The National Institute of Standards and Technology (NIST), in cooperation with the External RNA Controls Consortium (ERCC), has awarded a contract to Commonwealth Biotechnologies, Inc. (CBI, Richmond, Va.) to produce suites of RNA test samples that will be evaluated in two rounds of a collaborative study through this winter. The study represents a major milestone in the ERCC's program to develop a standard set of RNA control samples that will be used to assess the performance of gene expression experiments.
Gene expression, a measure of the activity of specific genes under various conditions, is a cornerstone of modern bioscience. Gene expression is often measured across entire genomes—measuring as many as 50,000 different chemical entities simultaneously—presenting a unique measurement challenge in assessing the validity of experimental results. The approximately 90 companies, universities and federal laboratories in the ERCC are developing materials and tools that can be used to benchmark the most widely used tools for gene expression, including quantitative, real-time reverse transcriptase polymerase chain reaction (QRT-PCR) and DNA microarrays. NIST is a founding member and host of the consortium.
NIST has assembled a sequence library of approximately 160 sequences that are intended to act as controls. Many of these are synthetic constructs that mimic mammalian genes, but which can be found in no known genome*. CBI will synthesize mixtures of these sequences as RNA for use in the collaborative study, which will establish a "reference set" of RNA controls. The eight registered testing sites represent companies that manufacture microarrays and reagents and one government laboratory that makes arrays: Affymetrix Inc. (Santa Clara, Calif.), Agilent Technologies Inc. (Santa Clara, Calif.), Applied Biosystems (Foster City, Calif.), GE Healthcare (Chalfont St. Giles, U.K.), Illumina Inc., San Diego, Calif.), the National Institute of Allergy and Infectious Diseases (NIH), Qiagen N.V. (The Netherlands) and Roche Molecular Systems (Pleasanton, Calif.)
"The ultimate goal of the collaborative study is to determine a set of sequences that will give reliable, repeatable values across a variety of gene expression assay techniques," notes Marc Salit, NIST's representative on the ERCC, "That will give the research community something that they're all interested in—a solid, quantitative way to establish performance and gain confidence in their data, regardless of platform or assay." The ERCC plans to announce the results of the collaborative study in a public meeting in September 2007.
*The sequences collected in the library to date were contributed by NIST and the Hollings Marine Laboratory (Charleston, S.C.), the National Institute of Allergy and Infectious Diseases, Stanford University, Affymetrix, Invitrogen Corporation (Carlsbad, Calif.), and Atactic Technologies Inc. (Houston, Texas).