Nature Biotechnology
- 24, 1151 - 1161 (2006)
Published online: 8 September 2006; | doi:10.1038/nbt1239
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurementsMAQC Consortium(Leming Shi 1, Laura H Reid2, Wendell D Jones2, Richard Shippy3, Janet A Warrington4, Shawn C Baker5, Patrick J Collins6, Francoise de Longueville7, Ernest S Kawasaki8, Kathleen Y Lee9, Yuling Luo10, Yongming Andrew Sun9, James C Willey11, Robert A Setterquist12, Gavin M Fischer13, Weida Tong1, Yvonne P Dragan1, David J Dix14, Felix W Frueh15, Federico M Goodsaid15, Damir Herman16, Roderick V Jensen17, Charles D Johnson18, Edward K Lobenhofer19, Raj K Puri20, Uwe Scherf21, Jean Thierry-Mieg16, Charles Wang22, Mike Wilson12, 18, Paul K Wolber6, Lu Zhang9, 23, Shashi Amur15, Wenjun Bao24, Catalin C Barbacioru9, Anne Bergstrom Lucas6, Vincent Bertholet7, Cecilie Boysen25, Bud Bromley25, Donna Brown26, Alan Brunner3, Roger Canales9, Xiaoxi Megan Cao27, Thomas A Cebula28, James J Chen1, Jing Cheng29, Tzu-Ming Chu24, Eugene Chudin5, John Corson6, J Christopher Corton14, Lisa J Croner30, Christopher Davies4, Timothy S Davison18, Glenda Delenstarr6, Xutao Deng22, David Dorris12, Aron C Eklund17, Xiao-hui Fan1, Hong Fang27, Stephanie Fulmer-Smentek6, James C Fuscoe1, Kathryn Gallagher31, Weigong Ge1, Lei Guo1, Xu Guo4, Janet Hager32, Paul K Haje33, Jing Han20, Tao Han1, Heather C Harbottle34, Stephen C Harris1, Eli Hatchwell35, Craig A Hauser36, Susan Hester14, Huixiao Hong27, Patrick Hurban19, Scott A Jackson28, Hanlee Ji37, Charles R Knight38, Winston P Kuo39, J Eugene LeClerc28, Shawn Levy40, Quan-Zhen Li41, Chunmei Liu4, Ying Liu42, Michael J Lombardi17, Yunqing Ma10, Scott R Magnuson43, Botoul Maqsodi10, Tim McDaniel4, Nan Mei1, Ola Myklebost44, Baitang Ning1, Natalia Novoradovskaya13, Michael S Orr15, Terry W Osborn38, Adam Papallo17, Tucker A Patterson1, Roger G Perkins27, Elizabeth H Peters38, Ron Peterson45, Kenneth L Philips19, P Scott Pine15, Lajos Pusztai46, Feng Qian27, Hongzu Ren14, Mitch Rosen14, Barry A Rosenzweig15, Raymond R Samaha9, Mark Schena33, Gary P Schroth23, Svetlana Shchegrova6, Dave D Smith47, Frank Staedtler45, Zhenqiang Su1, Hongmei Sun27, Zoltan Szallasi48, Zivana Tezak21, Danielle Thierry-Mieg16, Karol L Thompson15, Irina Tikhonova32, Yaron Turpaz4, Beena Vallanat14, Christophe Van7, Stephen J Walker49, Sue Jane Wang15, Yonghong Wang8, Russ Wolfinger24, Alex Wong6, Jie Wu27, Chunlin Xiao9, Qian Xie27, Jun Xu22, Wen Yang10, Liang Zhang29, Sheng Zhong50, Yaping Zong51 & William Slikker Jr1)1
National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA. 2
Expression Analysis, Inc., 2605 Meridian Parkway, Durham, North Carolina 27713, USA. 3
GE Healthcare, 7700 S. River Parkway, Suite 2603, Tempe, AZ 85284, USA. 4
Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA. 5
Illumina,Inc. 9885 Towne Centre Drive, San Diego, California 92121, USA. 6
Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, USA. 7
Eppendorf Array Technologies, rue du Séminaire 20a, 5000 Namur, Belgium. 8
NCI Advanced Technology Center, 8717 Grovemont Circle, Bethesda, Maryland 20892, USA. 9
Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA. 10
Panomics, Inc., 6519 Dumbarton Circle, Fremont, California 94555, USA. 11
Medical University of Ohio, 3000 Arlington Avenue, Toledo, Ohio 43614, USA. 12
Ambion, An Applied Biosystems Business, 2130 Woodward Street, Austin, Texas 78744, USA. 13
Stratagene Corp., 11011 North Torrey Pines Road, La Jolla, California 92130, USA. 14
Office of Research and Development, US Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, North Carolina 27711, USA. 15
Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA. 16
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA. 17
University of Massachusetts-Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125, USA. 18
Asuragen, Inc., 2150 Woodward, Austin, Texas 78744, USA. 19
CogenicsTM, A Division of Clinical Data, Inc., 100 Perimeter Park Drive, Suite C, Morrisville, North Carolina 27560, USA. 20
Center for Biologics Evaluation and Research, US Food and Drug Administration, 29 Lincoln Drive, Bethesda, Maryland 20892, USA. 21
Center for Devices and Radiological Health, US Food and Drug Administration, 2098 Gaither Road, Rockville, Maryland 20850, USA. 22
UCLA David Geffen School of Medicine, Transcriptional Genomics Core, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, California 90048, USA. 23
Solexa, Inc., 25861 Industrial Boulevard, Hayward, California 94545, USA. 24
SAS Institute, Inc., 100 SAS Campus Drive, Cary, North Carolina 27513, USA. 25
Vialogy Corp., 2400 Lincoln Avenue, Altadena, California 91001, USA. 26
Operon Biotechnologies, 2211 Seminole Drive, Huntsville, Alabama 35805, USA. 27
Z-Tech Corp., 3900 NCTR Road, Jefferson, Arkansas 72079, USA. 28
Center for Food Safety and Applied Nutrition, US Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708, USA. 29
CapitalBio Corp., 18 Life Science Parkway, Changping District, Beijing 102206, China. 30
Biogen Idec, 5200 Research Place, San Diego, California 92122, USA. 31
US Environmental Protection Agency, Office of the Science Advisor, 1200 Pennsylvania Avenue, NW, Washington, DC 20460, USA. 32
Yale University, W.M. Keck Biotechnology Resource Laboratory, Microarray Resource, 300 George Street, New Haven, Connecticut 06511, USA. 33
TeleChem ArrayIt, 524 E. Weddell Drive, Sunnyvale, California 94089, USA. 34
Center for Veterinary Medicine, US Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708, USA. 35
Cold Spring Harbor Laboratory, 500 Sunnyside Boulevard, Woodbury, New York 11797, USA. 36
Burnham Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA. 37
Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305, USA. 38
Gene Express, Inc., 975 Research Drive, Toledo, Ohio 43614, USA. 39
Harvard School of Dental Medicine, Department of Developmental Biology, 188 Longwood Avenue, Boston, Massachusetts 02115, USA. 40
Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232, USA. 41
University Texas Southwestern Medical Center, 6000 Harry Hines Boulevard/ND6.504, Dallas, Texas 75390, USA. 42
University of Texas at Dallas, Department of Computer Science, MS EC31 Richardson, Texas 75083, USA. 43
GenUs BioSystems, Inc., 1808 Janke Drive Unit M, Northbrook, Illinois 60062, USA. 44
Norwegian Microarray Consortium, Rikshospitalet - Radiumhospitalet Health Centre, Montebello, N0310 Oslo, Norway. 45
Novartis, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA. 46
MD Anderson Cancer Center, Breast Medical Oncology Department-Unit 1354, 1155 Pressler Street, Houston, Texas 77230, USA. 47
Luminex Corp., 12212 Technology Boulevard, Austin, Texas 78727, USA. 48
Harvard Medical School, Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology (CHIP@HST), Boston, Massachusetts 02115, USA. 49
Wake Forest University School of Medicine, Department of Physiology and Pharmacology, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA. 50
University of Illinois at Urbana-Champaign, Department of Bioengineering, 1304 W. Springfield Avenue, Urbana, Illinois 61801, USA. 51
Full Moon Biosystems, Inc., 754 N. Pastoria Avenue, Sunnyvale, California 94085, USA.
Correspondence should be addressed to Leming Shi leming.shi@fda.hhs.gov 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.
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