Sequencing 100,000 genomes to revolutionize Nigerian genomics

Rare variations in the human genome can have huge implications for understanding disease and developing new treatments. Scientists search for these rare variants by analyzing the genomes of as many people as they can, looking for that one diamond that reveals the key to curing a deadly disease. Most genetic databases have plenty of genomic sequence information from people of European and Asian descent, but they are missing a whole continent’s worth of genetic data from African people. There are likely rare genetic variants unique to African people that put them at greater risk for developing non-communicable diseases. The inclusion of this genetic data in future genome-wide association studies will allow scientists to more accurately predict how likely a person of African descent is to develop a particular disease, and the identification of new genetic variants may lead to the development of new therapeutics.

Living in more than 50 countries and as members of even more ethnic groups, African people are the most diverse population of people in the world. But in 2019, only 3% of genomic studies included African populations (1). Fast forward to 2021, and that number actually dropped to 1.1% (2).

“It's now worse,” said Segun Fatumo, a genomics researcher at the London School of Hygiene and Tropical Medicine and a co-leader of the African Centre for Translational Genomics (ACTG). “There's a need for more genomic studies to be done in African populations.”

To reverse this trend, Fatumo and his colleagues at ACTG along with the biotechnology company 54gene, based in Lagos and Washington DC, set out to sequence the genomes of 100,000 people in Nigeria — the most populous and ethnically  diverse country in Africa (3). There are 500 languages spoken in Nigeria, and it is home to 300 ethnic groups. Sequencing 100K Nigerians will give researchers a better picture of the genomic diversity in Africa compared to other sequencing efforts. Their Nigerian 100K Genome Project is the first of its kind on the African continent. With it, Fatumo and his team hope to better understand how non-communicable diseases such as cancer, heart disease, metabolic diseases, and many others affect Africans. The initiative will empower Nigerian and other African genomics researchers to identify potential disease genes and develop new therapeutics for them that will benefit Africans and others all over the world.

How did you first become interested in genetics and genomics?

I was born in Lagos, Nigeria in a family of six children. My little brother was in a lot of pain and crying all the time. We eventually found out that he had sickle cell disease, and everyone in the family also had sickle cell traits. Having sickle cell traits means that a person has just one sickle cell allele, whereas people with sickle cell disease have two alleles. As I was growing up, I also discovered that because I have sickle cell traits, I am protected against malaria. I wanted to understand what was going on, so that was how I started getting interested in genes and the role they play in health. 

What motivated you to start the Nigerian 100K Genome Project?

In Africa, the major problem over the years has been infectious disease. But in recent years, non-communicable diseases such as kidney disease and type two diabetes are rising at a faster rate in African countries than in high-income countries (4). That is concerning, so we want to reliably assess the prevalence of different non-communicable diseases in the Nigerian population. Nigeria has a lot of diversity in terms of the ethnicity and languages spoken, so it is a good place to start.

How much progress have you made on the Nigerian 100K Genome Project so far?

We are in the stage where we have collected our samples from the participants, and we are now doing genome sequencing and whole exome sequencing on the samples. Nigeria is divided into six geopolitical zones, so we’re sequencing people in each of them to make sure that we have a representative sample. We are looking at the genomic differences between rural and urban populations to assess the prevalence of different diseases. We also collected samples from people at different hospitals with specific non-communicable diseases. We are focusing on kidney disease and sickle cell disease. 

What sort of feedback have your received from people participating in the project?

People are really willing to participate, and one of the reasons for this is that before we started sampling, we did a lot of community engagement. We talked to stakeholders, cultural leaders, religious leaders, and other leaders in the community. People were aware of what we were planning to do and the potential benefit of our study, not just to them as an individual, but to a Black person living in Nigeria or a Black person living abroad. People are really excited to know what is going on in their bodies.

What challenges have you encountered?

We're doing something that's never been done before, so there are many challenges. Before we started doing the 100K sampling, we did pilot studies with a few samples to see if people would accept us. Some people are very skeptical about someone taking their blood. Some Nigerians believe that their blood can be used by others for juju to make money, so before we took blood, we made sure that we had their informed consent and explained how we would use their blood.

Because Nigeria is very diverse, we had to translate our questionnaire into many different languages, including Yoruba in the West and Southwest and Fulani or Hausa in the North. Along with that, it's very difficult to interpret everything in the local language. We don't have words that translate directly to “genomics” or “DNA” in Yoruba, Fulani, or Hausa. We have to describe those words by saying things like, “You are your dad's and your mom’s, and you resemble them because you share features with them.”

How has the African genomics community changed since you started working in it?

There have been so many changes in the genomics community in Africa. Years ago, people would come to Africa from high-income countries, collect samples from our countries, and fly the sample to their own country for analysis. They would do the study without taking into consideration the scientists here, but that has changed. Now we are in a place where we can empower our own people to collect samples from different parts of Africa, do the analysis, and publish our own papers. Of course, that doesn't mean that we're not collaborating. We are widely collaborating with other scientists globally, but we also want to take the lead in performing studies in Africa. We think that the Nigerian 100K Genome Project will propel a genomics revolution in Africa. We will not stop at 100,000 genomes; this will move forward into other countries in Africa in the future. We are very excited because we don't want Africa to be behind in genomics studies. We are in a state where Africans are setting the agenda for our own genomics studies, and that is very important.

What do you find most exciting about working on the Nigerian 100K Genome Project?

I'm excited about the potential benefits of this study. There is a gene called PCSK9 that is responsible for lowering blood cholesterol, which is a risk factor for heart disease. Years ago, this gene led to the discovery of a drug, which is now very important for lowering blood cholesterol. The only reason the researchers found this gene was because they included individuals with African ancestry in the research study. If they hadn’t included African ancestry individuals, we wouldn’t have this drug today.

I expect that the genetic variants we find will associate with different non-communicable diseases because we know that there are so many genetic variants present in the Nigerian population that are not in any other population. In five to ten years’ time, hopefully we will find a treatment for kidney disease, for type two diabetes, or for cancer, who knows? I'm very excited about the new medicine that may be discovered because of this study.

This interview has been edited for length and clarity.

References

1. Sirugo, G. et al. The Missing Diversity in Human Genetic Studies. Cell  177, 26-31 (2019).
2. Fatumo, S. et al. A roadmap to increase diversity in genomic studies. Nat Med  28, 243-250 (2022).
3. Fatumo, S. et al. Promoting the genomic revolution in Africa through the Nigerian 100K Genome Project. Nat Gen  54, 531-536 (2022).
4. Gouda, H.N. et al. Burden of non-communicable diseases in sub-Saharan Africa, 1990–2017: results from the Global Burden of Disease Study 2017. Lancet Glob Health  7, e1375-e1387 (2019).