Abstract
The emerging field of epigenetics is advancing our understanding of cellular biology. Epigenetic modifications including DNA methylation are now accepted as being responsible for a wide variety of human diseases including cancer and autoimmune disorders. Although technical advances to study methylation have evolved, the success ultimately depends on the quality of the sample being used. While the isolation of gDNA is relatively simple, most clinical samples are formalin-fixed and paraffin embedded (FFPE) and it is well known that this process introduces crosslinks in the DNA that can irreversibly modify the sample. How formalin fixation and degradation affect our ability to detect methylation is still fairly unknown. The Nucleic Acids Research Group (NARG) study evaluates how fixation and degradation affects the detection of DNA methylation using several analysis methods. Mouse breast cancer tissue was used to generate gDNA from matched source tissues that are both flash-frozen and formalin-fixed paraffin embedded. The resulting gDNA will be assayed using conventional methylation detection methods including methylation sensitive restriction digest coupled with qPCR, methylated CpG island capture coupled to microarrays or next gen sequencing. Results discussing differential methylation detection are presented.