The African Imperative
The importance of diversity in biobanking and genomic data
Aminu Yakubu | | Opinion
Humans are incredibly diverse. It stands to reason that this diversity would be reflected in our susceptibility and response to disease. Some illnesses are more prevalent in certain populations than in others. Not all populations respond similarly when treated in the same way for the same disease. Some populations even have higher survival rates than others.
Our genes have specific sequence variants that could explain these differences. By exploring these variants, we could learn how to better manage diseases in different populations, improve patient treatment selection and outcomes, and identify gene targets for the development of new drugs. However, one of the most widely used reference genomes applied to achieve these aims is largely comprised of genes from a single human being (1). Although more representative reference genome datasets are being developed, many are limited in diversity and representation – and others are developed ab initio to serve only a particular population group.
This limited diversity is even more concerning for those of African descent. Although these populations have the highest genetic diversity of all, they only provide about three percent of all genetic data used for research and drug discovery (2). This scenario does a great disservice to humanity. First, it has the potential to further exacerbate the disparity in disease morbidity, because those developing drugs from new target genes may lack the information needed to make such drugs effective for African populations. Second, the world is being denied access to novel genetic variants from the huge diversity inherent in African populations, as seen with the 300 million DNA letters from African populations reported missing from the human reference genome in 2018 (4). Equally, some 9.5 million variations identified in African populations have not been previously reported at all (5).
Some of these genetic variations could have informed the identification of valuable new drugs. For example, a mutation discovered in one African individual inactivates a gene that has been implicated in high cholesterol levels – and its identification has led to a drug used to better manage this condition (6). Another recently identified variant, said to have the potential to affect glycated hemoglobin levels, may inform research into better ways of managing diabetes (5) – a condition affecting many underrepresented populations. The findings of new variants among non-European populations, in particular those that can inform drug discovery, are a clear indication of the importance of diversity in genomics research. This diversity is achieved in two ways – by including more genomics data from underrepresented populations in research and drug discovery efforts and by further enriching the human reference genome to inform better imputation of genetic variants from other non-European populations and identification of novel variants.
New biobanking facilities and other efforts by academics to increase access to genomics data from African populations will go a long way towards addressing this gap. But there are important considerations in taking biobanking and genomics research to scale in underrepresented populations. African researchers and communities, for example, remain skeptical of the intent of research studies for which samples are collected and shipped to other countries. There are concerns about the use of the samples beyond the stated intent and researchers feel a sense of disempowerment once the samples leave the shores of their countries.
In a recent conference of oncologists in Maputo, Mozambique, African experts and researchers applauded a speech that frowned at the practice of transferring samples out of African countries for analysis and called for local capacity strengthening. Strategic location of biobanking facilities that also have gene sequencing capacities are important in this regard. With the preponderance of smaller biobanks in academic research institutions and hospitals, strategically located, well-resourced biobanks can help pool resources and maximize their collective potential.
Concerns about social value and benefit remain at the core of expectations from biobanking and genomics research – and yet, such research does not promise immediate benefit to participants. To address this concern, research efforts must include some degree of individual and institutional capacity building to sustain and drive future research by African scientists.
Overall, one thing is clear: if the world is to optimize the potential of the human genome in improving health, underrepresented populations, especially those from Africa, must be included. And not only in terms of their genomic data; researchers from underrepresented areas must be involved in these efforts. And, last but not least, African governments must provide an enabling environment, appropriate regulations, and support for biobanking and genomics research. This is vital for not only addressing the limited reach of current international funding, but also creating a sustainable industry in the long run.
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- RE Green et al., “A draft sequence of the Neandertal genome”, Science, 328, 710 (2010). PMID: 20448178.
- J Morales et al., “A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog”, Genome Biol, 19, 21 (2018). PMID: 29448949.
- J Wapner, “Cancer scientists have ignored African DNA in the search for cures” (2018). Available at: bit.ly/2O8DJ3f.
- RA Mathias et al., “A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome”, Nat Commun, 7, 12522 (2016). PMID: 27725671.
- D Gurdasani et al., “Uganda genome resource enables insights into population history and genomic discovery in Africa”, Cell, 179, 984 (2019). PMID: 31675503.
- K Jaworski et al., “PCSK9 inhibitors – from discovery of a single mutation to a groundbreaking therapy of lipid disorders in one decade”, Arch Med Sci, 13, 914 (2017). PMID: 28721159.