Monitoring Plasma Tumor DNA in Early-Stage Breast Cancer

This is a prospectively designed study. Up to 229 newly diagnosed invasive HER2-positive or
triple-negative breast cancer patients planning neoadjuvant therapy (NAT) will be enrolled.
Blood samples will be collected pre-operatively at the time of diagnosis/prior to NAT,
post-cycle 1/pre-cycle 2 of NAT, after all NAT/immediately before surgery, and
post-operatively at 6, 12, 24, and 36 months, and annually thereafter if funding allows.
Researchers will also collect representative tissue samples from the diagnostic biopsy (in
all participants) and definitive surgery (if available). Additionally, to look at feasibility
of tumor DNA analyses in urine samples, urine samples will be collected along with blood
samples (urine tumor DNA or utDNA).

Next generation sequencing will be performed on core biopsies of all enrolled patients for
tumor-specific mutations (TSM) discovery. Based on those findings, droplet digital PCR
(ddPCR) on plasma DNA samples will also be performed to confirm the presence of the TSM in
the plasma on diagnosis, and one TSM will be chosen to track as the plasma tumor DNA (ptDNA)
mutation of interest. Investigators will perform ddPCR on pre-operative plasma DNA samples
and will assess for the presence of ptDNA. Pathologists will assess surgical specimens for
pathologic response (such as complete response/pCR and residual cancer burden/RCB). As
primary endpoint, investigators will assess the number of patients with and without
preoperative ptDNA who have pCR versus residual disease. As exploratory endpoints, the
following will also be performed: (a) quantitative multiplex methylation-specific PCR
(QM-MSP) in diagnostic biopsy and definitive residual surgery specimen; and, (b) the
circulating methylated tumor DNA (cMethDNA) assay in plasma specimens (baseline and after
NAT), and evaluate associations with pathologic response.

Additional endpoints include the association between plasma and tissue markers at baseline,
after NAT, and (if available) during surveillance with long-term prognosis (invasive
disease-free survival/IDFS and distant disease-free survival/DDFS).

Inclusion Criteria:

- Newly diagnosed, histologically confirmed invasive breast cancer that is triple
negative (estrogen receptor [ER], progesterone receptor [PR], and HER2-neu negative)
or HER2-positive (any ER/PR status)

- Unresected, untreated breast cancer that is T2, T3, or T4a-c; any N (nodal status);
and M0 (not metastatic)

- ECOG Performance Status of 0 or 1

- Planning to receive a neoadjuvant chemotherapy regimen containing a taxane ± an
anthracycline for at least 4 cycles. Patients with HER2-positive disease must also be
planning to receive HER2-targeted therapy.

- Diagnostic tumor material must be available for correlative analyses

- Patients must have the ability to understand and the willingness to sign a written
informed consent document

Exclusion Criteria:

- No prior treatment for the current breast cancer, though prior use of selective
estrogen receptor modulators (SERMs) or aromatase inhibitors (AIs) for the prevention
of breast cancer is acceptable.

- Women who are pregnant or nursing are excluded.

- No history of another primary malignancy in the last 5 years prior to registration.
Patients with prior history of in situ cancer or basal or localized squamous cell skin
cancer are eligible.