SEATTLE — The External RNA Controls Consortium, a 2-year old organization that has joined the biochip industry with the US government and the biggest names in global pharma on a mission to standardize microarray data, will most likely have a set of group-endorsed standards in the hands of users by 2006. The consortium also plans to make pre-approved protocols available as soon as this summer, a leader of the ERCC told BioArray News at the Northwest Gene Expression Conference held here last week.
The controls will be the final product from a group of 70 members from more than a dozen countries and 50 different organizations that have come together to standardize the data that is coming out of microarray experiments conducted by the membership. Demand for these standards is on the rise as molecular diagnostics and pharmaceutical companies are increasingly using microarray data in their submissions to the US Food and Drug Administration.
Janet Warrington, vice president of research and development at Affymetrix and is head of the consortium, said that the ERCC finished collecting 140 sequences it plans to test across several platforms on May 18, following a group meeting in Boulder, Colo. She added that the consortium has completed a final draft of a document that will detail how testing sites will run the experiments.
Warrington said that the group has "collected 140 sequences that they need to test across all major microarray platforms to collectively identify a subset of controls." Warrington said that testing would be done on the dozen or so platforms of major array manufacturers, including Affy, Applied Biosystems, Agilent, Illumina, GE Healthcare and others.
"The test plan is to lay out how we are going to do that," she explained.
Warrington said that the ERCC will make the testing plan available for public commentary this summer, and that the final input from the user community will be taken into consideration when the group gathers at its next meeting in October.
"Once we get the blessing of the community, we will work to do the testing," Warrington said. "If everything goes well in the October meeting, testing could go forward in the fourth quarter of [this year], [which means] that we could have the controls in 2006," she said.
According to Warrington, while the standards will have a positive impact on all involved, the FDA is driving the work of the organization.
"The FDA wants to have some reference point on understanding probes and array data or RT-PCR data," she said.
According to Warrington, the ERCC holds open workshops once or twice a year. Members include chip makers, array-based diagnostic developers, and drug makers that wish to use array data in their FDA submissions. Among the 70 members are Affymetrix, ABI, Agilent, Illumina, Stratagene, Invitrogen, CombiMatrix, Expression Analysis, the Mayo Clinic, Eppendorf, Eli Lilly, Roche Molecular Diagnostics, BioMerieux, the US Centers for Disease Control, the FDA, Celera Diagnostics, and the National Institute of Standards and Technology, which hosts the ERCC.
Warrington added that once the testing plan is given the final thumbs-up in October, testing will proceed at multiple sites, and will be undertaken by microarray manufacturers, such as Affymetrix, so-called "neutral" sites like NIST and the CDC, and by diagnostic firms, like Affy collaborators Roche and BioMerieux.
To increase comparability across platforms, Warrington said that software tools are being developed by researchers at Agilent and Affymetrix for microarray analysis at all testing sites. The data will then be shared and the controls agreed upon by the ERCC.
"They will share data after testing and identify acceptable performance," Warrington said.
While the controls developed by the ERCC will help pharma and molecular diagnostics companies in 2006 by aiding them in creating data that is less questionable to regulatory agencies, Warrington told BioArray News that the ERCC understands that some companies cannot wait a year for the final controls to be released.
To meet the needs of this subset of end-users — who no doubt include Affy partners like Roche Molecular Diagnostics, Veridex, and BioMerieux — the ERCC may release a pre-approved document outlining protocols before the end of the year, Warrington said.
"They could be published this year and available for a nominal fee," she said. "It's a priority because people are coming out with tests," Warrington said. "So even if people aren't using the standard controls, it's something."
Warrington said that "end users need the controls, need to know how to use them, and need the software tools to analyze them." The early-access protocols will be available through the Clinical and Laboratory Standards Institute — a global, nonprofit, standards-developing organization.
BioArray News attempted to contact CLSI for further details, but the organization did not respond by press time.
ANOTHER STEP TOWARD STANDARDIZATION
If the ERCC does release its controls for sample preparation next year, then 2006 may very well be the first year that the microarray industry has some real documentation on how to standardize experiments and get results that are comparable from lab to lab and platform to platform.
ERCC's progress follows on the heels of a similar initiative at the Toxicogenomics Research Consortium, a large collaborative research program comprising six universities and the Microarray Group of the National Institute of Environmental Health Science's National Center for Toxicogenomics. Last month, the Toxicogenomics Research Consortium published a study that outlined protocols for standardizing gene expression analyses.
Entitled, 'Standardizing global gene-expression analysis between laboratories and across platforms,' and published in last month's issue of Nature Methods, the study highlighted protocols developed by seven laboratories running standard mouse RNA on 12 selected platforms that increased the comparability of data from lab to lab, platform to platform (see BAN 5/4/2005).
While that study generally dealt with synchronizing image analysis software, sample preparation, and array-production from lab to lab, researchers at NIEHS also plan to encourage a greater use of community-approved standards between microarray users.
In an interview with BioArray News this month, Brenda Weis, the lead author on the study said that the industry was "crying" for standardization.
"Every forum we go to, in every one of those communities, they are crying to know what to do, how to do it, and what is most important. The application is clearly there in the clinical, drug development, pharma arena," she said.
Still, the focus of the two organizations differs. The TRC has set out to provide standard protocols for use by the research community in general, and has developed protocols for researchers that use homebrew arrays as well as commercial arrays. The ERCC's angle is far more commercial, and these protocols will impact pharma and molecular diagnostics companies as they seek to use arrays in their application and production of data on their way through the FDA's approval process.
— Justin Petrone ([email protected])