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Ultrasensitive Detection and Monitoring of Circulating Tumor DNA Using Structural Variants in Early-Stage Breast

Mitchell J Elliott1, Karen Howarth2, Sasha Main3

  • 1Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada.

Clinical Cancer Research : an Official Journal of the American Association for Cancer Research
|January 9, 2025
PubMed
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Structural variants (SVs) in circulating tumor DNA (ctDNA) offer ultrasensitive detection for early-stage breast cancer recurrence. This method provides early warning and aids in monitoring treatment effectiveness.

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Area of Science:

  • Genomics
  • Oncology
  • Molecular Diagnostics

Background:

  • Circulating tumor DNA (ctDNA) detection post-therapy is prognostic for early-stage breast cancer recurrence.
  • Current ctDNA assays using single-nucleotide variants have variable sensitivity and specificity.
  • Structural variants (SVs) represent an underexplored area for ctDNA detection in breast cancer.

Purpose of the Study:

  • To evaluate a tumor-informed SV-based ctDNA assay for sensitivity and prognostic value in early-stage breast cancer.
  • To assess ctDNA dynamics and lead times to recurrence using SVs.
  • To explore the potential of SVs for improved ctDNA detection compared to single-nucleotide variants.

Main Methods:

  • Retrospective analysis of a cohort of 100 early-stage breast cancer patients.
  • Utilized a tumor-informed SV-based ctDNA assay with 568 timepoints.
  • Assessed ctDNA dynamics during neoadjuvant systemic therapy and in the postoperative period.

Main Results:

  • 96% of participants had detectable ctDNA at baseline.
  • ctDNA detection at cycle 2 of therapy correlated with higher distant recurrence risk.
  • SVs detected ctDNA prior to distant recurrence in 100% of cases, with a median lead time of 417 days.

Conclusions:

  • Ultrasensitive ctDNA detection and monitoring using SVs is clinically validated.
  • SV-based ctDNA assays show promise for early detection and monitoring of breast cancer recurrence.
  • Prospective trials are needed to investigate ctDNA-guided treatment strategies.