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FDA Spearheads Microarray Quality Control Project

  September, 13 2006 9:56
your information resource in human molecular genetics
A major, multi-center study comparing the reliability of an emerging technology for measuring human gene expression is reported in the September issue of Nature Biotechnology. The MicroArray Quality Control (MAQC) project examines the performance of seven different DNA microarray products with a view to assessing not only their reliability from experiment to experiment but also the best approaches for analyzing resulting data.

DNA microarrays are devices that contain thousands of short DNA sequences spotted onto a surface that can be used to detect the levels of specific molecules produced by human genes. They can be used, for example, to detect patterns of mRNA transcripts that are elevated in diseased tissues compared with healthy tissues. Although they have been employed in basic research for over a decade, one problem facing the technology is a lack of consensus concerning best practice not only for how to design microarray experiments and prepare tissue samples, but also the approaches used for acquiring and interpreting data.

To address this problem, the US Food and Drug Administration brought together more than 100 scientists from over 50 academic, industrial and government organizations to examine the performance of six commercial DNA microarray products and a custom-made DNA microarray conduct in measuring the expression levels of two 'reference' human RNA samples. The results from product to product were remarkably consistent in predicting which genes were differentially expressed and also correlated well with measurements from three more traditional methods of assaying mRNA transcript levels. The large amount of data generated by the consortium provides the community with a thoroughly characterized reference data set against which new refinements can be measured in the future.

The results of the MAQC project represent a first step in establishing guidelines and quality control procedures by regulatory agencies. DNA microarrays are likely to be at the forefront of future approaches that target the molecular causes of diseases rather than their symptoms, and the validation of the technology by a consortium headed by government scientists is an important step in realizing the potential of molecular approaches both in healthcare and environmental testing.

Articles/Papers available online:
Research Article 1.
Research Article 2.
Analysis Paper 1.
Analysis Paper 2.
Analysis Paper 3.
Analysis Paper 4.

Author contacts:

Leming Shi (National Center for Toxicological Research, US FDA, Jefferson, AR, USA)
E-mail: leming.shi@fda.hhs.gov

Federico Goodsaid (Center for Drug Evaluation and Research, US FDA, Silver Spring, MD, USA)
E-mail: Federico.Goodsaid@fda.hhs.gov

Weida Tong (National Center for Toxicological Research, US FDA, Jefferson, AR, USA)
E-mail: weida.tong@fda.hhs.gov

Tucker Patterson (National Center for Toxicological Research, US FDA, Jefferson, AR, USA)
E-mail: tucker.patterson@fda.hhs.gov

Richard Shippy (GE Healthcare, Tempe, AZ, USA)
E-mail: richard.shippy@ge.com

Lei Guo (National Center for Toxicological Research, US FDA, Jefferson, AR, USA)
E-mail: lei.guo@fda.hhs.gov

The following authors can also be contacted for additional comment:

Foreword Author
Daniel Casciano (University of Arkansas for Medical Sciences, Little Rock, AR, USA)
E-mail: dcasciano@sbcglobal.net

Commentary Author
Felix Frueh (Center for Drug Evaluation and Research, US FDA, Silver Spring, MD, USA)
E-mail: dix.david@epa.gov
Commentary Author
Hanlee Ji (Department of Medicine, Stanford University, CA, USA)
E-mail: genomics_ji@stanford.edu

(C) Nature Biotechnology press release.

Message posted by: Trevor M. D'Souza

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