Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects

Abstract

Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.

Keywords: Africa; African OMICs innovation ecosystem; bioinformatics; computational biology; diversity; foresight; public health.

FIG. 1.

Size of data entries by world region in the GWAS Catalog and PharmGKB databases. The illustration displays a notable bias toward European subjects and poor representation of subjects from Africa. (GMEs: Great Middle Easterns). GWAS, Genome-Wide Association Study; PharmGKB, PharmacoGenomics Knowledge Base.

FIG. 2.

Representation of Human genomic sequences with African origins in NCBI nucleotide database. Only entries with “country” qualifiers were mined from the database. A total of 21,456 human genome entries (sequences of some target loci) have been submitted by these African countries.

FIG. 3.

Primary Sub-Saharan African Ethno-Linguistic Groups. Data have been collected only for groups with populations of more than one million members. Data were extracted from the Joshua project database (https://joshuaproject.net/).

FIG. 4.

Primary challenges related to African OMICs data processing.

FIG. 5.

Key steps, actors, and skills needed during the whole life cycle of OMICs data.

FIG. 6.

R&D economic indicators in Africa. (A) Expenditure on R&D in some African countries and (B) Number of researchers per million inhabitants. Data in (A) and (B) are extracted from UNESCO Institute for Statistics (http://data.uis.unesco.org/). (C) Based on the expenditure data we calculated the average number of Whole genomes (916 USD$ per genome) that could be sequenced by every 100 researchers per country or the equivalent total number of CPUs (2.5 GHz Xeon E5420) purchased for every 100 researchers per country. These statistics do not consider the area of expertise for each researcher, and we assume that those working in life science are of the same proportion from country to country. (D) Total number of OMICs projects per African country funded by abroad organizations for the period 2015–2018. Data are extracted from NIH World Report (https://worldreport.nih.gov/). (E) Funding contribution of each HIRO for OMICs research in Africa. CPUs, Central Processing Units; HIRO, Heads of International Research organizations; R&D, Research and Development.