Comparison of capillary electrophoresis, AGE, and PAGE for MTHFR polymorphism analysis in FFPE cervical samples.

Abstract

Background. Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism analysis could help in diagnosis, treatment, and prognosis of some pathologies, since it has been associated with the development of cardiovascular diseases, defects in neural tube formation, psychiatric disorders, and cancer. Polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) is the most commonly used technique to analyze this polymorphism. Usually, RFLP products are evaluated by agarose gel electrophoresis (AGE) or polyacrylamide gel electrophoresis (PAGE). However, capillary electrophoresis (CE) may represent an alternative for MTHFR C677T polymorphism analysis by PCR-RFLP. Thus, the aim of this study was to compare CE, AGE, and PAGE to MTHFR C677T polymorphism analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) cervical samples. Methods. 150 biopsy blocks of cervical samples were analyzed. MTHFR polymorphism was evaluated by PCR-RFLP, and the products generated were analyzed by CE, AGE, and PAGE. Concordance between the methods was evaluated by rate agreement, Kappa coefficient, and McNemars’s Test. Results. Eight samples (5.4%) showed discordant results according to CE and PAGE or AGE. Differences of CC and CT frequencies were observed between CE and AGE (p=0.016): CC genotype varied from 68.0% to 72.7%, and CT varied from 23.3% to 27.3%. Besides, Kappa coefficient between CE and AGE, or PAGE was very high (κ>0.81). Conclusion. Capillary electrophoresis presented high agreement with PAGE and AGE, and may be an accurate, safe, and quick alternative method for MTHFR polymorphism analysis.