Evaluation of patient-specific cell free DNA assays for monitoring of minimal residual disease in solid tumors

Real time monitoring of disease status is an essential part of cancer management. The low sensitivity and specificity of serum markers and the constraints and risks associated with radiological scans prompt the need for accurate non-invasive means to monitor minimal residual disease (MRD) in solid tumors. In this study we describe MRD evaluation via profiling of patient-specific gene variants in cell free tumor DNA (i.e., ctMRD). We evaluate the feasibility of this approach for real time monitoring of tumor load dynamics in response to anticancer treatments. We prioritized 162 hot spot mutations for designing ctMRD assays based on literature review. These ctMRD assays were evaluated in 436 plasma specimens with a median of 6 (range 3-18) longitudinal evaluations in a cohort of 48 patients with various solid tumors. In patients with partial radiological response (PR), Mutant Allele Fraction (MAF) showed high correlation (84%) with radiological response and tumor volume (cm3) compared to conventional CA markers (53%). Total plasma ctDNA level was significantly higher in patients with 2-5 metastatic sites compared with single metastatic site (P = 0.04) and discriminated patients with stable disease (SD) and progressive disease (PD) from patients with partial response (PR) (P =0.01 and P = 0.04, respectively). Collectively, the present study shows that changes in mutation burden evaluated using patient specific ctMRD assays is a highly sensitive approach for monitoring of therapy response.