FDA to Advance Precision Medicine by Enabling Open Source Collaborative Informatics

Taha A. Kass-Hout, M.D., M.S., FDA’s Chief Health Informatics Officer and Director of FDA’s Office of Health Informatics.FDA plays an integral role in President Obama’s Precision Medicine Initiative, which foresees the day when an individual’s medical care will be tailored in part based on their unique characteristics and genetic make-up. Yet while more than 80 million genetic variants have been found in the human genome, we don’t understand the role that most of these variants play in health or disease. Achieving the President’s vision requires working collaboratively to ensure the accuracy of genetic tests in detecting and interpreting genetic variants. We are working towards that goal by developing an informatics community and supporting platform we call precisionFDA.

Sophisticated, relatively inexpensive technology known as next generation sequencing (NGS) already exists to sequence a person’s genome quickly. Developers and users of NGS tests must then comb these sequences to look for segments that suggest potentially meaningful differences and determine whether those differences provide useful and actionable information about the state of a person’s health, and their future risk of disease, behavior, or treatment choices.

Special features of this technology pose novel regulatory issues for FDA. Most diagnostic tests follow a one test-one disease paradigm that readily fits FDA’s current device review approaches for evaluating a test’s accuracy and clinical interpretation. Because NGS tests may be used in many ways in the clinic and can produce an unprecedented amount of data about a patient, we are working to evaluate whether a better option might simply be requiring each NGS test developer to show that the test meets certain standards for quality. Similarly, to demonstrate a test’s clinical value, we are assessing whether it may be more efficient for developers to refer to evidence in well-curated, validated, and shared databases of mutations instead of independently generating data to support a mutation-disease association.

David Litwack, Ph.D., Policy Advisor, Office of In Vitro Diagnostics and Radiological Health, at FDA’s Center for Devices and Radiological Health.To begin to realize this new vision, precisionFDA is designed as a crowd-sourced, cloud-based platform to advance the science needed to develop the necessary standards. PrecisionFDA will supply an environment where the community can test, pilot, and validate new approaches. For example, NGS test developers, researchers, and other members of the community can share and cross-validate their tests or results against crowd-sourced reference material in precisionFDA.

Planned for beta release (work in progress) in December 2015, precisionFDA will offer community members access to secure and independent work areas where, at their discretion, their software code or data can either be kept private, or shared with the owner’s choice of collaborators, FDA, or the public. Initially, precisionFDA’s public space will offer a wiki and a set of open source or open access reference genomic data models and analysis tools developed and vetted by standards bodies, such as the National Institute of Standards and Technology (e.g., Genome in a Bottle). We believe precisionFDA will help us advance the science around the accuracy and reproducibility of NGS-based tests, and in doing so, will advance consumer safety. We look forward to continuing to update the community on the development of these new tools.

Taha A. Kass-Hout, M.D., M.S., is FDA’s Chief Health Informatics Officer and Director of FDA’s Office of Health Informatics.

David Litwack, Ph.D., is Policy Advisor, Office of In Vitro Diagnostics and Radiological Health, at FDA’s Center for Devices and Radiological Health.