I need to perform a multiplex PCR (one of them with up to 30 primers) and very often the FFPE samples do not amplify (only 50% vs 98% of fresh samples). I am planning to use the qiagen deparaffinization solution instead of the heat to remove paraffin and see if there is any improvement. Plus I am planning to replace an in-house method for the DNA isolation from skin samples with one of the Qiagen kit but I am not sure wich one is better, especially considering that sometimes I have big chunks of tissue and I don't want to waste any material.
Thanks
I'm afraid I don't work in this area myself but I help out a Next-Generation Sequencing consulting company and I have heard a talk twice from a guy at Covaris at both Oxford and Dundee conferences about extracting NGS-grade DNA and RNA from FFPE samples. Here is the page that has details about the kits: http://covarisinc.com/products/ffpe-extraction/truxtrac-ffpe-dna-and-rna-kits/
Thermo also has some kits but again, I'm not sure how good they are: https://www.thermofisher.com/uk/en/home/life-science/dna-rna-purification-analysis/dna-extraction/genomic-dna-extraction/dna-extractions-working-with-ffpe-samples.html
I hope maybe this gives you some ideas or at least might generate some more answers from people! Best of luck!
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