Stranded bulk Illumina RNASeq of human mammary tumors before and after neoadjuvant chemotherapy treatment

This study is designed to find a reliable marker enabling to predict the response to treatment in patients with early breast cancers treated by neoadjuvant chemotherapy. This marker would allow on one hand to select more homogeneous patient cohorts requiring treatment escalation strategies, and on the other hand reduce the burden of toxicity (both treatment-related and financial) for the patients that will already derive high benefit from the conventional treatments. In this study, gene expression profiles were measured and correlated with the clinical response to neoadjuvant chemotherapy and other features like the epithelial to mesenchymal transition and the tumor immune cell infiltration. Overall design: The gene expression of 95 tumors samples of primary breast cancer patients were analyzed pre-neoadjuvant chemotherapy by bulk stranded RNA sequencing. Among those 95 patients, 29 did not respond completely to the neoadjuvant chemotherapy, and the residual tumor after treatment were sequenced by the same technique.