Abstract 535: Development of a liquid biopsy assay to longitudinally monitor changes in mutations’ allelic frequency in response to treatment with KB-0742

Abstract

Abstract Liquid biopsies analyzing cell-free DNA (cfDNA) released by tumors are emerging as a powerful noninvasive sampling approach. As opposed to single-site solid tumor biopsy, liquid biopsies allow for better representation of the tumor mutational landscape. In the clinic, liquid biopsies are utilized for early detection of disease, to help inform treatment decisions, to monitor for disease recurrence, and to identify potential resistance mechanisms. Here we describe our approach to developing a liquid biopsy assay that will allow us to monitor, in real time, longitudinal changes in mutations’ allelic frequency in patients with solid tumors. Our approach combines two powerful technologies: next-generation sequencing, that enables the identification of a broad array of mutations, and droplet digital PCR (ddPCR) that provides speed and a cost-effective advantage to monitor mutations in cfDNA obtained from patient plasma samples. In order to maximize the effectiveness of using liquid biopsy assays in our clinical trial, we prioritized developing an approach that enabled us to meet the following criteria: 1) generating a baseline and end-of-treatment mutational profile for each patient using either a tumor tissue sample or liquid biopsy to identify both driver and potential resistance mutation markers, 2) longitudinal sampling and real-time analysis over the course of treatment, 3) high assay sensitivity to detect low frequency alleles, 4) overall cost-effectiveness, and 5) ability to examine allelic frequency of multiple mutations of interest from limited input of cfDNA isolated from plasma. Assay development included custom quantification of cfDNA and optimization of a pre-amplification step, which amplified the material allowing us to analyze multiple mutations of interest while ensuring that the quantitative nature of the assay was not impacted. For each individual mutation, gBlocks™ and/or cell-line−derived cfDNA were utilized to optimize annealing temperature and time, cycle number, and input amount to attain an assay with a target 0.1% limit of detection. These customized mutation assays can potentially serve as an accelerated cost-effective surrogate approach, compared to imaging, to monitor in real time the response to KB-0742 (CDK9i) in the ongoing phase 1/2 clinical trial NCT04718675. Citation Format: Suha Naffar-Abu Amara, Christina Noe, Tressa Hood, Sara Paganini, Crystal MacKenzie, Melinda A. Day, Pavan Kumar. Development of a liquid biopsy assay to longitudinally monitor changes in mutations’ allelic frequency in response to treatment with KB-0742 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 535.