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Standardized microarrays show promise

5 May 2005   |   By Dr Philippa Brice   |   News story

Three new reports published in the latest edition of Nature Methods agree that the use of microarrays can yield more reproducible results than previous analyses have suggested, provided that standardized protocols and data processing are used. Microarrays are platforms that allow the simultaneous analysis of expression from thousands of genes, allowing researchers to identify patterns of gene expression that are associated with specific tissues and diseases. They are already being used in clinical trials for use in determining the prognosis and hence treatment options for breast cancer patients.

A study led by the US National Institute of Environmental Health Sciences (NIEHS) funded Toxicogenomics Research Consortium, comprising seven different centres, to assess the causes of variation between gene expression experiments and different microarray platforms has been running since 2001.These researchers report that using a standardized process led to more consistent results, and that using commercially manufactured microarrays made results more reproducible [Bammler T et al. (2004) Nat Methods 2, 351-356]. Dr Brenda Weis, one of the authors of the report, commented: "So far, gene expression data have been very useful in understanding diseases and biological processes…But if we standardize protocols the knowledge we gain from microarray studies can be used to improve clinical practice", adding: "If microarrays are to be used effectively in the clinic to diagnose patients and design patient-tailored therapies, they will need to be like any other clinical tests; they will need to be standardized" (see NIH press release).

A further two studies lend weight to these conclusions. One compared gene expression between two microarray platforms and using different experimental treatments, and concluded that biological treatment had a far greater overall impact on measured gene expression than the use of different platforms [Larkin JE et al. (2005) Nat Methods 2, 337-344]. The second compared microarray analysis data from ten different laboratories generated using identical RNA samples on three different platforms. This group found that different labs using the same RNA and the same microarray platform could produce significantly divergent data; but that the “best-performing” laboratories produced fairly consistent results [Irizarry RA et al. (2005) Nat Methods 2, 345-350]. Taken together, these results are encouraging endorsements of the potential value of microarrays in harnessing genomic information for clinical benefit.

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