Germline mutation landscape of Oesophageal Squamous Cell Cancer in South African patients

Abstract

Oesophageal squamous cell cancer is highly prevalent in the Black South African populaDon, yet its germline mutaDon landscape remains poorly understood. This study aimed to idenDfy pathogenic germline variants in known cancer predisposiDon genes in a cohort of 16 Black South African paDents diagnosed between the ages of 26 and 38. Whole exome sequencing data were generated using the Agilent SureSelect Human All Exome Capture assay (version 8) and sequenced on the Illumina NextSeq 2000 plaaorm. Sequencing data were analysed using a curated set of 109 genes implicated in oesophageal squamous cell cancer, derived from literature, clinical panels, and the Fanconi Anaemia pathway. Variants were filtered and prioriDsed using a stepwise approach: exonic and splicing variants were retained, while downstream, upstream, intergenic, intronic, and synonymous single nucleoDde variants were excluded. PopulaDon frequency filtering was applied using gnomAD exomes, removing variants with a minor allele frequency >1%. Variants classified as benign or likely benign based on American College of Medical GeneDcs and AssociaDon for Molecular Pathology guidelines were excluded, while pathogenicity was further assessed using in silico predicDon tools. Seventeen candidate variants were idenDfied in 14 genes, including 15 missense variants classified as variants of uncertain significance and two frameshif deleDons classified as likely pathogenic. Notably, rs5742973, a “hot VUS,” was idenDfied in PMS1, and two frameshif deleDons were found in MSH3 (rs766700228 and rs759756736). The findings highlight the potenDal involvement of the mismatch repair and Fanconi Anaemia pathways in oesophageal squamous cell cancer . This study highlights the importance of germline studies in underrepresented populaDons, providing a basis for future research on the geneDc aeDology of oesophageal squamous cell cancer and its potenDal applicaDons in risk predicDon, early diagnosis, and targeted therapies.