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BioInform Guidelines on the Way? FDA Delves into Microarray Data


By Bernadette Toner

The US Food and Drug Administration is rolling up its sleeves and diving elbow-deep into the messy world of microarray data as it girds for a potential wave of genomics-derived information submitted as part of the drug approval process.

At a June meeting of the FDA’s pharmacology/toxicology subcommittee on pharmacogenomics, the agency took its first steps toward tackling the questions of whether, when, and how it will accept data from microarray experiments submitted under investigational new drug or new drug applications.

“[FDA reviewers] haven’t seen microarray data,” says William Mattes, associate director at Pfizer’s Kalamazoo Genomics Center of Excellence, who attended the subcommittee meeting. “They’re concerned about how to handle it, they’re concerned about its analysis, they basically are concerned about what does it look like, what does one do with it?”

As a first step in familiarizing itself with the nuances of microarray data, the FDA’s Office of Testing and Research has embarked upon two separate gene expression database projects. One, in collaboration with Iconix, will introduce FDA reviewers to the basics of microarray data via the company’s DrugMatrix toxicogenomics database. A second project, with Schering-Plough and Affymetrix services provider Expression Analysis, will create an internal “mock submission” database for gene expression data. The outcome of these database projects will shape a draft guidance document the FDA is preparing on the submission of microarray data that may be out as early as this month.

The FDA has had access to the DrugMatrix database since March, when it began a collaboration with Iconix to gain hands-on experience with toxicogenomics data and tools. Iconix is training FDA reviewers in quality control and quality assurance for microarray data generation, as well as analysis of data across multiple microarray product platforms, and the validation of biomarkers from integrated chemogenomic datasets.

The goals of the planned internal gene expression database are a bit different than the Iconix project. In this effort, FDA, Expression Analysis, and Schering-Plough will build a framework to support the mock submission of data from a drug project Schering discontinued. “We’re taking that data, which includes microarray data, histology data, clinical chemistry data, and phenotype data, and helping FDA to understand the appropriate format, content, and context of microarray-based submissions,” says Steve McPhail, CEO of Expression Analysis. A final report on that project is planned for November.

Parallel Effort

The FDA’s database activities are not without precedent. A project spearheaded by the International Life Sciences Institute consortium and the European Bioinformatics Institute has been developing a centralized, public gene expression database using EBI’s ArrayExpress for more than a year, with plans to bring it online by the first quarter of 2004.

“The intent of the ILSI effort was to establish some public offering that could be helpful in developing standards,” says Pfizer’s Mattes, who is on the ILSI database working group. Building on the MIAME (minimum information about a microarray experiment) guidelines, the project has drafted a revised version of the standard called MIAME/Tox that aims to establish some consensus on the minimal descriptors for array-based toxicogenomics experiments.

FDA could save itself some duplication of effort — and perhaps a lot of headaches — by communicating with the ILSI group. They have made some headway into the very issues that FDA plans to address with its own database, but so far there has been no formal involvement between the two groups, Mattes says.

No matter what, a great deal of work remains before the FDA is able to determine when and how microarray data should be included in the regulatory process, Mattes says. “I think we’re trying to work out the nuts and bolts before we get there.”

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