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UNC-Chapel Hill ENVR 442 - Impact of microarray data quality on genomic data submissions to the FDA

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NATURE BIOTECHNOLOGY VOLUME 24 NUMBER 9 SEPTEMBER 2006 1105Impact of microarray data quality on genomic data submissions to the FDAFelix W FruehHow can microarray data best be exploited and integrated into the regulatory decision-making process?Five years ago, the completion of the sequenc-ing of the human genome was announced1,2, triggering many comments about the value of this knowledge for new approaches and insights into drug development. However, although genomics is used in an increasing number of drug development programs, the genomics-led ‘revolution’ in drug development has not hap-pened yet. This can be attributed to a variety of reasons; one reason is the lack of a thorough evaluation of the quality of novel technologies such as DNA microarrays as well as the man-ner in which the results of such experiments are analyzed and interpreted.To investigate the challenges presented to regulators by microarray data, the US Food and Drug Administration (FDA) spearheaded the formation of the MicroArray Quality Consortium (MAQC), which brings together researchers from the government, industry and academia to assess the key factors contributing to variability and reproducibility of microarray data. Ultimately, the data from this initiative will help determine a new set of standards and guidelines for the use of DNA microarray data.Genomic data maturesSeveral factors have encouraged the adoption and integration of genomic data in drug devel-opment and regulatory assessment, including a better understanding of disease pathophysi-ology and targeted drug molecules to sites of action. However, there are challenges to further expansion of genomics use; one key issue fre-quently discussed is that genomic science has evolved more quickly than technologies suitable for generating consistent, high-quality genomic data. Before 2004, genomic information was largely absent from the investigational new drug submissions or new drug applications received by the FDA; today, that situation is chang-ing (Fig. 1). This more than likely reflects the timelines associated with the drug development process overall and the integration of genomics within that process. It is therefore logical that by this time, we should be starting to see an increase in submissions to the FDA containing genomic information; indeed, the number of data submissions containing genomic informa-tion is increasing significantly (Fig. 1).On the basis of 20 voluntary genomic data submissions that have been submitted to the FDA so far, it appears that the technologies for generating genomic data have only recently become a commodity of broader applica-tion. Recently, the integration of large-scale screening approaches (e.g., gene expression profiling or whole genome single-nucleotide polymorphism (SNP) scans has been observed in different stages of drug discovery and now also in drug development. Consequently, at this point, the generation and exploitation of genomic data generated from such large-scale efforts in modern drug development requires a regulatory environment adequately equipped to review such data.The agency respondsShortly after the human genome sequence was announced, a seminal paper by the FDA’s Lesko and Woodcock3 was published highlighting Felix W. Frueh, US Food and Drug Administration, Office of Clinical Pharmacology, Center for Drug Evaluationand Research, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA.e-mail: [email protected] of submissionsQ1 '04 Q2 '04 Q3 '04 Q4 '04 Q1 '05 Q2 '05 Q3 '05 Q4 '05 Q1 '06 Q2 '06Quarter of yearConsultsVGDS Figure 1 Increase in formal requests (consults) for genomic data review (data submitted as part of regular INDs, NDAs or BLAs) to the Office of Clinical Pharmacology, and voluntary genomic data submissions (VGDS) to the FDA, since 2004. IND, investigational new drug; NDA, new drug application; BLA, biologic license application.COMMENTARY© 2006 Nature Publishing Group http://www.nature.com/naturebiotechnology1106 VOLUME 24 NUMBER 9 SEPTEMBER 2006 NATURE BIOTECHNOLOGYthe importance of new guidance for regula-tory submissions containing genomic infor-mation. This ‘call to arms’ was followed by a series of workshops organized by FDA/the Drug Information Association (Horsham, PA, USA)/and the Pharmaceutical Researchers and Manufacturers of America (PhRMA; Washington, DC, USA) on pharmacogeno-mics, which led to the development of a guid-ance document and ultimately facilitated a new type of voluntary data submission process—voluntary genomic data submission (VGDS). This process allowed for a new informal inter-action between sponsors of voluntary submis-sions and regulators to discuss the science of novel, exploratory uses of pharmacogenomics. The Guidance for Industry: Pharmacogenomic Data Submissions4, released as a final guid-ance document in 2005, was accompanied by two additional documents explaining the newly created VGDS path and the function/responsibilities of a newly created FDA-wide Interdisciplinary Pharmacogenomic Review Group (IPRG), respectively.At the same time, the FDA launched a new website (http://www.fda.gov/cder/genomics), which serves as a portal for regulatory infor-mation in the area of genomics. Together, these new regulatory resources allow and promote the submission of exploratory, cutting-edge genomic data to the FDA. This exploratory information is not used by regulators or industry as part of regulatory decision mak-ing, which is a critical aspect as it is understood that many of the data sets generated with this new technology are not yet sufficiently mature to contribute to critical regulatory decisions that have a wide-ranging impact on entire drug development programs. Nonetheless, these data are of value to regulators in understand-ing the changes underway in the processes, approaches and direction of drug research and development programs. It is also impor-tant to note that the Guidance for Industry: Pharmacogenomic Data Submissions4 is not a guidance about ‘voluntary’ submissions alone; instead, in very general terms, it explains what types of genomic data need to be submitted to the FDA and when, and what types of data can be submitted on a voluntary basis.Voluntary genomic data submissionThe VGDS program creates a forum for sci-entific data exchange and discussions with the FDA outside of the regular review process. The VGDS program is used for a variety of strategic purposes


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UNC-Chapel Hill ENVR 442 - Impact of microarray data quality on genomic data submissions to the FDA

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