What size of DNA can be expected?
This can vary significantly and strongly depends on the DNA quality present in the original FFPE sample. Formalin fixation, paraffin embedding, and storage conditions are factors that affect the DNA size distribution and may cause significant fragmentation of nucleic acids. To limit the extent of nucleic acid fragmentation, be sure to:
- Fix tissue samples in 4%–10% formalin as quickly as possible after surgical removal.
- Use a fixation time of 14–24 hours (longer fixation leads to more fragmentation, reducing performance in downstream assays).
- Thoroughly dehydrate samples prior to embedding (residual formalin can inhibit Proteinase K digestion).
Store FFPE tissue samples at 4–8°C.