Longitudinal monitoring of circulating tumor DNA to detect relapse early and predict outcome in early breast cancer

Abstract

Purpose: Detection of molecular residual disease (MRD) allows for the identification of breast cancer patients at high-risk of recurrence, with the potential that early initiation of treatment at early stages of relapse could improve patient outcomes. The Invitae Personalized Cancer Monitoring™ assay (PCM) is a newly developed next-generation sequencing approach that utilizes up to 50 patient-specific, tumor-informed DNA variants, to detect circulating tumor DNA (ctDNA). The ability of the PCM assay to detect MRD before clinical relapse was evaluated.

Methods: The cohort included 61 female patients with high-risk breast cancer who underwent neoadjuvant chemotherapy. Plasma samples were collected before and during neoadjuvant therapy, after surgery and during monitoring. PCM was used to detect ctDNA at each time point.

Results: The sensitivity to detect ctDNA in plasma from patients who relapsed during the monitoring phase was 76.9% (10/13). Specificity and positive predictive values were both 100% with all (10/61, 16%) of the patients who had ctDNA detected during the monitoring phase subsequently relapsing. Detection of ctDNA during monitoring was associated with a high-risk of future relapse (HR 37.2, 95% CI 10.5-131.9, p < 0.0001), with a median lead-time from ctDNA detection to clinical relapse of 11.7 months.

Conclusion: PCM detected ctDNA in patients who relapsed with a long lead-time over clinical relapse, shows strong association with relapse-free survival and may be used to identify patients at high-risk for relapse, allowing for earlier intervention.

Keywords: Breast cancer; CtDNA; Liquid biopsy; Minimal residual disease; Relapse.

Fig. 1

Baseline characteristics a Proportion of baseline samples per subtypes (center) and ctDNA detection status (present, absent and indeterminate) for HR + (blue), HER2 + (pink), TNBC (green) and unknown (orange) subtypes; b Heatmap showing the clinical characteristics of the 56 patients with baseline ctDNA characterization. MRD call (Positive =  + , Negative = -, Indeterminate = Ind.) at baseline is represented along with log₁₀ Max detected allele frequency (AF) in the plasma. Patients are grouped per subtype and sorted by Max AF

Fig. 1

Baseline characteristics a Proportion of baseline samples per subtypes (center) and ctDNA detection status (present, absent and indeterminate) for HR + (blue), HER2 + (pink), TNBC (green) and unknown (orange) subtypes; b Heatmap showing the clinical characteristics of the 56 patients with baseline ctDNA characterization. MRD call (Positive =  + , Negative = -, Indeterminate = Ind.) at baseline is represented along with log₁₀ Max detected allele frequency (AF) in the plasma. Patients are grouped per subtype and sorted by Max AF

Fig. 2

Swimmer plot representing longitudinal ctDNA tracking for all patients in the study For each patient, baseline and monitoring ctDNA results are represented as well as patients characteristics (Age at diagnostic, menopausal status, pre-chemotherapy tumor grade, pCR, panel size and subtype at diagnostic). Of note, for patient 20,000,004,710 ctDNA was detected shortly before relapse, with the symbol for relapse (red X) partially obscuring the symbol for ctDNA detection (green diamond)

Fig. 3

Sankey plot of disease progression and its relationship to ctDNA detection over time in the patient cohort Baseline samples are grouped together, then additional samples are grouped into 6 month bins, labeled by the last time point post-surgery in that bin. All patients that convert from ctDNA negative (blue) to ctDNA positive (yellow) eventually relapse (maroon), indicating a 100% positive predictive value. Patient 20,000,006,307 was not included due to a missing surgery date

Fig. 4

Proportional hazards model of time to relapse for all patients participating in the study ctDNA status during monitoring was treated as a time-dependent covariate. The hazard for relapse of ctDNA + was significantly higher than for ctDNA- patients (HR = 37.161, likelihood ratio p-value = 2.84e–09.). Patient 20,000,006,307 was not included due to a missing surgery date