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Different microarray systems more alike than previously thought

n agree rather well, and that there is a large lab effect that accounts for why others thought comparisons revealed inconsistencies."

"This is good news for many people," said Forrest Spencer, Ph.D., associate professor at Johns Hopkins' McKusick-Nathans Institute of Genetic Medicine. "Given appropriate and careful analysis, it should be possible to compare historical data to future experiments, even if the technology changes or people make different choices in their platform."

When the study began roughly two years ago, microarray platforms were an exciting technology in the medical and biological sciences, but comparisons of results from different platforms had proved inconsistent. Previous studies indicated that Affymetrix GeneChips, for example, the commercially available and most expensive of the three platforms tested, provided different results from other platforms.

Affymetrix GeneChips provided highly reproducible, or consistent results, but for a laboratory on a budget, more cost-effective in-house systems were attractive.

"Technical choice of microarray platforms is a key issue for people who want to look at changes in gene expression. It is important for both cost and quality of data," she said. "But people are in need of clear information in making the choice."

For the study, five expert labs used Affymetrix GeneChips, three used "homemade" versions called two-color spotted cDNA arrays, and two used another commercial platform called two-color long oligonucleotide arrays. In general, the study showed Affymetrix GeneChips generated more reproducible data than the other microarrays.

But the researchers also showed that any of the platforms can be quite good -- or bad. The overall best performance came from one of the labs using a two-color long oligonucleotide array, with better statistical results in accuracy and precision than the remaining nine labs. However, the other lab using the two-color long oligonuc
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Source:John Hopkins Medicine


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