Genomic medicine in Africa: promise, problems and prospects

Cross-population applications of genomics to understand the risk of multifactorial traits involving inflammation and immunity

The interplay between genetic and environmental factors plays a significant role in interindividual variation in immune and inflammatory responses. The availability of high-throughput low-cost genotyping and next-generation sequencing has revolutionized our ability to identify human genetic variation and understand how this varies within and between populations, and the relationship with disease. In this review, we explore the potential of genomics for patient benefit, specifically in the diagnosis, prognosis and treatment of inflammatory and immune-related diseases. We summarize the knowledge arising from genetic and functional genomic approaches, and the opportunity for personalized medicine. The review covers applications in infectious diseases, rare immunodeficiencies and autoimmune diseases, illustrating advances in diagnosis and understanding risk including use of polygenic risk scores. We further explore the application for patient stratification and drug target prioritization. The review highlights a key challenge to the field arising from the lack of sufficient representation of genetically diverse populations in genomic studies. This currently limits the clinical utility of genetic-based diagnostic and risk-based applications in non-Caucasian populations. We highlight current genome projects, initiatives and biobanks from diverse populations and how this is being used to improve healthcare globally by improving our understanding of genetic susceptibility to diseases and regional pathogens such as malaria and tuberculosis. Future directions and opportunities for personalized medicine and wider application of genomics in health care are described, for the benefit of individual patients and populations worldwide.

Stakeholder knowledge and attitudes toward the use of predictive genetic testing in South Africa

The use of predictive genetic testing, particularly for risk profiling in non-communicable diseases (NCDs), has the potential to benefit public health by decreasing the disease burden and alleviating the pressure on healthcare. It is thus important to assess knowledge and uptake among stakeholders. This study aimed to assess end users' (community, medical practitioners and medical students) knowledge and attitudes regarding the use and support of genomic medicine. A descriptive cross-sectional survey was conducted in Kwazulu-Natal (KZN) among 3 groups of stakeholders (n = 170): medical practitioners from both private and public healthcare, medical students from UKZN and community members represented by teachers. Three structured questionnaires using a Likert scale were administered. Responses were stratified by practice type, and a scoring scale was developed. Principal component analysis (PCA) was used to reduce data on all constructs that made up each variable. All three groups showed adequate knowledge and a positive attitude towards use, apart from medical students who were not as keen to support future use in their own practice. Although medical practitioners supported the use of this technology, with necessary guidelines, expertise and affordability, only 18% from private practice reported having used it. PCA reduced data to fewer parsimonious constructs for all 3 groups: common threads included an awareness that genetic testing may improve health and disease outcomes; guidelines for use; and the provision of education to increase awareness, training to bolster expertise and confidence to use these services. Participants in this study attributed a lack of uptake to limited expertise and professional support, and a lack of legislative guidelines. We recommend updating continuing professional development for medical practitioners and promoting community education concomitantly. Provision of guidelines and increased accessibility to resources are important.

Modeling factors critical for implementation of precision medicine at health systems-level: an IRT approach

BACKGROUND

Through recent advances in omics technologies, precision medicine (PM) promises to fundamentally change the way we approach health, disease and illness. Imperative applications of omics-based biomarkers are gradually moving from research to clinical settings, with huge long-term clinical and public health implications. Whereas much of research in PM is mainly focused on basic biomedical discoveries, currently there is little research on the clinical implementation of omics biomarkers, especially at health systems level.

AIM AND METHODS

This study investigated the application of multidimensional item response theory (IRT) models to validate a hypothesized PM implementation measurement model. This is a contribution to PM implementation at health systems level. Data obtained through an item-sort procedure involving 496 observations from 124 study participants formed the basis of a 22-item PMI measurement model.

CONCLUSION

Statistical significance of the bifactor model suggests PM implementation may have to be examined using factors that reflect a single common underlying implementation construct, as well as factors that reflect unique variances for the identified four content-specific 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 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.

Has translational genomics come of age in Africa?

The rapid increase in genomics research in Africa and the growing promise of precision public health 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 is 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 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 precision public health 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.

Catalyzing clinical implementation of pharmacogenomics and personalized medicine interventions in Africa

Pharmacogenomics is considered to be the low-hanging fruit in the tree of genomic medicine with numerous examples of its successful implementation in the clinic. In this perspective, we provide details about the potential clinical application of pharmacogenomics in African populations by using relevant drug cases and high-throughput genomics approaches; involving numerous countries and stakeholders; and most importantly exploiting the existing knowledge of respective large-scale initiatives. We emphasize on the necessity of constructing appropriate frameworks for government policies in African countries. We also provide input about different initiatives in the field of genomics medicine implementation in Africa, not only for their potential for synergy and collaboration among them, but also as models for replication in other regions worldwide, aiming for healthcare improvement.

Understanding Ethical, Legal and Societal Issues (ELSIs) in Human Biobanking and Genomics for Research and Healthcare in Zimbabwe: The Genomics Inheritance Law Ethics and Society (GILES) initiative

Biobanks and human genomics applications are key for understanding health, disease and heredity in Africa and globally. Growing interest in these technologies calls for strengthening relevant legal, ethical and policy systems to address knowledge disparities and ensure protection of society, while supporting advancement of science. In Zimbabwe there is limited understanding of ethical, legal, and societal issues (ELSI) for biobanking and genomics. The Genomics Inheritance Law Ethics and Society (GILES) initiative was established in 2015 to explore the current status and gaps in the ethical and legal frameworks, knowledge among various stakeholders, and to establish capacity for addressing ELSI of biobanking and genomics as applied in biomedical and population research, and healthcare. The project was conducted over a countrywide geographical region and established one of the most comprehensive studies for ELSI of human biobanking and genomics in Africa. This paper outlines the strategy undertaken during the implementation of the GILES initiative and discusses the importance of such an initiative for characterisation of ELSI of human biobanking and genomics in Zimbabwe and Africa.

The African Genomic Medicine Training Initiative (AGMT): Showcasing a Community and Framework Driven Genomic Medicine Training for Nurses in Africa

The potential of genomic medicine in improving the quality of healthcare both at population and individual-level is well-recognized globally. However, successful adoption of genetic and genomic evidence into clinical practice depends on training the healthcare workforce and clinical researchers in genomic medicine. Due to limited expertise in the medical genetics and genomics field, widespread uptake largely depends on task-shifting for the implementation of genomic medicine implementation to key healthcare professionals such as nurses. Their knowledge would be developed through courses aimed at professional development. Globally, trainers, and training initiatives in genomic medicine are in early stages of development, but resource limited settings such as the African continent face additional logistical and institutional challenges. The African Genomic Medicine Training (AGMT) Initiative was conceived during a combined conference of the African Society of Human Genetics (AfSHG) and the Human Heredity and Health in Africa Consortium (H3Africa) in 2016, Senegal, in response to the needs for developing knowledge and skills in genomic medicine. AGMT was established to implement a sustainable genomic medicine training initiative primarily for healthcare professionals who are not geneticists but are nurses, doctors, and pharmacists in Africa. This paper reports on the establishment of the AGMT initiative and the strategies developed and piloted by this initiative in designing and implementing an accredited frame-work and community-based blended learning course for nurses across 11 African countries. The global implementation experiences, outcomes and lessons learnt are highlighted. The AGMT initiative strategy takes advantage of existing research consortia and networks to train and create a pool of trainers and has adopted evidence-based approaches to guide curriculum and content development/adaptation. This initiative established the first Africa-wide online blended learning genomic medicine course which forms the basis from which to develop courses for other healthcare professionals and the wider public.

Diversity and dysmorphology

PURPOSE OF REVIEW

Dysmorphic features result from errors in morphogenesis frequently associated with genetic syndromes. Recognizing patterns of dysmorphic features is a critical step in the diagnosis and management of human congenital anomalies and genetic syndromes. This review presents recent developments in genetic syndromes and their related dysmorphology in diverse populations.

RECENT FINDINGS

Clinical findings in patients with genetic syndromes differ in their heterogeneity across different population groups. Some genetic syndromes have variable features in different ethnicities, in part due to specific background exam characteristics such as flat facial profiles or nasal differences; however, other genetic syndromes are similar across different ethnicities. Facial analysis technology is accurate in diagnosing genetic syndromes in populations around the world and is a powerful adjunct to conventional clinical examination. This accuracy also reinforces the concept that genetic syndromes can and should be diagnosed in any ethnicity.

SUMMARY

The increasing amount of data from studies on genetic syndromes in diverse populations is significantly improving our knowledge and approach to dysmorphic patients from various ethnic backgrounds. Optimal management of genetic syndromes requires early diagnosis, including in developing countries.

Blueprint for building a biorepository in a resource-limited setting that follows international best practices

BACKGROUND

Genetic diversity is abundant on the African continent. However, genomic research has been hampered by a lack of high quality and extensively annotated biospecimens and the necessary infrastructure to support such a technology-intensive effort.

OBJECTIVE

The Institute of Human Virology Nigeria (IHVN) partnered with the H3Africa Consortium and the Coriell Institute for Medical Research to build an internationally recognised biorepository for the receipt, processing, storage and distribution of biospecimens for biomedical research. Here, the authors describe the procedures, challenges and results encountered.

RESULTS

Key requirements for a high-quality biorepository were identified: (1) institutional support of infrastructure and services, (2) on-site trained staff with primary commitment to the biorepository, (3) reliance on best practices from globally recognised biorepository groups, (4) early implementation of a quality management system, (5) adoption of a laboratory information management system with demonstrated versatility in functions, (6) collaboration with external experts and sharing of experience through abstracts, newsletters, published manuscripts, and attendance at meetings and workshops, (7) strict adherence to local and national ethical standards and (8) a sustainability plan that is reviewed and updated annually.

CONCLUSION

Utilising published best practices of globally recognised experts in the biorepository field as a benchmark, IHVN expanded and reorganised its existing laboratory facility and staff to take on this new purpose.

Use of broad consent and related procedures in genomics research: Perspectives from research participants in the Genetics of Rheumatic Heart Disease (RHDGen) study in a University Teaching Hospital in Zambia

The use of broad consent for genomics research raises important ethical questions for the conduct of genomics research, including relating to its acceptability to research participants and comprehension of difficult scientific concepts. To explore these and other challenges, we conducted a study using qualitative methods with participants enrolled in an H3Africa Rheumatic Heart Disease genomics study (the RHDGen network) in Zambia to explore their views on broad consent, sample and data sharing and secondary use. In-depth interviews were conducted with RHDGen participants (n = 18), study staff (n = 5) and with individuals who refused to participate (n = 3). In general, broad consent was seen to be reasonable if reasons for storing the samples for future research use were disclosed. Some felt that broad consent should be restricted by specifying planned future studies and that secondary research should ideally relate to original disease for which samples were collected. A few participants felt that broad consent would delay the return of research results to participants. This study echoes findings in other similar studies in other parts of the continent that suggested that broad consent could be an acceptable consent model in Africa if careful thought is given to restrictions on re-use.

Genomics for All: International Open Science Genomics Projects and Capacity Building in the Developing World

Genomic medicine applications have the potential to considerably improve health care in developing countries in the coming years. However, if developing countries do not improve their capacity for research and development (R&D) in the field, they might be left out of the genomics revolution. Large-scale and widely accessible databases for storing and analyzing genomic data are crucial tools for the advancement of genomic medicine. Building developing countries' capacity in genomics is accordingly closely linked to their involvement in international human genomics research initiatives. The purpose of this paper is to conduct a pilot study on the impact of international open science genomics projects on capacity building in R&D in developing countries. Using indicators we developed in previous work to measure the performance of international open science genomics projects, we analyse the policies and practices of four key projects in the field: the International HapMap Project, the Human Heredity and Health in Africa Initiative, the Malaria Genomic Epidemiology Network and the Structural Genomics Consortium. The results show that these projects play an important role in genomics capacity building in developing countries, but play a more limited role with regard to the potential redistribution of the benefits of research to the populations of these countries. We further suggest concrete initiatives that could facilitate the involvement of researchers from developing countries in the international genomics research community and accelerate capacity building in the developing world.

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.

The critical needs and challenges for genetic architecture studies in Africa

Human genetic studies have long been vastly Eurocentric, raising a key question about the generalizability of these study findings to other populations. Because humans originated in Africa, these populations retain more genetic diversity, and yet individuals of African descent have been tremendously underrepresented in genetic studies. The diversity in Africa affords ample opportunities to improve fine-mapping resolution for associated loci, discover novel genetic associations with phenotypes, build more generalizable genetic risk prediction models, and better understand the genetic architecture of complex traits and diseases subject to varying environmental pressures. Thus, it is both ethically and scientifically imperative that geneticists globally surmount challenges that have limited progress in African genetic studies to date. Additionally, African investigators need to be meaningfully included, as greater inclusivity and enhanced research capacity afford enormous opportunities to accelerate genomic discoveries that translate more effectively to all populations. We review the advantages, challenges, and examples of genetic architecture studies of complex traits and diseases in Africa. For example, with greater genetic diversity comes greater ancestral heterogeneity; this higher level of understudied diversity can yield novel genetic findings, but some methods that assume homogeneous population structure and work well in European populations may work less well in the presence of greater heterogeneity in African populations. Consequently, we advocate for methodological development that will accelerate studies important for all populations, especially those currently underrepresented in genetics.

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

Africa may be heading for an era of genomics medicine. There are also expectations that genomics may play a role in reducing global health inequities. However, the near lack of genomics studies on African populations has led to concerns that genomics may widen, rather than close, the global health inequity gap. To prevent a possible genomics divide, the genomics 'revolution' has been extended to Africa. This is motivated, in part, by Africa's rich genetic diversity and high disease burden. What remains unclear, however, are the prospects of using genomics technology for healthcare in Africa. In this qualitative study, we explored the views of 17 genomics researchers in Africa on the prospects and challenges of genomics medicine in Africa. Interviewees were researchers in Africa who were involved in genomics research projects in Africa. Analysis of in-depth interviews suggest that genomics medicine may have an impact on disease surveillance, diagnosis, treatment and prevention. However, Africa's capacity for genomics medicine, current research priorities in genomics and the translation of research findings will be key defining factors impacting on the ability of genomics medicine to improve healthcare in Africa.

Implementation of genomics research in Africa: challenges and recommendations

BACKGROUND

There is exponential growth in the interest and implementation of genomics research in Africa. This growth has been facilitated by the Human Hereditary and Health in Africa (H3Africa) initiative, which aims to promote a contemporary research approach to the study of genomics and environmental determinants of common diseases in African populations.

OBJECTIVE

The purpose of this article is to describe important challenges affecting genomics research implementation in Africa.

METHODS

The observations, challenges and recommendations presented in this article were obtained through discussions by African scientists at teleconferences and face-to-face meetings, seminars at consortium conferences and in-depth individual discussions.

RESULTS

Challenges affecting genomics research implementation in Africa, which are related to limited resources include ill-equipped facilities, poor accessibility to research centers, lack of expertise and an enabling environment for research activities in local hospitals. Challenges related to the research study include delayed funding, extensive procedures and interventions requiring multiple visits, delays setting up research teams and insufficient staff training, language barriers and an underappreciation of cultural norms. While many African countries are struggling to initiate genomics projects, others have set up genomics research facilities that meet international standards.

CONCLUSIONS

The lessons learned in implementing successful genomics projects in Africa are recommended as strategies to overcome these challenges. These recommendations may guide the development and application of new research programs in low-resource settings.

Pharmacogenomic implications of the evolutionary history of infectious diseases in Africa

As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations. Here, we examine Africa's large burden of infectious disease, discuss key examples of known genetic variation modulating disease risk, and provide examples of clinically relevant variants critical for establishing dosing guidelines. We propose that a more systematic characterization of the genetic diversity of African ancestry populations is required if the current benefits of precision medicine are to be extended to these populations.

Embracing an "African Ethos" to facilitate African immigrants participation in medical genetics and genomics research

BACKGROUND

Limited published research exists on perceptions and potentials for black African immigrants' participation in medical genetics and genomics research.

PURPOSE

This study explores the inclination and disinclination of African immigrants to be involved in genetics and genomics research.

METHODS

In-depth qualitative interviews were employed in which a sample of black African immigrants 18 years and older (n = 34) were interviewed.

DISCUSSION

Barriers included contrary beliefs and customs about disease and the human body that differs from Western conceptions, and lack of genuine connection to the health care system. Facilitators included promotion of an "African ethos," wherein Africans unite with one another in a communal extension of self and robust community involvement across the life span of genetic studies.

CONCLUSION

It is important for researchers and genetic counselors to understand the sociocultural underpinnings of African immigrants about genetics and genomics research as an initial step to encouraging their participation.

Building local capacity for genomics research in Africa: recommendations from analysis of publications in Sub-Saharan Africa from 2004 to 2013

Background

The poor genomics research capacity of Sub-Saharan Africa (SSA) could prevent maximal benefits from the applications of genomics in the practice of medicine and research. The objective of this study is to examine the author affiliations of genomic epidemiology publications in order to make recommendations for building local genomics research capacity in SSA.

Design

SSA genomic epidemiology articles published between 2004 and 2013 were extracted from the Human Genome Epidemiology (HuGE) database. Data on authorship details, country of population studied, and phenotype or disease were extracted. Factors associated with the first author, who has an SSA institution affiliation (AIAFA), were determined using a Chi-square test and multiple logistic regression analysis.

Results

The most commonly studied population was South Africa, accounting for 31.1%, followed by Ghana (10.6%) and Kenya (7.5%). About one-tenth of the papers were related to non-communicable diseases (NCDs) such as cancer (6.1%) and cardiovascular diseases (CVDs) (4.3%). Fewer than half of the first authors (46.9%) were affiliated with an African institution. Among the 238 articles with an African first author, over three-quarters (79.8%) belonged to a university or medical school, 16.8% were affiliated with a research institute, and 3.4% had affiliations with other institutions.

Conclusions

Significant disparities currently exist among SSA countries in genomics research capacity. South Africa has the highest genomics research output, which is reflected in the investments made in its genomics and biotechnology sector. These findings underscore the need to focus on developing local capacity, especially among those affiliated with SSA universities where there are more opportunities for teaching and research.

Genetics and genomic medicine in Mali: challenges and future perspectives

Genetics and genomic medicine in Mali: challenges and future perspectives.

Perspectives in Genetics and Sickle Cell Disease Prevention in Africa: Beyond the Preliminary Data from Cameroon

Management of sickle cell disease (SCD) in Africa needs to be accompanied by various preventive strategies, including early detection via prenatal genetic diagnosis (PND). Contrary to Cameroonian doctors who considered termination of an affected pregnancy (TAP) for SCD in 36.1%, the majority of parents (62.5%) with affected children accepted TAP in principle. In practice, most women opted for TAP (90%), justified by a huge psycho-social burden. The ethical and legal challenges of PND prompted the need to explore the use of genetics for secondary prevention of SCD. In 610 Cameroonian SCD patients, the genomic variations in two principal foetal haemoglobin-promoting loci were significantly associated with foetal haemoglobin levels. In addition, the co-inheritance of a 3.7-kb α-globin gene deletion and SCD was associated with a late disease onset and possibly improved survival: there was a much higher allele frequency of the 3.7-kb α-globin gene deletion in SCD patients (∼ 40%) than in haemoglobin AA controls (∼ 10%). The data indicate the urgent need to develop and implement policy actions in sub-Saharan Africa on at least four levels: (1) the implementation of SCD screening practices and early neonatal follow-up; (2) the development and incorporating of socio-economic support to alleviate the burden of SCD on affected families; (3) the exploration of the appropriateness of the medical abortion laws for SCD, and (4) the development of national plans for genetic medicine, including research on genomic variants that affect the phenotypes of SCD, in order to potentially use them for anticipatory guidance.

The H3Africa policy framework: negotiating fairness in genomics

Human Heredity and Health in Africa (H3Africa) research seeks to promote fair collaboration between scientists in Africa and those from elsewhere. Here, we outline how concerns over inequality and exploitation led to a policy framework that places a firm focus on African leadership and capacity building as guiding principles for African genomics research.