More attention should be paid on the interpretation of gene expression data

Abstract

Molecular profiling of gene expression is important for determining signatures in cancer progression and diagnosis. For this purpose, polymerase chain reaction-based techniques are preferentially used as a feasible and sensitive approach. Nevertheless, when relative quantitative analyses are performed on gene expression, the interpretation of mathematical equations must be carefully done. This letter to the editor is focused on recently published gene expression data in World Journal of Gastroenterology by Ozmen et al demonstrating increased levels of LYVE-1, VEGFR-3 and CD44 genes in gastric cancer samples compared to non-neoplastic gastric tissues. However, there are major concerns about misinterpretation of the gene expression data obtained with the 2^-ΔΔCt relative quantitative method. In the study, 2^-ΔΔCt values calculated for many samples were smaller than 1 (2^-ΔΔCt < 1) which indicate decreased levels of LYVE-1, VEGFR-3 and CD44 gene expression in the gastric cancer tissues. This unfortunate mistake is an important example showing how a simple error in the interpretation of relative-quantitative gene expression data may result in misleading scientific conclusions. In this letter, a brief explanation of the 2^-ΔΔCt method is given. In addition, the importance of technical quality and interpretation in gene expression studies is discussed.

Keywords: Gene expression; 2^-ΔΔCt method; Real-time polymerase chain reaction