Ultrasensitive ctDNA detection for relapse and response prediction in melanoma patients treated with immunotherapy.

Abstract

9572 Background: Immune checkpoint inhibitors (ICIs) have markedly improved outcomes in melanoma and are now standard of care in advanced and adjuvant settings. However, substantial toxicities remain, and up to 50% of patients derive no clinical benefit. Conventional clinicopathological factors lack sufficient precision for risk stratification, resulting in under- and overtreatment. Circulating tumor DNA (ctDNA) has emerged as a highly specific biomarker for molecular residual disease (MRD) detection, enabling real-time, minimally invasive monitoring to guide personalized ICI strategies. Methods: We analyzed 847 plasma timepoints from 98 melanoma patients treated with ICI in either the unresectable advanced (metastatic) setting (25 patients) or adjuvant setting following complete resection of the primary and/or loco-regional metastases (73 patients). Plasma samples were analyzed using NeXT Personal, a whole-genome-sequencing-based tumor-informed assay designed to track up to 1,800 patient-specific variants. This ultrasensitive liquid biopsy approach achieves detection limits of down to ~1 part per million (PPM) at high specificity (>99.9%), enabling identification of MRD and early molecular relapse that may inform timely therapeutic intervention. Results: Baseline ctDNA was detected in 100% of 25 patients with unresectable melanoma. Within this group, an early molecular response defined by a ≥30% decrease in ctDNA by cycle 3 predicted an 80% reduction in the risk of progression or death (PFS HR 0.2, P=0.01; OS HR 0.2, P=0.03). In the adjuvant cohort, landmark ctDNA positivity at 3 months post-surgery prior to immunotherapy, was 35% and identified patients with significantly inferior outcomes, with a >3-fold increase for the risk of distant metastasis or death (DMFS HR 3.8, P=4.9510−3; OS HR 4.1, P=3.61×10−3). Longitudinal monitoring further established that any ≥20% increase in ctDNA during adjuvant treatment was highly prognostic of poor survival (DMFS HR 3.0, P=0.01; OS HR 3.5, P=0.02). These molecular increases identified recurrences a median of 212 days prior to radiographic detection. The clinical necessity of ultrasensitive assays was underscored by the fact that 71% of these early detections occurred at ultra-low levels below 100 PPM. Real-time variant tracking revealed mutations druggable mutations such as BRAF V600E. Conclusions: Detection of MRD with PPM sensitivity represents a major advance in treatment monitoring for both unresectable and completely resected melanoma. Early on-treatment ctDNA decreases identify responders in advanced disease, while postoperative ctDNA positivity identifies adjuvant patients at highest relapse risk. Early MRD-based detection of loco-regional or distant relapse enables timely adaptation of therapeutic strategies.