The aims of our analyses were (1) to identify a set of gene DNA methylation markers predictive of ER/PR status in a training dataset of invasive breast cancer samples from an ethnically diverse patient cohort (the Breast Cancer Care in Chicago (BCCC) study); (2) to validate DNA methylation markers identified in the training data using a different, publically available validation dataset; and (3) to associate these DNA methylation markers with corresponding gene expression changes. Here, PGR is linked to breast cancer.