Evaluating circulating tumor DNA methylation patterns of a multi-gene panel for colorectal cancer diagnosis: A pilot...

Colorectal cancer (CRC) is a leading cause of cancer-related mortality globally and a major public health burden in the Gaza Strip. As CRC is often asymptomatic in its early stages, early detection is critical. This study evaluates the diagnostic performance of circulating tumor DNA (ctDNA) methylation biomarkers (SEPT9, SPG20, ALX4, MGMT, and RASSF1A) for non-invasive CRC detection. A pilot case-control study was conducted with 50 participants, comprising 25 confirmed CRC patients and 25 colonoscopy-verified CRC-free controls. Plasma cell-free DNA was extracted, bisulfite-converted, and analyzed via methylation-specific PCR. Diagnostic performance was assessed using receiver operating characteristic curve analysis, and multi-gene panels were evaluated using an OR-based logic model. Individual and combined methylation markers demonstrated robust diagnostic potential. The combination of SEPT9 and SPG20 achieved excellent discrimination between CRC patients and controls (AUC = 1.00). Other combinations, such as SPG20 + MGMT and SPG20 + ALX4, also exhibited high accuracy (AUC = 0.994 and 0.990, respectively). The inclusion of additional genes provided marginal diagnostic improvement, suggesting redundancy in larger panels. The two-gene panel of SEPT9 and SPG20 represents a highly sensitive and specific non-invasive biomarker combination for CRC detection. However, these preliminary findings should be interpreted with caution given the small sample size and require validation in larger, independent screening cohorts before clinical implementation.