gQuant: A Robust and Generalizable Algorithm for Identifying Normalizer Genes in qRT-PCR Data: A Case Study on Urinary Exosomal miRNAs

Abstract

AbstractThe emergent role of nucleic acid-based biomarkers, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs), is becoming increasingly prominent in the realms of disease diagnostics and risk assessment. Quantitative reverse transcription PCR (qRT-PCR) is the primary analytical method for quantitative measurement of biomarkers. Yet, the relative infancy of non-coding RNAs’ (ncRNAs) recognition as biomarkers poses a challenge due to the absence of a consensus on a universally accepted normalizer gene, which is pivotal for accurate quantification. Current tools for selecting normalizer genes in qRT-PCR are fraught with limitations, including inadequate handling of null values, reliance on elementary statistical tools, use of a biased integrated approach, outlier sensitivity, and suboptimal graphical user interface for data visualization. These deficiencies underscore the necessity for a more nuanced and algorithmically balanced tool tailored to handle qRT-PCR datasets and facilitate the discernment of the most appropriate normalizer gene for specific datasets.Addressing the identified challenges, we have developed ‘gQuant,’ a tool crafted to address the limitations present in existing methods. In ‘gQuant’ we employed voting classifiers as an ensemble technique that combines predictions from multiple statistical methods to make more accurate rankings than any individual statistical measures. The tool’s efficacy was substantiated through rigorous validation against datasets from the Gene Expression Omnibus (GEO) database and corroborated with experimental data derived from urinary exosomal miRNAs. Comparative analysis with existing tools revealed that their integrated methodologies could skew the ranking of normalizer genes, whereas ‘gQuant’ consistently yielded rankings characterized by lower standard deviation, reduced covariance, and enhanced kernel density estimation (KDE) values. Given ‘gQuant’s’ promising performance, normalizer gene identification will be greatly improved, improving the precision of gene expression quantification in a variety of research scenarios.