precisionFDA Launches to Help With NGS Assay Validation, Data Sharing

Posted 15 December 2015 | By Zachary Brennan 

precisionFDA Launches to Help With NGS Assay Validation, Data Sharing

In the spirit of sharing, the US Food and Drug Administration (FDA) on Tuesday launched precisionFDA, a new online, cloud-based platform where genomics experts from industry, academia, government and elsewhere can come together and securely share data on next-generation sequencing (NGS).

The beta-launch of the site opens the door for accessing and sharing datasets, analysis pipelines, bioinformatics tools and other approaches that also could advance regulatory science.

“While precisionFDA does not serve a regulatory role, it is expected to generate knowledge to inform future regulatory pathways and decision making,” FDA explains.

The Personalized Medicine Coalition commended FDA for engaging with stakeholders as it decides whether and how to use curated databases for regulatory oversight of NGS technologies.

The launch of the site coincides with new research (written about by NIH Director Francis Collins today) that could lead to the development of a simple urine test to help identify which individuals with chronic kidney disease would benefit the most from aggressive disease management and clinical follow-up.


NGS allows scientists to compile a vast amount of data on a person’s DNA, which could potentially be mined to discover meaningful differences that suggest a person’s risk of disease, possible response to treatment and current health.

The agency has previously held a meeting on how it’s looking to curate databases establishing the clinical relevance of genetic variations, and how to use these databases to evaluate new technology.

FDA released a discussion paper, Use of Databases for Establishing the Clinical Relevance of Human Genetic Variants, in which it discussed the strategies to "ensure that NGS tests produce accurate and reliable results."

And the agency’s Division of Antiviral Products (DAVP) has already begun assessing NGS resistance data for at least three new drug applications (NDAs), including Gilead’s Sovaldi, which was the first antiviral drug approved by FDA based on resistance data from pivotal Phase II and III clinical trials using NGS data, DAVP’s Eric Donaldson, Damon Deming, Julian O’Rear and Lisa Naeger noted in a recent study in Biomarkers in Medicine.

Through the new precisionFDA portal, FDA envisions a place where genome test or software providers, pharma and biotech companies (Roche and Illumina are participating), academic medical centers (including the famous Broad Institute) and others can conduct genome analysis and reference material comparisons.

VCF Files

According to the guide on the new site, the concept of comparing two sets of genetic variants (VCF files) is central to the exploration of regulatory science, and to the evaluation of NGS assays.

“The problem of comparing VCF files constitutes an active area of research. The precisionFDA building crew is represented in the Global Alliance for Genomics and Health (GA4GH) Benchmarking Task Team, which is expected (within the next year) to provide recommendations and/or software solutions for comparing VCFs and for counting, classifying, and reporting results.”

For now, FDA has put together an initial VCF comparison framework which can compare two variant sets: a test set and a benchmark set.

“The underlying comparison methodology is mostly symmetric with respect to each assignment; however, reporting of the results is based on the assumption that the benchmark set represents the truth, and that the test set represents predictions. Therefore, the results of a comparison constitute an implicit evaluation of the performance of whatever method was used to generate the predictions,” FDA says.

In addition to the VCF files, participants may provide up to two BED files, which “dictate the genomic regions inside which you want the comparison to be performed. If no BED files are provided, the comparison will be performed across the whole genome, and will compare all entries of each of the test and benchmark variant files.”

More information on how the system will work, including information on files, comparisons, apps, creating apps, notes, tracking and publishing can be found at precisionFDA.

FDA Launches precisionFDA to Harness the Power of Scientific Collaboration


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