Circulating Tumor DNA Based Minimal Residual Disease Detection for Patients With Early-Stage Breast Cancer

PRIMARY OBJECTIVES: I. To determine the pathologic response rate and presence of ctDNA post-neoadjuvant therapy in stage I-III breast cancer patients receiving neoadjuvant systemic therapy followed by curative-intent surgical resection, separately for Subgroup 1A: human epidermal growth factor receptor 2 positive (HER2+) (any estrogen receptor \[ER\]/progesterone receptor \[PR\] status) and Subgroup 1B: triple negative breast cancer (TNBC). (Cohort 1) II. To determine ctDNA detectability before and after curative-intent surgical resection in Cohort 2 ER+/any progesterone receptor (PR)/HER2- stage I-III breast cancer patients. (Cohort 2) SECONDARY OBJECTIVES: I. To determine ctDNA detectability before and after adjuvant chemotherapy and/or radiation therapy, by cohort and subgroup. II. To determine ctDNA detectability during the follow-up period of up to 3 years after definitive treatment, by cohort and subgroup. III. To describe, by cohort and subgroup, the association between detectable ctDNA measured post-neoadjuvant treatment and post-surgery with recurrence free survival (RFS). IV. To describe, by cohort and subgroup, ctDNA levels at baseline and during neoadjuvant treatment and their association with clinical and pathologic response. V. To describe, by cohort and subgroup, changes in ctDNA levels during systemic treatment (neoadjuvant and adjuvant) and association with clinical response determined radiographically. VI. To describe, by cohort and subgroup, the difference in time between ctDNA detection (molecular recurrence) and radiographic evidence of disease recurrence following definitive treatment among patients who achieved undetectable ctDNA levels after surgery. EXPLORATORY OBJECTIVE: I. To explore the performance of up to two cancer detection assays - BestSEEK and enACT - in development by Dr. Tomasetti at TGen and City of Hope. OUTLINE: Patients are assigned to 1 of 2 cohorts. COHORT 1: Patients undergo collection of blood samples for ctDNA testing at 14-21 days post cycle 1, day 1 of standard of care (SOC) neoadjuvant chemotherapy, on the day of SOC surgery, at 3-6 weeks after SOC surgery, at 1-2 weeks after SOC adjuvant radiation therapy (if receiving), at 2-4 weeks after SOC adjuvant systemic therapy (if receiving), every 3 months for 1 year after surgery, and then every 6 months up to year 3 after surgery. Patients may also undergo collection of tumor tissue during SOC surgery on study. COHORT 2: Patients undergo collection of blood samples for ctDNA testing on the day of SOC surgery, at 3-6 weeks after SOC surgery, at 1-2 weeks after SOC adjuvant radiation therapy (if receiving), at 2-4 weeks after SOC adjuvant systemic therapy (if receiving), every 3 months for 1 year after surgery, and then every 6 months up to year 3 after surgery. Patients may also undergo collection of tumor tissue during SOC surgery on study.