Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets

TLDR

Accurate normalization is essential for correct gene‑expression measurement; while a single constitutive control gene is commonly used, no gene is universally stable, so its stability must be verified for each experiment. The study proposes a novel, robust strategy to identify stably expressed genes among candidate normalization genes. The approach uses a mathematical model to estimate overall and subgroup variation of candidate genes, providing a direct measure of expression variability and enabling identification of suitable normalization genes for colon and bladder cancer. Compared to a prior method, the model‑based strategy proved more robust and less sensitive to coregulation, identified UBC, GAPD, and TPT1 for colon and HSPCB, TEGT, and ATP5B for bladder, and can be applied broadly to improve RT‑PCR normalization.

Abstract

Accurate normalization is an absolute prerequisite for correct measurement of gene expression. For quantitative real-time reverse transcription-PCR (RT-PCR), the most commonly used normalization strategy involves standardization to a single constitutively expressed control gene. However, in recent years, it has become clear that no single gene is constitutively expressed in all cell types and under all experimental conditions, implying that the expression stability of the intended control gene has to be verified before each experiment. We outline a novel, innovative, and robust strategy to identify stably expressed genes among a set of candidate normalization genes. The strategy is rooted in a mathematical model of gene expression that enables estimation not only of the overall variation of the candidate normalization genes but also of the variation between sample subgroups of the sample set. Notably, the strategy provides a direct measure for the estimated expression variation, enabling the user to evaluate the systematic error introduced when using the gene. In a side-by-side comparison with a previously published strategy, our model-based approach performed in a more robust manner and showed less sensitivity toward coregulation of the candidate normalization genes. We used the model-based strategy to identify genes suited to normalize quantitative RT-PCR data from colon cancer and bladder cancer. These genes are UBC, GAPD, and TPT1 for the colon and HSPCB, TEGT, and ATP5B for the bladder. The presented strategy can be applied to evaluate the suitability of any normalization gene candidate in any kind of experimental design and should allow more reliable normalization of RT-PCR data.