Investigator elected to end the study

The primary objective is to examine the impact on progression-free survival of targeted therapy for breast cancer suggested by proteomic and genomic profiling.

To explore the impact of targeted therapy for breast cancer suggested by proteomic and genomic profiling using RPMA, targeted resequencing, IHC analysis, WGS, RNA-seq, and Exome sequencing on progression-free survival. When a molecular target cannot be identified, the patient will be treated with a therapy selected on an empirical basis by the investigator/treating physician at the individual site and will be followed for survival status. Only available, FDA-approved agents will be used.

Inclusion Criteria:

• Life expectancy of >3 months
• Diagnosis of metastatic breast cancer or an advanced gynecological malignancy with measurable disease
• Age greater than or equal to 18 years
• ECOG performance status of 0-1
• Able to undergo two biopsies to obtain tissue with first biopsy required and second biopsy optional
• Have failed or unable to tolerate previous treatment regimen
• Adequate organ and bone marrow function as defined by ANC ≥ 1.5 x 109/L; Hgb 9 g/dL; platelets greater than 100 x 109/L; creatinine ≤ 1.5 mg/dL; bilirubin ≤ 2.5 x ULN; AST and ALT ≤ 2.5 x ULN (or ≤ 5 x ULN if due to underlying liver metastases); INR ≤ 1.5 x ULN (except in the case of anticoagulation therapy)

Exclusion Criteria:

• Metastatic lesions that are not accessible to biopsy
• Symptomatic CNS metastasis
• Previous history of another malignancy within 5 years of study entry
• Uncontrolled concurrent illness
• Known HIV, HBB, and/or HCV infection
• Pregnant or breast feeding or childbearing potential and not using adequate birth control