MammaTrace - a cell-free DNA methylation plasma only assay for minimal residual disease detection in breast cancer patients

Abstract

Introduction: Metastatic breast cancer (MBC) remains an incurable disease with a 5-year overall survival rate below 25%. Metastases often emerge from subclinical, disseminated tumor cells that persist despite systemic therapy of primary disease - referred to as minimal residual disease (MRD). Detecting MRD is critical for identifying patients at high risk of recurrence and enabling timely intervention.

Methods: In this study, we developed MammaTrace, a plasma-only cell-free DNA (cfDNA) methylation-based MRD assay, informed by differentially methylated regions (DMRs) identified in MBC using whole genome bisulfite sequencing. MammaTrace was evaluated in an independent longitudinal cohort of early-stage breast cancer patients treated with curative intent.

Results: MammaTrace achieved a sensitivity of 91% and specificity of 83%, with a median follow-up of 12.4 months. A positive MammaTrace score, indicative of MRD, preceded clinical or radiologic recurrence by a median of 457 days, providing a substantial lead time for therapeutic intervention to prevent progression to metastatic disease.

Conclusions: MammaTrace enables detection of minimal residual disease in breast cancer patients, offering a substantial lead time before clinical recurrence. This approach may improve risk stratification and guide early therapeutic strategies to delay or prevent metastatic progression.