Unique considerations for advancing genomic medicine in African populations

Childhood-Onset Systemic Lupus Erythematosus (cSLE): An International Perspective

PURPOSE OF REVIEW

Childhood-onset systemic lupus erythematosus (cSLE) is a severe and potentially life-threatening chronic autoimmune disease. cSLE is more aggressive and has poorer outcomes than adult-onset disease. The global burden of cSLE is poorly understood, with most publications on cSLE originating from high-resourced settings. The reports from less resourced settings indicate high morbidity and mortality in these populations.

RECENT FINDINGS

In this article, we review the disparities in global access to rheumatology care and research for patients with cSLE. We highlight recent cSLE advances from all regions of the globe. We describe current obstacles to cSLE clinical care and research in all settings. Finally, we propose a path forward for high quality, equitable and accessible care to individuals with cSLE everywhere. Individuals with cSLE are at risk for morbidity and death, yet patients worldwide face challenges to adequate access to care and research. Sustained, collaborative efforts are needed to create pathways to improve care and outcomes for these patients.

The implementation and utility of clinical exome sequencing in a South African infant cohort

Genetic disorders are significant contributors to infant hospitalization and mortality globally. The early diagnosis of these conditions in infants remains a considerable challenge. Clinical exome sequencing (CES) has shown to be a successful tool for the early diagnosis of genetic conditions, however, its utility in African infant populations has not been investigated. The impact of the under-representation of African genomic data, the cost of testing, and genomic workforce shortages, need to be investigated and evidence-based implementation strategies accounting for locally available genetics expertise and diagnostic infrastructure need to be developed. We evaluated the diagnostic utility of singleton CES in a cohort of 32 ill, South African infants from two State hospitals in Johannesburg, South Africa. We analysed the data using a series of filtering approaches, including a curated virtual gene panel consisting of genes implicated in neonatal-and early childhood-onset conditions and genes with known founder and common variants in African populations. We reported a diagnostic yield of 22% and identified seven pathogenic variants in the NPHS1, COL2A1, OCRL, SHOC2, TPRV4, MTM1 and STAC3 genes. This study demonstrates the utility value of CES in the South African State healthcare setting, providing a diagnosis to patients who would otherwise not receive one and allowing for directed management. We anticipate an increase in the diagnostic yield of our workflow with further refinement of the study inclusion criteria. This study highlights important considerations for the implementation of genomic medicine in under-resourced settings and in under-represented African populations where variant interpretation remains a challenge.

A scoping review of genetics and genomics research ethics policies and guidelines for Africa

BACKGROUND

Genetics and genomics research (GGR) is increasingly being conducted around the world; yet, researchers and research oversight entities in many countries have struggled with ethical challenges. A range of ethics and regulatory issues need to be addressed through comprehensive policy frameworks that integrate with local environments. While important efforts have been made to enhance understanding and awareness of ethical dimensions of GGR in Africa, including through the H3Africa initiative, there remains a need for in-depth policy review, at a country-level, to inform and stimulate local policy development and revision on the continent.

METHODS

To identify and characterize existing ethics-related guidelines and laws applicable to GGR across much of Africa, we conducted a scoping review of English language policy documents identified through databases, repositories, and web searches. Thirty-six documents were included and coded using a framework that contained a range of themes across five analytical categories: (1) respect, (2) beneficence, (3) justice, (4) independent oversight, and (5) bans and prohibitions. Data analysis software (NVivo 12) was used to organize, code, and tabulate information according to document characteristics and topics. Illustrative examples of policy requirements were selected for inclusion.

RESULTS

Documents that met inclusion criteria spanned 20 years; published between 1996 and 2018, with the majority (58%) published after 2009. About two-thirds were denoted as "guidelines," and slightly more than half were non-exclusive to GGR. Very few (six) country-level documents identified were specific to GGR. Requirements related to the principle of "respect" appeared most often across all documents, relative to other principles and processes. The most commonly stated ban was on reproductive cloning. Other prohibitions applied to germline editing, undue inducements in research, sample use for commercial purposes, employee mandatory DNA testing, fetal sex selection, stem cell use, eugenics, and research without public health benefits.

CONCLUSIONS

Enforceable policies that are indispensable to the ethical conduct and review of GGR are either deficient or missing in many African countries. Existing international, GGR-specific ethics guidelines can be used to inform GGR policy development at a country-level, in conjunction with insight from country specific ethics committees and other local stakeholders.

Dissecting in silico Mutation Prediction of Variants in African Genomes: Challenges and Perspectives

Genomic medicine is set to drastically improve clinical care globally due to high throughput technologies which enable speedy in silico detection and analysis of clinically relevant mutations. However, the variability in the in silico prediction methods and categorization of functionally relevant genetic variants can pose specific challenges in some populations. In silico mutation prediction tools could lead to high rates of false positive/negative results, particularly in African genomes that harbor the highest genetic diversity and that are disproportionately underrepresented in public databases and reference panels. These issues are particularly relevant with the recent increase in initiatives, such as the Human Heredity and Health (H3Africa), that are generating huge amounts of genomic sequence data in the absence of policies to guide genomic researchers to return results of variants in so-called actionable genes to research participants. This report (i) provides an inventory of publicly available Whole Exome/Genome data from Africa which could help improve reference panels and explore the frequency of pathogenic variants in actionable genes and related challenges, (ii) reviews available in silico prediction mutation tools and the criteria for categorization of pathogenicity of novel variants, and (iii) proposes recommendations for analyzing pathogenic variants in African genomes for their use in research and clinical practice. In conclusion, this work proposes criteria to define mutation pathogenicity and actionability in human genetic research and clinical practice in Africa and recommends setting up an African expert panel to oversee the proposed criteria.

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.

The African Lupus Genetics Network (ALUGEN) registry: standardized, prospective follow-up studies in African patients with systemic lupus erythematosus

Background

The prevalence and severity of systemic lupus erythematosus (SLE) differs between ethnic groups and geographical regions. Although initially reported as rare, there is growing evidence that SLE is prevalent and runs a severe course in Africa. There is a paucity of prospective studies on African SLE patients.

Objective

The African Lupus Genetics Network (ALUGEN) is a multicentred framework seeking to prospectively assess outcomes in SLE patients in Africa. Outcomes measured will be death, hospital admission, disease activity flares, and SLE-related damage. We will explore predictors for these outcomes including clinical, serological, socio-demographic, therapeutic and genetic factors. Further, we will investigate comorbidities and health-related quality of life amongst these patients.

Methods

Data of patients recently (≤5 yrs) diagnosed with SLE will be collected at baseline and annual follow-up visits, and captured electronically. The ALUGEN project will facilitate standardized data capture for SLE cases in Africa, allowing participating centres to develop their own SLE registries, and enabling collaboration to enrich our understanding of inter-ethnic and regional variations in disease expression.

Conclusion

Comprehensive, high-quality multi-ethnic data on African SLE patients will expand knowledge of the disease and inform clinical practice, in addition to augmenting research capacity and networking links and providing a platform for future biomarker and interventional studies.