Don't know if you can get larger fragments from FFPE-samples ... Do you use punched samples or section slides ....
Promega ReliaPrep are quite good. Work better than many competitors.
https://www.promega.co.uk/products/dna-purification-quantitation/genomic-dna-purification/reliaprep-ffpe-gdna-miniprep-system/
However, you cannot expect very high quality DNA from FFPE, especially if your samples are old.
Dear Baiba, you can try to use QIAamp DNA FFPE Tissue Kit (qiagen) or promega for DNA isolation. I agree with Maxim Freidin, with time nucleic acids especially RNA can degrade in FFPE tissue.
The following paper can also help your studies.
Virchows Arch. 2012 Feb;460(2):131-40. doi: 10.1007/s00428-011-1184-9.
Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses.
Best regards.
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