Breast cancer genomes often undergo severe hypomethylation, much of which is found at interspersed repeats. There have been some studies that have linked the hypomethylation found in cancer with genomic instability and possibly the reactivation of oncogenes. One limitation in previous studies is that the details of which particular repeats that undergo demethylation could not be mapped on a genome-wide scale.

We are combining genome-wide methylation mapping data using Methyl-MAPS with high-resolution transcriptome profiles using RNA-Seq to understand the transcriptional effects of demethylation of repetitive elements.

We are also mapping rearrangements with low-pass genomic sequencing and comparing these with genome-wide methylation data to understand how demethylation events in breast cancer can play a role in mediating rearrangement events in cancer.