African Global Representation in Biomedical Sciences

Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit

Microbiome research has made significant gains with the evolution of sequencing technologies. Ensuring comparability between studies and enhancing the findability, accessibility, interoperability and reproducibility of microbiome data are crucial for maximizing the value of this growing body of research. Addressing the challenges of standardized metadata reporting, collection and curation, the Microbiome Working Group of the Human Hereditary and Health in Africa (H3Africa) consortium aimed to develop a comprehensive solution. In this paper, we present the Microbiome Research Data Toolkit, a versatile tool designed to standardize microbiome research metadata, facilitate MIxS-MIMS and PhenX reporting, standardize prospective collection of participant biological and lifestyle data, and retrospectively harmonize such data. This toolkit enables past, present and future microbiome research endeavors to collaborate effectively, fostering novel collaborations and accelerating knowledge discovery in the field. Database URL: https://doi.org/10.25375/uct.24218999.v2.

Clinical Practice Patterns in IgA Nephropathy: A Global Questionnaire-Based Survey

Introduction

IgA nephropathy (IgAN) displays ethnic differences in disease phenotype. We aimed to examine how this common disease is managed worldwide.

Methods

An online 2-step questionnaire-based survey was conducted among nephrologists globally focusing on various management strategies used in IgAN.

Results

A total of 422 nephrologists responded to the initial survey and 339 to the follow-up survey. Of the nephrologists, 13.7% do not get MEST-C scores in biopsy reports; 97.2% of nephrologists use renin-angiotensin-aldosterone system (RAAS) blockade with angiotensin-converting-enzyme inhibitors (ACEi) / angiotensin receptor blockers (ARB) as initial treatment. Other supportive treatments commonly employed are fish oil (43.6%) and sodium-glucose co-transporter-2 (SGLT2) inhibitors (48.6%) with regional differences. Immunosuppression is generally (92.4%) initiated when proteinuria >1 g/d persists for ≥3 months.Main considerations for initiating immunosuppression are level of proteinuria (87.9%), estimated glomerular filtration rate (eGFR) decline (78.7%), lack of response to RAAS blockade (57.6%) and MEST-C score (64.9%). Corticosteroids (89.1%) are universally used as first-line immunosuppression; mycophenolate mofetil is commonly used in resistant patients (49.3%). Only 30.4% nephrologist enroll patients with persistent proteinuria >1 g/d in clinical trials. Nephrologists in Europe (63.6%), North America (56.5%), and Australia (63.6%) are more likely to do so compared to South America (31.3%) and Asia (17.2%). Only 8.1% nephrologists in lower-middle income countries (LMICs) enroll patients in clinical trials, though 40% of them are aware of such trials in their nations.

Conclusion

Although most nephrologists agree on common parameters to assess clinical severity of IgAN, use of RAAS blockade, and blood pressure control, there is heterogeneity in use of other supportive therapies and initiation of immunosuppression. There is reluctance to enroll patients in clinical trials with novel treatments, principally in LMICs.

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available.