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J Biomol Tech. 2007 February; 18(1): 87.
PMCID: PMC2292031

SP23A Proficiency Testing in Microarray Laboratories using Human MAQC Samples


Several studies, including the MicroArray Quality Control (MAQC) project, have reported that concordant results in relative expression measures can be obtained in different microarray laboratories using the same RNA samples. These encouraging results have led to increased interest in and utilization of microarray technology in clinical and diagnostic assays, which require stringent regulatory approval. Many laboratories monitor microarray quality metrics calculated from each hybridization image, such as background or percent present. While these internal metrics provide essential information for individual hybridizations, they are not sufficient for validating overall competency of the facility, including precision and accuracy of the results, which may vary between laboratories and over time. Comprehensive assessments of laboratory performance must include inter-laboratory comparisons, such as a proficiency testing program, where identical samples are tested in multiple facilities.

We have initiated a proficiency testing program for microarray laboratories using the Affymetrix platform. In previous testing rounds, we compared data from 18 laboratories over a nine-month period using rat samples. Now we are expanding the program to additional laboratories using human samples. Three replicates of the two human MAQC reference RNA samples were repeatedly tested in multiple facilities. The poster will show the results of several analyses to assess the repeatability and comparability of each laboratory’s results with a variety of microbiomes to understand complex metabolic interactions and their impact on the host health and nutritional status.

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