Deconvolution of the confounding variations for reverse transcription quantitative real-time polymerase chain reaction by separate analysis of biological replicate data.

Reverse transcription quantitative real-time polymerase chain reaction (RT–qPCR) uses threshold cycles (Ct values) for measuring relative gene expression. Ct values are signal-to-noise data composed of target gene expression and multiple sources of confounding variations. Data analysis is to minimize technical noises, evaluate biological variances, and estimate treatment-attributable expression changes of particular genes. However, this function is not sufficiently fulfilled in current analytic methods. An important but unrecognizable problem is that Ct values from all biological replicates and technical repeats are pooled across genes and treatment types. This violates the sample-specific association between target and reference genes, leading to inefficient removal of technical noises. To resolve this problem, here we propose to separate Ct values into replicate-specific data subsets and iteratively analyze expression ratios for individual data subsets. The individual expression ratios, rather than the raw Ct values, are pooled to determine the final expression change. The variances of all biological replicates and technical repeats across all target and reference genes are summed up. Our results from example data demonstrate that this separated method can substantially minimize RT–qPCR variance compared with the traditional methods using pooled Ct profiles. This analytic strategy is more effective in control of technical noises and improves the fidelity of RT–qPCR quantification.