Development and clinical application of PredicineBEACON next-generation minimal residual disease assay for genitourinary cancers.

Abstract

539 Background: Tumor-informed minimal residual disease (MRD) assay has been studied in muscle invasive bladder cancer (MIBC) in IMvigor010 study. However, the current methods require the use of tumor tissue and lacking actionable insights. In this study, a tumor-agnostic and actionable MRD assay (PredicineBEACON) is developed with high sensitivity and capability to detect actionable mutations in blood- or urine-based circulating tumor DNA. Methods: PredicineBEACON tumor-agnostic MRD assay includes three components, i.e., baseline mutation identification, personalized panel design, and ultra-deep next generation sequencing of cancer variants. Step 1: whole exon sequencing with boosted depth in 600 cancer-related genes is performed using baseline tumor tissue or liquid biopsy (blood or urine) to identify somatic mutations. Step 2: Up to fifty somatic mutations are selected for personalized MRD panel design, in combination with the use of a fixed core panel of 500 actionable/hotspot variants. Step 3: MRD and actionable mutations were called from ultra-deep sequencing (100,000X). A companion low-pass whole-genome sequencing (LP-WGS) is performed to monitoring copy number variation (CNV). In the current study of patients with MIBC, urine samples at baseline were used for personalized variant generation. Urine samples under neoadjuvant immunotherapy and blood samples after radical cystectomy were collected and tested with the PredicineBEACON MRD assay. Results: PredicineBEACON MRD assay demonstrated a sensitivity of 0.005% tumor fraction. In patients of MIBC, urine-based MRD assay detected the dynamic changing of disease evolution under neoadjuvant therapy and preceded the radiographic response. Actionable mutations, including FGFR3, TERT and PIK3CA mutations, were detected. Copy number burden revealed by LP-WGS correlated with disease evolution. Plasma-based MRD assay on the patients after radical cystectomy is currently ongoing. Conclusions: PredicineBEACON tumor-agnostic MRD assay provides an ultra-sensitive and actionable MRD detection with high sensitivity and specificity. Assessment of MRD could potentially be leveraged, for example, to avoid overtreatment of early stage of genitourinary cancers such as non-metastatic prostate cancer, non-muscle invasive bladder cancer and muscle invasive bladder cancer.