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New RNA control standards will improve ability to characterize performance of gene expression assays
July 2007
by Jeffrey Bouley  |  Email the author
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SANTA CLARA, Calif.—The External RNA Controls Consortium (ERCC) recently brought approximately 100 of its selected external RNA controls into a final testing phase, which will be completed by the end of 2007. Once the phase is complete, The National Institute of Standards and Technology (NIST) will advance the controls through its Standards Program to make the set available to researchers around the world as a standardized DNA reference material—marking the first-ever standardized DNA control reference set created in this way.
 
"What we're trying to do is give people a set of tools—standards that we are developing, analysis approaches and defined protocols—by which they can characterize the technical performance of their gene expression assays," says Dr. Marc Salit, a research chemist at NIST who in May took on the responsibilities of chairing the ERCC from previous chair Dr. Janet A. Warrington, who is vice president, Advanced Applications and Standards Development at Affymetrix. "So, using these external controls which are added to a normal study sample of interest, you can assess the performance of the assay independent of your sample of interest. And what that does is give you an idea of the technical veracity, if you will, for your data."
 
Salit is quick to point out that these new control standards won't be able to give any potential drugs a green light, because there are "too many things that go into samples and too much biological variability." But some of the key things it can do is to ensure that no steps were skipped and that the testing platform's measurement process works well.
 
"What is does is give you a 'yellow light' to keep moving forward if things check out OK, or it gives you a 'red light' if they don't," he explains. "That way, you don't spend six months trying to characterize something when all along you've had some sort of data anomaly going on."
 
The ERCC is an international group of close to 200 scientists who represent more than 90 organizations in 16 countries. The team is working together to define a set of well-characterized standard RNA controls and protocols for gene expression assays. NIST will help guide the controls through the final testing phase, which includes validation by a second independent characterization method.
 
"The ERCC is a great example of the public and private sector, including competitors, coming together for the common goal of developing a set of controls that will help accelerate development and adoption of expression-based clinical applications," Warrington says. "Soon, scientists everywhere performing gene expression experiments will benefit from a common set of standardized controls of known provenance and have a better understanding of sources of variability and data quality."
 
The biggest interest in using these controls will be among those using microarrays, Salit says, but that doesn't mean that is the only market. He says the controls are also useful for other gene expression assays, both current and next-generation, that are not microarrays.
 
The results from the first round of collaborative testing look promising, Salit reports, and that involved five different platforms at four sites, with a "great concordance of results," he notes. The ERCC is now moving into more complex tests and expects to have standards out for the sequence library in about a year and RNAi standards probably around six months thereafter.
 
Code: E070714

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