Pre-treatment is one of the most critical steps in the fluorescence in situ hybridization (FISH) assay for formalin-fixed, paraffin-embedded (FFPE) tissue.
The pre-treatment step is required because formalin fixation results in protein cross-linkage. The purpose of the pre-treatment step is to break these linkages, expose the genes, and allow the probes to penetrate. The pre-treatment step must also maintain the tissue's morphology and the DNA's integrity in the cells of interest.
Pre-treatment strategies typically use a sodium thiocyanate solution or a citric acid buffer, commonly used in clinical laboratories. This course's historical standard FISH method uses sodium thiocyanate, and the second uses citric acid.
Sodium thiocyanate is much harsher on tissue/cells than sodium citrate.
