Getting on the same page

Gene Logic-FDA collaboration sets stage for establishing quality control standards for submission of genomics data

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GAITHERSBURG, Md.—GeneLogic Inc. recently entered into a collaboration with the United States Foodand Drug Administration (FDA) to share quality control methods and metrics thatmay be useful in better understanding disparate genomic data that are sent bypharmas and biotechs as part of regulatory submissions.

According to Gene Logic, the collaboration is part of theFDA's Critical Path Initiative, an effort to stimulate and facilitate the useof new scientific and technical methods, such as computer-based predictivemodels and biomarkers for safety and effectiveness. The overriding goal of thatinitiative is to improve the predictability and efficiency of drug developmentfrom laboratory concept to commercially approved medicines.

The reasons for pursuing this specific genomicscollaboration are critical on both the pharmaceutical and government sides ofthe equation, notes Dr. Donna Mendrick, Gene Logic scientific fellow and vicepresident of toxicogenomics. With no federal or industry standards in place forassessment of the quality of genomic data submissions to the FDA, it is hard toknow which data are good and which data aren't. The results of theFDA-Gene Logic collaboration will be released publicly, she says, as an earlystep in creating industry-wide standards for genomic data assessment. Theoutcomes of the collaboration won't be the final word, most likely, but theywill be a step toward achieving a common understanding of key microarray QCprocedures that will help shape microarray data standards for the submission ofmicroarray data to the FDA.

"Industry and FDA consensus is that biomarkers are valuabletools for assessing the safety and efficacy of drug candidates," Mendrick says."Regulatory agencies want to know if the data they get is good enough toanalyze," she notes. "From the pharma side, companies feel more comfortablesending data to a regulatory agency when they know up-front what the agencywants in terms of standards and what they are looking for."
At an FDA workshop on emerging safety science in April, theimportance of genomic markers was highlighted by Dr. Felix W. Frueh, associatedirector of genomics for the Office of Clinical Pharmacology at the FDA'sCenter for Drug Evaluation and Research. He noted, for example, that theemergence of new molecular biomarkers for drug safety will help bridge thesafety gap between the preclinical and clinical research.

As for Gene Logic's credentials to help achieve this,according to the company it has assembled one of the world's largest and mostdetailed knowledge bases of gene expression profiles from human tissues andcells. The company has processed more than 200,000 microarrays to obtaingenomic data and has developed proprietary methods and software— including morethan 40 quality metrics—to help ensure data are accurate.

To the best of Gene Logic's knowledge, the FDA isn'tcurrently in any similar collaborations with other genomics-oriented companiesto develop metrics. The FDA was not available for comment on that issue, butthe Gene Logic news release quotes a senior FDA official as saying that"projects focused on understanding the QC issues will help drive thedevelopment of baseline standards for the submission of microarray data to theFDA in the future."

Foreveryone to benefit, QC metrics have to be in the public domain and everyonehas to agree what the best metrics are, just as they have in other areas ofpharmaceutical and healthcare work, Mendrick says. No specific timeframe forreleasing a "first draft" exists as yet, though, she adds, noting thatGene Logic and the FDA are still addressing issues such as the bandwidth needed toanalyze data and other technical and logistical matters

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