NEW YORK (GenomeWeb) – A recent perspectives article appearing in Science Translational Medicine described several regulatory research challenges that remain in the way of fulfilling the diagnostic testing potential of next-generation sequencing.
Stanford University's Russ Altman and his colleagues outlined nine main challenges that must be tackled if next-generation-based diagnostic testing, under the broader umbrella of the Precision Medicine Initiative, is to become routine. The PMI has spurred research on everything from the clinical validation, utility, and applicability of a given test to the appropriate regulatory frameworks for next-generation sequencing-based tests by the US Food and Drug Administration, the team explained.
The latter's precisionFDA effort, in turn, is expected to set the stage for bioinformatics methods and tools that are tailored to the types of genomic tests that are developed for various medical conditions and settings.
For their part, Altman and his colleagues recommended a roadmap for those involved in regulatory research related to next-generation sequencing tests, which can span sequences beyond a region of interest and may involve variants of unknown clinical significance.
"In order to organize precisionFDA as a community platform and to ensure an effective means of developing robust methods for evaluating [next-generation sequencing]-based diagnostics, we propose a research roadmap that highlights nine areas of potential regulatory science investigation for DNA (including precisionFDA) accompanied by a discussion of aims, research milestones, software tools, and data services," they wrote.
For example, the team highlighted the need for systems to store genomic data and related software tools in a manner that's secure, but allows for data sharing when needed. It also touched on the importance of accurately comparing error models and pipelines for different next-generation technologies, as well as coming up with validated reference data sets and standards for clinical variant database use.
On the variant interpretation side, the researchers noted that it will be necessary to establish appropriate population-based frameworks for interpreting genetic variants in the clinical context, along with effective strategies for returning genetic information to physicians and patients in way that's understandable and, ideally, improves care.
They noted that researchers will need to explore the most effective methods for benchmarking next-generation sequencing methods, both on the data generation and informatics sides.
Finally, the team argued that cost-effectiveness studies are needed to determine if and when next-generation sequencing-based testing is warranted, since some types of genetic information may be superfluous and difficult to obtain.