Abstract
DNA methylation is a well-established biomarker for cancer diagnosis, and most studies have focused on cancer-type-specific markers. However, methylation biomarkers applicable to multiple cancer types remain largely unexplored, posing a challenge for multi-cancer detection. Here, we identified pan-cancer differentially methylated regions (DMRs) by analyzing 197 whole-genome bisulfite sequencing datasets spanning 11 malignancies. Compared to cancer-type-specific DMRs, pan-cancer DMRs exhibited conserved methylation alterations across tumor types and significantly greater differential methylation in both tissue and cell-free DNA (cfDNA). A diagnostic model leveraging pan-cancer DMRs accurately detected seven cancer types in a plasma cfDNA dataset (n = 1,108), achieving 77% sensitivity and 96.9% specificity in the test set, with sensitivities of 69.6% and 70.4% for stage I and II patients, respectively. Overall, our findings establish pan-cancer DMRs as promising biomarkers for non-invasive diagnosis of multiple cancer types.