Evaluation of external RNA controls for the assessment of microarray performance

• Published in: Nature biotechnology Vol. 24; no. 9; pp. 1132 - 1139
• Main Authors: Tong, Weida, Lucas, Anne Bergstrom, Shippy, Richard, Fan, Xiaohui, Fang, Hong, Hong, Huixiao, Orr, Michael S, Chu, Tzu-Ming, Guo, Xu, Collins, Patrick J, Sun, Yongming Andrew, Wang, Sue-Jane, Bao, Wenjun, Wolfinger, Russell D, Shchegrova, Svetlana, Guo, Lei, Warrington, Janet A, Shi, Leming
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.09.2006; Nature Publishing Group
• Subjects: Agriculture; Algorithms; analysis; Arrays; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Equipment Failure Analysis - methods; Gene Expression Profiling - instrumentation; Gene Expression Profiling - standards; Hybridization; Life Sciences; Oligonucleotide Array Sequence Analysis - instrumentation; Oligonucleotide Array Sequence Analysis - standards; Performance assessment; Quality control; Reference Values; Reproducibility of Results; Research methodology; Ribonucleic acid; RNA; RNA - analysis; RNA - genetics; RNA - standards; Sensitivity and Specificity; United States; United States
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt1237

External RNA controls (ERCs), although important for microarray assay performance assessment, have yet to be fully implemented in the research community. As part of the MicroArray Quality Control (MAQC) study, two types of ERCs were implemented and evaluated; one was added to the total RNA in the samples before amplification and labeling; the other was added to the copyRNAs (cRNAs) before hybridization. ERC concentration-response curves were used across multiple commercial microarray platforms to identify problematic assays and potential sources of variation in the analytical process. In addition, the behavior of different ERC types was investigated, resulting in several important observations, such as the sample-dependent attributes of performance and the potential of using these control RNAs in a combinatorial fashion. This multiplatform investigation of the behavior and utility of ERCs provides a basis for articulating specific recommendations for their future use in evaluating assay performance across multiple platforms.