Detection of genomic variants in BRCA1 and BRCA2 across gastric cancer patients using next generation sequencing

Objectives: To explore the landscape of BRCA1/2 mutations in gastric cancer patients.

Methods: Next-generation sequencing (NGS), Sanger sequencing, reverse transcription quantitative polymerase chain reaction (RT-qPCR), Immunohistochemistry, The Cancer Genome Atlas (TCGA), gnomAD, and DAVID.

Results: With 95% of bases boasting a phred score surpassing 30 and a minimum coverage depth of 500X, our NGS approach ensures high-quality data acquisition. Analyzing BRCA1 and BRCA2 sequences revealed 11 and 4 mutations, respectively, with one pathogenic mutation identified in each gene. This emphasizes the prominence of BRCA1 mutations in gastric cancer. Sanger sequencing validation confirmed the presence of pathogenic mutations in select cases, consolidating our findings. Frequency analysis utilizing the gnomAD database elucidated the rarity of these mutations in the Asian population, underscoring their uniqueness. Exploring TCGA data further corroborated this rarity, emphasizing the distinctive nature of these mutations in gastric cancer. RT-qPCR analysis unveiled a significant reduction in BRCA1/2 expression in samples harboring pathogenic mutations, hinting at their potential role in down-regulating gene expression. Immunohistochemistry confirmed diminished protein expression in samples with pathogenic mutations, solidifying our observations. Kaplan-Meier survival analysis demonstrated significantly poorer survival outcomes for patients with pathogenic BRCA1/2 mutations compared to those without, emphasizing their potential role in prognosis. Additionally, KEGG pathway analysis highlighted the involvement of BRCA1/2 in critical cancer-associated pathways, emphasizing their role in tumorigenesis.

Conclusion: Our comprehensive findings underscore the clinical significance of BRCA1/2 mutations in gastric cancer, advocating for further research to elucidate their mechanistic implications and therapeutic opportunities.