DNA quality challenges in breast cancer samples from three low-middle income African countries: a straightforward protocol for research in cancer genomics

Sub-Saharan African women often develop breast cancer at a younger age, with a high prevalence of aggressive subtypes such as triple-negative breast cancer and elevated mortality. Genetic factors may underlie these patterns, but African populations remain underrepresented in genomic research. As an initial step toward addressing this gap, we evaluated DNA extracted from formalin-fixed paraffin-embedded (FFPE) breast cancer blocks collected in anatomic pathology laboratories in Gabon, Togo, and Benin. Although DNA could be successfully extracted, its functional quality was significantly impaired. Quantitative PCR revealed progressive degradation, with poor amplification efficiency for larger fragments, and next-generation sequencing (NGS) libraries exhibited degraded electropherogram profiles, low coverage, and elevated duplication rates. These limitations likely stem from socio-economic constraints, including delayed processing and prolonged formalin fixation, which promote nucleic acid fragmentation and crosslinking. To overcome these barriers, we established a preservation protocol adapted to the resource and infrastructural limitations of the region: storage of biopsies in physiological saline at -20 °C. This method requires only basic equipment widely available in local hospitals, yet yielded DNA of high integrity, enabled efficient library construction, and produced significantly superior NGS performance compared with FFPE-derived DNA. This cost-effective and scalable approach provides a feasible solution for genomic research in resource-limited settings. Future efforts should focus on complementary strategies for RNA preservation and tumor enrichment to enable comprehensive molecular profiling and advance precision oncology in West Africa.