SHORT REPORT

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

V Zsikla, M Baumann and G Cathomas

Laboratory for Pathology of Infectious Diseases, Cantonal Institute of Pathology, 4410 Liestal Switzerland

Correspondence to:
Correspondence to:
Professor G Cathomas
Laboratory for Pathology of Infectious Diseases, Cantonal Institute of Pathology, Rheinstrasse 37, 4410 Liestal, Switzerland; gieri.cathomas{at}ksli.ch; http://www.infectpathology.ch

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 ß actin DNA extracted from upper gastrointestinal tract biopsies fixed in buffered and unbuffered formalin.

Methods: Amounts of ß 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 ß actin DNA was significantly higher in biopsies fixed in buffered formalin than in those fixed in unbuffered formalin (median 2.8 x 10⁴ and 5.3 x 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.

Keywords: unbuffered formalin fixation; gastric and duodenal biopsy; paraffin wax embedding; real-time (TaqMan) polymerase chain reaction; human ß actin

Abbreviations: PCR, polymerase chain reaction

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