In Search of Microarray Standards

An industry/academia/government coalition puts microarray reproducibility to the test

Jeffrey M. Perkel
Apr 1, 2006

There's no denying the popularity of DNA microarrays: 1.8 billion data points in the Stanford Microarray Database don't lie. But a lack of standards and quality control metrics for everything from RNA preparation to probe design to data analysis has led to the perception, at least, that gene expression profile concordance between, and even within labs is, shall we say, spotty.

That technical ambivalence could be ending, however. As you read this, a team of researchers led by Leming Shi of the US Food and Drug Administration's National Center for Toxicological Research is preparing 10 research papers to be submitted jointly to Nature Biotechnology for September publication. The subject of this decology: the Microarray Quality Control (MAQC) project.

The impetus behind MAQC was a series of highly critical papers questioning microarray reliability and reproducibility. In one particularly damning study1 Margaret Cam of the National Institute of Diabetes and Digestive...

References

1. P.K. Tan et al., "Evaluation of gene expression measurements from commercial microarray platforms," Nucleic Acids Res, 31:5676-84, 2003.