Detection of circulating tumor DNA in colorectal cancer patients using a methylation-specific droplet digital PCR multiplex

Despite the use of conventional biomarkers and imaging methods for treatment monitoring of colorectal cancer (CRC) patients, limitations remain in detecting minimal residual disease and early relapse. Circulating tumor DNA (ctDNA) offers a promising noninvasive and cost-effective alternative for monitoring disease progression and relapse, potentially improving patient outcomes. In this study, we developed a methylation-specific droplet digital PCR (MS-ddPCR) multiplex assay designed to detect ctDNA through a combination of tumor-specific and tissue-conserved methylation markers. Our objective was to evaluate the performance of this assay in patients with CRC and assess ctDNA dynamics as a prognostic tool in those with metastatic CRC (mCRC). The assay demonstrated high specificity (96.7%) and sensitivity in detecting ctDNA in both patients with localized tumors (64.4%) and mCRC (89.2%). Notably, ctDNA dynamics from baseline to after the first treatment cycle were significantly associated with progression-free survival (PFS) and overall survival (OS) in mCRC. Classifying patients based on ctDNA-RECIST (Response Evaluation Criteria in Solid Tumors) and the percent reduction in ctDNA fraction revealed pronounced differences in PFS and OS. Median PFS and OS were 11.4 and 35.3 months for good responders compared with 7.6 (HR = 1.71, 95% CI 0.9-3.25) and 18.4 (HR = 2.15, 95% CI 1.16-3.99) for poor responders, while patients with progressive disease had a median PFS and OS of 5.1 (HR = 4.36, 95% CI 1.91-9.92) and 6.85 (HR = 4.73, 95% CI 2.09-10.7) months. Our multiplex MS-ddPCR assay provides a sensitive, cost-effective approach for detecting and quantifying ctDNA in CRC patients, especially in metastatic disease. The ability to monitor ctDNA dynamics holds potential for early treatment response assessment, prognosis, and guiding personalized therapeutic strategies, making it a valuable tool for clinical practice.