- Africa is the most genetically diverse continent on Earth and the birthplace of modern humans.
- Despite this, African populations are severely underrepresented in global genomic databases.
- A massive collaborative project, coordinated by researchers at Wits, helped to change this.
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It looks increasingly likely that modern medicine will lean more on genetic data, but the vast majority of that data comes from people of European descent. A significant collaborative project, coordinated through Wits, helped change this.
Last month, a paper was published in the journal Nature describing the process undertaken by a group of researchers to collect and sequence the entire genetic code of 1 000 individuals from African communities underrepresented in global genomic databases.
The research was made possible through a massive partnership of research institutions collectively called the Assessing Genetic Diversity in Africa (AGenDA) project.
Essentially, the researchers set out to sample and sequence the genomes of many African ethnolinguistic communities, some of which had never been represented in global genomic databases before.
This matters because genetic data is increasingly used to unravel mysteries of human evolution and to advance a growing field called precision medicine, in which disease prevention and treatment are tailored to differences in people’s genes, environments, and lifestyles.
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Genomics is still a relatively new field. The first, essentially complete human genome was sequenced in April 2003 by the Human Genome Project.
While Africa is the birthplace of modern humans and widely considered the most genetically diverse continent on Earth, it is severely underrepresented in global genetic databases.
A separate study published in 2022 in Nature Medicine showed that 86.3% of the data points in the Genome-wide Association Studies (GWAS) catalogue, a prominent database that compiles data from multiple studies, came from people of European descent.
Only 1.1% of the samples came from people of African descent.
Increasing database diversity creates opportunities to improve our understanding of precision medicine and to gain insights into human evolution.
The AGenDA project, while sequencing a relatively small number of individuals, may make a significant contribution to database diversity.
Closing the data gap
Over a few years, the AGenDA project collected and generated whole-genome sequence data for 1 000 individuals from eight African countries, representing underrepresented ethnolinguistic groups.
Samples were collected from participants living in Angola, the Democratic Republic of Congo, Kenya, Libya, Mauritius, Rwanda, Tunisia, and Zimbabwe.
This included populations with substantial hunter-gatherer ancestry, Niger-Congo-speaking populations from Central and Central-Southern areas of the continent, and African islander populations that are not adequately represented in current public datasets.
Michèle Ramsay, the director of the Sydney Brenner Institute for Molecular Bioscience (SBIMB) at Wits and lead author of the study, told News24 that the researchers picked which communities to target by looking at existing data, identifying where the biggest gaps were, and assessing the feasibility of filling them given their resources and the legal frameworks around matters like data privacy in a given country.
Ramsay said that the project team spent a long time getting local partners on board, securing ethical and legal approvals, and engaging with communities before collecting samples.
The paper said that the people who collected samples made it clear to the participants that while their participation would help inform the genetic background for research studies, which would help their community benefit from precision medicine in the future, it would not be of personal benefit to them.
Massive potential
Ramsay said that this is not the first project of its kind.
She said that a study published in Nature in 2020, produced by the H3Africa Consortium, a pan-African initiative established to strengthen genomics research capacity on the continent, collected 300 whole human genomes from African individuals.
She said that researchers identified around three million DNA variants that had never been documented before in the 2020 study, underlining how much African genetic diversity is still missing from global databases.
“What we realised is that Africa is so diverse. People talk about putting all people with African ancestry into one box, those with European ancestry into one box, and those with Asian ancestry into another box.
“But what we realised is that the African box is enormous and is made up of a lot of smaller boxes that have genetic variation which is much wider than what you would expect,” said Ramsay.
She said that adding 1 000 people from underrepresented communities will “add significantly to our understanding of variation within the African continent”.
Impact
To explain the possible solutions that greater diversity in genomic databases might offer, Ramsay referenced the field of pharmacogenomics, a branch of precision medicine focused on how people with different genetic profiles respond to drugs.
“Instead of starting somebody on a particular drug because that’s what you usually do, by doing a genetic test, it could tell you that drug is not going to work on this person, because of their genetics, you need to try another drug, or you need another dose of the drug,” she said.
She said that some precision medicine interventions are reaching a stage where they are ready to be implemented.
She caveated this by recognising that public health officials face difficult trade-offs and that, at present, some precision medicine interventions can be quite expensive.
For example, Ramsay said that there is now a cure for sickle cell disease through gene editing; however, it costs in the order of $3 million per patient.
The other thing that Ramsay hopes will come out of the project is more information on human history.
The genome is a history book. Our past encounters, selection through either food insecurity, climate change, or infectious diseases, all modulate what comes out in the genome. So we are really interested and fascinated in using the data that we have to understand the history better.
Future plans
With the data now collected, Ramsay said the team intends to analyse it and make it available in a database accessible through a data committee.
The data committee’s job will be to assess what the person requesting the data intends to use the data for and whether that request aligns with the consent the researchers obtained from the participants.
Ramsay said the intention is to build analysis skills within the organisations they worked with on the project so that more people can conduct genomic research on the continent.
She said the project wants to ensure that future genomic research on Africa can be led, analysed, and interpreted by African researchers.
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