African researchers are shaping the future of human genomics

In 2003, the human genome was fully identified and mapped. It took several years and cost billions of dollars, but that cost has exponentially gone down since. Today, it is possible to obtain your entire genome (a sequence of about 3 billion genetic units) for a few hundred dollars in a couple of days. A genome is the complete set of genetic information found in a cell, and genomics is concerned with characterizing mapping and editing genomes. This means an entire industry, including new kinds of healthcare services, has emerged, built on the back of genomics data. Almost 20 years since the Human Genome Project, genetic information from Africans represents only about 2% of studies that link genome data to diseases that could inform diagnosis or cures. This is changing. The Uganda Genome Resource (UGR) - a collection of genetic and phenotypic information from over 6,400 individuals in Uganda - represents a landmark in genomics research on the continent where such data is sorely lacking. African-led initiatives like UGR and many others in the pipeline are enabling genomics research to benefit Africans.

Humans share 99.9% of the same genetic makeup. The 0.1% that is left is enough to make us all different from each other. That 0.1% determines our physical features (phenotype) and our predisposition to certain diseases. The variation in genomes across different populations is therefore an important marker for understanding disease biology. The 1000 Genomes Project, which analyzed genomes globally, showed that African people have the most variant site per genome, which means there are consistent structural variations in the genetic units of Africans when compared to a reference human genome. However, characterizing the phenotypic and clinical consequences of these variations required more data from African cohorts. This kind of information is what resources like UGR may provide. For example, genetic variants developed by Africans in malaria-endemic areas to confer protection to the disease offers clues into the diagnosis of diabetes in regions where a particular blood disorder is common. Such insights and many others, including population history in East Africa, were obtained from analyzing the UGR.

UGR is borne out of collaborations and programs of Human Hereditary & Health in Africa (H3Africa). Inarguably, the establishment of H3Africa about a decade ago remains the most significant turning point in genomics research on the continent. It was designed to be a consortium of genomics laboratories and researchers across the continent and spearheaded by Dr. Charles Rotimi, a Nigerian epidemiologist whose distinguished career is characterized by many firsts in genomics for African ancestry populations. Funded by the US National Institute of Health and Wellcome Trust, the H3Africa initiative has enabled groundbreaking research in genetic and environmental determinants of diseases in Africans. The initiative has also funded several students and researchers, produced genome-wide and sequencing data on 79,254 individuals across 30 African countries, and funds three bio-repositories (in Nigeria, Uganda, and South Africa).

With little support from local governments, genomics researchers on the continent have often looked to international donors for funding. By considering alternative funding models, and Covid-19 bringing pandemic preparedness to a global focus, things may be changing.

As a case in point, Dr. Christian Happi leads an H3Africa project on surveillance of microbial threats in West Africa. To anyone who has been paying attention to epidemiology on the continent lately, his name may sound familiar. Dr. Happi was born in Sangmélima, Cameroun, where he studied before moving to Nigeria for a Master's and then to the USA, where he spent 12 years at Harvard as a scientist and professor. Dr. Happi is a global scientific leader. In 2011, he relocated again to Nigeria. His lab has been at the forefront of tackling diseases like Ebola and Lassa Fever (a highly asymptomatic hemorrhagic illness that kills thousands yearly) in the region. His team was among the first to sequence and publish the SARS-CoV2 virus genome in the world. A feat that they achieved 48 hours after the first case was reported in Nigeria. Dr. Happi is building a 1,300 sq. m facility in southwest Nigeria to enable world-class research on the continent. The center will enable researchers to pay less money to send samples and reagents abroad for their experiments. Dr. Happi is looking to reduce his group’s reliance on grants by providing a commercial service to other researchers on the continent.

There is an enormous commercialization potential of genomics in Africa, which has direct implications for the research community. Drugs are often only available on the continent several years after they are discovered and only when their patents expire. But according to 54Gene's CEO, Abasi Ene-Obong, the two-year-old startup wants to "create novel drugs out of Africa." The company has already raised more than 45 million US dollars and is composed of a brilliant team of mostly Africans. 54Gene is planning to sequence the genomes of 100,000 Nigerians, a plan that will significantly increase the data available for scientific research.

Nonetheless, the commercialization of human genomics requires serious ethical considerations. And even more so in Africa, where "parachute science" and resource exploitation isn't uncommon. Furthermore, scientists putting their careers at risk by raising ethical concerns within their organizations need to be better protected by society. Deepti Gurdasani co-led the UGR project. She has been at the forefront of research into the genetic basis for disease susceptibility in African populations for several years. In 2019, Wellcome Sanger Institute in England tried to commercialize the data and analysis from DNA samples of the Nama people in Southern Africa even though they had not consented to such use of their samples. Dr. Gurdasani, while working at Sanger, blew the whistle and lost her job as a result. Still, the expertise and leadership of African scientists are shaping new frameworks for biomedical research. H3Africa has published guidelines for informed consent and a framework for best practices in genomic research on the continent, with one core principle being respect for African values and cultures.

The future of genomics relies on genomics research done in Africa. Given the genetic variation Africans possess, we get a complete picture of what is happening in the human biological system. African scientists and entrepreneurs are blazing the trail with new insights, groundbreaking research, and innovative business models. Genomics is being used for drug discovery, precision medicine, and improved diagnostics, transforming the healthcare industry. It is imperative that African governments pay more attention to genomics research, fund scientists, and create the enabling environment for African scientists to train and work as investigators, clinicians, and genetic counselors in the field and develop intellectual property. African governments should also consider genomics data as a critical part of their healthcare infrastructure and ensure proper legislation and data privacy regulations.