precisionFDA Challenges Support Innovation

The U.S. Food and Drug Administration (FDA) has put its innovative platform, precisionFDA, to work promoting next-generation sequencing (NGS) with two projects inviting industry participants to process datasets with their own sequencing pipelines and comparing results on precisionFDA. The FDA described precisionFDA upon its launch last year as a “crowd-sourced, cloud-based platform to advance the science needed to develop the necessary standards” for evaluating NGS tests. According to the FDA’s latest update concerning the platform, the cloud-based “community” encompasses “more than 1,500 users from 600 organizations, with more than 10 terabytes of genetic data stored.”

The first of two challenge projects, the Consistency Challenge, required participants to use an informatics pipeline to identify genetic variants in whole genome sequences from a known human sample. Results were to be checked for consistency against results in FDA-provided datasets. This first challenge was completed in April and winners announced at the end of May. Winners included teams from Sentieon and Sanofi-Genzyme and the 21 entries included participants from organizations such as Roche, Pathway Genomics, Avera, and the Broad Institute. The challenge has yielded a dataset that the FDA indicates is available for others to study via archived files accessible on precisionFDA.

The Truth Challenge, closed at the end of May, required participants to “identify genetic variants in one known and one unknown sample dataset.” “The goal is to see how close they come to the truth when analyzing data from a human sample with variant results unknown to them, which we will reveal at the end of the challenge,” said the FDA. The Genome in a Bottle consortium and the Global Alliance for Genomics and Health worked with the FDA to design this challenge and Genome in a Bottle will provide a “truth dataset”—releasing “for the first time new high confidence variant calls for the unknown sample dataset.”

A recent FDA Voice blog explained the purpose of these challenges is to encourage collaboration and further the Precision Medicine Initiative: “These competitions are motivating community members to demonstrate the effectiveness of their tools, test the capabilities of the precisionFDA platform, and engage the community in discussions and data analysis that will provide new insights and serve as a comprehensive source of information about reference data and software pipelines used to analyze sequencing results.”

Takeaway: The FDA continues to encourage sharing of data and collaboration among industry stakeholders to maximize the potential of genetic testing and next-generation sequencing.