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

Leming Shi, Laura H. Reid, Wendell D. Jones, Richard Shippy, Janet A. Warrington, Shawn C. Baker, Patrick J. Collins, Francoise De Longueville, Ernest S. Kawasaki, Kathleen Y. Lee, Yuling Luo, Yongming Andrew Sun, James C. Willey, Robert A. Setterquist, Gavin M. Fischer, Weida Tong, Yvonne P. Dragan, David J. Dix, Felix W. Frueh, Federico M. GoodsaidDamir Herman, Roderick V. Jensen, Charles D. Johnson, Edward K. Lobenhofer, Raj K. Puri, Uwe Scherf, Jean Thierry-Mieg, Charles Wang, Mike Wilson, Paul K. Wolber, Lu Zhang, William Slikker, Shashi Amur, Wenjun Bao, Catalin C. Barbacioru, Anne Bergstrom Lucas, Vincent Bertholet, Cecilie Boysen, Bud Bromley, Donna Brown, Alan Brunner, Roger Canales, Xiaoxi Megan Cao, Thomas A. Cebula, James J. Chen, Jing Cheng, Tzu Ming Chu, Eugene Chudin, John Corson, J. Christopher Corton, Lisa J. Croner, Christopher Davies, Timothy S. Davison, Glenda Delenstarr, Xutao Deng, David Dorris, Aron C. Eklund, Xiao Hui Fan, Hong Fang, Stephanie Fulmer-Smentek, James C. Fuscoe, Kathryn Gallagher, Weigong Ge, Lei Guo, Xu Guo, Janet Hager, Paul K. Haje, Jing Han, Tao Han, Heather C. Harbottle, Stephen C. Harris, Eli Hatchwell, Craig A. Hauser, Susan Hester, Huixiao Hong, Patrick Hurban, Scott A. Jackson, Hanlee Ji, Charles R. Knight, Winston P. Kuo, J. Eugene LeClerc, Shawn Levy, Quan Zhen Li, Chunmei Liu, Ying Liu, Michael J. Lombardi, Yunqing Ma, Scott R. Magnuson, Botoul Maqsodi, Tim McDaniel, Nan Mei, Ola Myklebost, Baitang Ning, Natalia Novoradovskaya, Michael S. Orr, Terry W. Osborn, Adam Papallo, Tucker A. Patterson, Roger G. Perkins, Elizabeth H. Peters, Ron Peterson, Kenneth L. Philips, P. Scott Pine, Lajos Pusztai, Feng Qian, Hongzu Ren, Mitch Rosen, Barry A. Rosenzweig, Raymond R. Samaha, Mark Schena, Gary P. Schroth, Svetlana Shchegrova, Dave D. Smith, Frank Staedtler, Zhenqiang Su, Hongmei Sun, Zoltan Szallasi, Zivana Tezak, Danielle Thierry-Mieg, Karol L. Thompson, Irina Tikhonova, Yaron Turpaz, Beena Vallanat, Christophe Van, Stephen J. Walker, Sue Jane Wang, Yonghong Wang, Russ Wolfinger, Alex Wong, Jie Wu, Chunlin Xiao, Qian Xie, Jun Xu, Wen Yang, Liang Zhang, Sheng Zhong, Yaping Zong

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724 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1151-1161
Number of pages11
JournalNature biotechnology
Issue number9
StatePublished - Sep 1 2006

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering


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