APC, CDH13 and RARβ methylation was significantly associated with ERα-negative DCIS (P = 0.017, P = 0.017 and P <0.001 respectively) and CDH13 and RARβ methylation were also significantly associated with PgR-negative DCIS (P <0.001 and P = 0.001). Here, APC is linked to ductal breast carcinoma in situ.