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MAQC Consortium Prolongs Data Analysis to Feb. 06; Publication Delayed Until Next Fall


After determining that it needs an additional meeting to discuss data analysis, the Microarray Quality Control consortium has decided to hold another meeting in Boston on Feb. 3-4, and to delay publication of its results until next fall, according to several MAQC leaders.

MAQC, which aims to establish QC metrics for assessing performance across microarray platforms and evaluating the advantages and disadvantages of different data-analysis methods, had planned on wrapping up data analysis and finalizing a publication schedule during a meeting in Palo Alto earlier this month, but leaders said they just needed more time (see BAN 12/7/2005).

"We realized that we didn't have sufficient time to really put the effort into data analysis, so we decided to have additional meetings that will be held in Boston," said Weida Tong, director of the Center for Toxicoinformatics at the US Food and Drug Administration's National Center for Toxicological Research.

While Tong called the Palo Alto meeting a success, he said members of MAQC's data analysis team had requested more time to be confident in the analysis. Tong said that in some cases the information presented earlier this month was only days old at the time.

"Most of the results are quite consistent," he said, "but it is difficult to say because everybody had such little time to look into the results, and they all expressed a desire to analyze more. Hopefully, we'll have more concrete conclusions from the data analysis in the Boston meeting."

"Some of the 22 million data points had only been received a few days before and many of us were still preparing PowerPoint slides as we walked to the podium."

MAQC member Roderick Jensen, director of the Center for Environmental Health, Science, and Technology at the University of Massachusetts, Boston, will host the February meeting. He said that it would include MAQC's analysis groups, authors of manuscripts, and industry representatives. The location of the meeting on UMass' Boston campus has yet to be determined, Jensen told BioArray News this week.

In Boston, data analysis teams will sort through 22 million data points collected from 30 test sites on seven microarray platforms and three alternative technologies, all of which ran the same four human RNA reference samples.

"The data presented at the Palo Alto meeting was very preliminary," explained Jensen. "Some of the 22 million data points had only been received a few days before and many of us were still preparing PowerPoint slides as we walked to the podium," he said.

"Each presenter only had 10 minutes to describe their preliminary results and there were many open questions about the interpretation of the data and error flags from the different manufacturers and in the choice of metrics to be used to compare the data," he said.

"Finally, there was little time to discuss any discrepancies in the conclusions from different presentations. All of these questions should be resolved in the next six weeks by careful comparisons of the different analyses and, most importantly, the many different assumptions that underlie any particular comparative analysis," Jensen said.

The Eighth Platform

The extension of the data analysis deadline to February has enabled MAQC to take on an eighth platform for the project, according to Damir Herman, a National Center for Biotechnology Information investigator who is a steering member of MAQC's probe-sequence based cross platform comparison group.

Herman told BioArray News this week that TeleChem International's whole-human-genome array had been added as the official eighth platform of MAQC. MAQC platforms are also 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.

According to Mark Schena, a consultant with TeleChem, the company's data was generated using testing sites at Yale University and Wake Forest University, and should be ready for submission to MAQC soon. The testing was done on TeleChem's H25K Human Genome platform.

"Our expectation is that the data will be available literally in days," he told BioArray News this week.

Publication Delayed … Rats!

Because the MAQC project will not be able to finalize its data analysis until February, Tong said that the consortium will most likely submit manuscripts for a supplementary issue of Nature Biotechnology in May, and that it will probably take until September for that publication to review the manuscripts and publish them.

However both Tong and Herman said that MAQC is looking for alternative ways to get the QC metrics and the data to the public before September.

Tong said that after the manuscripts are submitted, MAQC will make the data available on its website using the FDA's free ArrayTrack microarray data management and analysis software. Herman added that MAQC may "advertise" its progress in an earlier issue of Nature Biotechnology.

"We are discussing the possibility of having a forerunner publication that predates the complete MAQC study by a few months, preferably in the same journal," he said. "In that paper we would like to advertise the MAQC project and send out a strong optimistic message to the microarray community about the present status of the technology," he said.

Tong also said that MAQC will be holding brainstorming meetings over the next few months to discuss the consortium's future plans. He said that MAQC may embark on a similar project to develop QC metrics for array experiments that use the rat model.

"We will conduct a rat experiment, but not exactly the same as human because the nature of the rat is different from human. We will be able to do a more controlled experiment for the rat, so we would probably be more interested looking into the biological questions along with the quality control for the rat project," Tong said.

Tong said the rat project could coalesce by the MAQC meeting scheduled for Research Triangle Park, NC, in February 2007.

— Justin Petrone ([email protected])

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