Evaluation of Urinary Circulating Tumor DNA to Detect Minimal Residual Disease in Patients with High-Risk Non-Muscle Invasive Bladder Cancer

Purpose Restaging transurethral resection of bladder tumor (reTURBT) is the standard-of-care for some patients with high-risk non-muscle invasive bladder cancer (NMIBC). However, it may lead to complications and biomarkers to avoid unnecessary reTURBT are needed. Materials and Methods Patients with high-risk NMIBC undergoing reTURBT were prospectively enrolled. Whole-exome sequencing along with low-pass whole-genome sequencing were performed on index TURBT samples to generate mutational profiles and copy number variation. Up to 50 personalized mutations and a fixed panel of 500 hotspot mutations were used for detecting variants from urine samples collected prior to reTURBT. Using a prespecified algorithm, tumor fraction (TF) and copy number burden (CNB) score were used to measure minimal residual disease and correlated with reTURBT pathology. Results Overall, 72/76 urine samples collected from patients with high-risk NMIBC prior to reTURBT passed quality check. From the indext TURBT specimens, a median of 39 personalized variants from the index TURBT were used for disease tracking. Overall, median TF was 0.206 vs. 0.001 in patients with and without residual tumor, respectively (p<0.001). Similarly, CNB score was elevated (7.34 vs. 4.02, p<0.001). utDNA achieved sensitivity of 97.8% and specificity of 69.2%, with area under the curve (AUC) of 0.932 in predicting disease found on reTURBT. Analyses of the index and reTURBT tissue and urine mutational profiles provided evidence for underdiagnosis of subclinical disease at the time of reTURBT. Conclusion Paired personalized and panel utDNA can be used to accurately detect residual disease in patients with high-risk NMIBC with potentially wide-ranging clinical applications.