve just graduated their first cohort of genetic counselors. But you won’t find genetic counselors anywhere else.”

This can be a big problem for patients with cancer in countries like Cameroon, where even if targeted therapies are available, the lack of genetic testing opportunities means that therapies cannot be matched with the right patients.

“Let me take the example of ovarian cancer, which has such poor survival rates even in the most developed countries. In the last ten years, PARP inhibitor drugs have been developed, like olaparib and niraparib. They’re more effective in patients who either have a BRCA1/2 pathogenic variant or who carry some kind of homologous repair deficiency gene,” explained Joko Walburga.

“In sub-Saharan Africa, we have a lot of patients who are diagnosed young, but who will never get tested, who will never receive a BRCA1/2 test, who don’t know if they are triple negative. You’re not tailoring their treatment to their cancer type, as a result of which there could be a lot of waste of resources as well, because you could give treatment which doesn’t necessarily benefit the patient.”

The formation of a more active biotech and pharma industry in Africa could help improve infrastructure and bring precision medicine to the region on a more advanced and larger scale. “There needs to be some industry that’s kind of taking the innovations and packaging them into products, which could be helpful in keeping the skills we produce,” said Choudhury.

Inevitably, the more active companies in a region, the easier it is for new startups to join them because existing companies build infrastructure and attract investors. Being the first, or one of the first, in an area can be difficult.

54Gene was one such company, founded in Nigeria in 2019, and was aiming to create a diverse African biobank, improve drug efficacy for African people, boost translational genomics research, and develop new medicinal products. Sadly, despite a great initial fundraise of $45 million and a good premise, the company shut down in 2023.

It is unclear exactly why the company folded, but financial troubles, leadership changes, and legal issues were all cited as possible reasons in the media. “I hope they will be able to recover and be able to get back to continue what they were doing in Nigeria,” said Adebiyi.

There is a small biotech sector in South Africa and a few companies beginning to make a name for themselves in other countries, for example, Yemaachi Biotech is based in Ghana and trying to revolutionize how cancer is treated in Africa. But ultimately, more financial, government, and regulatory support is needed for more startups to be launched and to succeed in the region.

New directions

The African continent may not yet have widely accessible and affordable precision medicine, but there is no doubt that the region is a hotbed of research and new genomic projects that will drive precision medicine forward.

The success of H3Africa has sparked interest in African genomics and a wave of new African projects, biobanks, and companies have either started or are in the process of launching. For example, a new initiative to build a network of Genomic Centers of Excellence (GenCoE) across Africa aims to improve the continent’s ability to address rare and emerging diseases through the application of cutting-edge science.

Adebiyi is a contributor to this project. “GenCoE is already working with also a new initiative, namely the Partnership for Accelerating Genomics research in Africa, and in their first pilot project, the collaboration will fund the sequencing of up to 25,000 genomes.”

Working with Jjingo and U.S.-based collaborator Melissa Gymrek, PhD, an associate professor at UC San Diego, Adebiyi and colleagues are currently using data from H3Africa and AWI-Gen to look for tandem repeat mutations in African populations.

“Most expansion disorder loci were discovered in European populations, and so they’re actually more common in European populations,” noted Gymrek. “Part of our goal was to find repeats that are specifically expanded in African populations now that we have this other data to look at. Even though we don’t yet have the disease phenotypes to tie them to, we actually did find multiple regions of the genome that are very commonly expanded in African individuals, but almost never expanded in European or other non-African populations.”

Fatumo is expanding on earlier projects through the newly set up KidneyGenAfrica Research Partnership Program. “It’s a partnership to deliver research and training excellence in genomics of kidney disease in Africa,” he explained.

Persuading local government and regulatory authorities to spend time and money on developing precision medicine in Africa can be a challenge.

Adebiyi believes one strategy is to show governments that precision medicine can help save money. “The governments are interested in cost saving. We need to tell them that precision medicine will strengthen the public health system, and the scarce resources available will be used to directly benefit the population.”

Moosa advocates for adopting a model like the one used to roll out precision medicine in Thailand, as they are a similar size country with an equivalent economy. “They’ve moved centuries beyond us already in the last five years, because they’ve incorporated this into public health and because they have serious buy in and support from their government,” she emphasized.

She also cautioned that it is important to fix problems locally and not rely on international help. “We can’t always depend on the NIH or the European Union or somebody else to help us. This needs to be something that is also led and co-led by local governments.”

Costs for patients also need to be affordable or limited. “There’s a push for universal health care. It’s not all bleak,” said Joko Walburga. “There are some countries like Kenya, like Nigeria, which are pushing for universal health care, meaning that patients with cancers would benefit from access to better treatment.”

There are still challenges that need to be overcome, but genomic resource and capacity building is increasing in many countries across the region, bringing hope that patients will gradually have access to more genomic and precision medicine services over the next few years.

Helen Albert is senior editor at Inside Precision Medicine and a freelance science journalist. Prior to going freelance, she was editor-in-chief at Labiotech, an English-language, digital publication based in Berlin focusing on the European biotech industry. Before moving to Germany, she worked at a range of different science and health-focused publications in London. She was editor of The Biochemist magazine and blog, but also worked as a senior reporter at Springer Nature’s medwireNews for a number of years, as well as freelancing for various international publications. She has written for New Scientist, Chemistry World, Biodesigned, The BMJ, Forbes, Science Business, Cosmos magazine, and GEN. Helen has
academic degrees in genetics and anthropology, and also spent some time early in her career working at the Sanger Institute in Cambridge before deciding to move into journalism.