Breast Cancer Genome Guided Therapy Study (BEAUTY) (BEAUTY)

• DNA from the germline and breast tumor for the identification of novel somatic changes within gene and gene pathways. [ Time Frame: 5 years ]
  To obtain DNA from the germline and breast tumor for the identification of novel somatic changes within gene and gene pathways that are potentially "druggable" in men or women with breast cancer undergoing a standard neoadjuvant paclitaxel (with or without trastuzumab), followed by a standard anthracycline containing regimen (e.g. doxorubicin and cyclophosphamide) for breast cancer.
• Frequency of known tumor mutations for which current drug therapies already exist. [ Time Frame: 5 years ]
  To determine the frequency of known tumor mutations for which current drug therapies already exist (e.g. BRAF, C-KIT, EGFR mutation, KRAS, PTEN, PI3K).
• Breast cancer tissue to develop tumor xenograft cell lines for mechanistic and functional studies. [ Time Frame: 5 years ]
  Using breast cancer tissue obtained prior to chemotherapy in all patients and following the completion of chemotherapy (in patients with residual tumors > 2 cm or residual nodal disease), to develop tumor xenograft cell lines for mechanistic and functional studies to determine whether mutations identified are associated with the malignant phenotype and response to associated drugs which target the gene and/or pathways.
• Somatic alterations identified are associated with pathologic complete response to therapy. [ Time Frame: 5 years ]
  To determine whether somatic alterations identified above are associated with pathologic complete response to therapy.

Inclusion Criteria:

• Age ≥18 years.
• Histological confirmation of invasive breast cancer.

• Confirmation of breast cancer lesion ≥ 1.5 cm in size by any clinical (physical examination measurement) or radiographic criteria (mammogram, ultrasound or MRI) in the ipsilateral breast.

  • Note: Benign breast disease, LCIS or DCIS in the contralateral breast is allowed. Contralateral invasive breast cancer is allowed if disease is of clinically lower stage and the higher stage lesion will be the study lesion for all biopsies and tissue samples.
  • Note: Disease in axilla only is not eligible.
  • Note: Patients that have a contraindication or inability to have an MRI may still be enrolled on study and not participate in the MRI at any of the study specific time points.
  • Note: For patients with bilateral disease the higher clinical stage disease will be the study lesion that will undergo study biopsies and tissue samples from surgery and the contralateral lesion will NOT undergo research biopsies and tissue samples.

• Men or women who are to begin neoadjuvant chemotherapy for treatment of Stage I-III Her 2 negative breast cancer with paclitaxel followed by either the combination of 5-fluorouracil, epirubicin and cyclophosphamide (FEC) or the combination of doxorubicin and cyclophosphamide (AC). OR Men or women who are to begin neoadjuvant chemotherapy for treatment of Stage I-III Her 2 positive breast cancer with paclitaxel followed by either the combination of 5-fluorouracil, epirubicin and cyclophosphamide (FEC) or the combination of doxorubicin and cyclophosphamide (AC). MC1137 Trastuzumab will be given concurrently with the taxane portion and can be given concurrently with FEC (but not AC) at the discretion of the medical oncologist.

  • Note: Her2 positive disease is defined to be: HER2 score of 3+ by IHC or HER2 gene amplification by FISH.
• Provide informed written consent.
• Willing to return to Mayo Clinic in Rochester, MN, Mayo Clinic in Arizona, or Mayo Clinic in Florida for imaging correlative, surgery, and follow-up.
• Willing to provide blood samples for correlative research purposes.
• Willing to provide tissue samples for correlative research purposes.
• ECOG Performance Status ≤ 2.

Exclusion Criteria:

• Receiving any investigational agent which would be considered as a treatment for the primary neoplasm.

• Other active malignancy ≤ 5 years prior to registration. EXCEPTIONS: Non-melanotic skin cancer or carcinoma-in-situ of the cervix.

  • Note: If there is a history or prior malignancy, they must not be receiving any other treatment for their cancer.
• Patients who are not planning to receive neoadjuvant chemotherapy.
• Biopsy proven Stage IV disease.
• Patients who are pregnant or nursing.