With its samples run and data collected, one could say that the Microarray Quality Control consortium is getting closer to accomplishing what it set out to do: To establish QC metrics for assessing performance across microarray platforms and evaluating the advantages and disadvantages of different data-analysis methods.
Still, when the members of the US Food and Drug Administration-led group convene in Palo Alto, Calif., on Dec. 1-2, those holding leadership positions in MAQC are certain there will be much to discuss.
According to Weida Tong, director of the Center for Toxicoinformatics at the FDA's National Center for Toxicological Research, MAQC has three main objectives for the Palo Alto meeting.
"[The first is] to exchange analysis results on the microarray data generated from seven microarray platforms and three alternative platforms based on four human reference RNA samples," he wrote to BioArray News in an e-mail this week. "[The second is] to agree on the main focus of the next step of the project," which may include using mouse and rat as models in the organization's continuing effort to create QC standards. MAQC used human RNA samples from Ambion and Stratagene to create its initial dataset, according to MAQC's website.
Tong said that the third ambition of the December MAQC meeting will be "to agree on the topics for and the teams who will work on about 10 manuscripts that describe the main outcomes of the project."
Of the three aims, Tong, whose NCTR is one of six FDA centers involved in the project, said that the need to finalize a publication schedule for the results of the MAQC project was the most important objective for Palo Alto.
MAQC member Roderick Jensen, the director of the Center for Environmental Health, Science, and Technology at the University of Massachusetts, Boston, told BioArray News this week that another important objective will be reaching consensus on the QC metrics that have been determined. He noted that MAQC is a fairly large group.
"There are more than 40 different companies, universities, and national laboratories involved in this study," Jensen said. "The goal of the Palo Alto meeting will be to compare the preliminary analyses of a large data set containing gene-expression data for two standard, commercially available RNA samples on six human whole-genome microarray platforms," he said. The platforms are made by Applied Biosystems, Affymetrix, Agilent, GE Healthcare, Illumina, as well an array using oligos made by Operon and printed by the National Cancer Institute, Jensen said.
"The meeting will be a success if there is a consensus on QC metrics that can be used to evaluate the relative performance of the DNA microarary platforms which can then be used to clearly demonstrate the high concordance of the different commercial DNA microarray platforms with each other and with QRT-PCR," Jensen said.
Damir Herman, a National Center for Biotechnology Information investigator who is a steering member of MAQC's probe-sequence based cross platform comparison group, told BioArray News this week that he believed MAQC has done well in terms of timing, and that the data from the project "will be publicly available once the first round of work has been submitted in a series of publications in February next year."
"The timeline now is to see where we are at in Palo Alto and to discuss what the next step is," Herman said. He said that MAQC will meet again in autumn 2006 to discuss microarray quality control and data analysis project ideas.
Herman added that the FDA plans to issue a guidance on microarray quality control and data analysis stemming from the MAQC project in late 2007.
— Justin Petrone ([email protected])