Nucleic acid extraction kit for FFPE tissue is unstable, is there any recommendation?

FFPE samples are preferably labeled with a kit that is compatible with FFPE/paraffin sectioning, rather than just generic DNA for cells or blood. Focus on the protease K digestion system after dewaxing, whether there is a de-crosslinking step, and the pH of the elution buffer. A260/280 Low often indicates protein or phenolic residues, which can be compared to whether the supplier provides low residue washing solutions, automatic magnetic bead adaptation, and batch quality inspection reports. When selecting models, historical samples can be used for parallel verification: the same slice, the same dewaxing conditions, compare the yield, fragment distribution, library insertion fragments, and coverage, not just OD.

If the kit is not changed for the time being, the FFPE process can be standardized first: the slice thickness, dewaxing time, ethanol washing, protease K dosage and temperature should be fixed. When the paraffin tissue is cross-linked heavily, it can be incubated for a short time at 70-80 °C after cleavage and then cooled to reduce insufficient de-cross-linking; protease K can also be added twice to avoid insufficient digestion. It is recommended to use low-salt and weak-base buffer for elution, and the elution volume should not be too small, otherwise the subsequent dilution error will be large. After extraction, Qubit can be used to see the actual recovery, and the fragment analyzer can be used to see whether it is excessively degraded, and then it is decided whether to adjust the digestion and washing.