Bridging the genomic data gap in Africa: implications for global disease burdens

Governments by far have the highest level of influence on society especially including decisions that could affect the socioeconomic and health outcomes of a population. Investments towards anything that could improve these outcomes are therefore important for any country. Since research is an important aspect of health, investing in genomics research in Africa can prove vital for the improvement of health globally. What this implies for global health inclusion of African genome data would improve precision medicine through solutions like vaccines and drug development, reduce the chances of disease re-infection, drug resistance, and even future pandemics. We suggest the following policy recommendations to bridge the genomic data gap in Africa.

Building a representative genomic repository for Africans

Concerns about intercontinental genomics data inequalities had risen as far back as 2009 when it was reported [33] that 96% of participants in genome-wide association studies (GWAS) were of European descent. Africa has been established to be a genetically diverse continent representing 54 countries with over 3000 ethnic groups. However, much of its genomic data is attributed to Africans living in the diaspora, which is not an adequate representation of the diverse genome that span the continent [5]. Some of these diasporans are not fully African as they have deep interracial relations with people from other continents (e.g., children from interracial marriages). Some are often affected by the environment in which they live too. Hence, the possible influence of inter-racial relations and gene-environment interaction must be considered if we would get the best of African genomic data.

Now, organizations like the H3Africa, ACEGID, 54Gene, Institute of Human Virology, African Collaborative Center for Microbiome and Genomics Research, African Research Group for Oncology, and Center for Genomic and Precision Medicine, amongst others, have risen to fill this gap. Today, Nigeria, with one-fourth of the total African population is taking the lead in the generation of genomic data for the continent, as demonstrated by Fatumo et al., 2022 [11]. However, African data in GWAS still accounts for < 1% [34]. To tackle this gross underrepresentation, local researchers, i.e., those domiciled within the continent, must be empowered with the funds and tools to contribute their quota to building a larger genomic data repository that can cater to the larger population without having to collect data abroad.

Developing research capacity across countries on the continent

A key consideration in addressing this status quo is developing research capacities through improved research facilities and technical expertise in Africa. African researchers do not lack the knowledge or skill for this genomic revolution, rather, they lack the key infrastructure, strategic partnership, favourable policy, and sufficient funding, as earlier mentioned. Hundreds of African researchers have acquired knowledge and expertise in well-equipped laboratories and institutes overseas through funded graduate studies, postdoctoral fellowships, grants, and collaborations. The challenge is coming back home to find that there is little or no opportunities for (world-class) research and genomic infrastructure for them to contribute their expertise.

However, we can take a cue from what already exists and the difference that such facilities are contributing. The H3Africa project, in its 12 years of commencement, has spearheaded many breakthrough research findings in Africa, most of which cumulates to form a huge chunk of the < 1% African data in global GWAS. This was achieved through a $176 million grant provided by the U.S. National Institute of Health (NIH) and Wellcome Trust [19]. H3Africa has established its presence in 30 African countries and facilitated the following research [35]:

a.

the AWI-Gen research that revealed that hypertension is highly prevalent in Eastern and Southern Africa;

b.

the Genomic Characterization and Surveillance of Microbial Threats in West Africa, which led to the development of SHERLOCK- a low-cost genomics test to rapidly identify three types of fever - which was deployed during the Lassa fever outbreak;

c.

Immunoglobulin gene diversity in an African population and impact on antibody function in HIV infection, clinical and genetics studies of hereditary neurological disorders in Mali and many others.

The NIH has proved very instrumental in addressing the genomic data gap in Africa. Recently, it granted $46 million for Alzheimer’s Disease Genetic Study, which will involve the genetic study of 5000 Africans and 4000 African Americans, among others [36].

In Africa, the financial allocation to support education and scientific research is insignificant compared to the volume of work that needs to be done. The reason for this is not far-fetched: the burden of other competing needs in the region, inarticulate communication of research findings to a non-science audience to foster the understanding of the importance of science, and significantly, corruption and misappropriation of scarce resources. This has led to brain drain of the continent. The International Development Research Centre in 2011 [37] identified that there are more African scientists and engineers in the United States than in the entire continent; most of whom have migrated for career prospects, better working conditions, and academia. But some strides have been made on the continent too. In 2018, South Africa recorded the highest scientific expenditure - 0.83% of its GDP [38]. Because of this seemingly extraordinary spending compared to other African countries, the country was ranked the 53rd most innovative country in the world by the Global Innovative Index [39]. This reveals that there are willing and capable hands on the continent and, if given the needed support in research capacity and technology development, they can contribute significantly to global health equity.

For robust results, setting strong local research ethics, laws and agendas that are of priority to the continent should be the foundation and should serve as templates for building local research capacity. The approach of scientists from High-Income Countries (HIC) coming to conduct “extractive or helicopter” research in Africa has not proven sustainable due to conflict of interest, ethical issues, claims on patent and data ownership, and dissemination of findings [40]. Hence, building local research capacity in- and about Africa’s health priorities is important for acquiring genomic data on the continent. However, local researchers should consider forming a partnership with HIC collaborators who understand the context and needs of the African region, teach agenda-setting skills, and assist in agenda development. African governments should also implement local specialized funding bodies seeking to finance research of African origin and relevance. Currently, the most frequent sponsors of research in Africa include the National Research Foundation and Medical Research Council in South Africa, the U.K. Department for International Development, The Bill & Melinda Gates Foundation, the German research-funding organization DFG, the WHO, the World Bank, USAID, NZAID, AUSAID, NIH, and Wellcome Trust [41, 42]. While these contributions have significantly advanced science and technology on the continent, much more is needed to fill the genomic data gap in Africa, notably at the grassroots. More commitment to funding and sponsorship from the Government, private and corporate establishments, and individuals in Africa will also go a long way.

Building African science to be self-sustainable

An aspect of concern with foreign grants is the continuity of these grants and the adverse regression that science and genomics research in Africa would face if these foreign funding bodies pull out. More so, these funding bodies have their objectives already set, which sometimes might not be Africa’s health priority. The long-term goal would then be to build African research to be self-sustainable through the commercialization of research findings translated into innovations, industrial processes, or tangible products for human use. Wanjiru [43] and John Ayisi [44] examined the role and crucial steps for research commercialization for sustainable development and economic growth in South Africa and Kenya, respectively. Typically, the Bayh-Dole Act of 1980 of the United States established the legal framework for commercializing research developed within university settings by transferring ownership of intellectual property from publicly funded granting agencies to universities [45]. And this sole Act has contributed well over $1.3 trillion to U.S. economic growth and created more than 4.2 million jobs and over 11,000 new startups [46]. Similar models can be adopted and adapted for sustainable science in Africa. In the long term, research capacities should be developed in Africa to build self-sustainable facilities and capacities that can lead the course of total transformation in genomics and the entire science field in Africa.

Developing capacity for high-end scientific publications and data analysis

The paradox of most research conducted in Africa is that they are not properly documented or not documented at all. For instance, Nigeria has over 170 universities (polytechnics, technical and vocational schools excluded). In 1996/1997, the country produced about 50,000 graduates, out of which 18,805 were reported to be science/science-related graduates [47]. While this figure has progressed geometrically in recent years, Nigeria’s scientific publication stands at 0.3% of global scientific and technical journal articles in 2020, which when pooled with other African countries give less than 1% of scientific publications globally [9].

There is a dire need to develop the capacity of Africans especially young and early career scientists to produce scientific publications that are of international standard. Tertiary institutions in Africa that teach research writing skills are barely a handful and are not enough to bring Africa to par with other continents, hence the need for training, especially from the baccalaureate level is important. Also, bioinformatics skills are needed to analyze and interpret data from genomics research. Without bioinformatics expertise, health and genomics research in Africa is largely going to be suboptimal. There is an enormous need for bioinformaticians in Africa as this field is largely untapped in the region [48]. Consequently, evaluating the interplay of genomics, transcriptomics, and proteomics [49] in the African populace will be essential to better understand any data from genomic research. Bioinformatics and data science research have boundless potential across Africa due to its high level of genetic diversity and the burden of infectious diseases.

Strategic funding and partnership

Most public institutions with genomic sequencing capabilities are non-profit and have been funded by external bodies on projects they keenly focus on. The fortunate researchers in these institutions represent very few percentages of the African research population. The top funded researchers represent a small fraction (about 2%) of researchers on the continent and are primarily from Agriculture and Health Sciences [42]. This leaves a gap in other disciplines. Private companies like Inqaba Biotec and 54 Gene are contributing their quota to grant African scientists access to their Next Generation Sequencing platforms. Development in sequencing technologies has come a long way, becoming less expensive in recent years. Whole Genome sequencing now costs about $1000 compared to the Human Genome Project, which cost about $3 billion [50]. However, due to no or poor funding, few African researchers can afford to own this infrastructure or pay for such services in a continent where most graduate studies and research (M.Sc and Ph.D.) are self-funded by students who still face the harsh economic realities of the African continent. For context, about 460,065,747 (33%) of the African population are living in extreme poverty (on ≤ $1.90 a day) [51].

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