Targeted Next-Generation Sequencing Identifies Clinically Important Somatic Variants in Urothelial Bladder Cancer Patients

Abstract Background This study aimed to analyze the mutational status of 25 genes associated with urothelial bladder carcinoma (UBC) in Slovak patients. Methods Tumor tissue samples from 36 patients were analyzed alongside matched whole blood samples as germline controls. Targeted next-generation sequencing (NGS) was employed to identify pathogenic and likely pathogenic single-nucleotide variants and short insertions/deletions. Results We detected well-established mutations commonly associated with UBC. FGFR3 mutations were found in 47.2% of tumor samples, making it the most frequently altered gene in our cohort, followed by TSC1 (16.7%), PIK3CA (16.7%), and TP53 (13.9%). A statistically significant correlation (p < 0.05) was observed between FGFR3 and TP53 mutations and tumor invasiveness and grade; FGFR3 mutations also correlated significantly with TNM stage. Additionally, we identified seven variants in KDM6A, ARID1A, TSC1 , and CDKN1A, not previously reported in association with UBC in major cancer mutation databases. Conclusion Our results confirm global trends in the mutational landscape of UBC and provide novel insights into rare genetic variants in the Slovak population. To our knowledge, this is the first molecular profiling study of UBC in Slovakia, contributing to the understanding of regional genetic variation. These findings underscore the potential of NGS-based testing in supporting personalized clinical management of bladder cancer.