(A) Sample flow chart to show how samples were selected. Starting with 305 patients, specimens were removed for multiple reasons including incomplete clinical data, low RNA yields, a normal-like non-tumor expression profile, being part of the TL= lapatinib and paclitaxel arm, thus leaving 203 patients. Of these, 137 had DNA exomes results, with this final 137 sample set also being split into a training and test set. (B) Clinical and intrinsic expression subtype characteristics with pCR rates using the 137 patient data set. P-values were calculated by Chi-aquare test. TH, trastuzumab and paclitaxel arm; THL, trastuzumab, lapatinib and paclitaxel arm; ER, estrogen-receptor; PgR, progesterone receptor.