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A Simple Method for Optimization of Reference Gene Identification and Normalization in DNA Microarray Analysis

Federico M. Casares

Department of Bioinformatics, Mitogenetics Research Institute, Farmingdale, NY, USA

Med Sci Monit Basic Res 2016; 22:45-52

DOI: 10.12659/MSMBR.897644

Available online: 2016-04-28

Published: 2016-04-28


BACKGROUND: Comparative DNA microarray analyses typically yield very large gene expression data sets that reflect complex patterns of change. Despite the wealth of information that is obtained, the identification of stable reference genes is required for normalization of disease- or drug-induced changes across tested groups. This is a prerequisite in quantitative real-time reverse transcription-PCR (qRT-PCR) and relative RT-PCR but rare in gene microarray analysis. The goal of the present study was to outline a simple method for identification of reliable reference genes derived from DNA microarray data sets by comparative statistical analysis of software-generated and manually calculated candidate genes.
MATERIAL AND METHODS: DNA microarray data sets derived from whole-blood samples obtained from 14 Zucker diabetic fatty (ZDF) rats (7 lean and 7 diabetic obese) were used for the method development. This involved the use of software-generated filtering parameters to accomplish the desired signal-to-noise ratios, 75th percentile signal manual normalizations, and the selection of reference genes as endogenous controls for target gene expression normalization.
RESULTS: The combination of software-generated and manual normalization methods yielded a group of 5 stably expressed, suitable endogenous control genes which can be used in further target gene expression determinations in whole blood of ZDF rats.
CONCLUSIONS: This method can be used to correct for potentially false results and aid in the selection of suitable endogenous control genes. It is especially useful when aimed to aid the software in cases of borderline results, where the expression and/or the fold change values are just beyond the pre-established set of acceptable parameters.

Keywords: Gene Expression Profiling - methods, Animals, Gene Expression Regulation, Oligonucleotide Array Sequence Analysis - standards, Rats, Rats, Zucker, Real-Time Polymerase Chain Reaction, Reference Standards, signal-to-noise ratio, Software, Statistics as Topic - methods