The research focus of the lab is in developing and using new experimental and computational tools in genomics to understand epigenetic abnormalities in cancer. Cancer genomes are known to undergo focal hypermethylation (increase in DNA methylation) in a background of genomic hypomethylation (decrease in methylation). Hypermethylation events tend to occur at the promoters of some genes and may result in transcriptional repression. Hypomethylation tends to occur at interspersed repeats and has been understudied due to many technological limitations.

We have recently developed Methyl-MAPS (Methylation Mapping Analysis by Paired-end Sequencing), which combines an enzymatic approach for fractionating DNA according to methylation status with the power of Next-Gen sequencing to understand genome-wide DNA methylation profiles. We are using this technology to understand the patterns found in methylation abnormalities in breast cancer and how they affect transcription. In particular, one goal is to determine the effects of demethylation of interspersed repeats (such as SINE and LINE elements) on various processes, including transcription of nearby genes, chromosomal rearrangements and chromatin structure. In addition, we are exploring the use of subsets of the genome-wide methylation patterns we obtain as stable biomarkers that may be used as prognostic indicators of aspects, such as survival and response to drug treatment.

The lab does have openings for new graduate students.  Projects tend to have both experimental and computational components. Some projects are primarily experimental based with a small computational component, while others are primarily computationally based. If you are interested in a rotation in the lab please contact John Edwards directly at jedwards <at> dom.wustl.edu.