Our WSI-based deep-learning models can identify the point mutation status of six genes (RB1, CDH1, NF1, NOTCH2, TP53, and MAP3K1) and the copy number alteration of another six genes (FGFR1, EIF4EBP1, KAT6A, HEY1, ZNF217, and RAB25) in breast cancer. Here, CDH1 is linked to breast cancer.