The behavior of breast cancers and their response to neoadjuvant systemic therapy depend on their phenotype which is to a large extent determined by gene expression programs within the cancer cell. The purpose of the analysis was to compare matched gene expression profiles of pretreatment cancer with post-neoadjuvant systemic therapy, residual cancer. Overall design: Pre-treatment FNA from primary tumors or post-treatment surgical specimens were obtained and RNA extracted and hybridized to afymetrix microarrays according to manufacturer protocol.