Liquid biopsy-based detection of MTAP gene loss in non-muscle invasive bladder cancer.

844 Background: MTAP, located at chromosome 9p21.3 adjacent to CDKN2A/B, is frequently co-deleted with the CDKN2A in cancer. Homozygous 9p21 deletions (encompassing CDKN2A/MTAP) occur in ~15% of all cancers, and MTAP loss is observed in ~30% of bladder cancers. MTAP deletion creates a therapeutic vulnerability through dependence on the PRMT5/MAT2A pathway, a target of emerging synthetic-lethal therapies. A non-invasive liquid biopsy assay to detect MTAP loss may enable biomarker-driven patient selection in clinical drug development. Methods: Urine samples from patients with non-muscle invasive bladder cancer (NMIBC) were analyzed using the PredicineCARE 200-gene NGS assay, which covers MTAP and CDKN2A coding regions and includes a genome-wide SNP backbone, enabling detection of MTAP gene deletion events independent of CDKN2A. Results: MTAP gene loss was identified in 137/409 (33%) and CDKN2A loss in 141/409 (34%) selected patient urine samples. Results of a subset urine samples with matched tissues were confirmed by tissue NGS results. The assay distinguished MTAP-specific deletions from CDKN2A deletions despite their < 30 kb proximity. Notably, four patients showed MTAP deletions with intact CDKN2A, and seven patients had CDKN2A deletions with preserved MTAP. Both heterozygous (HETD) and homozygous (HOMD) deletions were resolved, including 15 cases with CDKN2A homozygous deletion and MTAP heterozygous loss. Conclusions: This study demonstrates the feasibility of urine liquid biopsy-based detection of MTAP gene loss in bladder cancer, differentiating MTAP deletions from adjacent CDKN2A losses and resolving both HETD and HOMD events. These findings highlight the potential of liquid biopsy-based cancer diagnostics for patient selection and therapy monitoring in clinical drug development and personalized patient care.