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Scaling for African inclusion in high-throughput whole cancer genome bioinformatic workflows
Jiang, J. Samaha, G. Willet, C. E. Chew, T. Hayes, V. M. Jaratlerdsiri, W.
Jiang, J.
Samaha, G.
Willet, C. E.
Chew, T.
Hayes, V. M.
Jaratlerdsiri, W.
Abstract
Sub-Saharan Africa is experiencing the highest mortality rates for several cancer types. While cancer research globally has entered the genomic era and advanced the deployment of precision oncology, Africa has largely been excluded and has received few benefits from tumour profiling. Through a thorough literature review, we identified only five whole cancer genome databases that include patients from Sub-Saharan Africa, covering four cancer types (breast, esophageal, prostate, and Burkitt lymphoma). Irrespective of cancer type, these studies report higher tumour genome instability, including African-specific cancer drivers and mutational signatures, suggesting unique contributory mechanisms at play. Reviewing bioinformatic tools applied to African databases, we carefully select a workflow suitable for large-scale African resources, which incorporates cohort-level data and a scalable design for time and computational efficiency. Using African genomic data, we demonstrate the scalability achieved by high-level parallelism through physical data or genomic interval chunking strategies. Furthermore, we provide a rationale for improving current workflows for African data, including the adoption of more genomic techniques and the prioritisation of African-derived datasets for diverse applications. Together, these enhancements and genomic scaling strategies serve as practical computational guidance, lowering technical barriers for future large-scale African-inclusive research and ultimately helping to reduce the disparity gap in cancer mortality rates across Sub-Saharan Africa.
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Date
2025
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Jiang J, Samaha G, Willet CE, Chew T, Hayes VM, Jaratlerdsiri W. Scaling for African Inclusion in High-Throughput Whole Cancer Genome Bioinformatic Workflows. Cancers (Basel). 2025 Jul 26;17(15). PubMed PMID: 40805180. Pubmed Central PMCID: PMC12346427. Epub 2025/08/14. eng.