Mutational analysis of exon 14 and 15 of the APC gene in esophageal squamous cell carcinoma in Mthatha-South Africa: A cross-sectional study

Esophageal cancer is a major public health challenge in the Eastern Cape region of South Africa. Although changes in the APC gene are frequently implicated in various forms of cancer, few studies have examined its mutations in esophageal cancer, particularly in this highly endemic region. This study aimed to analyze mutations in exons 14 and 15 of the APC gene in esophageal cancer patients at the Nelson Mandela Hospital in Mthatha. To achieve this, biopsy samples of cancerous and normal tissues were collected from ESCC patients, then DNA was extracted and amplified by PCR targeting exons 14 and 15 of the APC gene before being sequenced using the Sanger method. Sequencing data were processed from both ab1 and FASTA formats, aligned to the hg19 reference genome, and variants were identified via comparison with the transcripts NM_001354905.2 (exon 14) and NM_001354906.2 (exon 15) using custom alignment and variant-calling scripts. All variants were annotated using HGVS nomenclature and cross-referenced against publicly available databases including ClinVar, dbSNP, and Ensembl VEP. The results showed a total of 37 mutation events, with 83.8% detected in tumour tissues and 16.2% in histologically normal tissues. Tumour samples from exon 15 exhibited the highest mutation frequency (88.5%). In contrast, there were fewer mutations in normal tissues and were mostly novel. In sum, this study highlights the key role of mutations in the APC gene, particularly its exon 15, in the etiology of esophageal cancer. These findings emphasize the predominance of APC disruption in tumor tissues but also support the need to further explore mutational processes in adjacent normal tissue, particularly for early detection strategies,