Detection of postoperative minimal residual disease in colorectal cancer using a novel ultrasensitive whole-genome sequencing-based ctDNA test

Introduction: Accurate detection of minimal residual disease (MRD) after curative intent surgery remains a major limitation in colorectal cancer (CRC) management. Current ctDNA assays identify only 30-50% of patients who later develop clinical recurrence, restricting their utility for both escalation and safe de-escalation of adjuvant therapy. We evaluated a novel, ultrasensitive, tumor-informed, whole-genome sequencing (WGS)-based ctDNA test engineered to maximize detection sensitivity while simplifying clinical implementation by eliminating the need for bespoke patient-specific capture panels, reducing turnaround time, and requiring only 1mL of plasma. Methods: Pre- and postoperative plasma samples (drawn 14 and 30 days after operation) from 300 stage II-III CRC patients (median follow-up 35.7 months) were collected. At the time of abstract submission, 161 patients have been analyzed, but complete cohort results (n = 300) will be presented at AACR 2026. The test ( AccuScan ) utilizes rolling-circle amplification to convert single-stranded cfDNA into concatemers, enabling >1000-fold error suppression at modest sequencing depth (median 28×). Tumor-informed variant tracking was derived from paired tumor/germline WGS. ctDNA detection was done blinded to clinical information. Performance was evaluated against recurrence outcomes. Results: Among the 161 analyzed patients, 43 (26.7%) recurred. A median of 11,822 tumor-derived variants per patient were tracked with a mean error rate of 4.97 × 10⁻⁷. Preoperatively, the novel WGS test detected ctDNA in 98.1% of samples. Postoperatively, ctDNA was detected in at least one sample (day 14 or 30) in 69.8% of recurrence patients with a specificity of 91.5%. Sensitivity and specificity were 55.8% and 96.6% at day 14 and 62.8% and 94.1% at day 30. ctDNA levels in recurrence patients reached as low as 2.7 ppm (median 162 ppm). Extrapolating the performance to an unselected stage III population indicates a ~10% 3-year recurrence rate for postoperative ctDNA-negative individuals, comparable to low-risk stage II disease, for which adjuvant therapy is generally not recommended. Postoperative ctDNA status was a strong predictor of recurrence-free survival (HR 11.9; 95% CI, 6.2-23.1; p<0.001). In a head-to-head comparison, tumor-informed digital PCR using 8mL plasma aliquots achieved substantially lower sensitivity both preoperative (75.4%) and postoperative (33.3% day 14; 51.5% day 30). Conclusion: The novel WGS-based test delivers exceptional sensitivity in both preoperative and postoperative settings while requiring minimal plasma. The streamlined workflow is compatible with real-world clinical implementation. Sensitive detection at day 14 offers an opportunity for earlier therapeutic intervention, and the assay's performance supports its use in future therapy de-escalation trials.