I guess routine tissue preparation might degrade methylation status of genomic DNAs and there must be increasing possibility of contamination than fresh tissue. I know there are many studies using FFPE tissue though. But can anyone share any comments on this issue?
We have validated the use of FFPE tissue, which was up to 30 years old, using Methylation Sensitive-High Resolution Melting (MS-HRM) and Sensitive Melting Analysis after Real-Time-Methylation Specific PCR (SMART-MSP), with a successful result:
BMC Cancer. 2009 Dec 21;9:453.
Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM.
Kristensen LS, Wojdacz TK, Thestrup BB, Wiuf C, Hager H, Hansen LL.
Genetic methylation is an enzymatic reaction adding a methyl group to carbon 2 , formalin fixation would occur at the amine group of the cytosine but this is unlikely as these charges will be interacting with their base pairs and not the solution (in theory)
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