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What is the current state of African genomics?

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    African genes are not well represented in research databases. Here’s why that’s a problem
     
    The Human Genome Project, which took 13 years to complete from 1990 to 2003 was the first successful global effort involving public and private scientists towards sequencing the DNA of the human genome.[1] It had one major shortcoming – an under-representation of the African population in the sampling. In fact, only about 2% of the genomes mapped globally are African.[2], [3] But that is now beginning to change as multinational pharmaceutical firms are scouring the length and breadth of the continent to get their hands on a rich repository of genes. In the article, I highlight the economics that underpins the various African genomics initiatives currently underway and flag concerns of what could happen if governments do not seize the initiative of mapping the continent’s human genome.

     

     

    What is genomics and why is it important?

    According to the National Human Genome Research Institute (NHGRI), genomics is the study of a person’s genes (the genome), including interactions of those genes with each other and with the person’s environment.[4] Whether in health or in wealth, genes underpin the human condition, including what ails man. Genomics enable better and more accurate diagnosis of diseases based on a patient’s genomes, allowing for optimal variations in treatment that are particular to the person. In fact, drugs can be specifically designed to match the genomics of each patient, reducing incidences of drug resistance and adverse reactions.

    What is the current state of African genomics?

    African DNA does not feature much in global genetics research. In fact, research published in Nature found that 300 million letters of DNA from 910 people of African descent were not found in the reference genome that underlies the basis of modern genetic and genomic research (Nawrat, 2019). This is in part due to the antipathy of peoples of African-origin to the study of genomics given its long and painful association with racism. Present-day western scientists are also reticent about studying African DNA knowing well the role this branch of science of played in the popularisation of race theories. The problem is compounded by infrastructural in Africa itself.[5] Besides, Africa is not a significant player in the global market for new drugs, which is estimated to be worth US$20bn, with annual growth of as much as 12%.[6] The absence, however, of a key element of human genetic history, creates an in-built handicap to these efforts – a realisation that is beginning to make global pharmaceutical firms pay attention to African genomics for the potential it has to advance ground-breaking discoveries in medicine.[7]

    Even so, there have been recent efforts by some African scientists to correct this lacuna, albeit with Western funding and support. At the moment, they are largely focused on researching diseases mostly found in Africans like sickle cell disease or predominant ones like tuberculosis and stroke, under the aegis of the Western-funded Human Heredity and Health in Africa (H3Africa) initiative, for instance.[8] Naturally, there is worry that the increasing support for African genomics research will inevitably perpetuate the continued dependence of African countries on the West, with most of the benefits and knowhow ringfenced to the continent’s detriment.[9] That could mean the sale of medical drugs to Africans at a premium even as the DNA that led to its development was African. Failure to protect such intellectual property has been a folly that has resulted in Africa losing millions of dollars in revenue from multinational corporations over the years.

    There are costs to science from scant African genomic data. In 2019, for instance, a “genome-wide analysis of Type 2 diabetes in sub-Saharan African populations [found] a previously unreported gene, Zinc Finger RANBP2-Type Containing 3.”[10] New insights are increasingly being found from African genomic data.[11] This is not surprising. After all, Africa is widely regarded as the cradle of human civilization.[12] It is from here that the first humans stepped out to begin populating the world. There is still much that we do not know about the human genome owing to the lack of African genetic samples. Notable efforts, however, are being made to map the African genetic pool. Institutions and laboratories like 54gene (Nigeria), African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University (Nigeria), Institute of Infectious Disease and Molecular Medicine, University of Cape Town (South Africa),[13] African Computational Genomics (TACG) Research group at the MRC/UVRI & LSHTM Uganda Research Unit (Uganda), Africa CDC Institute of Pathogen Genomics (Ethiopia), Centre for Proteomic and Genomic Research (South Africa)[14] and H3Africa-funded Africa Wits-INDEPTH Partnership for Genomics Research (South Africa) are just such initiatives.

    In collaboration with hospitals in Nigeria, 54gene, which was established by Abasi Ene-Obong in 2019, aims to sequence the DNA of at least 100,000 samples of spit, blood or body tissue of willing patients, with plans to expand further afield across more African countries.[15] 54gene makes revenue by providing this genetic data to global pharmaceutical firms looking to produce more effective and bespoke drugs. African genomic data will also reduce the time lag between when new medicines hit the global market and Africans get access to them, often taking more than a decade, after patents have expired or rich countries have moved on to better drugs. Global genomic data with ample African samples will facilitate a broader and diversified drug-testing process and thus ensure African genomes will be receptive to new drugs as well as their counterparts in the developed world. Another significant African genomics research effort is by renowned microbiologist Christian Happi at the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID) in Nigeria.[16] ACEGID, which has been getting good reviews for its surveillance work on Lassa fever, Ebola and Covid-19, has received more than US$9m in grants and funding from myriad institutions, including the World Bank, evidence of growing global interest. Led by Segun Fatumo, an assistant professor and genetic epidemiologist, who trained at the University of Cambridge and was part of the team at the Wellcome Sanger Institute in the UK that conducted what is still considered one of the most significant analysis of the African genome yet, studies by the African Computational Genomics Research group at the MRC/UVRI & LSHTM Uganda Research Unit focuses on the genes associated with diseases that frequently ail Africans.[17] 

    A database of the genetic information of the African population will be invaluable. The Three Million African Genomes (3MAG) project is a major step in this direction but would cost US$450m a year and would take 10 years to complete, according to Ambroise Wonkam, a professor of medical genetics and one of the champions of the endeavour.[18]  The Covid-19 pandemic brought to fore the importance of knowhow and resources on the African genome. According to the World Health Organisation (WHO) genomic sequencing was crucial to rapidly identifying the coronavirus and developing a robust response towards containing it. Africa’s shortcoming in this regard has been writ large, with the continent accounting for “just 1% of the more than 3.5m Covid-19 sequences carried out to date worldwide.”[19] The Africa Centre for Disease Control Institute of Pathogen Genomics, US CDC, Bill & Melinda Gates Foundation, Microsoft, Illumina (a genomics sequencing technology firm), and Oxford Nanopore Technologies are collaborating on a US$100m 4-year initiative to “integrate pathogen genomics and bioinformatics into public health surveillance, outbreak investigations, and improved disease control and prevention in Africa.”[20]

    Perhaps the foremost African genomics research endeavour is the Human Heredity and Health in Africa (H3Africa) programme sponsored by the African Society of Human Genetics founded by Charles Rotimi, the scientific director at America’s National Human Genome Research Institute (NHGRI). It is supported by the UK-based Wellcome Trust and the American National Institutes of Health (NIH). H3Africa, which is headquartered in Cape Town, South Africa, but has sites across Africa is enabling African scientists do genomics research on African populations in Africa.[21] “Most of H3Africa’s projects (roughly three dozen or so) fall under the so-called capacity-building [viz.] establishing collaborative research centres; biorepositories (in Uganda, Nigeria and South Africa); a coordinating centre; ethical, legal and social implications (ELSI) research projects; an informatics network; and bioinformatics training programmes (LeMieux, 2021).” In the Africa Wits-INDEPTH Partnership for Genomics Research in South Africa, for instance, funding by H3Africa was used for a “transcontinental study on genetic and environmental contributions to cardiometabolic diseases and traits in Ghana, Burkina Faso, Kenya, and South Africa (LeMieux, 2021).”

    Western institutions remain the main champions and may eventually be forced to take ownership of data if African apathy continues. A dearth of political will, scarce funding for research and development, limited local supporting infrastructure, and lack of human resources are impeding progress.[22] The scientists and data produced by H3Africa, may become dispersed after the programme concludes in June 2022 if there are no new sponsors willing to maintain the current format. Considering the huge economic potential of African genomics, it would be more than a tad surprising if that happens. At present the loci of programmes like H3Africa is on the continent. Qualified African institutions and scientists receive funding and support to pursue their own research interests and then share the research findings for global benefit. For the system to endure, however, African governments and investors must be similarly enthused. But of course, there are private ventures like 54gene which are already reaping profits. For-profit ventures will not suffice, however. Research by academia supported by governments and global pharma will be required to complement such ventures. Incidentally, the NIH launched the Harnessing Data Science for Health Discovery and Innovation in Africa in October 2021, a US$74.5m initiative (LeMieux, 2021). Besides, global genetics research firms like Illumina and Regeneron are increasingly interested in African genomics and its potential for advancing the medical sciences, owing in part to initiatives such as H3Africa (LeMieux, 2021). In fact, the issue is now no longer about how African genomics is important or its huge economic potential but rather to ensure that an inequity is not fixed via another inequity. The history of colonial exploitation and the business model that sustained it should not be repeated with African genomics research. To ensure that this is not the case, a great deal of investment would be required from the firms and governments of African countries and their international partners.[23]

    The economic potential of African genomics is huge

    The real potential of genomics lies in pooling genetic and clinical data from across the world. The Covid-19 pandemic has accelerated progress in genome sequencing, as data from every corner of the globe has been sought to effectively check the spread of the coronavirus and manage future pandemics. Hitherto, however, so-called whole genome sequencing (WGS) required for such surveillance was expensive and capacity was both scarce and sparse. Thus it was available only in a few selected centres around the world. This is no longer the case. Based on work by scientists from 16 countries led by Neil Hall at the Earlham Institute, the so-called 10,000 Salmonella genomes research consortium (10KSG), which successfully “sequenced and analysed 10,000 Salmonella genomes from Africa and Latin America,” efficient large-scale genome sequencing is now accessible.[24] Furthermore, mechanisms have to be put in place by governments and other stakeholders to enable easier acquisition of genomic data from clinical records, which should also ensure a good balance is struck with legacy ethical and cultural considerations. There are also more basic constraints; the huge cost of data storage, for instance, which could range from as little as 2EB to as much as 40EB annually, that is, about as much as all of YouTube’s video data. Challenging as it is, there is a “real need to link clinical records to genomic data”; a federated data system that enables the sharing of data across borders with security, privacy, and interoperability, argues the World Economic Forum.[25]

    Apart from pre-existing power and telecommunications infrastructure constraints African genomic data would ultimately reside in foreign-owned local servers without investment by African governments and firms in the continent’s cloud storage infrastructure. A global consortium that allows for the seamless sharing and analysis of genomic data from clinical records will ultimately leave Africa at the mercy of developed countries yet again. There is already a recognition of this weakness by the likes of China, which is not only building the Africa CDC headquarters in Addis Ababa but has its firms like Huawei building data centres across the continent, most recently in Senegal.[26] The worry about potential Western exploitation is not without precedent. According to an investigative report published by The Telegraph in February 2019, Ebola blood samples from West Africa that were supposedly destroyed ended up in Europe and America,.[27] An international protocol to prevent such mishaps were put in place in 2014. The so-called Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization or “Nagoya Protocol” in short, is worth rallying around. It has thus far not enjoyed universal support.[28]

    To the global pharmaceutical industry a person’s genetic data is worth US$1,900. When combined with medical records its value can go up to as much as US$6,400 each, according to research on the United Kingdom’s National Health Service (NHS) by EY, a global consulting firm.[29] The indicative market value of the integrated genetic and clinical data of the estimated 55 million patient records in the UK NHS database could be as much as US$6.4bn per annum, with benefits of about US$5.8bn to patients yearly, EY estimates. When applied to the African scenario, especially as an integrated African genetics and clinical records database will likely be more valuable as it will harbour secrets to many potentially ground-breaking innovations in medicine, we could be talking of indicative market values to the tune of US$17.5bn per annum for a country the size of Nigeria. For this to be realised, however, the identified myriad challenges must first be overcome.

    African countries can adapt the Singapore model

    Singapore is a kindred spirit of sorts. In October 2019, Cell magazine published a study of the “world’s largest whole-genome sequencing (WGS) analysis of Asian populations” which involved about 5,000 Singaporeans.[30][31] Singapore’s main three ethnic groups – the Chinese, Malay and Indians – made it an ideal market study. In December 2019, Nature published the first Asia-wide genome mapping study by GenomeAsia 100K, a consortium of Nanyang Technological University, Singapore, MedGenome US/India, and Macrogen Inc., Korea, which analysed the genomes of 1,739 people from 64 countries.[32],[33] Singapore’s National Precision Medicine (NPM) strategy is a 10-year “whole-of-government effort to establish the necessary frameworks and infrastructure to realise precision medicine on a national scale, enhance disease prevention and to identify the right treatments for the right individuals and groups.”[34] African countries looking to beef up genomics research have in Singapore a viable model to follow. In the Singaporean case, for instance, the authorities centralised the NPM effort in an entity called Precision Health Research, Singapore (PRECISE). While I am not suggesting that ongoing privately-funded genomics research efforts in Africa should be nationalised, there is a need for state oversight and co-ordination to ensure that the ownership of the African genomic data remains in African hands.

    Conclusion and recommendations

    African DNA does not feature much in global genetics research. In fact, genomic data of African origin constitute less than 2% of global genomewide association studies (GWAS). This tallies with the fact that Africa is not a major player in the global pharmaceutical industry, especially for new drugs. However, this shortcoming is impeding the growth of the US$20bn global market for new drugs as African DNA has been proven to contain invaluable insights for the development of medicines that will benefit all of humanity. The global pharmaceutical industry has already taken steps to tap into the huge potential of African genomics. There are, however, significant downsides to this global effort owing to lacklustre interest by African governments and firms. True, African firms like 54gene in Nigeria are beginning to build profitable business models. But these are largely independent initiatives with little surveillance and governance by African authorities.  There are viable models that African governments can look at. I recommend Singapore’s National Precision Medicine (NPM) strategy, which if emulated by African governments, provides a comprehensive framework to regulate and support the work of private genomic firms like 54gene while at the same time ensuring that the scientific know-how remains in African hands.

    References

    References

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    [2] Schutz, E. (2021, November 2). Why Africa urgently needs its own genetic library. BBC News. Retrieved from https://www.bbc.com/news/business-58788040

     

    [3] Sirugo, G., Williams, S.M., Tishkoff, S.A. (2019). The missing diversity in human genetics studies. Cell, 177 (1), pp. 26-31. Retrieved from https://www.cell.com/fulltext/S0092-8674(19)30231-4

     

    [4] National Human Genome Research Institute. (n.d.). A brief guide to genomics. Retrieved from https://www.genome.gov/about-genomics/fact-sheets/A-Brief-Guide-to-Genomics

     

    [5] Nawrat, A. (2019, October 1). Unseen genes: boosting African DNA in medical research. Pharmaceutical Technology. Retrieved from https://www.pharmaceutical-technology.com/features/boosting-african-dna-in-medical-research/

     

    [6] Onukwue, A. (2021, September 16). Africa’s top DNA research startup has secured $25 million for drug discovery and pharma talent. Quartz. Retrieved from https://qz.com/africa/2060175/nigeria-based-54gene-raises-25-million-extra-for-drug-discovery/

     

    [7] Monks, K. (2019, September 26). Unlocking the life-saving secrets of African DNA. CNN. Retrieved from https://edition.cnn.com/2019/09/26/health/unlocking-the-life-saving-secrets-of-african-dna-intl/index.html

     

    [8] Kelland, K. (2010, June 22). Research projects takes genetics to African roots. Reuters. Retrieved from https://www.reuters.com/article/genetics-africa/research-project-takes-genetics-to-african-roots-idUSLDE65L1YI20100622

     

    [9] Munshi, N. (2020, March 5). How unlocking the secrets of African DNA could change the world. Financial Times. Retrieved from https://www.google.com/amp/s/amp.ft.com/content/eed0555c-5e2b-11ea-b0ab-339c2307bcd4

     

    [10] Jackson, C. (2020, September 8). Africa’s missing genomic data and its impact on healthcare. Genetic Engineering & Biotechnology News. Retrieved from https://www.genengnews.com/insights/africas-missing-genomic-data-and-its-impact-on-health-care/

     

    [11] Choudhury, A., Aron, S., Botigue, L.R. et al. (2020). High-depth African genomes inform human migration and health. Nature, 586, pp. 741-748. Retrieved from https://www.nature.com/articles/s41586-020-2859-7

     

    [12] Wayman, E. (2011, October 17). How Africa became the cradle of humankind. Smithsonian Magazine. Retrieved from https://www.smithsonianmag.com/science-nature/how-africa-became-the-cradle-of-humankind-108875040/

     

    [13] Baker, C. (2021, January 1). African genomics: The scientists unlocking cures encoded in DNA. Aljazeera. Retrieved from https://www.aljazeera.com/features/2021/1/1/african-genomics-the-scientists-unlocking-cures-encoded-in-dna

     

    [14] Schutz, E. (2021, November 2). Why Africa urgently needs its own genetic library. BBC News. Retrieved from https://www.bbc.com/news/business-58788040

     

    [15] Olewe, D. (2019, November 12). How decoding African DNA could help fight disease. BBC News. Retrieved from https://www.bbc.com/news/world-africa-50205190

    [16] Maxmen, A. (2020, February 19). The next chapter for African genomics. Nature. Retrieved from https://www.nature.com/articles/d41586-020-00454-1

    [17] Pennisi, E. (2021, February 4). Genomes arising: Africans have begun to study their continent’s rich human diversity – but what comes after current grants end? Science. Retrieved from https://www.science.org/content/article/africans-begin-take-reins-research-their-own-genomes#:~:text=Africans%20begin%20to%20take%20the%20reins%20of%20research%20into%20their%20own%20genomes,-By%20Elizabeth%20Pennisi&text=In%201987%2C%2010%2Dyear%2D,put%20food%20on%20the%20table

    [18] Wonkam, A. (2021, February 10). Sequence three million genomes across Africa. Nature. Retrieved from https://www.nature.com/articles/d41586-021-00313-7

    [19] World Health Organization. (2021, September 30). Scaling up genomic sequencing in Africa [Press release]. Retrieved from https://www.afro.who.int/news/scaling-genomic-sequencing-africa

    [20] Makoni, M. (2020). Africa’s $100-million pathogen genomics initiative. The Lancet, 1, p.e318. Retrieved from https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(20)30206-8/fulltext

    [21] LeMieux, J. (2021, December 3). H3Africa funds scientists, advances genomics, and fosters collaboration in Africa. Genetic Engineering & Biotechnology News. Retrieved from https://www.genengnews.com/topics/omics/h3africa-funds-scientists-advances-genomics-and-fosters-collaboration-in-africa/

    [22] Happi, C. (2022, February 17). What’s next for R&D in health for Africa? In A.U. Ordu & C. Golubski (Eds). Foresight Africa: Top Priorities for the Continent in 2022(pp. 44). Brookings: Washington DC. Retrieved from https://www.google.com/amp/s/www.brookings.edu/blog/africa-in-focus/2022/02/17/whats-next-for-rd-in-health-for-africa/amp/

    [23] Mabuka-Maroa, J. (2019, April 4). Africa needs a heavy dose of investment in genomics research. The Conversation. Retrieved from https://theconversation.com/africa-needs-a-heavy-dose-of-investment-in-genomics-research-114456

    [24] Feasay, N.A., Hinton J.C.D., Hall, N., et al. (2021). An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes. Genome Biology, 22 (349). Retrieved from https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02536-3

    [25] Atkins, D., Boughtwood, T. & Chediak, L. (2020, July 30). This system unleashes the power of data to transform health outcomes for millions of patients. World Economic Forum. Retrieved from https://www.weforum.org/agenda/2020/07/value-of-genomic-data-with-global-data-consortia-governance-model-precision-medicine/

    [26] Huawei invests in data centres in Africa (2021, December 15). Africanews. Retrieved from https://www.africanews.com/2021/12/15/huawei-invests-in-data-centres-in-africa//

    [27] Freudenthal, E. (2019, February 6). Ebola’s lost blood: row over samples flown out of Africa as ‘big pharma’ set to cash in. The Telegraph. Retrieved from https://www.telegraph.co.uk/global-health/science-and-disease/ebolas-lost-blood-row-samples-flown-africa-big-pharma-set-cash/

    [28] Mckenna, M. (2019, March 3). Colonialists are coming for blood – literally. Wired. Retrieved from https://www.wired.com/story/ebola-epidemic-blood-samples/

    [30] Genome Institute of Singapore (2019, October 18). Singapore completes world’s largest whole genome sequencing analysis of multi-ethnic Asian populations [Press release]. Retrieved from https://www.a-star.edu.sg/News/a-star-news/news/press-releases/singapore-completes-world-s-largest-whole-genome-sequencing-analysis-of-multi-ethnic-asian-populations

    [31] Wu, D., Dou, J., et al. (2019). Large-scale whole-genome sequencing of three diverse Asian populations in Singapore. Cell, 179, pp. 736-749. Retrieved from https://www.cell.com/cell/pdf/S0092-8674(19)31070-0.pdf

    [32] Nanyang Technological University, MedGenome & Macrogen (2019, December 4). Asia-wide genome mapping project reveals insights into Asian ancestry and genetic diversity [Press release]. Retrieved from https://www.ntu.edu.sg/science/news-and-events/news/detail/-asia-wide-genome-mapping-project-reveals-insights-into-asian-ancestry-and-genetic-diversity

    [33] GenomeAsia 100K Consortium (2019). The GenomeAsia 100K project enables genetic discoveries across Asia. Nature, 576, pp. 106-111. Retrieved from https://www.nature.com/articles/s41586-019-1793-z

    [34] Duke-NUS Medical School (2021, April 7). Singapore launches next phase of national precision medicine programme [Press release]. Retrieved from https://www.npm.sg/singapore-launches-next-phase-of-national-precision-medicine-programme/

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