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The MAQC (Microarray Quality Control) Project: Calibrated RNA Samples, Reference Datasets, and QC Metrics and Thresholds

L. Shi¹ , F. W. Frueh² , U. Scherf³ , R. K. Puri⁴ , S. A. Jackson⁵ , H. C. Harbottle⁶ , J. A. Warrington⁷ , J. Collins⁸ , D. Dorris⁹ , G. P. Schroth¹⁰ , L. Lamarcq¹¹ , Y. Wang¹² , T. J. Sendera¹³ , S. C. Baker¹⁴ , G. M. Fischer¹⁵ , B. Bromley¹⁶ , D. J. Dix¹⁷ , M. Salit¹⁸ , Z. Szallasi¹⁹ , E. S. Kawasaki²⁰ , C. Wang²¹ , R. V. Jensen²² , J. Han⁴ , F. M. Goodsaid² , G. A. Pennello³ , T. A. Cebula⁵ , J. E. LeClerc⁵ , W. Tong¹ , J. C. Fuscoe¹ , T. A. Patterson¹ , T. Han¹ , L. Guo¹ , H. Fang¹ , J. J. Chen¹ , Y. P. Dragan¹ , W. Slikker, Jr.¹ , D. A. Casciano¹ , ¹NCTR, FDA, Jefferson, AR, ²CDER, FDA, Rockville, MD, ³CDRH, FDA, Rockville, MD, ⁴CBER, FDA, Bethesda, MD, ⁵CFSAN, FDA, Laurel, MD, ⁶CVM, FDA, Laurel, MD, ⁷Affymetrix, Santa Clara, CA, ⁸Agilent, Palo Alto, CA, ⁹Ambion, Austin, TX, ¹⁰Applied Biosystems, Foster City, CA, ¹¹BD Clontech, Palo Alto, CA, ¹²Full Moon BioSystems, Sunnyvale, CA, ¹³GE Healthcare, Chandler, AZ, ¹⁴Illumina, San Diego, CA, ¹⁵Stratagene, La Jolla, CA, ¹⁶ViaLogy, Altadena, CA, ¹⁷NHEERL, EPA, Research Triangle Park, NC, ¹⁸NIST, Gaithersburg, MD, ¹⁹Harvard, Boston, MA, ²⁰NCI, Bethesda, MD, ²¹UCLA, Los Angeles, CA, ²²UMass, Boston, MA

FDA's Critical Path Initiative identifies pharmacogenomics and toxicogenomics as key opportunities in advancing medical product development and personalized medicine, and the ¡°Guidance for Industry: Pharmacogenomic Data Submissions¡± has been released. Microarrays represent a core technology in pharmacogenomics and toxicogenomics; however, before this technology can successfully and reliably be used in clinical practice and regulatory decision-making, standards and quality measures need to be developed.

The Microarray Quality Control (MAQC) project involves six FDA Centers, major providers of microarray platforms and RNA samples, EPA, NIST, academic laboratories, and other stakeholders. The MAQC project aims to establish QC metrics and thresholds for objectively assessing the performance achievable by various microarray platforms and evaluating the advantages and disadvantages of various data analysis methods. Two RNA samples will be selected for three species, human, rat, and mouse, and differential gene expression levels between the two samples will be calibrated with both microarrays and QRT-PCR. The resulting microarray datasets will be used for assessing the precision and cross-platform/laboratory comparability of microarrays, and the QRT-PCR datasets will enable evaluation of the nature and magnitude of any systematic biases that may exist between microarrays and QRT-PCR. The availability of the calibrated RNA samples combined with the resulting microarray and QRT-PCR datasets, which will be made readily accessible to the microarray community, will allow individual laboratories to more easily identify and correct procedural failures. The MAQC project will help improve the microarray technology and foster its proper applications in discovery, development and review of FDA regulated products.