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Study: 'homemade' gene expression technology unreliable

r these were of greatest importance.

Spencer's group is using the technology in two National Institute of Environmental Health Sciences (NIEHS) centers led by CROET ?one with Oregon State University and the Battelle-run Pacific Northwest National Laboratory focuses on mechanisms underlying Superfund chemicals with neurotoxic properties; the other with the OHSU School of Medicine's Department of Pediatrics focuses on neurotoxicogenomics and child health.

Srinivasa Nagalla, M.D., associate professor of pediatrics, and cell and developmental biology, OHSU School of Medicine, led the initial bioinformatics research that supported the Nature Methods publication.

"The gene chip is a revolution in technology that is hoped rapidly to advance understanding of biological mechanisms and methods to assess the actions and effects of drugs and chemicals," said Spencer, who estimates there are "hundreds, if not thousands" of laboratories around the country using DNA microarrays.

Microarray platforms came into widespread use about five years ago. Pioneers in the field constructed their own gene chips, but these have now been replaced by much more reliable commercial platforms that generate highly reproducible data. One of these is used by CROET and another by OHSU's West Campus microarray resource facility.

"It's possible to buy a robot which will take some copies of RNA on a small pin and then write that on a glass slide repetitively until one can build up hundreds of thousands of different spots on this glass array," Spencer said.

But as commercial platforms improved over time, many laboratory or "home-built" platforms have not, he said. "The fruits of the research done on some of the early homemade and early commercial platforms have entered the literature, but the platforms were not reliable because they did not produce reproducible results."

Spencer co-authored the Nature Methods study, titled "Standardizing Global Gene E
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Source:Oregon Health & Science University


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