ESR1 and breast cancer: While the ER gene (ESR1) did not show significantly altered transcript levels within either the early neoplasias or breast cancers in our sequencing dataset, IHC staining for ER showed elevated protein levels in both the early neoplasias (57/61 cases with strong or intermediate staining) and breast cancers (79/99 with strong or intermediate staining; Figure 4C; Table S10 in Additional file 1).