Real-time Quantitative Polymerase Chain Reaction Assay for Detecting 1p and 19q Codeletion in Glioma

Abstract

Abstract Background: Glioma is a type of tumor that occurs in the brain and spinal cord. Gliomas begin in the gluey supportive cells (glial cells) that surround nerve cells and help them function. Gliomas are classified according to the type of glial cell involved in the tumor, as well as the tumor’s genetic features, which can help predict how the tumor will behave over time and the treatments most likely to work. Among the molecular markers for the classification of glioma, loss of the 1p/19q fragments is by far the most well-characterized and most widely studied. In this study, we used real-time polymerase chain reaction (PCR) as an alternative technique to fluorescence in situ hybridization (FISH) to detect 1p/19q deletion mutations in adult gliomas. Methods: This was a cross-sectional study. Specific primers were designed for target genes represented for 1p and 19q areas. Real-time PCR was performed for 60 formalin-fixed paraffin-embedded samples which were randomly divided into two groups: whole tissue DNA extraction and tumor-only area DNA extraction. FISH was used as a confirmation method. Results: Real-time PCR results from DNA isolated from whole tissue showed a low similarity with FISH results (56.6% for 1p and 66.6% for 19q), while real-time PCR results from DNA of tumor-only area showed high similarity with FISH results for both markers (80%). For samples with 1p/19q deletion, real-time PCR showed a relatively low sensitivity as this technique only detected 5 out of 11 samples with 1p/19q deletion. Conclusions: Using DNA extracted from the tumor-only area, real-time PCR has a similarity of 80% compared with FISH in detecting 1p/19q deletion.