From Competition to Collaboration: precisionFDA Challenges

By: Taha Kass-Hout, M.D., M.S., Zivana Tezak, Ph.D., and Elaine Johanson

Next week, we will announce the winners of the first precisionFDA challenge.

Taha Kass-Hout

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

We set up precisionFDA as an online, cloud-based, virtual research space to allow scientists from academia, industry, health care organizations, and government to work together on creating tools to evaluate a method of “reading” DNA known as next generation sequencing (or NGS). The ultimate goal of precisionFDA is to foster innovation and develop regulatory science around NGS tests, which are essential to achieving the promise of President Obama’s Precision Medicine Initiative. So far, the response to precisionFDA has been gratifying, with participants calling precisionFDA “refreshing”, “innovative,” and “a new paradigm in regulatory science.” The community currently boasts more than 1,500 users from 600 organizations, with more than 10 terabytes of genetic data stored.

To engage users and encourage sharing of data and ideas, precisionFDA has offered two competitions to date. 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.

Zevana Tezak

Zivana Tezak, Ph.D., Associate Director for Science and Technology at FDA’s Office of In Vitro Diagnostics and Radiological Health, Center for Devices and Radiological Health

The first precisionFDA challenge, the Consistency Challenge, closed in April 2015, with 21 entries from 17 submitters. Participants were given two datasets of whole genome sequences from a known human sample, sequenced at two different sites and generously donated to precisionFDA by Garvan Institute of Medical Research and Human Longevity, Inc. Challenge participants were instructed to use the informatics pipeline (software) of their choice to identify genetic variants and check for consistency between results in the provided datasets. The top performers will be announced in person by FDA Commissioner Robert Califf on May 25, 2016. At the time of his announcement, we will post detailed information here on all the recognitions and how the top performers were selected. So stay tuned!

The second challenge, the Truth Challenge, closes on May 26, 2016, and was designed in collaboration with the Genome in a Bottle consortium and the Global Alliance for Genomics and Health. Participants are expected 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. An exciting characteristic of this challenge is that the Genome in a Bottle consortium will release for the first time new high confidence variant calls for the unknown sample dataset (we refer to in this challenge as “truth dataset”) for the human sample at the end of the contest.

Elaine Johanson

Elaine Johanson, precisionFDA Project Manager and Deputy Director of FDA’s Office of Health Informatics.

The knowledge generation potential for precisionFDA is immense, and leverages the collaboration of the global community to help solve challenges that will ultimately provide insight to regulation to ensure the safety and efficacy of genetic tests. The platform offers users the ability to assemble and run apps, learn from other experts, share lessons learned, participate in competitions, and help to develop standards for assessing the effectiveness of genetic tests.

With new challenges and opportunities for ongoing discussions and collaborations between FDA and the global community, we look forward to the precisionFDA community facilitating and advancing development and assessment of new tools and tests in this fast growing field of genetic testing.

 

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

Zivana Tezak, Ph.D., is Associate Director for Science and Technology at FDA’s Office of In Vitro Diagnostics and Radiological Health, Center for Devices and Radiological Health

Elaine Johanson, is precisionFDA Project Manager and Deputy Director of FDA’s Office of Health Informatics

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