IntroductionWe compared associations of DNA methylation with tumor features and clinical variables in n = 99 women with breast cancer. Hundreds of hypermethylated genes have been described in breast cancer, yet the nature and contribution of these genes in their methylated state to overall risk and prognosis is undercharacterized in non-sporadic breast cancers. The inherent heterogeneity of breast cancer and its myriad subtypes pose a challenge in any research undertaking. In an effort to limit heterogeneity, we narrowed the inclusion criteria for this study to an at risk cohort of women with the rationale that distinct epigenetic factors common to those with familial breast cancers and/ or known BRCA1 or BRCA2 genetic mutations, are at differing Background: hundreds of hypermethylated genes have been described in breast cancer, yet the nature and contribution of these genes in their methylated state to overall risk and prognosis is under-characterized in non-sporadic breast cancers. We therefore compared associations of DNa methylation with tumor stage, hormone/growth receptor status and clinical outcomes in a familial breast cancer cohort. Because few previous methylation studies have considered the oncogenic or tumor suppressor properties of their gene sets, this functional status was included as part of our correlative analysis.Results: We found methylation of oncogenes was associated with better prognostic indicators, whereas tumor suppressor gene methylation was associated with a more severe phenotype in women that were either heR2 + or lymph node positive at diagnosis, and/or tended to recur or develop distant metastases. For example, the methylation of the tumor suppressor gene apC was strongly associated with a specific subset of tumors that were both eR + and heR2