What size of DNA can be expected?
Size distribution of the extracted DNA can vary significantly and first and foremost 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 h (longer fixation times lead to more severe DNA fragmentation, resulting in poor 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