LIQUID BIOPSY APPROACHES FOR CANCER DETECTION

Cell-free DNA (cfDNA), acquired through non-invasive liquid biopsies, provides a new opportunity for cancer detection and monitoring of therapeutic response. To evaluate the utility of cfDNA for cancer detection and intervention we used a machine learning model to identify tumor-derived cfDNA through genome-wide analyses of cfDNA fragmentation in a prospective study of 365 individuals at risk for lung cancer. We validated this cancer detection model using an independent cohort of 385 non-cancer individuals and 46 lung cancer patients. Combining fragmentation features, clinical risk factors, and CEA levels, followed by CT imaging, detected 94% of patients with cancer across stages and subtypes, including 91% of stage I/II and 96% of stage III/IV, at 80% specificity. We found that a higher fragmentation score represented an independent prognostic indicator of survival. To further explore the potential of circulating tumor DNA (ctDNA) as a biomarker of response to guide therapy selection and monitor treatment response we evaluated plasma from participants in the prospective phase III CAIRO5 clinical trial. We assessed whether ctDNA based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC) derived DNA. The combined cfDNA and WBC analysis prevented false-positives due to germline or hematopoietic variants in 40% of patients. Patient-matched tumor tissue sequencing did not provide additional information. Longitudinal analyses of ctDNA were more predictive of overall survival than standard-of-care radiological response evaluation. We further developed a novel approach to evaluate genome-wide fragmentation patterns to molecularly detect disease progression in the phase 1 study of entinostat and nivolumab ± ipilimumab in advanced solid tumors (ETCTN-9844, NCT02453620). Patients with metastatic or unresectable solid tumors received an entinostat run-in 2 weeks prior to the addition of anti-PD-1 and anti-CTLA-4 immune checkpoint inhibitors (ICIs). Genome-wide cfDNA fragmentation features were included in a Bayesian model to approximate a tumor fraction as compared to best response by RECIST v1.1. Molecular responders and non-responders at week 10 experienced a median PFS that was not reached and 4.5 months (HR = 5.4; 95% CI 1.7-17; p = 0.004) while patients with RECIST response and non-response at week 10 had similar PFS (median 6.4 vs. 6.7 months; HR = 1.7; 95% CI 0.54-5.3; p = 0.36). Here, we demonstrate a cfDNA fragmentation based approach for molecular detection of disease progression that could guide future trials with ICIs. Collectively, these diverse analyses highlight the utility of ctDNA for the detection of cancer as well as monitoring responses to therapy using mutation and non-mutation-based approaches