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Federal microArray quality control study

DTI Globalwatch : 18 October, 2006  (Technical Article)
The FDA-led MicroArray Quality Control project findings announced show that microarray gene expression data from the commercial platforms tested in the study show high degrees of correlation. The results, published in the peer-reviewed journal Nature Biotechnology, indicates that scientists have the ability to choose a gene expression platform based on value, ease of use and quality of content, with little to no legacy data concerns.
The MAQC project successfully compared multiple whole-genome gene expression profiles across various commercial platforms at an unprecedented scale. It showed that there was a relatively high level of agreement between all platforms as well concordance with reverse transcription PCR technology, a separate technique for measuring differential gene expression, confirming that microarray data is directly comparable, accurate and biologically significant.

'The MAQC project observed intraplatform reproducibility across test sites as well as high interplatform concordance in terms of genes identified as differentially expressed,' said Leming Shi, MAQC project director at the U.S. Food and Drug Administration's National Center for Toxicological Research. 'One major result was that platforms with divergent approaches often generated comparable results of differential gene expression. In other words, the differential gene expression patterns generated were reflective of biology regardless of the difference in technology platforms.'

'Given such high levels of concordance, choosing a gene expression platform should primarily be driven by such factors as cost, ease of use and quality of content,' said Shawn Baker, Illumina's gene expression scientific product manager. 'Illumina's BeadChips, which were shown to consistently be among the very best performers across the various technical measurements assessed by the MAQC, are also substantially less expensive than all other commercial whole-genome arrays used in the study. With array and reagent costs less than half that of other commercial arrays, the use of Illumina BeadChips allows for experimental designs to be expanded, yielding more powerful and farther-reaching results with the same research budget.'

The MAQC results pave the way for microarray researchers to tackle the legacy data issue. Until now, researchers have hesitated to use the latest microarray gene expression technology due to concerns around inconsistent data when comparing new findings against research derived from older or different microarray technology. Similar results have been validated elsewhere. Illumina is working with industry leaders to develop tools that will facilitate migration of legacy data to its gene expression platform.

The MAQC project was established to generate a set of quality control tools and standards for the microarray research community and advance pharmacogenomics and bioinformatics for more effective medicines and medical products. The project involved 137 participants representing 51 organizations, including the FDA, NIH, EPA and USDA, all major whole-genome gene expression platform providers including Illumina as well as several alternative gene expression platform providers. MAQC included validated reference samples, a large collection of multiplatform reference datasets as well as analysis tools. As a MAQC project participant, Illumina has posted its gene expression data at
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