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. The gene discussed is SOX9; the disease is ductal breast carcinoma in situ.