United States: FDA Holds Back-To-Back Workshops On Next-Generation Sequencing Diagnostic Tests

Last week, FDA held two workshops to gather information on developing a flexible approach for the regulation of next generation sequencing ("NGS") in vitro diagnostic tests. NGS tests facilitate the rapid sequencing and analysis of segments of DNA, yielding information that can be used to tailor medical therapies to the individual characteristics of a patient. Specifically, the workshops focused on best practices and potential standards regarding NGS tests and the use of curated databases as sources of valid clinical evidence in the evaluation of NGS tests. The workshops featured the perspectives of industry leaders and regulators and continue the dialogue from similar workshops held by FDA in February 2015.

On November 12, 2015, the first workshop focused on a standards-based approach to evaluating NGS tests. Deputy Commissioner Califf kicked off the event with remarks on the emerging field of personalized medicine. He indicated a major regulatory challenge is that NGS testing often lacks a specific intended use, because the tests are used by clinicians who initially do not know what condition they will be diagnosing. In addition to exploring standards for these new technologies, FDA is developing open-source tools such as precisionFDA, a cloud-based platform for sharing genomic sequencing data and methodologies and for supporting the development of a data commons for evidence on the clinical relevance of genetic variation.

During a panel on bioinformatics strategies and tools, industry representatives and clinicians discussed their experiences developing and using bioinformatics and the analytical benchmarking of tests. The panelists' "wish list" for new tools includes ways to access scientific literature in a more user-friendly manner, such as semantically tagging literature to bioinformatics tools, and improved clinical education so that sequencing pipelines are actually relevant to patients' therapeutic needs. Some panelists spoke of the importance of incremental, adaptive standards to account for unique circumstances in NGS testing, while one of the clinicians expressed concern about the risks associated with relying on fully automated systems for diagnosis.

A second workshop was held on November 13, 2015, focusing on the ways that well-curated databases of genetic variants can be used to inform clinical interpretation of NGS test results and serve as a source of clinical evidence of new genetic variants identified through NGS tests. Panelists discussed the attributes of existing databases, such as the National Center for Biotechnology Information's ClinVar database, and the potential challenges of harmonizing across databases. Such noted challenges include variation in the meaning and interpretation of data points, and lack of consistency in the expression of genotypic and phenotypic metadata. Panelists also discussed the challenge of tracking and accounting for real-time changes in data, particularly data uploaded from electronic medical records, and the utility of incomplete data sets. The curation of databases was also discussed, including desired qualifications for curators, sources of information queried by curators, and standard curation procedures.

It is unclear what policies FDA will ultimately develop for NGS tests, but the Agency has stated that the meetings held this year are intended to lead to a flexible, adaptive regulatory approach for NGS tests. The deadline for public comments on both workshops is November 25, 2015.

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Authors
Colleen Heisey
Christian Fulda
 
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