This story has been updated to reflect the accurate sources of the RNA samples used in the MAQC project.
VANCOUVER, BC — Despite being forced to extend its data analysis and discussion period by two additional months, the US Food and Drug Administration-sponsored Microarray Quality Control Consortium will release the project data and publish its results on time, according to a MAQC project leader.
Roderick Jensen, director of the Center for Environmental Health, Science, and Technology at the University of Massachusetts, Boston, affirmed last week that MAQC was still on track to release all of its data from the project this summer and publish 10 papers summarizing the results in a special issue of Nature Biotechnology in September.
MAQC will submit the manuscripts in May, Jensen told attendees at the World Microarray Congress, held here last week.
When all 200 members of the MAQC met in their last face-to-face meeting in Palo Alto, Calif., in December, the data was literally so fresh that MAQC members were putting their slides together shortly before they were scheduled to present it, Jensen told BioArray News this week.
Although MAQC members agreed in Palo Alto on a timeline to publish their results, Jensen and others in the project decided the group needed to add another invite-only meeting to its agenda to discuss the data more thoroughly, Jensen told BioArray News at the time (see BAN 12/21/2005). A preliminary timeline was scrapped in favor of the autumn publication, and the meeting was held last month in Boston. If the data analysis did not go smoothly, there was the threat that the project could be delayed further.
"Prior to this study, there was no objective way of evaluating performance."
However, the additional discussion did not slow down MAQC's progress, Jensen said. "The Boston meeting gave everyone a chance to express their concerns, worries, and positions," he said. "We are on schedule to submit a manuscript in May," he said, adding that, so far, the manuscript proofs have been a "tremendous success."
Weida Tong, a fellow MAQC leader and the director of the FDA's Center for Toxicoinformatics at the National Toxicological Research Center, confirmed the timeline and said the data will be available this summer.
"We will turn in all the papers by the end of May and the single issue on the MAQC should be out in September for Nature Biotechnology," Tong said.
"Thus, the data release date will be sometimes between June 1 and September, depending on when the manuscripts will be accepted for publication," he said.
The goal of MAQC is to provide the microarray community with metrics and thresholds to compare different gene expression platforms, and over the past year, MAQC has run two "standard" RNA samples — from Ambion and Stratagene — across eight different microarray platforms at six separate testing sites to identify the QC controls.
Jensen said that in total, the project has resulted in 10 papers and 22 million data points. He added that once users have access to the data and [analysis] they will "know what the answers should be across platforms."
"With this data set, everyone in the gene expression community will have reference data and reference samples where there's no question that there are thousands of genes that are differentially expressed," he said.
Jensen said that he is already using the QC samples in his lab to assess everything from the optimization of his scanner to technician performance.
"I have used [these controls] to evaluate scanners and reagents," he said. "If I use a new scanner, and I run the reference RNA and lose genes, then I know there's a problem," Jensen said. "Prior to this study, there was no objective way of evaluating performance."
TeleChem and the 11th Publication
Jensen said that one difference between the MAQC that went into Boston and the MAQC that came out of Boston is that data from TeleChem International's ArrayIt platform will not be included in the initial 10 papers published by the consortium.
Although TeleChem told BioArray News in December that it would be submitting data to MAQC using the controls in time for the Boston meeting, Jensen said last week that, in the end, there was just not enough time to add TeleChem to the project (see BAN 12/21/2005).
Instead, the number of official platforms used will remain seven, with arrays provided by Applied Biosystems, Affymetrix, Agilent, GE Healthcare, Eppendorf, Illumina, and an array using oligos made by Operon and printed by the National Cancer Institute, Jensen said.
Though TeleChem will be excluded from the first 10 publications, Jensen said the company will be free to publish its own data or papers on the material after MAQC publishes its results.
However, Paul Haje, a spokesperson for TeleChem, disagrees. TeleChem is in the MAQC and will be authoring the eleventh manuscript, which will be published with the other papers in September, he said.
"The MAQC project consists of a certain amount of manuscripts and we are in the one-color/two-color manuscript," Haje told BioArray News this week. Haje said the paper examines whether or not it is it "better" to use a one-color or two-color approach in a microarray experiment.
"It's a very juicy thing," he said of the project. "There are all these platforms being done [and evaluated] in regards to probe design, bioinformatics, and how the chips perform in labs. All this is being sorted out now in the final manuscripts which will be presented in Nature Biotechnology," Haje said.
Jensen also said that the data produced by the study had biological content that may interest future investigators as well. "There's actually real biology in this data, so there will be many more opportunities for people to investigate."
— Justin Petrone ([email protected])