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

## TL;DR

This study used broad genomic sequencing to identify different molecular subgroups and prognostic markers in bladder cancer patients.

## Contribution

The study demonstrates that pan-cancer sequencing reveals new prognostic markers and molecular subgroups in urothelial bladder cancer.

## Key findings

- TP53 mutations are linked to worse survival, while STAG2 mutations are associated with better outcomes.
- FGFR3 mutations are common in non-muscle-invasive tumors but have limited independent prognostic value.
- Pan-cancer sequencing uncovers additional actionable alterations like BRCA1 and ALK mutations.

## Abstract

Bladder cancer shows substantial biological heterogeneity, and patients with similar clinical stages may experience markedly different outcomes. In this study, we analyzed tumor samples from 100 patients with urothelial bladder cancer using a broad targeted sequencing panel designed for pan-cancer testing. We confirmed that TP53 mutations were associated with worse overall survival, whereas STAG2 mutations were linked to a favorable prognosis. FGFR3 mutations were frequent and more common in non–muscle-invasive tumors, although their prognostic impact was weaker after accounting for other clinical factors. Analysis of combined mutation patterns further highlighted distinct molecular subgroups. In addition to common bladder cancer drivers, we detected recurrent alterations in genes, such as ERBB2 and ATM, which may have clinical relevance. In summary, our findings support the value of broader panel-based genomic profiling for identifying prognostic subgroups and better understanding molecular heterogeneity in real-world bladder cancer cohorts.

Background: 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. Methods: 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). Results: Recurrent alterations were identified in FGFR3 (≈50%), TP53 (≈35%), STAG2 (≈25%), and PIK3CA (≈20%), consistent with established molecular pathways in UBC. Less frequent but potentially actionable alterations, including mutations in BRCA1 and ALK, were also detected, reflecting the extended coverage of the panel. TP53 mutations were independently associated with worse OS, whereas STAG2 alterations were associated with improved OS, particularly in tumors without concurrent TP53 mutations. FGFR3 mutations showed a favorable but non-independent trend. No gene retained independent prognostic significance for DFS. Co-occurrence analysis revealed an FGFR3/PIK3CA-associated pathway and relative mutual exclusivity between FGFR3 and TP53. Copy-number alterations were modest overall. Comparison with TCGA data demonstrated a higher frequency of FGFR3 alterations in our cohort, likely reflecting the larger proportion of non–muscle-invasive tumors. Conclusions: 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 TP53 and STAG2 as prognostic markers highlights the potential value of broader genomic profiling for biologically informed risk stratification in urothelial bladder cancer.