SPOP and breast neoplasm: Besides HER2 gene amplifications, HER2-positive breast tumors were detected with more copy number amplification in genes including CDK12 (p < 0.001), retinoic acid receptor alpha (RARA; p < 0.001), and speckle-type POZ protein (SPOP; p < 0.001) and significantly higher TP53 mutation rates (p < 0.001) as compared with HER2-zero (Fig. 3A, Additional file 1: Fig. S2A) and HER2-low breast tumors (Fig. 3B, Additional file 1: Fig. S2B).