Serial Postoperative Circulating Tumor DNA Assessment Has Strong Prognostic Value During Long-Term Follow-Up in Patients With Breast Cancer

Abstract

Purpose: Here, we report the sensitivity of a personalized, tumor-informed circulating tumor DNA (ctDNA) assay (Signatera) for detection of molecular relapse during long-term follow-up of patients with breast cancer.

Methods: A total of 156 patients with primary breast cancer were monitored clinically for up to 12 years after surgery and adjuvant chemotherapy. Semiannual blood samples were prospectively collected, and analyzed retrospectively to detect residual disease by ultradeep sequencing using ctDNA assays, developed from primary tumor whole-exome sequencing data.

Results: Personalized Signatera assays detected ctDNA ahead of clinical or radiologic relapse in 30 of the 34 patients who relapsed (patient-level sensitivity of 88.2%). Relapse was predicted with a lead interval of up to 38 months (median, 10.5 months; range, 0-38 months), and ctDNA positivity was associated with shorter relapse-free survival (P < .0001) and overall survival (P < .0001). All relapsing triple-negative patients (n = 7/23) had a ctDNA-positive test within a median of 8 months (range, 0-19 months), while the 16 nonrelapsed patients with triple-negative breast cancer remained ctDNA-negative during a median follow-up of 58 months (range, 8-99 months). The four patients who had negative tests before relapse all had hormone receptor-positive (HR+) disease and conversely, five of the 122 nonrelapsed patients (all HR+) had an occasional positive test.

Conclusion: Serial postoperative ctDNA assessment has strong prognostic value, provides a potential window for earlier therapeutic intervention, and may enable more effective monitoring than current clinical tests such as cancer antigen 15-3. Our study provides evidence that those with serially negative ctDNA tests have superior clinical outcomes, providing reassurance to patients with breast cancer. For select cases with HR+ disease, decisions about treatment management might require serial monitoring despite the ctDNA-positive result.

FIG 1.

EBLIS study flow diagram and patient timeline summaries showing detection of ctDNA ahead of clinical relapse. (A) Patient recruitment and collection of clinical samples. For the 156 women with breast cancer monitored in this study, exonic alterations were determined through paired-end sequencing of FFPE tumor-tissue specimens and matched normal DNA. Patient-specific Signatera assays were designed to include 16 somatic mutations identified from whole-exome sequencing data. Serial plasma samples were analyzed with the corresponding custom assay panels using the Signatera workflow in a blinded manner in a CLIA-certified laboratory. A total of 1,141 plasma samples were analyzed for ctDNA detection. (B) Each patient's time since surgery showing longitudinal ctDNA assay samples, treatment and relapse status and results summary of each patient's (n = 156) treatment regimen by subgroup along with results of serial plasma samples (n = 1,136) analyzed. CLIA, Clinical Laboratory Improvement Amendments; ctDNA, circulating tumor DNA; EBLIS, Exploratory Breast Lead Interval Study; FFPE, formalin-fixed paraffin-embedded; QC, quality control; TNBC, triple-negative breast cancer; WES, whole-exome sequencing.

FIG 2.

Personalized ctDNA detection in serial plasma samples predicts relapse-free survival and overall survival. (A) Relapse-free survival according to the detection of ctDNA in any follow-up plasma sample after surgery (HR, 52.98 [95% CI, 18.32 to 153.20]; P < .0001). (B) Overall survival according to the detection of ctDNA in any follow-up plasma sample after surgery (HR, 53.69 [95% CI, 7.01 to 411.49]; P < .0001). (C) Relapse-free survival according to the detection of ctDNA in the first postsurgical plasma sample (HR, 30.15 [95% CI, 13.76 to 66.05]; P < .0001). (D) Overall survival according to the detection of ctDNA in the first postsurgical plasma sample (HR, 19.32 [95% CI, 6.66 to 56.01]; P < .0001). n = 156 patients. ctDNA, circulating tumor DNA; HR, hazard ratio; OS, overall survival; RFS, relapse-free survival.