African-led genomics takes centre stage in global precision oncology push

In September 2025, more than 160 researchers, clinicians, bioinformaticians, policymakers and patient advocates from 21 countries gathered in Windhoek, Namibia, for the inaugural

The report behind this article is explicitly a conference synthesis and narrative review rather than a primary research study, and its authors are careful to say so. It does not present new clinical trial results, new sequencing data, or new statistical analyses. Instead, it distils four days of expert-led presentations, panel discussions and delegate engagement sessions into thematic priorities, and then situates those themes against a targeted review of literature published mainly from 2015 onwards, supplemented by grey literature such as WHO and World Bank reports. The authors also acknowledge that the thematic development did not involve systematic coding, inter-coder reliability assessment or formal saturation analysis, and that the perspectives captured may not represent every stakeholder group or health-system context across Africa.

The epidemiological backdrop the delegates discussed is stark. In 2022, Africa recorded roughly 1.2 million new cancer cases and about 800,000 deaths, with projections pointing to approximately 2.1 million cases and 1.4 million deaths by 2040. The most common malignancies across sub-Saharan Africa are breast, cervical, prostate, liver and colorectal cancers, and late-stage diagnosis at stages III or IV is prevalent in 70% to 80% of cases. Five-year survival rates frequently fall below 50%, compared with over 80% in high-income countries. The report attributes this trajectory to population aging, lifestyle changes, environmental exposures, genetic susceptibility, epigenetic modifications, microbiome disruption and a high prevalence of oncogenic infections such as human papillomavirus and Epstein–Barr virus, all unfolding against health systems that often prioritise infectious diseases and depend heavily on primary care facilities with some of the lowest doctor-to-patient ratios globally.

A recurring theme was the mismatch between Africa’s genetic richness and its visibility in global genomic datasets. The continent harbours the greatest human genetic diversity, containing most allelic variation despite representing roughly 19% of the global population, yet much of this variation remains unrecognised in commercially available cancer panels. The report recalls that when the first two African genomes were sequenced, belonging to Archbishop Desmond Tutu of South Africa and a Namibian man named !Gubi, researchers identified 1.3 million previously unknown genetic variants from just those two individuals, at the time the largest single addition to global databases. Despite such milestones, individuals of African ancestry still account for less than 3% of participants in genome-wide association studies and only 2% of all human genome sequences available worldwide.

Delegates argued that this underrepresentation has direct clinical consequences. Genomic reference panels, variant databases, analytical algorithms and diagnostic benchmarks have been derived predominantly from European ancestry datasets, which can lead to variant misclassification, reduced predictive sensitivity for African genomic variants and limited access to precision therapies. The report offers prostate cancer as a concrete illustration: germline testing panels derived from European populations reduce predictive accuracy by more than half for southern African patients, while nearly doubling the frequency of variants of unknown significance. Whole-genome studies of prostate tumours from southern African men have revealed a greater tumour mutational burden, higher structural variant complexity, and population-specific driver genes and therapeutic targets. Meanwhile, African men carry the highest prostate cancer mortality rates, with southern Africa ranking highest globally, yet patients continue to be risk-stratified using prostate-specific antigen thresholds largely calibrated to European cohorts, increasing the risk of misclassification and delayed diagnosis.

Against this backdrop, the report positions next-generation sequencing as the technological backbone of contemporary cancer genomics. NGS enables cost-effective and highly accurate profiling that simultaneously detects single-nucleotide variants, insertions and deletions, structural and copy-number variations, gene fusions, mutational burden and microsatellite instability. Real-world applications cited include FoundationOne CDx for targeted panel sequencing, Guardant360 and Grail Galleri for liquid biopsies, and MSK-IMPACT, which uses a 468-gene panel to match patients with clinical trials. Large-scale data resources such as The Cancer Genome Atlas and the International Cancer Genome Consortium’s ARGO programme were also referenced as drivers of discovery. Delegates emphasised that NGS has redefined cancer classification by revealing molecular distinctions within tumours previously grouped together histologically, generating new subtypes in glioma, breast, prostate and lung cancers. At the same time, the report cautions that NGS findings must be interpreted alongside rigorous histopathological evaluation, particularly in African settings characterised by high tumour heterogeneity and late-stage presentation, and it notes that African prostate cancer genomics studies have demonstrated a 1.6 to 2.5-fold higher burden of structural variation compared with other populations.

The report also explores integrative multi-omics, which combines genomics with proteomics, metabolomics and other biological layers to capture the molecular interplay driving cancer heterogeneity. Proteomic profiling of accessible biofluids such as plasma or serum can identify biomarkers for early detection, prognostic stratification and real-time monitoring of therapeutic response. A cited example is a SWATH-MS proteomic analysis of gallbladder cancer patients of African ancestry from southern Africa, which identified dysregulated proteins and plasma-detectable biomarkers linked to extracellular matrix and metabolic pathways. In metabolomics, prostate cancer metabolic profiling has been used to identify hyper-aggressive subgroups defined by specific lipoprotein signatures, and similar stratification has been observed in pancreatic cancer. The report describes initiatives such as the South African Clinical Multiome Atlas Platform, in partnership with The African Cancer Atlas, which according to programme descriptions from the Council for Scientific and Industrial Research seek to generate pan-African integrated multiome datasets and support technologies including 3D patient-derived organoids, single-cell sequencing and AI-guided target discovery. The authors note, however, that the long-term translational impact of these initiatives remains to be evaluated.

Artificial intelligence featured prominently in discussions of diagnostics and screening. The report distinguishes AI in pathology, meaning computer-based systems that analyse medical images, from digital pathology, which converts physical histology slides into high-resolution digital files for remote viewing and analysis. These technologies are framed as especially relevant across many sub-Saharan African countries, where there are roughly three pathologists per million inhabitants compared with about 65 per million in developed countries. Examples cited include deep-learning algorithms capable of detecting lung nodules on chest radiographs that radiologists initially overlooked, and early pilot data from an AI-assisted iris imaging application in Lubumbashi, which the report explicitly describes as preliminary and requiring independent validation in larger prospective studies before clinical adoption can be recommended. Barriers to implementation are also catalogued: paper-based records, gaps in national registries, unstable electricity, limited digital connectivity, shortages of local expertise in AI and bioinformatics, a linguistic landscape of more than 2,000 languages, and trust challenges shaped by low scientific literacy and misinformation.

Ethical data governance emerged as another central pillar. The report describes how the continent has historically been subject to “parachute research” and “ethics dumping”, in which external entities exploit local resources without equitable benefits. Emerging strategies discussed include federated data models that allow analyses to be performed locally without transferring raw data across borders, trusted research environments integrating high-performance computing and cybersecurity, tiered access and data segregation, and treatment of data centres as critical national assets. Delegates also highlighted homomorphic encryption, a technique that allows computation directly on encrypted data without decryption, as a promising framework for privacy-preserving genomic analysis. Questions of national data sovereignty received particular attention, with the report noting that custodians manage datasets but do not possess unilateral authority over data release, which must remain under the jurisdiction of the originating nation.

Cost considerations were addressed with specific figures. Sequencing costs have fallen from over 100 million dollars for the first human genome in 2001 to approximately 500 dollars per genome today. A micro-costing analysis presented for paediatric Burkitt lymphoma liquid biopsy showed pathology costs of 173 dollars per test compared with 600 dollars for NGS technology, with cost-effectiveness falling within the WHO bracket of three times GDP per capita. Yet the report stresses that even cost-effective genomic tests may remain inaccessible to patients because of reimbursement restrictions and upfront payment requirements. Existing initiatives discussed include the H3Africa Consortium, the World Bank-funded Genomic Centres of Excellence, the proposed Three Million African Genomes project, the US Department of Defence-funded Prostate Cancer Precision Health Africa1K project, and the NIH–Cancer Research UK-funded SAMBAI Grand Challenge project, though the report notes that much of the current dataset in the latter programmes focuses on African American and West African populations.

The authors close with a candid appraisal of limitations. Several recommendations remain conceptual and were not evaluated through formal implementation, economic or outcomes-based analyses. The supporting literature review was narrative rather than systematic, and conference priorities were inherently influenced by the programme structure and the expertise of invited speakers. They caution that AI models developed primarily using non-African datasets may underperform locally without validation, that multi-omics approaches remain analytically complex and dependent on population-specific reference datasets still being developed, and that an exclusive focus on advanced technologies could divert resources from foundational interventions such as cancer awareness programmes, earlier diagnosis, pathology services and access to standard treatments. The report is best read, therefore, as a structured agenda for discussion and investment rather than a demonstration of clinical outcomes.

Subject of Research: A conference synthesis report on advancing cancer genomics and precision oncology in Africa

Article Title: Africa’s emerging role in precision oncology: translational insights from the harnessing functional genomics in cancer research conference, Windhoek, 23-26 September 2025

Article References: Rix, C. L., Buberwa, E. B., Amofa, J., Maurihungirire, U., Hosea, R., Ratjama, L., Kandanda, G. K., Nangolo, L. N., Stanley, C., Schäfer, G., Cacciatore, S., Banda, R., Schuh, A., Hayes, V. M., Sarkar, D., Hansen, R., Wedge, D., Onywera, H., Niyonzima, N., … Mwapagha, L. M. (2026). Africa’s emerging role in precision oncology: translational insights from the harnessing functional genomics in cancer research conference, Windhoek, 23-26 September 2025. BMC Proceedings, 20(S28), Article 30. https://doi.org/10.1186/s12919-026-00387-z

Image Credits: AI Generated

DOI: 10.1186/s12919-026-00387-z

Keywords: precision oncology, cancer genomics, Africa, functional genomics, next-generation sequencing, artificial intelligence, data governance, cancer registries, genomic diversity, Windhoek conference, health equity, multi-omics