Field Effect-Informed Urine Liquid Biopsy Analysis for Assessment of Adjuvant BCG Response in Non-Muscle Invasive Bladder Cancer

The goal of this study was to develop a urine tumor DNA-based minimal residual disease liquid biopsy assay for bladder cancer that improves specificity by considering field effect mutations. We performed targeted cell free DNA sequencing on tumor, adjacent normal, and urine cell free DNA (cfDNA) from non-muscle invasive bladder cancer patients and urine cfDNA from healthy controls. We developed a method called RePhyNERX and used it to identify three molecular response classes: complete responders to surgery, responders to adjuvant Bacillus Calmette-Guérin immunotherapy, and non-responders. These molecular classifications correlated with patient outcome. We also performed RNA sequencing on tumor tissues to identify expression differences between the response classes.]]>