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Nat Biotechnol 2006 Sep 8;24(9):1151-1161

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

Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Scherf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, Leclerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr

Shi LM, US FDA, Natl Ctr Toxicol Res, 3900 NCTR Rd, Jefferson, AR 72079 USA US FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA Express Anal Inc, Durham, NC 27713 USA GE Healthcare, Tempe, AZ 85284 USA Affymetrix Inc, Santa Clara, CA 95051 USA Illuminia Inc, San Diego, CA 92121 USA Agilent Technol Inc, Santa Clara, CA 95051 USA Eppendorf Array Technol, B-5000 Namur, Belgium NCI, Ctr Adv Technol, Bethesda, MD 20892 USA Appl Biosyst Inc, Foster City, CA 94404 USA Panomics Inc, Fremont, CA 94555 USA Med Univ Ohio, Toledo, OH 43614 USA Ambion, Austin, TX 78744 USA Stratagene Corp, La Jolla, CA 92130 USA US EPA, Off Res & Dev, Res Triangle Pk, NC 27711 USA US FDA, Ctr Drug Evaluat & Res, Silver Spring, MD 20993 USA NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA Univ Massachusetts, Boston, MA 02125 USA Asuragen Inc, Austin, TX 78744 USA Cogenics, Morrisville, NC 27560 USA US FDA, Ctr Biol Evaluat & Res, Bethesda, MD 20892 USA US FDA, Ctr Devices & Radiol Hlth, Rockville, MD 20850 USA Univ Calif Los Angeles, Cedars Sinai Med Ctr, David Geffen Sch Med, Los Angeles, CA 90048 USA Solexa Inc, Hayward, CA 94545 USA SAS Inst Inc, Cary, NC 27513 USA Vialogy Corp, Altadena, CA 91001 USA Operon Biotechnol, Huntsville, AL 35805 USA Z Tech Corp, Jefferson, AR 72079 USA US FDA, Ctr Food Safety & Appl Nutr, Laurel, MD 20708 USA CapitalBio Corp, Beijing 102206, Peoples R China Biogen Idec, San Diego, CA 92122 USA US EPA, Off Sci Advisor, Washington, DC 20460 USA Yale Univ, WM Keck Biotechnol Resource Lab, New Haven, CT 06511 USA TeleChem Arraylt, Sunnyvale, CA 94089 USA US FDA, Ctr Vet Med, Laurel, MD 20708 USA Cold Spring Harbor Lab, Woodbury, NY 11797 USA Burnham Inst, La Jolla, CA 92037 USA Stanford Univ, Sch Med, Stanford, CA 94305 USA Gene Express Inc, Toledo, OH 43614 USA Harvard Univ, Sch Dent Med, Dept Dev Biol, Boston, MA 02115 USA Vanderbilt Univ, Nashville, TN 37232 USA Univ Texas, SW Med Ctr, Dallas, TX 75390 USA Univ Texas, Dept Comp Sci, Richardson, TX 75083 USA GenUs BioSyst Inc, Northbrook, IL 60062 USA Natl Hosp Norway, Radium Hosp Hlth Ctr, Norwegian Microarray Consortium, N-0310 Oslo, Norway Novartis, Cambridge, MA 02139 USA MD Anderson Canc Ctr, Breast Med Oncol Dept, Unit 1354, Houston, TX 77230 USA Luminex Corp, Austin, TX 78727 USA Harvard Univ, Sch Med, Childrens Hosp, Informat Program,Harvard MIT Div Hlth Sci & Tech, Boston, MA 02115 USA Wake Forest Univ, Sch Med, Dept Physiol & Pharmacol, Winston Salem, NC 27157 USA Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA Full Moon Biosyst Inc, Sunnyvale, CA 94085 USA


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.

Category: Journal Article
PubMed ID: #16964229
Includes FDA Authors from Scientific Area(s): Toxicological Research, Drugs, Biologics, Medical Devices, Animal and Veterinary
Entry Created: 2011-10-04 Entry Last Modified: 2012-08-29