Genome-wide profiling of 5-methylcytosine and 5-hydroxymethylcytosine in breast cancer

Breast cancer is one of the most common cancers in women worldwide. Epigenetic changes, in particular DNA methylation and its modifications, play a crucial role in the development and progression of breast cancer. In this study, high throughput sequencing was performed to identify genome-wide methylation and hydroxymethylation profile of breast cancer. Tumor samples consisted of Invasive ductal carcinoma (IDC) and ductal carcinoma in situ (DCIS) tissues. The adjacent / marginal tissues of the respective IDC tissues were considered as paired normal and normal tissues from patients undergoing surgery for breast diseases other than malignancy were classified as absolute normal samples. Tumor tissue samples were histopathologically confirmed to contain more than 70% tumor cells. DNA isolated from these tissues was enriched with MEDIP and RRBS methods followed by deep sequencing (150X2 PE).