PTEN and breast neoplasm: HER2-low breast tumors had significantly more frequent mutations in phosphatase and tensin homolog (PTEN; p < 0.001), GATA binding protein 3 (GATA3; p < 0.001), core-binding factor subunit beta (CBFB; p < 0.001), and AKT serine/threonine kinase 1 (AKT1; p < 0.001) than HER2-positive breast tumors (Fig. 3B, Additional file 1: Fig. S2B).