Abstract PR015: Novel digital PCR ctDNA monitoring assay evaluating exceptional responders to combination immune-oncology (IO) therapy
Authors: Stetson Daniel 
Published: November 2024

Non-invasive monitoring of ctDNA following curative intent IO therapy has been used to build an understanding of the dynamics of clinical response. Defining clinical response for patients identified with stable disease has always been difficult with imaging. To improve the resolution of ctDNA dynamics, we examined the plasma from a set of exceptional responders to combination IO therapy. These patients did not progress by imaging, however, the measurement of ctDNA showed that there was a persistent level of disease burden throughout the time on study. By evaluating these patients, we gained a comprehensive understanding of the response dynamics including the depth of Molecular Response (MR), the level of molecular persistence and the timing of molecular progression. Current NGS based methods for evaluating ctDNA have been shown to have considerable variability particularly at lower Tumor Fractions (TF). MR dynamics of ctDNA utilize a decrease of 50% TF, which may be related to the accuracy and resolution of assay rather than being a biologically relevant limit. We describe a comprehensive monitoring ctDNA platform using a novel digital PCR assay strategy that achieves a dynamic range not achievable by any current assay. METHODS: Plasma samples from the exceptional responders were evaluated using a novel tumor informed ctDNA platform. Personalized panels, targeting 3-5 variants, were selected from patient tumor data. In total, 225 unique timepoints were extracted (avg 25 timepoints per patient). A novel PCR primer algorithm was designed which showed improved amplification for the individual reactions and optimized multiplexing of the assays. Utilizing machine learning methods, the aggregated data analysis calculates quantitative TF and an accurate percent change between each timepoint. RESULTS: By examining the entire treatment cycle of these patients, we found that the patient timeline separated into molecular response, molecular persistence, and molecular progression. The maximum decrease in TF (molecular response) was found by C4D1 with the largest decrease occurring at either C1D1 or C2D1. Molecular persistence was found in one patient to continue for 55 cycles of treatment (1381 days on trial). Molecular progression occurred in 2 of the 3 exceptional responders. One patient had progression at cycle 12, while the second occurred at cycle 43. Progression occurred very rapidly with the TF doubling from baseline value in 28 days. While patient 1 did see a decrease in the TF for 3 cycles, progression was observed, prompting the end of treatment. To our knowledge this is the first study to evaluate the complete treatment cycle of exceptional responders to IO therapy. The ddPCR assay provided a unique and expansive window into the ctDNA dynamics of treatment suggesting that longitudinal monitoring provides valuable insights. Future studies utilizing this assay will allow for better understanding of the complex tumor dynamics during treatment.

Citation Format: Daniel Stetson. Novel digital PCR ctDNA monitoring assay evaluating exceptional responders to combination immune-oncology (IO) therapy [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr PR015.