Genomic Research In Africa Research Articles

Implementation of a genotyped African population cohort, with virtual follow-up: A feasibility study in the Western Cape Province, South Africa

Background There is limited knowledge regarding African genetic drivers of disease due to prohibitive costs of large-scale genomic research in Africa. Methods We piloted a cost-effective, scalable virtual genotyped cohort in South Africa, with participant recruitment using a tiered informed consent model and DNA collection by buccal swab. Genotype data was generated using the H3Africa Illumina micro-array, and phenotype data was derived from routine health data of participants. We demonstrated feasibility of nested case control genome wide association studies using these data for phenotypes type 2 diabetes mellitus (T2DM) and severe COVID-19. Results 2267346 variants were analysed in 459 participant samples. 78.6% of SNPs and 74% of samples passed quality control (QC). Principal component analysis showed extensive ancestry admixture in study participants. For 1780 published COVID-19-associated variants, 3 SNPs in the pre-imputation data and 23 SNPS in the imputed data were significantly associated with severe COVID-19 cases compared to controls. For 2755 published T2DM associated variants, 69 SNPs in the pre-imputation data and 419 SNPs in the imputed data were significantly associated with T2DM cases when compared to controls. Conclusions The results shown here are illustrative of what will be possible as the cohort expands in the future. Here we demonstrate the feasibility of this approach, recognising that the findings presented here are preliminary and require further validation once we have a sufficient sample size to improve statistical significance of findings. We implemented a genotyped population cohort with virtual follow up data in a resource-constrained African environment, demonstrating feasibility for scale up and novel health discoveries through nested case-control studies.

African Cultivated, Wild and Weedy Rice (Oryza spp.): Anticipating Further Genomic Studies.

Rice is a staple crop in sub-Saharan Africa, and it is mostly produced by Asian cultivars of Oryza sativa that were introduced to the continent around the fifteenth or sixteenth century. O. glaberrima, the native African rice, has also been planted due to its valuable traits of insect and drought tolerance. Due to competition and resistance evolution, weedy rice has evolved from O. sativa and O. glaberrima, posing an increasing threat to rice production. This paper provides an overview of current knowledge on the introduction and domestication history of cultivated rice in Africa, as well as the genetic properties of African weedy rice that invades paddy fields. Recent developments in genome sequencing have made it possible to uncover findings about O. glaberrima's population structure, stress resilience genes, and domestication bottleneck. Future rice genomic research in Africa should prioritize producing more high-quality reference genomes, quantifying the impact of crop-wild hybridization, elucidating weed adaptation mechanisms through resequencing, and establishing a connection between genomic variation and stress tolerance phenotypes to accelerate breeding efforts.

Ethical considerations for biobanking and use of genomics data in Africa: a narrative review

BackgroundBiobanking and genomic research requires collection and storage of human tissue from study participants. From participants’ perspectives within the African context, this can be associated with fears and misgivings due to a myriad of factors including myths and mistrust of researchers. From the researchers angle ethical dilemmas may arise especially with consenting and sample reuse during storage. The aim of this paper was to explore these ethical considerations in the establishment and conduct of biobanking and genomic studies in Africa.MethodsWe conducted a narrative synthesis following a comprehensive search of nine (9) databases and grey literature. All primary research study designs were eligible for inclusion as well as both quantitative and qualitative evidence from peer reviewed journals, spanning a maximum of 20 years (2000–2020). It focused on research work conducted in Africa, even if data was stored or analysed outside the region.ResultsOf 2,663 title and abstracts screened, 94 full texts were retrieved and reviewed for eligibility. We included 12 studies (7 qualitative; 4 quantitative and one mixed methods).Ethical issues described in these papers related to community knowledge and understanding of biobanking and genomic research, regulation, and governance of same by research ethics committees, enrolment of participants, types of informed consents, data collection, storage, usage and sharing as well as material transfer, returning results and benefit sharing. ca. Biospecimen collection and storage is given in trust and participants expect confidentially of data and results generated. Most participants are comfortable with broad consent due to trust in researchers, though a few would like to be contacted for reconsenting in future studies, and this would depend on whether the new research is for good cause. Sharing data with external partners is welcome in some contexts but some research participants did not trust foreign researchers.ConclusionBiobanking and genomic studies are a real need in Africa. Linked to this are ethical considerations related to setting up and participation in biobanks as well as data storage, export, use and sharing. There is emerging or pre-existing consensus around the acceptability of broad consent as a suitable model of consent, the need for Africans to take the lead in international collaborative studies, with deliberate efforts to build capacity in local storage and analysis of samples and employ processes of sample collection and use that build trust of communities and potential study participants. Research ethics committees, researchers and communities need to work together to work together to adapt and use clearly defined ethical frameworks, guidelines, and policy documents to harmonize the establishment and running of biobanking and genomic research in Africa.

Building blocks for better biorepositories in Africa

BackgroundBiorepositories archive and distribute well-characterized biospecimens for research to support the development of medical diagnostics and therapeutics. Knowledge of biobanking and associated practices is incomplete in low- and middle-income countries where disease burden is disproportionately high. In 2011, the African Society of Human Genetics (AfSHG), the National Institutes of Health (NIH), and the Wellcome Trust founded the Human Heredity and Health in Africa (H3Africa) consortium to promote genomic research in Africa and established a network of three biorepositories regionally located in East, West, and Southern Africa to support biomedical research. This manuscript describes the processes established by H3Africa biorepositories to prepare research sites to collect high-quality biospecimens for deposit at H3Africa biorepositories.MethodsThe biorepositories harmonized practices between the biorepositories and the research sites. The biorepositories developed guidelines to establish best practices and define biospecimen requirements; standard operating procedures (SOPs) for common processes such as biospecimen collection, processing, storage, transportation, and documentation as references; requirements for minimal associated datasets and formats; and a template material transfer agreements (MTA) to govern biospecimen exchange. The biorepositories also trained and mentored collection sites in relevant biobanking processes and procedures and verified biospecimen deposit processes. Throughout these procedures, the biorepositories followed ethical and legal requirements.ResultsThe 20 research projects deposited 107,982 biospecimens (76% DNA, 81,067), in accordance with the ethical and legal requirements and established best practices. The biorepositories developed and customized resources and human capacity building to support the projects. [The biorepositories developed 34 guidelines, SOPs, and documents; trained 176 clinicians and scientists in over 30 topics; sensitized ethical bodies; established MTAs and reviewed consent forms for all projects; attained import permits; and evaluated pilot exercises and provided feedback.ConclusionsBiobanking in low- and middle-income countries by local skilled staff is critical to advance biobanking and genomic research and requires human capacity and resources for global partnerships. Biorepositories can help build human capacity and resources to support biobanking by partnering with researchers. Partnerships can be structured and customized to incorporate document development, ethics, training, mentorship, and pilots to prepare sites to collect, process, store, and transport biospecimens of high quality for future research.

Regulating human genomic research in Africa: why a human rights approach is a more promising conceptual framework than genomic sovereignty.

This article revisits the debate on the regulation of human genomic research, with a focus on Africa. The article comprehensively examines the concept of genomic sovereignty, which was invoked mainly in the global South as a conceptual framework for state regulation of human genomic research. It demonstrates that genomic sovereignty has no utility value in human genomic research as it violates the rights of individuals and researchers. By analysing Mexico's regulatory approach based on genomic sovereignty and a divergent regulatory approach, viz Finland's human genomic research framework, we show that a human rights approach is more promising as it aligns with the state obligations under the right of everyone to participate in and benefit from scientific progress and its applications in international human rights law. We conclude by recommending that African states should anchor regulation of human genomic research on a human rights framework based on the right to science.

Stakeholders’ Perspectives on Community Engagement for Genomics Research in Africa – A Literature Review

Stakeholders’ Perspectives on Community Engagement for Genomics Research in Africa – A Literature Review

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.

Guideline for feedback of individual genetic research findings for genomics research in Africa

As human genomics research in Africa continues to generate large amounts of data, ethical issues arise regarding how actionable genetic information is shared with research participants. The Human Heredity and...

The Africa Ethics Working Group (AEWG): a model of collaboration for psychiatric genomic research in Africa.

The Africa Ethics Working Group (AEWG) is a South-South-North collaboration of bioethics and mental health researchers from sub-Saharan Africa, working to tackle emerging ethical challenges in global mental health research. Initially formed to provide ethical guidance for a neuro-psychiatric genomics research project, AEWG has evolved to address cross cutting ethical issues in mental health research aimed at addressing equity in North-South collaborations. Global South refers to economically developing countries (sub-Saharan Africa in this context) and Global North to economically developed countries (primarily Europe, UK and North America). In this letter we discuss lessons that as a group we have learnt over the last three years; lessons that similar collaborations could draw on. With increasing expertise from Global South as an outcome of several capacity strengthening initiatives, it is expected that the nature of scientific collaborations will shift to a truly equitable partnership. The AEWG provides a model to rethink contributions that each partner could make in these collaborations.

Has translational genomics come of age in Africa?

The rapid increase in genomics research in Africa and the growing promise of precision public health (PPH) begs the question of whether African genomics has come of age and is being translated into improved healthcare for Africans. An assessment of the continent's readiness suggests that genetic service delivery remains limited and extremely fragile. The paucity of data on mutation profiles for monogenic disorders and lack of large genome-wide association cohorts for complex traits in African populations is a significant barrier, coupled with extreme genetic variation across different regions and ethnic groups. Data from many different populations are essential to developing appropriate genetic services. Of the proposed genetic service delivery models currently used in Africa-Uncharacterized, Limited, Disease-focused, Emerging and Established-the first three best describe the situation in most African countries. Implementation is fraught with difficulties related to the scarcity of an appropriately skilled medical genetic workforce, limited infrastructure and processes, insufficient health funding and lack of political support, and overstretched health systems. There is a strong nucleus of determined and optimistic clinicians and scientists with a clear vision, and there is a hope for innovative solutions and technological leapfrogging. However, a multi-dimensional approach with active interventions to stimulate genomic research, clinical genetics and overarching healthcare systems is needed to reduce genetic service inequalities and accelerate PPH on the continent. Human and infrastructure capacity development, dedicated funding, political will and supporting legislation, and public education and awareness, are critical elements for success. Africa-relevant genomic and related health economics research remains imperative with an overarching need to translate knowledge into improved healthcare. Given the limited data and genetic services across most of Africa, the continent has not yet come of 'genomics' age.

Sickle Cell Disease Genomics of Africa (SickleGenAfrica) Network: ethical framework and initial qualitative findings from community engagement in Ghana, Nigeria and Tanzania

ObjectivesTo provide lay information about genetics and sickle cell disease (SCD) and to identify and address ethical issues concerning the Sickle Cell Disease Genomics of Africa Network covering autonomy and...

Promoting cancer genomics research in Africa: a roadmap

Cancer genomics research in Africa is crucial to understanding the genetic architecture of cancer and tailoring cancer diagnoses and therapies to African populations. Creating this research enterprise in Africa has to be purposeful with a roadmap that incorporates individual scientist-, international collaborator-, university or institution-, and scientific organization-level factors.

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 forsuch governance to be grounded in principles of justice, equity and solidarity. However, there is a near absence ofconceptual 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 researchin 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 differentmacro-levelethical 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.

Genomics and bioinformatics capacity in Africa: no continent is left behind.

Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States' National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities.

Qualitative study of comprehension of heritability in genomics studies among the Yoruba in Nigeria

BackgroundWith growth of genomics research in Africa, concern has arisen about comprehension and adequacy of informed consent given the highly technical terms used in this field. We therefore decided to study whether there are linguistic and cultural concepts used to communicate heritability of characters, traits and diseases in an indigenous African population.MethodsWe conducted Focus Group Discussions among 115 participants stratified by sex, age and socio-economic status and Key Informant Interviews among 25 stakeholders and Key Opinion Leaders among Yoruba living in Ibadan, Nigeria. We used Atlas-ti v.8.3.17 software to analyze the data, using thematic approach.ResultsThe study participants identified several linguistic and cultural concepts including words, proverbs, and aphorisms that are used to describe heritable characters, traits and diseases in their local dialect. These included words that can be appropriated to describe dominant and recessive traits, variations in penetrance and dilution of strength of heritable characteristics by time and inter-marriage. They also suggested that these traits are transmitted by “blood”, and specific partner’s blood may be stronger than the other regardless of sex.ConclusionsIndigenous Yoruba populations have words and linguistic concepts that describe the heritability of characters, traits and diseases which can be appropriated to improve comprehension and adequacy of informed consent in genomics research. Our methods are openly available and can be used by genomic researchers in other African communities.

Evolutionary Genomics at the Human-Environment Interface in Africa.

We report on the first meeting of SMBE in Africa. SMBE Malawi was initiated to bring together African and international researchers who use genetics or genomics to study natural systems impacted by human activities. The goals of this conference were 1) to reach a world-class standard of science with a large number of contributions from Africa, 2) to initiate exchange between African and international researchers, and 3) to identify challenges and opportunities for evolutionary genomics research in Africa. As repored, we think that we have achieved these goals and make suggestions on the way forward for African evolutionary genomics research.

Stigma in African genomics research: Gendered blame, polygamy, ancestry and disease causal beliefs impact on the risk of harm.

A recurring concern in genomics research is the possibility that it could lead to stigma for participants, their families and the population groups they belong to. Little evidence exists to explain how and when this ought to be a concern in genomics research in Africa whilst there is growing international evidence drawing into question the direct link between stigma and genetics. In this paper, we interrogate practical instances from African genomics research where stigma was identified as a concern in an attempt to nuance and refine accounts of when stigma should be considered as an ethical issue. The paper describes examples involving gendered blame, polygamy, beliefs in supernatural disease causation and sensitive information about group lineage. We propose that the concern may not be about stigma so much as broader research-related harm, including for instance reputational harm to population groups. Furthermore, we propose to shift the analytical gaze from establishing causal relationships to exploring the intersection of genomics with pre-existing stigma. Finally, we emphasize the importance of ensuring genomics researchers are culturally competent, meaning able to recognise when cultural factors impact on the possibility that genomics research could cause harm.

The governance of genomic biobank research in Africa: reframing the regulatory tilt

Genomic biobank research has experienced exponential growth in recent years. It represents a real opportunity to remedy global health inequity that has seen limited investment in diseases affecting populations from low- and middle-income countries. Previous research in Africa was limited to so-called parachute research, whereby samples were taken from local populations for use in high-income countries with no local oversight or use of the sample. These exploitative practices must be guarded against, but the current regulation of genomic research in Africa adopts a precautionary approach that at times is restrictive in nature. We argue that the regulation and oversight of genomic biobank research should guard against exploitative research, but in a manner that promotes reciprocal benefit and not restrictive research practices. To achieve this, there must be a rebalancing of the regulatory tilt.

Unraveling the Ethical, Legal, and Social Implications of Neurobiobanking and Stroke Genomic Research in Africa: A Study Protocol of the African Neurobiobank for Precision Stroke Medicine ELSI Project.

The ethical, legal, and social implications (ELSI) of emerging neurobiobanks and data resources are unclear in an African scientific landscape with unique cultural, linguistic, and belief systems. The overarching goal of the African Neurobiobank for Precision Stroke Medicine—ELSI Project is to identify, examine, and develop novel approaches to address ELSI issues of biobanking and stroke genomic research in sub-Saharan Africa (SSA). To accomplish the goal we will (1) explore knowledge, attitude, perceptions, barriers, and facilitators influencing ELSI issues related to biobanking and stroke genomic research; (2) use information obtained to craft a community intervention program focused on ELSI issues; and (3) build capacity and careers related to genomics and biobanking for effective client/community engagement while enhancing regulatory, governance, and implementation competences in biobanking science in SSA. A community-based participatory research and mixed-methodological approach, focused on various levels of the social ecological model, will be used to identify and examine relevant ELSI issues. Contextual intervention tools, platforms, and practices will be developed to enhance community understanding and participation in stroke biobanking and genomics research activities while facilitating enduring trust, and equitable and fair utilization of biobanking resources for genetic and trans-omics research. A concurrent capacity building program related to genetic counseling and biobanking will be implemented for early career researchers. The huge potential for neurobiobanking and genomics research in Africa to advance precision medicine applicable to stroke and other neurological disorders requires addressing ELSI challenges while building sustainable research, career, and regulatory capacities in trans-omics and biobanking science.

A framework for tiered informed consent for health genomic research in Africa

A generic framework for providing participant information and implementing a tiered consent process for health genomic research in Africa can help to harness global health benefits from sharing and meta-analysis of African genomic data while simultaneously respecting and upholding the autonomy and individual choices of African research participants.