Evaluating the performance of a plasma dual-target test developed based on sense-antisense and dual-MGB probe technique for colorectal cancer detection

Abstract Background Detecting colorectal cancer (CRC) via blood-based methylation tests shows good patient compliance and convenience, but some use to fail due to the low abundance of plasma cfDNA fragments. To address this issue, we designed this study to identify potential markers and enhance their performance to detect CRCs using sense-antisense and dual-MGB probe (SADMP) technique. Methods The study was conducted in three steps: identifying eligible methylation markers in our discovery set, developing assay using the sense-antisense and dual-MGB probe (SADMP) technique, and evaluating the test performance for CRC detection in training and validation cohorts. Results Findings of the discovery step indicated that adenoma and cancer samples exhibited similar methylation profiles and both had lower methylation levels than normal samples. Hypermethylated NTMT1 and MAP3K14-AS1 were recognized as the most promising candidate markers. The SADMP technique showed an ability to improve methylation signals by 2-fold than single-strand and single-MGB probe techniques. The MethyDT test, incorporating the SADMP technique, obtained an average sensitivity of 84.47% for CRC detection, higher than any single target alone, and without significant attenuation in specificity (average specificities of 91.81% for NTMT1 and 96.93% for MAP3K14-AS1 vs. 89.76% for MethyDT). For early (I-II) and late- (III-IV) stage CRC, the sensitivities were 82.61% and 88.64%, respectively. Meanwhile, the test performance was independent of patient age and gender. Conclusion The MethyDT test incorporating the SADMP technique exhibits a higher sensitivity to perceive methylation signals and may serve as a promising noninvasive tool for CRC detection.