FDA Platform Seeks to Enable Genomic Testing Breakthroughs

The Food and Drug Administration has launched a cloud-based portal enabling researchers to work together to improve the quality and accuracy of next-generation sequencing (NGS) genomic tests, which compile a vast amount of data on a person’s exact sequence of DNA.

Tuesday’s beta launch of the collaborative platform—precisionFDA—is being described as a “research sandbox” for the genomics community where scientists and test developers can explore NGS methodologies to develop necessary standards for the testing technology that quickly sequences a person’s genome to detect and interpret genetic variants.

The crowd-source portal will “help perfect the science to foster innovation needed to ensure the accuracy of the software that reads the DNA, also known as next-generation sequencing,” says Taha Kass-Hout, M.D., FDA’s chief health informatics officer and director of its Office of Health Informatics.

Part of the Obama administration’s Precision Medicine Initiative (PMI), precisionFDA offers researchers cloud-hosted work space where their software code or data can be shared with collaborators. They also can use open source reference genomic data models and analysis tools to help them compare their results to previously validated results. These 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.

“FDA’s part of the PMI is essentially to develop a new regulatory approach for next-generation sequencing,” adds Elizabeth Mansfield, deputy office director for personalized medicine at FDA’s Center for Devices and Radiological Health. “Next-generation sequencing is a relatively new technology that can rapidly and reasonably inexpensively provide almost the entire human genome sequence.”

Given that many diseases have genetic underpinnings, next-generation sequencing tests provide patients’ individual genomic data that can be leveraged to tailor medical treatments designed to improve their health outcomes, according to Mansfield.

Also See: Regulatory Reforms Needed to Leverage Data for Precision Medicine

In preparation for the launch of precisionFDA, the agency granted access to a variety of stakeholders to participate in an early feasibility version of the portal. Some of the early adopters included: 23andMe, Broad Institute of MIT, Emory University, Friends of Cancer Research, Harvard University, Illumina, Intel, National Institutes of Health, National Organization of Rare Diseases, Roche, and Stanford University. DNAnexus, a Mountain View, Calif.-based cloud solutions vendor for the genomics industry, was contracted by the FDA to build the underlying compute and data management infrastructure for precisionFDA, a secure cloud-based platform.

Richard Daly, CEO of DNAnexus, says that users are able to isolate their own data and software in a secure environment, but still have the option of exposing their developed software and any reference data in a community collaboration space.

As precisionFDA scales from a beta program to full-up launch early next year, Daly believes the platform is well-positioned to accommodate the vast amount of genomic data collected using next-generation sequencing technology. “That’s the great thing about the cloud. For all practical purposes, it’s an infinite resource and scale is not a problem,” he comments. “We routinely deploy jobs that scale from 100 servers to 10,000 servers—and that can be done in minutes. It’s highly elastic and very much responds to the demand for its use at any given point in time.”

According to George Asimenos, director of strategic projects for DNAnexus, the beta launch of precisionFDA will end in March 2016 when “it becomes a more hardened environment.” Toward that end, FDA is now accepting applications for participation in precisionFDA. So far, more than 190 participants have requested user accounts.