Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR

The isolation of good quality DNA from routinely fixed and processed biopsy samples is crucial for the success of subsequent molecular analysis.

To compare the amount of beta actin DNA extracted from upper gastrointestinal tract biopsies fixed in buffered and unbuffered formalin.

Amounts of beta actin DNA extracted from forceps biopsies of the upper gastrointestinal tract fixed in unbuffered (n = 22) and buffered formalin (n = 16) were estimated by quantitative real-time polymerase chain reaction.

The yield of beta actin DNA was significantly higher in biopsies fixed in buffered formalin than in those fixed in unbuffered formalin (median 2.8 x 10(4) and 5.3 x 10(2) DNA molecules, respectively; p < 0.005). Furthermore, fixation in buffered formalin led to a more reproducible DNA extraction, as indicated by the coefficient of variation (1.0 and 2.2, respectively).

This study indicates that tissue samples should be fixed in buffered formalin to facilitate the use of molecular pathology analysis in routine biopsy material.