Minimal Residual Disease Detection using a Plasma-only Circulating Tumor DNA Assay in Patients with Colorectal Cancer

Abstract

Purpose: Detection of persistent circulating tumor DNA (ctDNA) after curative-intent surgery can identify patients with minimal residual disease (MRD) who will ultimately recur. Most ctDNA MRD assays require tumor sequencing to identify tumor-derived mutations to facilitate ctDNA detection, requiring tumor and blood. We evaluated a plasma-only ctDNA assay integrating genomic and epigenomic cancer signatures to enable tumor-uninformed MRD detection.

Experimental design: A total of 252 prospective serial plasma specimens from 103 patients with colorectal cancer undergoing curative-intent surgery were analyzed and correlated with recurrence.

Results: Of 103 patients, 84 [stage I (9.5%), II (23.8%), III (47.6%), IV (19%)] had evaluable plasma drawn after completion of definitive therapy, defined as surgery only (n = 39) or completion of adjuvant therapy (n = 45). In "landmark" plasma drawn 1-month (median, 31.5 days) after definitive therapy and >1 year follow-up, 15 patients had detectable ctDNA, and all 15 recurred [positive predictive value (PPV), 100%; HR, 11.28 (P < 0.0001)]. Of 49 patients without detectable ctDNA at the landmark timepoint, 12 (24.5%) recurred. Landmark recurrence sensitivity and specificity were 55.6% and 100%. Incorporating serial longitudinal and surveillance (drawn within 4 months of recurrence) samples, sensitivity improved to 69% and 91%. Integrating epigenomic signatures increased sensitivity by 25%-36% versus genomic alterations alone. Notably, standard serum carcinoembryonic antigen levels did not predict recurrence [HR, 1.84 (P = 0.18); PPV = 53.9%].

Conclusions: Plasma-only MRD detection demonstrated favorable sensitivity and specificity for recurrence, comparable with tumor-informed approaches. Integrating analysis of epigenomic and genomic alterations enhanced sensitivity. These findings support the potential clinical utility of plasma-only ctDNA MRD detection.See related commentary by Bent and Kopetz, p. 5449.

Figure 1.

(A) Guardant Reveal plasma-only ctDNA assay schema and (B) patient enrollment and analysis groups

Figure 2.

ctDNA assay results and timing of treatment for each patient. Patients are ordered by total days of clinical follow up from surgery for (A) patients that received curative intent surgery alone and (B) for patients that received curative intent surgery followed by adjuvant therapy. Patients receiving neoadjuvant therapy are designated by a yellow square. Specimens obtained on the day of surgery were obtained pre-operatively.

Figure 3.

(A) Recurrence-free survival by landmark one-month post-therapy ctDNA detection for patients with >1 year follow up. Bar graph displays recurrence rates by ctDNA detection status with Venn diagram of ctDNA detection by calling methods (epigenomic only, genomic only, or both). (B) Sensitivity analysis for landmark, longitudinal, and surveillance cohorts and Venn diagram of ctDNA detection for longitudinal and surveillance analyses by calling method. (C) Recurrence sensitivity and Venn diagram of ctDNA detection by individual calling methods.

Figure 4.

Recurrence-free survival by landmark one-month post-therapy CEA analysis for patients with >1 year follow up. Bar graph displays recurrence rates by CEA status.