Southern blot analysis of DNA extracted from formalin-fixed pathology specimens

We have developed a method for the extraction of DNA from formalin-fixed, paraffin-embedded pathology specimens. High-molecular-weight DNA was recovered from well-fixed nonautolyzed samples of viable tissue. DNA recovered from samples exposed to picric acid or mercuric chloride containing fixatives was not intact. Increasing the formalin fixation time decreased the amount of intact DNA available. When these limitations were taken into consideration, the procedure allowed for the removal of degraded and chemically modified DNA from the preparation, and the final product was suitable for quantitative and qualitative analysis by Southern or dot blotting techniques. Digestion with methylation-sensitive restriction endonucleases showed that DNA methylation patterns were not altered after formalin fixation.