The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

• Published in: Nature biotechnology Vol. 24; no. 9; pp. 1151 - 1161
• Main Authors: Shi, Leming, Reid, Laura H, Jones, Wendell D, Shippy, Richard, Warrington, Janet A, Baker, Shawn C, Collins, Patrick J, de Longueville, Francoise, Kawasaki, Ernest S, Lee, Kathleen Y, Luo, Yuling, Sun, Yongming Andrew, Willey, James C, Setterquist, Robert A, Fischer, Gavin M, Tong, Weida, Dragan, Yvonne P, Dix, David J, Frueh, Felix W, Goodsaid, Federico M, Herman, Damir, Jensen, Roderick V, Johnson, Charles D, Lobenhofer, Edward K, Puri, Raj K, Scherf, Uwe, Thierry-Mieg, Jean, Wang, Charles, Wilson, Mike, Wolber, Paul K, Zhang, Lu, Amur, Shashi, Bao, Wenjun, Barbacioru, Catalin C, Lucas, Anne Bergstrom, Bertholet, Vincent, Boysen, Cecilie, Bromley, Bud, Brown, Donna, Brunner, Alan, Canales, Roger, Cao, Xiaoxi Megan, Cebula, Thomas A, Chen, James J, Cheng, Jing, Chu, Tzu-Ming, Chudin, Eugene, Corson, John, Corton, J Christopher, Croner, Lisa J, Davies, Christopher, Davison, Timothy S, Delenstarr, Glenda, Deng, Xutao, Dorris, David, Eklund, Aron C, Fan, Xiao-hui, Fang, Hong, Fulmer-Smentek, Stephanie, Fuscoe, James C, Gallagher, Kathryn, Ge, Weigong, Guo, Lei, Guo, Xu, Hager, Janet, Haje, Paul K, Han, Jing, Han, Tao, Harbottle, Heather C, Harris, Stephen C, Hatchwell, Eli, Hauser, Craig A, Hester, Susan, Hong, Huixiao, Hurban, Patrick, Jackson, Scott A, Ji, Hanlee, Knight, Charles R, Kuo, Winston P, LeClerc, J Eugene, Levy, Shawn, Li, Quan-Zhen, Liu, Chunmei, Liu, Ying, Lombardi, Michael J, Ma, Yunqing, Magnuson, Scott R, Maqsodi, Botoul, McDaniel, Tim, Mei, Nan, Myklebost, Ola, Ning, Baitang, Novoradovskaya, Natalia, Orr, Michael S, Osborn, Terry W, Papallo, Adam, Patterson, Tucker A, Perkins, Roger G, Peters, Elizabeth H, Peterson, Ron
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.09.2006; Nature Publishing Group
• Subjects: Agriculture; Alternative technology; Arrays; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Data analysis; Design of experiments; DNA microarrays; Equipment Design; Equipment Failure Analysis; Experimental design; Gene expression; Gene Expression Profiling - instrumentation; Gene Expression Profiling - methods; Life Sciences; Oligonucleotide Array Sequence Analysis - instrumentation; Platforms; Quality Assurance, Health Care - methods; Quality Control; Reliability analysis; Reproducibility; Reproducibility of Results; Ribonucleic acid; RNA; Sensitivity and Specificity; Titration; United States; United States
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt1239

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.