Large-scale cross-platform study of research microarrays uncovers high concordance across platforms

BOSTON--Gene expression microarrays have made a profound impact on biomedical research. The current expectation is that this technology will extend its current role as an experimental tool for basic science research and be increasingly applied in clinical practice. Before this can occur, the issues of cross-platform comparison and integration of data must be addressed. The diversity of available platforms and analytical methods has made comparison of data from multiple platforms challenging. Different laboratories may use different platforms to profile the same genes, but how comparable are they?

Winston Patrick Kuo, DDS, MS, DMSc, post-doctoral researcher in the Department of Oral and Developmental Biology at the Harvard School of Dental Medicine, and colleagues tested nearly all the available commercial and "in-house" gene expression microarray platforms for cross-platform and cross-laboratory comparisons. They have produced a framework for comparisons across platforms and different laboratories, reported in the July 2 online edition of Nature Biotechnology.

This study comes on the heels of several large efforts to create standardized protocols for microarray experiments (from probe annotation to data analysis), such as the Minimum Information About a Microarray Experiment (http://mged.org/Workgroups/MIAME/miame.html), the External RNA Controls Consortium (http://www.cstl.nist.gov/biotech/Cell&TissueMeasurements/GeneExpression/ERCC.htm), and the Microarray Quality Control Project (http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/). In addition, major portals for deposition and retrieval of microarray data, such as the Gene Expression Omnibus and ArrayExpress, will only be truly useful if experiments a

Contact: Leah Gourley
Harvard Medical School

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