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Getting on the same page
by Jeffrey Bouley  |  Email the author

GAITHERSBURG, Md.—Gene Logic Inc. recently entered into a collaboration with the United States Food and Drug Administration (FDA) to share quality control methods and metrics that may be useful in better understanding disparate genomic data that are sent by pharmas and biotechs as part of regulatory submissions.
According to Gene Logic, the collaboration is part of the FDA's Critical Path Initiative, an effort to stimulate and facilitate the use of new scientific and technical methods, such as computer-based predictive models and biomarkers for safety and effectiveness. The overriding goal of that initiative is to improve the predictability and efficiency of drug development from laboratory concept to commercially approved medicines.
The reasons for pursuing this specific genomics collaboration are critical on both the pharmaceutical and government sides of the equation, notes Dr. Donna Mendrick, Gene Logic scientific fellow and vice president of toxicogenomics. With no federal or industry standards in place for assessment of the quality of genomic data submissions to the FDA, it is hard to know which data are good and which data aren't. The results of the FDA-Gene Logic collaboration will be released publicly, she says, as an early step in creating industry-wide standards for genomic data assessment. The outcomes of the collaboration won't be the final word, most likely, but they will be a step toward achieving a common understanding of key microarray QC procedures that will help shape microarray data standards for the submission of microarray data to the FDA.
"Industry and FDA consensus is that biomarkers are valuable tools for assessing the safety and efficacy of drug candidates," Mendrick says. "Regulatory agencies want to know if the data they get is good enough to analyze," she notes. "From the pharma side, companies feel more comfortable sending data to a regulatory agency when they know up-front what the agency wants in terms of standards and what they are looking for." At an FDA workshop on emerging safety science in April, the importance of genomic markers was highlighted by Dr. Felix W. Frueh, associate director of genomics for the Office of Clinical Pharmacology at the FDA's Center for Drug Evaluation and Research. He noted, for example, that the emergence of new molecular biomarkers for drug safety will help bridge the safety 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 most detailed knowledge bases of gene expression profiles from human tissues and cells. The company has processed more than 200,000 microarrays to obtain genomic data and has developed proprietary methods and software— including more than 40 quality metrics—to help ensure data are accurate.
To the best of Gene Logic's knowledge, the FDA isn't currently in any similar collaborations with other genomics-oriented companies to develop metrics. The FDA was not available for comment on that issue, but the Gene Logic news release quotes a senior FDA official as saying that "projects focused on understanding the QC issues will help drive the development of baseline standards for the submission of microarray data to the FDA in the future."
For everyone to benefit, QC metrics have to be in the public domain and everyone has to agree what the best metrics are, just as they have in other areas of pharmaceutical and healthcare work, Mendrick says. No specific timeframe for releasing a "first draft" exists as yet, though, she adds, noting that Gene Logic and the FDA are still addressing issues such as the bandwidth needed to analyze data and other technical and logistical matters
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