70. Microarray Quality Control Parameters Applied to a Genomics Platform: A Comprehensive Performance Analysis

JUAN MARTÍN SENDOYA; DANIELA CHIRICO; GERMÁN GONZALEZ; CECILIA ROTONDARO; CRISTOBAL FRESNO; ELMER FERNÁNDEZ; OSVALDO PODHAJCER; ANDREA LLERA

Rosario

Congreso; IV Congreso Argentino de Bioinformática y Biología Computacional (4CAB2C) y IV Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SoIBio); 2013

Microarray technology remains a highly convenient approach in transcriptomics studies that require the analysis of a large number of samples [1, 2], especially in current international cancer consortia. In this context of worldwide microarray studies, the assessment of quality control (QC) parameters is crucial in order to ensure good laboratory practice. Using the recently developed QC R library Agi4x44.2c [3], we analyzed microarray performance in our genomics platform by comparing all the arrays in a given project, which in turn provided feedback to optimize our experimental workflow on a daily basis. Here we describe a series of relevant microarray QC metrics applied to 172 two-color Agilent microarrays from our facility, as shown by Agi4x44.2c. For each QC parameter evaluated, we have analyzed the results, in terms of the principle on which it is based, acceptable values range, and experimental interpretation. The selection of an appropriate processing method is a critical step when analyzing microarray data. The assessed QC parameters show that our platform?s performance successfully met the minimum quality requirements (i.e. at least 9/12 metrics within the acceptable range) in 171/172 (99.4%) of the experiments, with a sustained increase in reproducibility. Coupling Agi4x44.2c to Agilent?s Feature Extraction software provides our platform with a wider range of possibilities when it comes to verifying the quality of our data, plus enabling a follow-up of the experimental performance. These easy-to-interpret quality control tools along with a constant monitoring of the experimental practices makes us able to assure high-quality, successful microarray services.