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Different microarray systems more alike than previously thought

A multicenter comparison of equipment that can analyze the expression of thousands of genes at once to create a genetic "fingerprint," suggests these different microarray technologies are more alike than once thought.

Published in the May 2005 issue of Nature Methods, the study provides new hope that the mounds of information generated by these systems might actually be comparable, even though many different systems are used by many different laboratories.

"Biologists occasionally ask me what is the best platform on which to run microarray experiments, but there hasn't been a good answer to that question," said Rafael Irizarry, Ph.D., associate professor of biostatistics at the Johns Hopkins Bloomberg School of Public Health. "Now we see the possibility that it may not make much difference as long as the systems are used properly and the results reported properly."

The impact of such a finding is not insignificant, experts say, because these systems may ultimately allow scientists to uncover critical differences between, say, healthy and cancerous tissue. Unless laboratories can rely on each others' results, such findings would not have much value.

For the study, 10 laboratories in the Washington, D.C./Baltimore area were given identical samples of RNA -- DNA's cousin -- to analyze using a microarray platform of their choice. Five laboratories used commercially available Affymetrix microarrays, and five labs used either of two more flexible systems.

The Hopkins researchers noted that in the scientific literature some comparisons of different microarray systems found compatibility and some did not, and no study explored the possibility that a laboratory's methods of using a particular system affected the results.

"Given the amount of tinkering that occurs in some labs, my intuition was that different labs might obtain very different answers even when using the same platform," said Irizarry. "But we show that platforms ca
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Source:John Hopkins Medicine


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