precisionFDA’s Next Challenge? Conduct an App-a-Thon!

By: Zivana Tezak, Ph.D., and Elaine Johanson

FDA is increasingly harnessing the power of supercomputers, the creative and collaborative culture of the scientific community, and novel approaches to technology to help achieve advances in diagnostics, therapeutics, and analytics that will ultimately benefit patients.

Zevana Tezak

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

Perhaps no program personifies these efforts more than the online research portal precisionFDA, which was developed by FDA scientists with the help of leading minds from Silicon Valley as part of President Obama’s Precision Medicine Initiative (PMI).

The goal of the PMI is to help translate scientific knowledge about genomics into clinical care. As part of this initiative, precisionFDA’s task is to advance the use of a core technology behind the PMI known as next generation sequencing or NGS, which is capable of mapping the entire human genome. To achieve that, precisionFDA is drawing upon the latest computing and storage technologies to provide an open source cloud-based space where experts can share data, ideas, and methodologies. Today, it boasts more than 1,600 participants, including researchers, test developers, industry, academics, statisticians, and clinicians.

One way we’ve been learning and growing is through contests designed to spark the creative thinking of members on behalf of important NGS questions about data, analytics, and sequencing tools.

We are happy to announce the next challenge: an “App-a-Thon,” inviting software developers to get together with their peers, collaborators, and friends to add NGS software apps to the precisionFDA app library. Apps in this case are executable commands using the Linux operating system that are “wrapped” around NGS software.

Elaine Johanson

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

Apps can be existing, modified, or completely new. Ultimately this challenge, which closes Oct. 28, 2016, is a contest to engage the NGS community in the development of new genome sequencing analytical tools for use on precisionFDA. These apps can do a variety of useful activities such as simulations, benchmarking, data integration, mapping portions of the genome, or identifying genetic variants. Members of precisionFDA are encouraged to try out these apps by running them on the platform.

Our goal is to build a robust reference library of apps and files so that precisionFDA can provide developers with everything they need to support development work on their software pipeline or tests.

If you’d like to set up an App-a-Thon, FDA provides the framework and all the materials, storage, and compute capacity to hold an App-a-Thon on precisionFDA. We encourage you to choose a timeframe, invite your researcher/developer friends, and follow the directions in FDA’s ‘App-a-Thon in a Box’ toolkit. This toolkit even contains video and results from a precisionFDA App-a-Thon held at Stanford University.

The results of this challenge will be highlighted by FDA Commissioner Robert Califf at the World Precision Medicine Congress on Nov. 14, 2016 in Washington D.C. Participating will benefit the entire NGS community, but most importantly, it will advance public health and benefit the patients we collectively serve.

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

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

FDA Launches precisionFDA to Harness the Power of Scientific Collaboration

By: Taha A. Kass-Hout, M.D., M.S. and Elaine Johanson

Imagine a world where doctors have at their fingertips the information that allows them to individualize a diagnosis, treatment or even a cure for a person based on their genes. That’s what President Obama envisioned when he announced his Precision Medicine Initiative earlier this year. Today, with the launch of FDA’s precisionFDA web platform, we’re a step closer to achieving that vision.

Taha Kass-Hout

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

precisionFDA is an online, cloud-based, portal that will allow scientists from industry, academia, government and other partners to come together to foster innovation and develop the science behind a method of “reading” DNA known as next-generation sequencing (or NGS). Next Generation Sequencing allows scientists to compile a vast amount of data on a person’s exact order or sequence of DNA. Recognizing that each person’s DNA is slightly different, scientists can look for meaningful differences in DNA that can be used to suggest a person’s risk of disease, possible response to treatment and assess their current state of health. Ultimately, what we learn about these differences could be used to design a treatment tailored to a specific individual.

The precisionFDA platform is a part of this larger effort and through its use we want to help scientists work toward the most accurate and meaningful discoveries. precisionFDA users will have access to a number of important tools to help them do this. These tools include reference genomes, such as “Genome in the Bottle,” a reference sample of DNA for validating human genome sequences developed by the National Institute of Standards and Technology. Users will also be able to compare their results to previously validated reference results as well as share their results with other users, track changes and obtain feedback.

Elaine Johanson

Elaine Johanson, precisionFDA Project Manager.

Through such collaboration we hope to improve the quality and accuracy of genomic tests – work that will ultimately benefit patients.

Over the coming months we will engage users in improving the usability, openness and transparency of precisionFDA. One way we’ll achieve that is by placing the code for the precisionFDA portal on the world’s largest open source software repository, GitHub, so the community can further enhance precisionFDA’s features.

precisionFDA leverages our experience establishing openFDA, an online community that provides easy access to our public datasets. Since its launch in 2014, openFDA has already resulted in many novel ways to use, integrate and analyze FDA safety information. We’re confident that employing such a collaborative approach to DNA data will yield important advances in our understanding of this fast-growing scientific field, information that will ultimately be used to develop new diagnostics, treatments and even cures for patients.

Taha A. Kass-Hout, M.D., M.S., is FDA’s Chief Health Informatics Officer and Director of FDA’s Office of Health Informatics. Elaine Johanson is the precisionFDA Project Manager.

Advancing precision medicine by enabling a collaborative informatics community

By: Taha A. Kass-Hout, M.D., M.S., and David Litwack, Ph.D.

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.

Taha Kass-Hout

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

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

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.