Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR
- Laboratory for Pathology of Infectious Diseases, Cantonal Institute of Pathology, 4410 Liestal Switzerland
- Correspondence to: Professor G Cathomas Laboratory for Pathology of Infectious Diseases, Cantonal Institute of Pathology, Rheinstrasse 37, 4410 Liestal, Switzerland; gieri.cathomasksli.ch; http://www.infectpathology.ch
- Accepted 26 January 2004
Abstract
Background: The isolation of good quality DNA from routinely fixed and processed biopsy samples is crucial for the success of subsequent molecular analysis.
Aims: To compare the amount of β actin DNA extracted from upper gastrointestinal tract biopsies fixed in buffered and unbuffered formalin.
Methods: Amounts of β 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.
Results: The yield of β actin DNA was significantly higher in biopsies fixed in buffered formalin than in those fixed in unbuffered formalin (median 2.8 × 104 and 5.3 × 102 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).
Conclusions: This study indicates that tissue samples should be fixed in buffered formalin to facilitate the use of molecular pathology analysis in routine biopsy material.
- unbuffered formalin fixation
- gastric and duodenal biopsy
- paraffin wax embedding
- real-time (TaqMan) polymerase chain reaction
- human β actin
