Whole genome-powered ctDNA detection predicts breast cancer relapse

A molecular residual disease (MRD) assay powered by whole genome sequencing (WGS) successfully detects breast cancer relapse, improving lead times for circulating tumour DNA (ctDNA) detection years ahead of clinical recurrence based on imaging.

“We show that tracking up to ∼1,800 somatic variants for the detection of MRD in plasma ctDNA, both before and after curative-intent treatment, improves the sensitivity of ctDNA detection at diagnosis compared with other MRD methods,” the investigators said. [Ann Oncol 2025;36:673-681]

“Our findings also show that residual disease immediately after neoadjuvant chemotherapy and surgery can be detected with an ultrasensitive approach, with subsequent adjuvant therapy clearing the low-level residual disease,” they added.

A total of 617 plasma samples (median 8) from 78 patients were included in the analysis. Of the patients, 23 had triple-negative breast cancer, 35 were human epidermal growth factor receptor 2 (HER2)-positive, 18 were hormone receptor (HR)-positive, and two were unknown.

A team of investigators collected samples at diagnosis prior to therapy, cycle 2 of neoadjuvant chemotherapy, postsurgery following neoadjuvant therapy if administered, every 3 months during the first year, and every 6 months thereafter.

The NeXT Personal MRD platform, a tumour-informed WHS approach to produce personalized ctDNA sequencing panels tracking a median of 1,451 variants per patient, was used for plasma DNA analysis. MRD detection was then associated with clinical outcomes.

ctDNA detection

The investigators detected ctDNA at levels ranging from 2.19 parts per million (PPM) to 204,900 PPM (median 405 PPM), with 39 percent of all detections occurring in the ultra-low range of <100 PPM. Forty-nine (98 percent) of 50 patients with samples at diagnosis had ctDNA detected prior to treatment.

At a median follow-up of 76 months, ctDNA detection showed a significant association with an increased risk of future relapse (log-rank p<0.0001) and a reduced overall survival (p<0.0001), with a median lead time from ctDNA detection to clinical relapse of 15 months.

All patients who relapsed (11/11, 100 percent) had MRD, with a median ctDNA level of 13.1 PPM at first MRD detection. No relapse occurred in patients with undetected ctDNA (64/64) throughout follow-up.

“Comparison with exome-powered MRD detection assays showed improved sensitivity and lead time,” the investigators said.

“These findings merit additional investigation through additional prospective studies that can further establish the clinical impact and utility of ultrasensitive MRD approaches in breast cancer,” they noted.

False negatives

The reduction of false-negative results compared with previous work is the primary benefit offered by more sensitive, earlier detection of residual and recurrent disease, according to the investigators. [JAMA Oncol 2019;5:1473-1478]

Elevated diagnosis ctDNA levels were associated with prognostic clinical factors that have been shown in previous studies to predict poor outcomes. [Br J Cancer 2022;127:592-602; Cancers (Basel) 2022;14:310]

These studies, however, mentioned gaps in diagnosis ctDNA sensitivity, particularly in HER2-positive and HR+/HER2-negative breast cancer. [JCO Precis Oncol 2024;8:e2300456; J Clin Oncol 2024;42:LBA507]

The current findings “contribute to the growing body of evidence supporting the use of ultrasensitive ctDNA testing for risk stratification, identifying patients who may derive the greatest benefit from adjuvant therapy, and predicting the likelihood of disease recurrence,” the investigators said. [Nat Med 2023;29:127-134; N Engl J Med 2022;386:2261-2272; Nature 2021;595:432-437]