Pan-Cancer Targeted Sequencing Reveals Genomic Heterogeneity and Prognostic Subgroups in Urothelial Bladder Cancer

<b>Background</b>: Urothelial bladder cancer (UBC) is a molecularly heterogeneous disease, and most sequencing studies have relied on bladder-specific or solid tumor-restricted panels. Whether broader pan-cancer assays provide additional clinically relevant information remains unclear. <b>Methods</b>: We performed targeted next-generation sequencing using an extended gene panel on tumor samples from 100 patients with UBC treated at a tertiary center. Somatic single-nucleotide variants, small insertions/deletions, copy-number alterations, and gene co-occurrence patterns were analyzed and correlated with clinicopathological features, disease-free survival (DFS), and overall survival (OS). <b>Results</b>: Recurrent alterations were identified in <i>FGFR3</i> (≈50%), <i>TP53</i> (≈35%), <i>STAG2</i> (≈25%), and <i>PIK3CA</i> (≈20%), consistent with established molecular pathways in UBC. Less frequent but potentially actionable alterations, including mutations in <i>BRCA1</i> and <i>ALK</i>, were also detected, reflecting the extended coverage of the panel. <i>TP53</i> mutations were independently associated with worse OS, whereas <i>STAG2</i> alterations were associated with improved OS, particularly in tumors without concurrent T<i>P53</i> mutations. <i>FGFR3</i> mutations showed a favorable but non-independent trend. No gene retained independent prognostic significance for DFS. Co-occurrence analysis revealed an <i>FGFR3/PIK3CA</i>-associated pathway and relative mutual exclusivity between <i>FGFR3</i> and <i>TP53</i>. Copy-number alterations were modest overall. Comparison with TCGA data demonstrated a higher frequency of <i>FGFR3</i> alterations in our cohort, likely reflecting the larger proportion of non-muscle-invasive tumors. <b>Conclusions</b>: Pan-cancer targeted sequencing provided a comprehensive genomic landscape of UBC, capturing canonical drivers and additional alterations that may be overlooked by bladder-restricted assays. The identification of <i>TP53</i> and <i>STAG2</i> as prognostic markers highlights the potential value of broader genomic profiling for biologically informed risk stratification in urothelial bladder cancer.