Genomics research in Africa and its impact on global health: insights from African researchers

Review of Genetic and Artificial Intelligence approaches to improving Gestational Diabetes Mellitus Screening and Diagnosis in sub-Saharan Africa

Background: Adverse outcomes from gestational diabetes mellitus (GDM) in the mother and newborn are well established. Genetic variants may predict GDM and Artificial Intelligence (AI) can potentially assist with improved screening and early identification in lower resource settings. There is limited information on genetic variants associated with GDM in sub-Saharan Africa and the implementation of AI in GDM screening in sub-Saharan Africa is largely unknown. Methods: We reviewed the literature on what is known about genetic predictors of GDM in sub-Saharan African women. We searched PubMed and Google Scholar for single nucleotide polymorphisms (SNPs) involved in GDM predisposition in a sub-Saharan African population. We report on barriers that limit the implementation of AI that could assist with GDM screening and offer possible solutions. Results: In a Black South African cohort, the minor allele of the SNP rs4581569 existing in the PDX1 gene was significantly associated with GDM. We were not able to find any published literature on the implementation of AI to identify women at risk of GDM before second trimester of pregnancy in sub-Saharan Africa. Barriers to successful integration of AI into healthcare systems are broad but solutions exist. Conclusions: More research is needed to identify SNPs associated with GDM in sub-Saharan Africa. The implementation of AI and its applications in the field of healthcare in the sub-Saharan African region is a significant opportunity to positively impact early identification of GDM.

Genetic and Genomic Researchers' Perspectives on Biological Sample Sharing in Collaborative Research in Uganda: A Qualitative Study

Numerous ethical, legal, and social issues arise with biological sample sharing. The study explored the perspectives of genetic and genomic researchers on the sharing of biological samples in international collaborative research. Qualitative in-depth interviews were conducted with 15 researchers. Participants expressed positive attitudes towards biobanking and appreciated the benefits of cross-border sharing of biological samples but noted that this practice had adversely affected local capacity building efforts. There was limited understanding of the ethical and regulatory frameworks governing sample sharing. Researchers emphasized the importance of respecting cultural values in biobanking research. Issues concerning poor governance and inequitable benefit sharing were also raised. There is a need for fair and equitable international collaborations where all researchers are treated with respect and as equal partners.

Towards equitable genomics governance in Africa: Guiding principles from theories of global health governance and the African moral theory of Ubuntu

The post-genomics era promises a revolution characterized by precision medicine and the integration of genomics into almost every area of biomedical research. At the same time, there are concerns that if care is not taken, the genomics revolution may widen global inequities in science and health. In Africa, these concerns are primarily linked to the underrepresentation of African populations in genomics research, limited genomics research capacity in Africa and associated macro-level justice issues such as benefit sharing, inequitable international research collaborations, and the contribution of genomics to the health and research priorities of Africa. Addressing these concerns requires an in-depth reflection on how the ideals of global justice and equity may be advanced in genomics research. To contribute to the limited but growing scholarship on global genomics equity, especially in the African context, we performed a conceptual analysis of three accounts of justice and governance namely, Ubuntu, shared health governance and global governance of health, with the aim of identifying principles that could inform genomics governance in Africa. We used a convergence approach in the conceptual analysis, resulting in the identification of nine principles namely: solidarity, furthering the ideals of health justice, reciprocity, shared decision-making, shared resources, shared responsibility, mutual trust, transparency, and mutual collective accountability. Examples of how the principles may be applied are provided. We recommend that these principles should form the foundation of any mechanism that seeks to systematically advance justice, fairness and equity in genomics research in Africa and more broadly, global health and science equity.

Open science, data sharing and solidarity: who benefits?

Research, innovation, and progress in the life sciences are increasingly contingent on access to large quantities of data. This is one of the key premises behind the "open science" movement and the global calls for fostering the sharing of personal data, datasets, and research results. This paper reports on the outcomes of discussions by the panel "Open science, data sharing and solidarity: who benefits?" held at the 2021 Biennial conference of the International Society for the History, Philosophy, and Social Studies of Biology (ISHPSSB), and hosted by Cold Spring Harbor Laboratory (CSHL).

Design of a FAIR digital data health infrastructure in Africa for COVID-19 reporting and research

The limited volume of COVID‐19 data from Africa raises concerns for global genome research, which requires a diversity of genotypes for accurate disease prediction, including on the provenance of the new SARS‐CoV‐2 mutations. The Virus Outbreak Data Network (VODAN)‐Africa studied the possibility of increasing the production of clinical data, finding concerns about data ownership, and the limited use of health data for quality treatment at point of care. To address this, VODAN Africa developed an architecture to record clinical health data and research data collected on the incidence of COVID‐19, producing these as human‐ and machine‐readable data objects in a distributed architecture of locally governed, linked, human‐ and machine‐readable data. This architecture supports analytics at the point of care and—through data visiting, across facilities—for generic analytics. An algorithm was run across FAIR Data Points to visit the distributed data and produce aggregate findings. The FAIR data architecture is deployed in Uganda, Ethiopia, Liberia, Nigeria, Kenya, Somalia, Tanzania, Zimbabwe, and Tunisia.

Genomics governance: advancing justice, fairness and equity through the lens of the African communitarian ethic of Ubuntu

There is growing interest for a communitarian approach to the governance of genomics, and for such governance to be grounded in principles of justice, equity and solidarity. However, there is a near absence of conceptual studies on how communitarian-based principles, or values, may inform, support or guide the governance of genomics research. Given that solidarity is a key principle in Ubuntu, an African communitarian ethic and theory of justice, there is emerging interest about the extent to which Ubuntu could offer guidance for the governance of genomics research in Africa. To this effect, we undertook a conceptual analysis of Ubuntu with the goal of identifying principles that could inform equity-oriented governance of genomics research. Solidarity, reciprocity, open sharing, accountability, mutual trust, deliberative decision-making and inclusivity were identified as core principles that speak directly to the different macro-level ethical issues in genomics research in Africa such as: the exploitation of study populations and African researchers, equitable access and use of genomics data, benefit sharing, the possibility of genomics to widen global health inequities and the fair distribution of resources such as intellectual property and patents. We use the identified the principles to develop ethical guidance for genomics governance in Africa.

Authorship Patterns in Cancer Genomics Publications Across Africa

PURPOSE

Authorship is a proxy indicator of research capacity. Understanding the research capacity is imperative for developing population-specific cancer control strategies. This is particularly apropos for African nations, where mortality from cancer is projected to surpass that from infectious disease and the populations are critically under-represented in cancer and genomics studies. Here, we present an analysis and discussion of the patterns of authorship in Africa as they pertain to cancer genomics research across African countries.

METHODS

PubMed metadata of relevant cancer genomics peer-reviewed publications on African populations, published between January 1, 1990, and December 31, 2019, were retrieved and analyzed for patterns of authorship affiliation using R packages, RISmed, and Pubmed.mineR.

RESULTS

The data showed that only 0.016% (n = 375) of cancer publications globally were on cancer genomics of African people. More than 50% of the first and last authors of these publications originated from the North African countries of Tunisia, Morocco, Egypt, and Algeria. South Africa (13.6% and 12.7%) and Nigeria (2.2% and 1.9%) were the Sub-Saharan African countries most represented by first and last authorship positions, respectively. The United States contributed 12.6% of first and last authored papers, and nearly 50% of all African countries had no contributing author for the publications we reviewed.

CONCLUSION

This study highlights and brings awareness to the paucity of cancer genomics research on African populations and by African authors and identifies a need for concerted efforts to encourage and enable more research in Africa, needed for achieving global equity in cancer outcomes.

Advancing global equity in cancer genomics - challenges and opportunities in Sub-Saharan Africa

Developments in genomics in the last decade has improved our understanding of the role of genetics in health and disease. One area where the impact of genomics is very noticeable is in oncology, specifically in terms of diagnosis and elucidating genetic predisposition to rare and common cancers. Sub-Saharan Africa (SSA) stands to benefit from cancer genomics, given recent spikes in the incidence of various types of cancers in the region. This mini review presents, from a health and science equity perspective, how genomics could shape cancer research and clinical care in SSA. We highlight some pan-African genomics and cancer initiatives that are facilitating cancer genomics research in SSA. We conclude with recommendations on how the ideals of equity may be advanced in cancer genomics initiatives in SSA.

Cancer Omics in Africa: Present and Prospects

During the last century, cancer biology has been arguably one of the most investigated research fields. To gain deeper insight into cancer mechanisms, scientists have been attempting to integrate multi omics data in cancer research. Cancer genomics, transcriptomics, metabolomics, proteomics, and metagenomics are the main multi omics strategies used currently in the diagnosis, prognosis, treatment, and biomarker discovery in cancer. In this review, we describe the use of different multi omics strategies in cancer research in the African continent and discuss the main challenges facing the implementation of these approaches in African countries such as the lack of training programs in bioinformatics in general and omics strategies in particular and suggest paths to address deficiencies. As a way forward, we advocate for the establishment of an "African Cancer Genomics Consortium" to promote intracontinental collaborative projects and enhance engagement in research activities that address indigenous aspects for cancer precision medicine.

Ubuntu philosophy and the consensus regarding incidental findings in genomic research: a heuristic approach

This study adopts a heuristic technique to argue the thesis that a set of norms rooted in the African philosophy of Ubuntu can usefully supplement current research guidelines for dealing with incidental findings discovered in genomic research. The consensus regarding incidental findings is that there is an ethical obligation to return individual genetic incidental findings that meet the threshold of analytic and clinical validity, have clinical utility, and are actionable, provided that research contributors have not opted out from receiving such information. This study outlines the hurdles that may hinder the integration of this consensus in mainstream clinical practice, and shows how an ethical theory from the global south may be used to address the same. This will advance the field of ethical, legal and social issues of personalized medicine by providing exposure to the under-represented African perspective on the ethical, legal, and social issues of genomics.

Role of genomics literacy in reducing the burden of common genetic diseases in Africa

BACKGROUND

In Africa, health practitioners and the current knowledge of the public on genetics and genomics is still very low and yet this has potential to reduce the burden of common genetic diseases. Many initiatives have promoted genomic research, infrastructure, and capacity building in Africa. What remains to be done is to improve genomics literacy among populations and communities while utilizing an array of strategies. Genomic literacy and awareness are key in the management of genetic diseases which includes diagnosis, prevention of complications and therapy. Africa is characterized by great cultural and language diversity thereby requiring a multidisciplinary approach to improving public and community genomics literacy and engagement. However, this is further complicated by having the fact that sub-Saharan Africa is comprised of countries with the lowest literacy rates in the world.

METHODS

We applied the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to review genomic literacy in Africa using PubMed database.

RESULTS

We found very limited evidence of genomics literacy for genetic diseases in Africa.

CONCLUSION

We propose a number of approaches that if adopted will significantly increase the genomic literacy and reduce the burden of genetic diseases in Africa.

The Emergence of Genomic Research in Africa and New Frameworks for Equity in Biomedical Research

Individuals with African ancestry have the greatest genomic diversity in the world, yet they have been underrepresented in genomic research. To advance our understanding of human biology and our ability to trace human history, we must include more samples from Africans in genomic research. Additionally, inclusion of more samples from participants of recent African descent is imperative to provide equitable health care as genomics is increasingly used for diagnosis, treatment, and to understand disease risk. The Human Heredity and Health in Africa initiative (H3Africa) seeks to expand the number of Africans included in genomic research and to do so by expanding the research capacity on the continent. In this article, we discuss how H3Africa is endeavoring to achieve these goals while promoting equitable research collaborations.

Genomic Interventions in Medicine

Lately, the term "genomics" has become ubiquitous in many scientific articles. It is a rapidly growing aspect of the biomedical sciences that studies the genome. The human genome contains a torrent of information that gives clues about human origin, evolution, biological function, and diseases. In a bid to demystify the workings of the genome, the Human Genome Project (HGP) was initiated in 1990, with the chief goal of sequencing the approximately 3 billion nucleotide base pairs of the human DNA. Since its completion in 2003, the HGP has opened new avenues for the application of genomics in clinical practice. This review attempts to overview some milestone discoveries that paved way for the initiation of the HGP, remarkable revelations from the HGP, and how genomics is influencing a paradigm shift in routine clinical practice. It further highlights the challenges facing the implementation of genomic medicine, particularly in Africa. Possible solutions are also discussed.