HOXB3 and neoplasm: There was a limited overlap in DEGs between the 2 comparisons, mostly including genes with lower expression in no pCR relative to pCR tumors (regardless of HER2 heterogeneity) and again including genes in the ERBB2 amplicon (e.g., ERBB2, HOXB3) and mesenchymal subtype–specific genes (e.g., FN1, TNC) (Supplemental Figure 3B), again highlighting the importance of ERBB2 amplification and tumor subtype in response to T-DM1+P treatment.