At an individual gene level, gains of PIK3CA, CDK12, MLF1, EVI1, SOX2, TFRC, ERG and MTCP1, and losses of PIK3R1, APC, FGFR2, PDGFRB, CD74, ITK, EBF1, RANBP17, TLX3, NPM1, NR4A3, IL6ST and MAP2K4 were more frequent in synchronous DCIS or IDC than those in pure DCIS. Here, EBF1 is linked to ductal breast carcinoma in situ.