South Africa: Scientists Warn African DNA Is Missing From the Global Genome Map

African scientists say the world is missing vital medical insights by ignoring the continent’s vast genetic diversity. Less than 2 percent of human genome sequencing worldwide comes from African populations.

“Diversity” was the buzzword at the Human Genome Organisation (HUGO) summit last month in Durban, South Africa. Genomic research depends on it – yet Africa remains one of the most under-studied regions.

Cameroonian researcher Ambroise Wonkam, who leads the African Society of Human Genetics, said this leads to serious problems in diagnosing and treating genetic conditions.

“If we don’t know which genes are the most important in terms of diagnosing genetic diseases in African populations, it is impossible for me, as a medical geneticist, to treat an African child in the same way as I treat a European child,” he said.

Wonkam described his experience in Switzerland, where a single gene test explained the cause of deafness in 50 percent of cases.

“When I returned to the African continent, I tested Cameroonian children and black South African children, and zero percent of them had mutations in these genes,” he said.

Aimé Lumaka, professor of genetics at the University of Kinshasa, said fewer patients in Africa receive a definitive diagnosis than in Europe or North America.

“We compare the profile of the individual who has come to us with the genetic profile that exists in the databases, and as we cannot find certain profiles, we do not know the significance of certain African genetic profiles,” he said.

Why local data matters

This lack of data is holding back efforts to treat conditions like sickle cell anaemia, which are more common in African populations. It’s also slowing global research. One anti-cholesterol drug, for instance, was developed by studying African people with naturally low cholesterol.

Although humans share more than 99.9 percent of their DNA, small genetic variations can affect how our bodies function. Since the first humans evolved in Africa, populations that stayed on the continent retained the most diverse range of genes – making African DNA key to understanding human health.

“In fact, we need more data from Africa than from the rest of the world,” explained South African geneticist Michèle Ramsay.

“Because if we look at the evolution of our species and the branches of our lineage, someone from West Africa has more genetic differences with someone from East Africa than someone from Europe has with someone from East Africa,” Ramsay said.

“So we can’t just look at general data on people of African descent across the continent, we need much more detailed, regional data.”

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Still, research is lagging behind. “Genome sequencing has historically been carried out on populations of European origin,” said Christopher Kintu, a Ugandan scientist at Queen Mary University in London.

“This is not surprising, as it requires a lot of time, money and resources, which are not necessarily available in Africa.”

That’s changing. In 2001, sequencing one genome took 10 years and cost more than $2 billion. Now it takes just a few days and costs under $1,000 to decipher the letters that make up our DNA, the filament that forms our 23 pairs of chromosomes.

Each of these chromosomes carries genes – veritable instruction manuals hidden at the heart of our cells, so that the body can develop and function.

‘Helicopter’ research

A $176 million programme called Human Heredity and Health in Africa (H3Africa) supported about 50 projects over 10 years. Although the funding has now ended, some scientists are continuing the work in their own countries to bridge the data gap.

In South Africa, a new initiative will begin by sequencing around 10,000 genomes, as part of a longer-term plan to study 110,000 individuals.

“We’re going to start by sequencing around 10,000 genomes from a group of patients we’re already following over the long term, as a pilot phase to study feasibility,” said project coordinator Rizwana Mia.

This first stage is being funded by the South African government.

Nigeria has begun collecting samples for a similar project, though sequencing will only begin once funding is secured. Crucially, African scientists are leading these efforts – a pushback against so-called “helicopter” research, where foreign scientists collect data and leave.

“This leaves African researchers feeling that they have been used – and also the participants, whose samples and data have been collected,” said Deborah Ekusai Sebatta of Uganda’s Makerere University. “Genomic research is based on trust.”

Wonkam wants to go even further. With colleagues Nicola Mulder from the University of Cape Town and Christian Happi from Nigeria’s Redeemer University, he plans to open 10 sequencing centres across Africa over the next 10 years, each with an annual budget of $10 million.

For the time being, the project plans to sequence 300,000 genomes, although Wonkam estimates that a database of 3 million participants would be needed to fully reflect African diversity.

The location of the coordination centre, however, could be an issue, as it is likely to be in Rwanda, which is accused of being involved in the conflict in the east of the Democratic Republic of Congo.

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Viruses and chronic diseases

Genomics still hasn’t delivered on all its promises. Scientists are only beginning to understand how different mutations interact with each other and with the environment.

Predictive tests, which are meant to flag up genetic risks for certain diseases, haven’t always worked well in African populations.

“We make hundreds, even thousands, of genetic discoveries, but it takes a lot longer to understand the consequences and then to come up with a drug,” said Philippe Froguel, a professor at Imperial College London and the University of Lille.

He discovered a gene linked to obesity in 1998. A drug based on that finding only became available three years ago.

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Some question whether it makes sense to invest in genetic science in Africa, where healthcare systems are under strain and access remains unequal. But the researchers RFI spoke to say it is essential, especially as chronic diseases like cancer and diabetes are on the rise.

New studies are also looking at how DNA can affect the way the body responds to viruses. South African scientist Veron Ramsuran said some people seem able to control HIV without medication.

“We have discovered that there are groups of individuals capable of controlling the progression of HIV and maintaining a low viral load, without being on anti-retroviral drugs. So we’re trying to identify which mutations or genes in these individuals might play a role.”

The study of variants in African populations is unlikely to reveal its secrets immediately, but researchers say Africa must not be left behind as the world moves towards precision medicine.

Despite the evaporation of American funding in the health sector and US President Donald Trump’s aversion to the word “diversity”, African researchers continue to be ambitious when it comes to deepening our knowledge of the human genome.

By RFI website.