To identify alternative exon usage in clinical subtypes of invasive ductal carcinoma, the tumor samples were stratified into ER+ HER2− (n = 493), ER− HER2− (n = 157), and HER2+ (n = 97) tumors based on copy number of ERBB2, and mRNA expression of ESR1 (see Supplementary Fig. S2 and Methods for details). Here, ESR1 is linked to invasive ductal breast carcinoma.