Sequence three million genomes across Africa

Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders

Complex structural variations (cxSVs) are often overlooked in genome analyses due to detection challenges. We developed ARC-SV, a probabilistic and machine-learning-based method that enables accurate detection and reconstruction of cxSVs from standard datasets. By applying ARC-SV across 4,262 genomes representing all continental populations, we identified cxSVs as a significant source of natural human genetic variation. Rare cxSVs have a propensity to occur in neural genes and loci that underwent rapid human-specific evolution, including those regulating corticogenesis. By performing single-nucleus multiomics in postmortem brains, we discovered cxSVs associated with differential gene expression and chromatin accessibility across various brain regions and cell types. Additionally, cxSVs detected in brains of psychiatric cases are enriched for linkage with psychiatric GWAS risk alleles detected in the same brains. Furthermore, our analysis revealed significantly decreased brain-region- and cell-type-specific expression of cxSV genes, specifically for psychiatric cases, implicating cxSVs in the molecular etiology of major neuropsychiatric disorders.

Bridging the Gap: Immune Checkpoint Inhibitor as an Option in the Management of Advanced and Recurrent Cervical Cancer in Sub-Saharan Africa

Cervical cancer remains a leading cause of cancer-related mortality in women in low and middle-income countries despite efforts to improve prevention and standard-of-care interventions. Sub-Saharan Africa (SSA) leads the numbers for global cervical cancer incidence and mortality, with the majority of the incidence diagnosed in the late stage of the malignancy. Although the global cervical cancer death rate has been on the decline for the last two decades owing to advancements in screening and treatment options, the mortality rate in SSA has not declined very much. Chemotherapy has been the treatment of choice for cervical cancer in SSA without meeting the expected survival outcomes in these patients, with the majority having advanced diseases at diagnosis. Immune checkpoint inhibitors have recently shown clinical promise in improving the survival of patients with advanced cervical cancer and have been integrated into the treatment guidelines in most high-income countries, which have helped further reduce the mortality rate of cervical cancer. However, many SSA countries are yet to fully benefit from using immune checkpoint inhibitors in cervical cancer. In this review, we discuss the challenges hindering the effective use of immune checkpoint inhibitors for advanced cervical cancer in Africa and possible solutions.

Promoting equity in polygenic risk assessment through global collaboration

The long delay before genomic technologies become available in low- and middle-income countries is a concern from both scientific and ethical standpoints. Polygenic risk scores (PRSs), a relatively recent advance in genomics, could have a substantial impact on promoting health by improving disease risk prediction and guiding preventive strategies. However, clinical use of PRSs in their current forms might widen global health disparities, as their portability to diverse groups is limited. This Perspective highlights the need for global collaboration to develop and implement PRSs that perform equitably across the world. Such collaboration requires capacity building and the generation of new data in low-resource settings, the sharing of harmonized genotype and phenotype data securely across borders, novel population genetics and statistical methods to improve PRS performance, and thoughtful clinical implementation in diverse settings. All this needs to occur while considering the ethical, legal and social implications, with support from regulatory and funding agencies and policymakers.

The generation of human induced pluripotent stem cell lines from individuals of Black African ancestry in South Africa

The lack of equitable representation of African diversity in scientific resources, such as genome-wide association studies and human induced pluripotent stem cell (hiPSC) repositories, has perpetuated inequalities in the advancement of health research. HiPSCs could be transformative in regenerative and precision medicine, therefore, the generation of diverse lines is critical in the establishment of African-relevant preclinical cellular models. HiPSC lines were derived from two healthy donors of Black African ancestry using Sendai virus reprogramming of dermal fibroblasts, and characterised to confirm stemness markers, trilineage differentiation, and genetic integrity. These hiPSCs represent a valuable resource for modelling African relevant disease biology.

Bioinformatics proficiency among African students

Bioinformatics, the interdisciplinary field that combines biology, computer science, and data analysis, plays a pivotal role in advancing our understanding of life sciences. In the African context, where the diversity of biological resources and healthcare challenges is substantial, fostering bioinformatics literacy and proficiency among students is important. This perspective provides an overview of the state of bioinformatics literacy among African students, highlighting the significance, challenges, and potential solutions in addressing this critical educational gap. It proposes various strategies to enhance bioinformatics literacy among African students. These include expanding educational resources, fostering collaboration between institutions, and engaging students in research projects. By addressing the current challenges and implementing comprehensive strategies, African students can harness the power of bioinformatics to contribute to innovative solutions in healthcare, agriculture, and biodiversity conservation, ultimately advancing the continent's scientific capabilities and improving the quality of life for her people. In conclusion, promoting bioinformatics literacy among African students is imperative for the continent's scientific development and advancing frontiers of biological research.

Bridging the gap between omics research and dental practice

AIM

The burgeoning field of omics research has witnessed exponential growth in both medicine and dentistry. However, despite more than a decade of advancements, clinical dentistry, particularly in Low- and Middle-Income Countries (LMICs), has seen limited progress in integrating omics-based approaches into routine practice. This review aims to provide a comprehensive overview of the integration of omics approaches in dentistry, focusing on the challenges and opportunities for translating research findings into clinical practice.

METHODS

we conducted a literature review using key databases to provide a brief overview of the history of genomics in dentistry. Additionally, we summarised recent breakthroughs in omics relevant to oral health practitioners, emphasising the inadequate translation of omics research into clinical practice.

RESULTS

Despite significant growth in omics research in both medicine and dentistry, its translation into routine clinical practice in dentistry remains limited. We summarise recent breakthroughs in omics and highlight the gap between research advancements and clinical implementation.

DISCUSSION AND CONCLUSION

The integration of omics approaches holds promise for enhancing diagnostics, personalised treatment strategies, and preventive measures in dental practice, ushering in a new era of precision oral healthcare. However, several challenges, including infrastructure limitations, cost-effectiveness, and education gaps, hinder the widespread adoption of omics-based approaches in clinical dentistry. A strong commitment to transforming dentistry is required to embrace this transition. This shift has the potential to revolutionise oral healthcare by advancing precision diagnostics and treatment strategies tailored to individual patient needs.

Precision Medicine for Whom? Public Health Outputs from "Genomics England" and "All of Us" to Make Up for Upstream and Downstream Exclusion

This paper problematizes the precision medicine approach embraced by the All of Us Research Program (US) and by Genomics England (UK) in terms of benefits distribution, by arguing that current "diversity and inclusion" efforts do not prevent exclusiveness, unless the framing and scope of the projects are revisited in public health terms. Grounded on document analysis and fieldwork interviews, this paper analyzes efforts to address potential patterns of exclusion upstream (from participating in precision medicine research) and downstream (from benefitting from precision medicine outputs). It argues that efforts for inclusion upstream are not corresponded downstream, and this unbalance jeopardizes the equitable capacities of the projects. It concludes that enhanced focus on socio-environmental determinants of health and aligned public health interventions as precision medicine outputs would be to the benefit of all and especially of those who are most at risk of (upstream as well as downstream) exclusion.

The Case for Pre-Emptive Pharmacogenetic Screening in South Africa

Lack of equitable representation of global genetic diversity has hampered the implementation of genomic medicine in under-represented populations, including those on the African continent. Data from the multi-national Pre-emptive Pharmacogenomic Testing for Preventing Adverse Drug Reactions (PREPARE) study suggest that genotype guidance for prescriptions reduced the incidence of clinically relevant adverse drug reactions (ADRs) by 30%. In this study, hospital dispensary trends from a tertiary South African (SA) hospital (Steve Biko Academic Hospital; SBAH) were compared with the drugs monitored in the PREPARE study. Dispensary data on 29 drugs from the PREPARE study accounted for ~10% of total prescriptions and ~9% of the total expenditure at SBAH. VigiLyze data from the South African Health Products Regulatory Authority were interrogated for local ADRs related to these drugs; 27 were listed as being suspected, concomitant, or interacting in ADR reports. Furthermore, a comparison of pharmacogene allele frequencies between African and European populations was used to frame the potential impact of pre-emptive pharmacogenetic screening in SA. Enumerating the benefit of pre-emptive pharmacogenetic screening in SA will only be possible once we initiate its full application. However, regional genomic diversity, disease burden, and first-line treatment options could be harnessed to target stratified PGx today.

A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data

Accurately predicting the effect of missense variants is a central problem in interpretation of genomic variation. Commonly used computational methods does not capture the quantitative impact on fitness in populations. We developed MisFit to estimate missense fitness effect using biobank-scale human population genome data. MisFit jointly models the effect at molecular level ( d ) and population level (selection coefficient, s ), assuming that in the same gene, missense variants with similar d have similar s . MisFit is a probabilistic graphical model that integrates deep neural network components and population genetics models efficiently with inductive bias based on biological causality of variant effect. We trained it by maximizing probability of observed allele counts in 236,017 European individuals. We show that s is informative in predicting frequency across ancestries and consistent with the fraction of de novo mutations given s . Finally, MisFit outperforms previous methods in prioritizing missense variants in individuals with neurodevelopmental disorders.

Polygenic risk scores for disease risk prediction in Africa: current challenges and future directions

Early identification of genetic risk factors for complex diseases can enable timely interventions and prevent serious outcomes, including mortality. While the genetics underlying many Mendelian diseases have been elucidated, it is harder to predict risk for complex diseases arising from the combined effects of many genetic variants with smaller individual effects on disease aetiology. Polygenic risk scores (PRS), which combine multiple contributing variants to predict disease risk, have the potential to influence the implementation for precision medicine. However, the majority of existing PRS were developed from European data with limited transferability to African populations. Notably, African populations have diverse genetic backgrounds, and a genomic architecture with smaller haplotype blocks compared to European genomes. Subsequently, growing evidence shows that using large-scale African ancestry cohorts as discovery for PRS development may generate more generalizable findings. Here, we (1) discuss the factors contributing to the poor transferability of PRS in African populations, (2) showcase the novel Africa genomic datasets for PRS development, (3) explore the potential clinical utility of PRS in African populations, and (4) provide insight into the future of PRS in Africa.

Genetic research and the collective good: participants as leaders to reconcile individual and public interests

This paper problematises the notions of public or common good as weighed against individual sovereignty in the context of medical research by focusing on genetic research. We propose the notion of collective good as the good of the particular collective in which the research was conducted. We conducted documentary and interview-based research with participant representatives and research leaders concerned with participant involvement in leading genetic research projects and around two recent genetic data controversies: the case of the UK Wellcome Sanger Institute, accused of planning unauthorised commercialisation of African DNA samples, and the case of the company Genuity Science, which planned genetic research on brain tumour samples in Ireland with no explicit patient consent. We advocate for greater specificity in circumscribing the collective to which genetic research relates and for greater efforts in including representatives of this collective as research coleaders in order to enable a more inclusive framing of the good arising from such research. Such community-based participant cogovernance and coleadership in genetic research is vital especially when minorities or vulnerable groups are involved, and it centrally requires community capacity building to help collectives articulate their own notions of the collective good.

From target discovery to clinical drug development with human genetics

The substantial investments in human genetics and genomics made over the past three decades were anticipated to result in many innovative therapies. Here we investigate the extent to which these expectations have been met, excluding cancer treatments. In our search, we identified 40 germline genetic observations that led directly to new targets and subsequently to novel approved therapies for 36 rare and 4 common conditions. The median time between genetic target discovery and drug approval was 25 years. Most of the genetically driven therapies for rare diseases compensate for disease-causing loss-of-function mutations. The therapies approved for common conditions are all inhibitors designed to pharmacologically mimic the natural, disease-protective effects of rare loss-of-function variants. Large biobank-based genetic studies have the power to identify and validate a large number of new drug targets. Genetics can also assist in the clinical development phase of drugs-for example, by selecting individuals who are most likely to respond to investigational therapies. This approach to drug development requires investments into large, diverse cohorts of deeply phenotyped individuals with appropriate consent for genetically assisted trials. A robust framework that facilitates responsible, sustainable benefit sharing will be required to capture the full potential of human genetics and genomics and bring effective and safe innovative therapies to patients quickly.

Evolving cardiovascular genetic counseling needs in the era of precision medicine

In the era of Precision Medicine the approach to disease diagnosis, treatment, and prevention is being transformed across medical specialties, including Cardiology, and increasingly involves genomics approaches. The American Heart Association endorses genetic counseling as an essential component in the successful delivery of cardiovascular genetics care. However, with the dramatic increase in the number of available cardiogenetic tests, the demand, and the test result complexity, there is a need not only for a greater number of genetic counselors but more importantly, for highly specialized cardiovascular genetic counselors. Consequently, there is a pressing need for advanced cardiovascular genetic counseling training, along with innovative online services, telemedicine, and patient-facing digital tools, as the most effective way forward. The speed of implementation of these reforms will be of essence in the translation of scientific advancements into measurable benefits for patients with heritable cardiovascular disease and their families.

Perspectives on the future of dysmorphology

The field of clinical genetics and genomics continues to evolve. In the past few decades, milestones like the initial sequencing of the human genome, dramatic changes in sequencing technologies, and the introduction of artificial intelligence, have upended the field and offered fascinating new insights. Though difficult to predict the precise paths the field will follow, rapid change may continue to be inevitable. Within genetics, the practice of dysmorphology, as defined by pioneering geneticist David W. Smith in the 1960s as "the study of, or general subject of abnormal development of tissue form" has also been affected by technological advances as well as more general trends in biomedicine. To address possibilities, potential, and perils regarding the future of dysmorphology, a group of clinical geneticists, representing different career stages, areas of focus, and geographic regions, have contributed to this piece by providing insights about how the practice of dysmorphology will develop over the next several decades.

WGS Data Collections: How Do Genomic Databases Transform Medicine?

As a scientific community we assumed that exome sequencing will elucidate the basis of most heritable diseases. However, it turned out it was not the case; therefore, attention has been increasingly focused on the non-coding sequences that encompass 98% of the genome and may play an important regulatory function. The first WGS-based datasets have already been released including underrepresented populations. Although many databases contain pooled data from several cohorts, recently the importance of local databases has been highlighted. Genomic databases are not only collecting data but may also contribute to better diagnostics and therapies. They may find applications in population studies, rare diseases, oncology, pharmacogenetics, and infectious and inflammatory diseases. Further data may be analysed with Al technologies and in the context of other omics data. To exemplify their utility, we put a highlight on the Polish genome database and its practical application.

Genomic medicine in Africa: a need for molecular genetics and pharmacogenomics experts

The large-scale implementation of genomic medicine in Africa has not been actualized. This overview describes how routine molecular genetics and advanced protein engineering/structural biotechnology could accelerate the implementation of genomic medicine. By using data-mining and analysis approaches, we analyzed relevant information obtained from public genomic databases on pharmacogenomics biomarkers and reviewed published studies to discuss the ideas. The results showed that only 68 very important pharmacogenes currently exist, while 867 drug label annotations, 201 curated functional pathways, and 746 annotated drugs have been catalogued on the largest pharmacogenomics database (PharmGKB). Only about 5009 variants of the reported ∼25,000 have been clinically annotated. Predominantly, the genetic variants were derived from 43 genes that contribute to 2318 clinically relevant variations in 57 diseases. Majority (∼60%) of the clinically relevant genetic variations in the pharmacogenes are missense variants (1390). The enrichment analysis showed that 15 pharmacogenes are connected biologically and are involved in the metabolism of cardiovascular and cancer drugs. The review of studies showed that cardiovascular diseases are the most frequent non-communicable diseases responsible for approximately 13% of all deaths in Africa. Also, warfarin pharmacogenomics is the most studied drug on the continent, while CYP2D6, CYP2C9, DPD, and TPMT are the most investigated pharmacogenes with allele activities indicated in African and considered to be intermediate metaboliser for DPD and TPMT (8.4% and 11%). In summary, we highlighted a framework for implementing genomic medicine starting from the available resources on ground.

Bridging the genomic data gap in Africa: implications for global disease burdens

This paper highlights the gap in the use of genomic data of Africans for global research efforts for disease cures. Genomic data represents an important tool used in disease research for understanding how diseases affect several populations and how these differences can be harnessed for the development of effective cures especially vaccines that have an impact at the genetic level e.g., RNA vaccines.This paper then provides a review of global genomic data status where three continents are reported to be the major contributor of genomic data to repositories used for disease research and the development of vaccines and medicines around the world.We reviewed the most recently published information about genetic data inclusiveness of populations, explaining how genomic data of Africans is lacking in global research efforts that cater towards the eradication of pandemics via the development of vaccines and other cures. We also discuss the implication of this non-inclusiveness for global disease burdens and indicate where changes need to be made in the last part of the paper.Lastly, the entire centers on some general policy recommendations to fully include African genomic data in such global genetic repositories. These recommendations can be implemented in African countries to improve genetic data collection, storage, and usage policies.

Global perspectives on CYP2D6 associations with primaquine metabolism and Plasmodium vivax radical cure

Clinical trial and individual patient treatment outcomes have produced accumulating evidence that effective primaquine (PQ) treatment of Plasmodium vivax and P. ovale liver stage hypnozoites is associated with genetic variation in the human cytochrome P450 gene, CYP2D6. Successful PQ treatment of individual and population-wide infections by the Plasmodium species that generate these dormant liver stage forms is likely to be necessary to reach elimination of malaria caused by these parasites globally. Optimizing safe and effective PQ treatment will require coordination of efforts between the malaria and pharmacogenomics research communities.

The genetic determinants of oral diseases in Africa: The gaps should be filled

Oral diseases are a major health concern and are among the most prevalent diseases globally. This problem is becoming more prominent in the rapidly growing populations of Africa. It is well documented that Africa exhibits the most diverse genetic make-up in the world. However, little work has been conducted to understand the genetic basis of oral diseases in Africans. Oral health is often neglected and receives low prioritisation from funders and governments. The genetic determinants of highly prevalent oral diseases such as dental caries and periodontal disease, and regionally prevalent conditions such as oral cancer and NOMA, are largely under-researched areas despite numerous articles alluding to a high burden of these diseases in African populations. Therefore, this review aims to shed light on the significant gaps in research on the genetic and genomic aspects of oral diseases in African populations and highlights the urgent need for evidence-based dentistry, in tandem with the development of the dentist/scientist workforce.

Importance of Including Non-European Populations in Large Human Genetic Studies to Enhance Precision Medicine

One goal of genomic medicine is to uncover an individual's genetic risk for disease, which generally requires data connecting genotype to phenotype, as done in genome-wide association studies (GWAS). While there may be clinical promise to employing prediction tools such as polygenic risk scores (PRS), it currently stands that individuals of non-European ancestry may not reap the benefits of genomic medicine because of underrepresentation in large-scale genetics studies. Here, we discuss why this inequity poses a problem for genomic medicine and the reasons for the low transferability of PRS across populations. We also survey the ancestry representation of published GWAS and investigate how estimates of ancestry diversity in GWASparticipants might be biased. We highlight the importance of expanding genetic research in Africa, one of the most underrepresented regions in human genomics research, and discuss issues of ethics, resources, and technology for equitable advancement of genomic medicine.

Whole Exome Sequencing in South Africa: Stakeholder Views on Return of Individual Research Results and Incidental Findings

The use of whole exome sequencing (WES) in medical research is increasing in South Africa (SA), raising important questions about whether and which individual genetic research results, particularly incidental findings, should be returned to patients. Whilst some commentaries and opinions related to the topic have been published in SA, there is no qualitative data on the views of professional stakeholders on this topic. Seventeen participants including clinicians, genomics researchers, and genetic counsellors (GCs) were recruited from the Western Cape in SA. Semi-structured interviews were conducted, and the transcripts analysed using the framework approach for data analysis. Current roadblocks for the clinical adoption of WES in SA include a lack of standardised guidelines; complexities relating to variant interpretation due to lack of functional studies and underrepresentation of people of African ancestry in the reference genome, population and variant databases; lack of resources and skilled personnel for variant confirmation and follow-up. Suggestions to overcome these barriers include obtaining funding and buy-in from the private and public sectors and medical insurance companies; the generation of a locally relevant reference genome; training of health professionals in the field of genomics and bioinformatics; and multidisciplinary collaboration. Participants emphasised the importance of upscaling the accessibility to and training of GCs, as well as upskilling of clinicians and genetic nurses for return of genetic data in collaboration with GCs and medical geneticists. Future research could focus on exploring the development of stakeholder partnerships for increased access to trained specialists as well as community engagement and education, alongside the development of guidelines for result disclosure.

Increasing African genomic data generation and sharing to resolve rare and undiagnosed diseases in Africa: a call-to-action by the H3Africa rare diseases working group

The rich and diverse genomics of African populations is significantly underrepresented in reference and in disease-associated databases. This renders interpreting the Next Generation Sequencing (NGS) data and reaching a diagnostic more difficult in Africa and for the African diaspora. It increases chances for false positives with variants being misclassified as pathogenic due to their novelty or rarity. We can increase African genomic data by (1) making consent for sharing aggregate frequency data an essential component of research toolkit; (2) encouraging investigators with African data to share available data through public resources such as gnomAD, AVGD, ClinVar, DECIPHER and to use MatchMaker Exchange; (3) educating African research participants on the meaning and value of sharing aggregate frequency data; and (4) increasing funding to scale-up the production of African genomic data that will be more representative of the geographical and ethno-linguistic variation on the continent. The RDWG of H3Africa is hereby calling to action because this underrepresentation accentuates the health disparities. Applying the NGS to shorten the diagnostic odyssey or to guide therapeutic options for rare diseases will fully work for Africans only when public repositories include sufficient data from African subjects.

Current profile of Charcot-Marie-Tooth disease in Africa: A systematic review

BACKGROUND AND AIMS

Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy characterised by a high clinical and genetic heterogeneity. While most cases were described in populations with Caucasian ancestry, genetic research on CMT in Africa is scant. Only a few cases of CMT have been reported, mainly from North Africa. The current study aimed to summarise available data on CMT in Africa, with emphasis on the epidemiological, clinical, and genetic features.

METHODS

We searched PubMed, Scopus, Web of Sciences, and the African Journal Online for articles published from the database inception until April 2021 using specific keywords. A total of 398 articles were screened, and 28 fulfilled our selection criteria.

RESULTS

A total of 107 families totalling 185 patients were reported. Most studies were reported from North Africa (n = 22). The demyelinating form of CMT was the commonest subtype, and the phenotype varied greatly between families, and one family (1%) of CMT associated with hearing impairment was reported. The inheritance pattern was autosomal recessive in 91.2% (n = 97/107) of families. CMT-associated variants were reported in 11 genes: LMNA, GDAP1, GJB1, MPZ, MTMR13, MTMR2, PRX, FGD4/FRABIN, PMP22, SH3TC2, and GARS. The most common genes reported are LMNA, GDAP1, and SH3TC2 and have been found mostly in Northern African populations.

INTERPRETATION

This study reveals that CMT is not rare in Africa, and describes the current clinical and genetic profile. The review emphasised the urgent need to invest in genetic research to inform counselling, prevention, and care for CMT in numerous settings on the continent.

Operationalizing "One Health" as "One Digital Health" Through a Global Framework That Emphasizes Fair and Equitable Sharing of Benefits From the Use of Artificial Intelligence and Related Digital Technologies

The operationalization of One Health (OH) through digitalization is a means to deploy digital technologies (including Artificial Intelligence (AI), big data and related digital technologies) to better capacitate us to deal with growing climate exigency and related threats to human, animal and plant health. With reference to the concept of One Digital Health (ODH), this paper considers how digital capabilities can help to overcome ‘operational brakes’ in OH through new and deeper insights, better predictions, and more targeted or precise preventive strategies and public health countermeasures. However, the data landscape is fragmented and access to certain types of data is increasingly restrictive as individuals, communities and countries seek to assert greater control over data taken from them. This paper proposes for a dedicated global ODH framework—centered on fairness and equity—to be established to promote data-sharing across all the key knowledge domains of OH and to devise data-driven solutions to challenges in the human-animal-ecosystems interface. It first considers the data landscape in relation to: (1) Human and population health; (2) Pathogens; (3) Animal and plant health; and (4) Ecosystems and biodiversity. The complexification from the application of advance genetic sequencing technology is then considered, with focus on current debates over whether certain types of data like digital (genetic) sequencing information (DSI) should remain openly and freely accessible. The proposed ODH framework must augment the existing access and benefit sharing (ABS) framework currently prescribed under the Nagoya Protocol to the Convention on Biological Diversity (CBD) in at least three different ways. First, the ODH framework should apply to all genetic resources and data, including DSI, whether from humans or non-humans. Second, the FAIRER principles should be implemented, with focus on fair and equitable benefit-sharing. Third, the ODH framework should adopt multilateral approaches to data sharing (such as through federated data systems) and to ABS. By operationalizing OH as ODH, we are more likely to be able to protect and restore natural habitats, secure the health and well-being of all living things, and thereby realize the goals set out in the post-2020 Global Biodiversity Framework under the CBD.

Five Priorities of African Genomics Research: The Next Frontier

To embrace the prospects of accurately diagnosing thousands of monogenic conditions, predicting disease risks for complex traits or diseases, tailoring treatment to individuals' pharmacogenetic profiles, and potentially curing some diseases, research into African genomic variation is a scientific imperative. African genomes harbor millions of uncaptured variants accumulated over 300,000 years of modern humans' evolutionary history, with successive waves of admixture, migration, and natural selection combining with extensive ecological diversity to create a broad and exceptional genomic complexity. Harnessing African genomic complexity, therefore, will require sustained commitment and equitable collaboration from the scientific community and funding agencies. African governments must support academic public research and industrial partnerships that build the necessary genetic medicine workforce, utilize the emerging genomic big data to develop expertise in computer science and bioinformatics, and evolve national and global governance frameworks that recognize the ethical implications of data-driven genomic research and empower its application in African social, cultural, economic, and religious contexts. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Hepatic Models in Precision Medicine: An African Perspective on Pharmacovigilance

Pharmaceuticals are indispensable to healthcare as the burgeoning global population is challenged by diseases. The African continent harbors unparalleled genetic diversity, yet remains largely underrepresented in pharmaceutical research and development, which has serious implications for pharmaceuticals approved for use within the African population. Adverse drug reactions (ADRs) are often underpinned by unique variations in genes encoding the enzymes responsible for their uptake, metabolism, and clearance. As an example, individuals of African descent (14-34%) harbor an exclusive genetic variant in the gene encoding a liver metabolizing enzyme (CYP2D6) which reduces the efficacy of the breast cancer chemotherapeutic Tamoxifen. However, CYP2D6 genotyping is not required prior to dispensing Tamoxifen in sub-Saharan Africa. Pharmacogenomics is fundamental to precision medicine and the absence of its implementation suggests that Africa has, to date, been largely excluded from the global narrative around stratified healthcare. Models which could address this need, include primary human hepatocytes, immortalized hepatic cell lines, and induced pluripotent stem cell (iPSC) derived hepatocyte-like cells. Of these, iPSCs, are promising as a functional in vitro model for the empirical evaluation of drug metabolism. The scale with which pharmaceutically relevant African genetic variants can be stratified, the expediency with which these platforms can be established, and their subsequent sustainability suggest that they will have an important role to play in the democratization of stratified healthcare in Africa. Here we discuss the requirement for African hepatic models, and their implications for the future of pharmacovigilance on the African continent.

Towards equitable and trustworthy genomics research

The representation of traditionally scientifically underserved groups in genomic research continues to be low despite concerns about equity and social justice and the scientific and clinical need. Among the factors that account for this are a lack of trust in the research community and limited diversity in this community. The success of the multiple initiatives that aim to improve representation relies on the willingness of underrepresented populations to make data and samples available for research and clinical use. In this narrative review, we propose that this requires building trust, and set out four approaches to demonstrating trustworthiness, including increasing diversity in the research workforce, and meaningful engagement with underrepresented communities in a culturally and linguistically appropriate manner. Capacity building globally will ensure that actual and perceived exploitation and ‘helicopter’ research could be eliminated.

A Method for Localizing Non-Reference Sequences to the Human Genome

As the last decade of human genomics research begins to bear the fruit of advancements in precision medicine, it is important to ensure that genomics' improvements in human health are distributed globally and equitably. An important step to ensuring health equity is to improve the human reference genome to capture global diversity by including a wide variety of alternative haplotypes, sequences that are not currently captured on the reference genome.We present a method that localizes 100 basepair (bp) long sequences extracted from short-read sequencing that can ultimately be used to identify what regions of the human genome non-reference sequences belong to.We extract reads that don't align to the reference genome, and compute the population's distribution of 100-mers found within the unmapped reads. We use genetic data from families to identify shared genetic material between siblings and match the distribution of unmapped k-mers to these inheritance patterns to determine the the most likely genomic region of a k-mer. We perform this localization with two highly interpretable methods of artificial intelligence: a computationally tractable Hidden Markov Model coupled to a Maximum Likelihood Estimator. Using a set of alternative haplotypes with known locations on the genome, we show that our algorithm is able to localize 96% of k-mers with over 90% accuracy and less than 1Mb median resolution. As the collection of sequenced human genomes grows larger and more diverse, we hope that this method can be used to improve the human reference genome, a critical step in addressing precision medicine's diversity crisis.

Toward a genome sequence for every animal: Where are we now?

In less than 25 y, the field of animal genome science has transformed from a discipline seeking its first glimpses into genome sequences across the Tree of Life to a global enterprise with ambitions to sequence genomes for all of Earth's eukaryotic diversity [H. A. Lewin et al., Proc. Natl. Acad. Sci. U.S.A. 115, 4325-4333 (2018)]. As the field rapidly moves forward, it is important to take stock of the progress that has been made to best inform the discipline's future. In this Perspective, we provide a contemporary, quantitative overview of animal genome sequencing. We identified the best available genome assemblies in GenBank, the world's most extensive genetic database, for 3,278 unique animal species across 24 phyla. We assessed taxonomic representation, assembly quality, and annotation status for major clades. We show that while tremendous taxonomic progress has occurred, stark disparities in genomic representation exist, highlighted by a systemic overrepresentation of vertebrates and underrepresentation of arthropods. In terms of assembly quality, long-read sequencing has dramatically improved contiguity, whereas gene annotations are available for just 34.3% of taxa. Furthermore, we show that animal genome science has diversified in recent years with an ever-expanding pool of researchers participating. However, the field still appears to be dominated by institutions in the Global North, which have been listed as the submitting institution for 77% of all assemblies. We conclude by offering recommendations for improving genomic resource availability and research value while also broadening global representation.

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).

Health and demographic surveillance systems in low- and middle-income countries: history, state of the art and future prospects

Health and Demographic Surveillance Systems (HDSS) have been developed in several low- and middle-income countries (LMICs) in Africa and Asia. This paper reviews their history, state of the art and future potential and highlights substantial areas of contribution by the late Professor Peter Byass.Historically, HDSS appeared in the second half of the twentieth century, responding to a dearth of accurate population data in poorly resourced settings to contextualise the study of interventions to improve health and well-being. The progress of the development of this network is described starting with Pholela, and progressing through Gwembe, Balabgarh, Niakhar, Matlab, Navrongo, Agincourt, Farafenni, and Butajira, and the emergence of the INDEPTH Network in the early 1990'sThe paper describes the HDSS methodology, data, strengths, and limitations. The strengths are particularly their temporal coverage, detail, dense linkage, and the fact that they exist in chronically under-documented populations in LMICs where HDSS sites operate. The main limitations are generalisability to a national population and a potential Hawthorne effect, whereby the project itself may have changed characteristics of the population.The future will include advances in HDSS data harmonisation, accessibility, and protection. Key applications of the data are to validate and assess bias in other datasets. A strong collaboration between a national HDSS network and the national statistics office is modelled in South Africa and Sierra Leone, and it is possible that other low- to middle-income countries will see the benefit and take this approach.

Hearing loss in Africa: current genetic profile

Hearing impairment (HI) is highly heterogeneous with over 123 associated genes reported to date, mostly from studies among Europeans and Asians. Here, we performed a systematic review of literature on the genetic profile of HI in Africa. The study protocol was registered on PROSPERO, International Prospective Register of Systematic Reviews with the registration number “CRD42021240852”. Literature search was conducted on PubMed, Scopus, Africa-Wide Information, and Web of Science databases. A total of 89 full-text records was selected and retrieved for data extraction and analyses. We found reports from only 17/54 (31.5%) African countries. The majority (61/89; 68.5%) of articles were from North Africa, with few reports found from sub-Saharan Africa. The most common method used in these publications was targeted gene sequencing (n = 66/111; 59.5%), and only 13.5% (n = 15/111) used whole-exome sequencing. More than half of the studies were performed in families segregating HI (n = 51/89). GJB2 was the most investigated gene, with GJB2: p.(R143W) founder variant only reported in Ghana, while GJB2: c.35delG was common in North African countries. Variants in MYO15A were the second frequently reported in both North and Central Africa, followed by ATP6V1B1 only reported from North Africa. Usher syndrome was the main syndromic HI molecularly investigated, with variants in five genes reported: USH2A, USH1G, USH1C, MYO7A, and PCDH15. MYO7A: p.(P1780S) founder variant was reported as the common Usher syndrome variant among Black South Africans. This review provides the most comprehensive data on HI gene variants in the largely under-investigated African populations. Future exomes studies particularly in multiplex families will likely provide opportunities for the discovery of the next sets of novel HI genes, and well as unreported variants in known genes to further our understanding of HI pathobiology, globally.

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.