Are EpiTect Methyl qPCR Arrays or Assays applicable to FFPE samples?

No. Under the current protocol, FFPE samples are not suitable for analysis with EpiTect Methyl qPCR Arrays and Assays. This is because genomic DNA from FFPE samples is single-stranded due to the heating step involved in the DNA isolation process, making it undigestible by either Methylation-sensitive or Methylation-dependent enzymes. Please refer to the User Manual of your chosen genomic DNA isolation kit. If there is a 95 ºC heating step involved, please do not use the kit to isolate genomic DNA for EpiTect Methyl qPCR Arrays or Assays.

Instead, use the recommended genomic DNA isolation Kit in the User Manual of EpiTect Methyl qPCR Arrays or Assays. For analyzing methylation status of DNA isolated from FFPE tissues, we recommend using EpiTect Plus FFPE Bisulfite Kits for one-step isolation and bisulfite conversion of the DNA, followed by any detection method optimized for use with FFPE samples (e.g., Pyrosequencing).