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.
撒哈拉以南非洲地区在多种癌症类型上正经历着最高的死亡率。尽管全球癌症研究已进入基因组时代并推动了精准肿瘤学的应用，但非洲在很大程度上被排除在外，从肿瘤基因谱分析中获益甚少。通过全面的文献回顾，我们发现仅存在五个包含撒哈拉以南非洲患者的全癌症基因组数据库，涵盖四种癌症类型（乳腺癌、食管癌、前列腺癌和伯基特淋巴瘤）。无论癌症类型如何，这些研究均报告了更高的肿瘤基因组不稳定性，包括非洲特有的癌症驱动因素和突变特征，表明存在独特的致病机制。在回顾应用于非洲数据库的生物信息学工具后，我们精心选择了一套适用于大规模非洲资源的工作流程，该流程整合了队列层面的数据，并采用可扩展设计以提高时间和计算效率。利用非洲基因组数据，我们展示了通过物理数据或基因组区间分块策略实现的高水平并行化所带来的可扩展性。此外，我们提出了改进当前非洲数据处理流程的理论依据，包括采用更多基因组技术，并优先将非洲来源的数据集用于多样化应用。这些改进措施与基因组扩展策略共同提供了实用的计算指导，降低了未来开展大规模非洲包容性研究的技术门槛，最终有助于缩小撒哈拉以南非洲地区癌症死亡率的差距。
Scaling for African Inclusion in High-Throughput Whole Cancer Genome Bioinformatic Workflows
肿瘤(癌症)患者之家