Somatic mutations of FGFR2, BRCA2, MET, SMARCA4, AR, GNAS, NCOA3, PDGFRA, ATM, BCOR, MLL3, NOTCH1 and SOX9, and CNAs in AKT1, ALK, FGFR2, GNAS, MDM2, MET, MYCL1, MYCN, NCOA3, FGFR2 (gains), BCOR, CDKN2C, GNAS, GATA3, MAP3K1, NOTCH2, PIK3R1, SMARCA4 and SOX9 (losses) were identified as synchronous DCIS-IDC-specific alterations in our study (Figure 4) that may cooperate for progression. This evidence concerns the gene ATM and ductal breast carcinoma in situ.