Last month, the Association for Biomolecular Resource Facilities’ Microarray Research Group committee expected to launch its industry-wide survey of microarray variability, based on an earlier study confined to MARG member labs. Led by chair Andrew Brooks, a professor at the University of Rochester Medical Center, MARG hopes that the study will create a benchmark for investigators to compare their microarray results.
Array users can find instructions on the ABRF website to deposit their array data at an FTP site located at Rochester’s genome center. Data collected will record the type of chip, lot number, species, and tissue type. Brooks emphasizes that to maintain anonymity, nothing will be recorded about biology or the particular experiment a chip was involved in. The goal is to analyze the same types of information as the pilot study, according to Brooks: “3’ and 5’ ratios for integrity, hybridization studies, control genes as indicators for chip reproducibility, overall number of genes, and their presence or absence.” The study is also expected to reveal sources of variability on Affy chips, “which we know is probably going to give us different results from what they see,” Brooks says.
The data collection should end late this month, with results published in a peer-reviewed publication. “We want people to have a benchmark to be able to see what everyone else is doing,” he says. One idea: “access to a database that says, ‘This is what 900 mouse liver arrays look like.’ It’ll be really helpful … to smaller labs and core facilities” in particular, Brooks says.
Even before the FTP site launched, a major pharma and large academic lab had committed to submit more than 1,000 arrays to the study. “I think it’s going to be a good turnout,” Brooks says.
— Meredith Salisbury