Pan-cancer survival modeling reveals structural limits of genomic feature integration in immunotherapy outcomes
BackgroundImmune checkpoint inhibitors (ICIs) have improved outcomes across multiple cancer types, yet reliable predictors of survival remain limited. While genomic features such as tumor mutational burden (TMB) are widely used, their contribution to predictive modeling in heterogeneous real-world cohorts remains unclear. We evaluated the relative contributions of clinical and whole-genome sequencing (WGS) features in pan-cancer survival modeling. MethodsWe analyzed 658 patients treated with ICIs with matched WGS data from the Genomics England. Using a leakage-controlled machine learning framework with strict train-test separation, we compared four models: TMB-only, clinical-only, clinical+TMB, and an integrated 11-feature clinico-genomic XGBoost survival model. Model performance was assessed using Harrells concordance index (C-index) with bootstrap confidence intervals. ResultsTMB alone demonstrated near-random discrimination (C-index 0.50; 95% CI 0.44-0.56). Clinical variables substantially improved predictive performance (0.59; 95% CI 0.53-0.64), with marginal gain from adding TMB (0.59). The integrated model achieved a C-index of 0.60 (95% CI 0.55-0.65). While improvement over TMB alone was significant, incremental gain beyond optimized clinical models was modest. Feature attribution analysis showed that model performance was dominated by clinical variables, with genomic features contributing limited additional signal. ConclusionsThese findings suggest that, in heterogeneous pan-cancer cohorts, predictive performance is constrained by the underlying data structure, in which dominant clinical signals overshadow genome-scale features. This study highlights fundamental limitations in integrating genomic data into survival models across diverse cancer types and provides a benchmark for future computational approaches.