BOSTON — The External RNA Controls Consortium, an ad hoc group of nearly 100 partners from industry, government, and academia seeking to develop a list of microarray and RT-PCR experimental controls, will initiate the first phase of testing the controls next month and plans to start the second round of testing in the spring of 2007, according to an ERCC official.
Janet Warrington, vice president of emerging markets and molecular diagnostics R&D at Affymetrix and an ERCC leader, told attendees of IBC Life Sciences’ Discovery 2 Diagnostics meeting, held here this week, that the project will be split into two testing phases and will be followed by a review of the results, a general meeting, and, eventually, publication of the controls in a scientific journal.
Warrington declined to commit to a date for when the controls will be published. An earlier date floated for completion was mid-2006, but with the testing sites just selected last month and testing scheduled into next spring, it is likely that the ERCC may not officially publish until the second half of 2007, at the earliest.
In a follow-up e-mail exchange with BioArray News this week, Warrington laid out the consortium’s agenda. “The first phase will be focused on confirming labeling, concentration response and will include testing for cross hybridization. We anticipate being ready to go in November 2006,” Warrington wrote. “That will be followed by testing to evaluate control performance when they are spiked into complex samples, concentration response, and modified Latin square experiments,” she added.
“Test sites will use protocols recommended by platform manufacturers. We anticipate that those experiments will be carried out in the spring of 2007,” she wrote.
As the ERCC said last month, the sites that have volunteered to participate in testing the controls include Affymetrix, Agilent, Applied Biosystems, GE Healthcare, Illumina, the National Institute of Allergy and Infectious Disease, Qiagen, and Roche Molecular Systems.
The controls will be tested according to the ERCC Test Plan published in BMC Genomics last year.
The test plan, a document that lays out approximately 100 controls for microarray and QT-PCR experiments and a plan on how to test them, was originally accepted by the ERCC in October 2005 (see BAN 10/12/2005).
As the project nears its conclusion, “a meeting will be held to report the results,” Warrington said. “The meeting will be open to the public and the results will also be reported in a publication and the data will be deposited publicly,” she added.
According to Warrington, the ranks of the ERCC have surged to 92 members from around 70 a year and a half ago, and many are interested in seeing the project through its conclusion.
“Standard controls and best practices are required to achieve success in implementation and acceptance in clinical studies, trials, and diagnostics,” Warrington said. “We believe that the cooperation of public and private sectors accelerates the development work and is a very efficient way to develop tools that will benefit everyone engaged in this area,” she added.
Though the official controls will not be available until sometime in 2007, or even 2008, the untested controls have been made available to those who can’t wait another 18 months, like pharma and biotechs. In August, the Clinical Laboratory Standards Institute, a global non-profit standards organization, announced the publication of the controls, which are for sale through CLSI.
The document, Use of External RNA Controls in Gene Expression Assays; Approved Guideline, is available to CLSI members for $60 and non CLSI members for $120.
Warrington explained the need to release the controls document early in an interview with BioArray News in May 2005."It's a priority [to release them early] because people are coming out with tests. So even if people aren't using the standard controls, it's something. End users need the controls, need to know how to use them, and need the software tools to analyze them," she said (see BAN 6/1/2005).
Warrington assured BioArray News this week that CLSI’s document will be updated when the ERCC publishes its final results. “CLSI has a regular process for review and revision of documents,” she said.