Although we found variabilities along the stages, which reflects the heterogeneity of this disease, COMMD4_AS2, MARK3, MATR3, POLDIP3, COMMD4_AS1, and GNAS underwent AS switches in almost all stages of breast cancer, while RHOC displayed significant AS switches during stage IIB (Supplementary Fig. 6K–Q). Here, MARK3 is linked to breast carcinoma.