Nature Biotechnology
- 24, 1132 - 1139 (2006)
Published online: 9 August 2006; | doi:10.1038/nbt1237
Evaluation of external RNA controls for the assessment of microarray performanceWeida Tong1, Anne Bergstrom Lucas2, Richard Shippy3, Xiaohui Fan1, 4, Hong Fang5, Huixiao Hong5, Michael S Orr6, Tzu-Ming Chu7, Xu Guo8, Patrick J Collins2, Yongming Andrew Sun9, Sue-Jane Wang6, Wenjun Bao7, Russell D Wolfinger7, Svetlana Shchegrova2, Lei Guo1, Janet A Warrington8 & Leming Shi11
National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. 2
Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, USA. 3
GE Healthcare, 7700 S. River Pkwy., Suite #2603, Tempe, Arizona 85284, USA. 4
Pharmaceutical Informatics Institute, Zhejiang University, Hangzhou 310027, China. 5
Z-Tech Corporation, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. 6
Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, Maryland 20993, USA. 7
SAS Institute Inc., SAS Campus Drive, Cary, North Carolina 27513, USA. 8
Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA. 9
Applied Biosystems, 850 Lincoln Centre Dr., Foster City, California 94404, USA.
Correspondence should be addressed to Weida Tong weida.tong@fda.hhs.gov 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.
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