Dear James,

I've been trying to analysis FFPE in metabolomics, I know it's a different kind of experimenti, but I think that you could have the same problem I had. Infact it's quite difficult to remove, completely, the wax from the FFPE. and the wax could compromise the entire analysis and so the results. I tried a lot of dewaxing tecniques, by solvents such as xylene, by temperature etc....but I didn't get good results.

so, mine answer is just ad advice for your experiment...

I wish could be useful

have nice day 

Hello,

DNA extracted from FFPE samples can be used for targeted Amplicon sequencing but be aware that DNA is usually of low quality (fragmented, with some base modification due to FA fixation). You need first to deparaffinise samples and to extract DNA. You should not use too long amplicons  as DNA is degraded. A usual approach to check the quality/fragmentation is to run a multiplex PCR with increasing in size amplicons (up to 400-500 bp). Samples quality vary a lot from sample to sample making difficult to use a standard protocol for the totality of samples. There are different commercial solutions for DNA deparaffinisation and extraction. En example here:

https://www.diagenode.com/p/ffpe-dna-extraction-kit-bioruptor-pico-50-rxns

https://www.diagenode.com/files/protocols/FFPE_DNA_extraction_protocol.pdf

I agree with Irina. You can perform targeted sequencing using the DNA extracted from FFPE samples. There are different kits available in the market to extract DNA from FFPE. Depends on the tissue size, the DNA yield will vary. De-paraffinization is an important step as well, you can use Hemo-De instead of Zylene. Assessing your DNA conc using fluorometer instead of normal spectrophotometer will be helpful in getting the DS-DNA conc.