Federal agency hopes its open-source precisionFDA web portal will aid in development of laboratory-developed tests and inform regulatory decision-making

One recent initiative launched by the Food and Drug Administration (FDA) to foster the greater sharing of genetic information may be of some value to pathologists and clinical laboratory scientists  who are developing laboratory-developed tests (LDTs) that incorporate molecular and genetic technologies.

The FDA unveiled an open-source platform for community sharing of genetic information. It is called precisionFDA, and the FDA describes its new web platform as an “online, cloud-based portal that will allow scientist from industry, academia, government, and other partners to come together to foster innovation and develop the science” of next-generation DNA sequencing processing.

precisionFDA Expected to Level the Playing Field for Smaller Test Developers

When cloud-based genome informatics and data-management company DNAnexus was awarded the research and development contract to build precisionFDA in August, 2015, the company predicted that the development of a new model for evaluating next-generation sequencing-based tests would “open up the process to a broader range of community members, who will benefit from open-source reference data and applications and pay-for-use compute and storage solutions, leveling the playing field for smaller test developers.”

Already participating in precisionFDA are about 20 public and private sector participants including:

National Institutes of Health (NIH);

Centers for Disease Control and Prevention (CDC);

National Institute of Standards and Technology (NIST);

• Pharmaceutical and biotech companies;

• Academic medical centers;

• Healthcare providers;

• Genome test providers and others.

On the organization’s website, the FDA stated that the new precisionFDA portal plays an “integral role” in advancing President Obama’s Precision Medicine Initiative and demonstrates the FDA’s evolving role in facilitating open source information resources.

Taha A. Kass-Hout, MD, MS (left), is the FDA’s Chief Health Informatics Officer and Director of the FDA’s Office of Health Informatics, and Elaine Johanson (right) is the precisionFDA Project Manager. In an article posted on FDA Voice, they stated that 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).” (Photo copyright: FDA Voice.)

Taha A. Kass-Hout, MD, MS (left), is the FDA’s Chief Health Informatics Officer and Director of the FDA’s Office of Health Informatics, and Elaine Johanson (right) is the precisionFDA Project Manager. In an article posted on FDA Voice, they stated that 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).” (Photo copyright: FDA Voice.)

precisionFDA Follows Success of openFDA

In launching precisionFDA, the agency is leveraging the success of the 2014 debut of openFDA, another free-to-use service that makes it easier for the public to access FDA data related to drug adverse events, drug labeling, medical devices, and food recalls.

“Since its launch, 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,” stated FDA Chief Health Informatics Officer Taha Kass-Hout, MD, MS, and precisionFDA Project Manager Elaine Johanson in a news release posted on the FDA’s blog, FDA Voice.

FDA Makes precisionFDA’s Source Code Available to All

The FDA is openly seeking feedback as users of the precisionFDA platform share their results, track changes, and compare their results to previously-validated reference results. As part of this effort, the precisionFDA website also includes the code for the portal of the world’s largest open-source software repository, GitHub. It is hoped that this will help the genomics community to further enhance precisionFDA’s features.

Officials Comment on precisionFDA

National Institutes of Health Director Francis Collins, MD, PhD, calls precisionFDA “a bold and innovative step towards advancing the regulatory science for precision medicine.”

The precisionFDA initiative also has won praise from the Personalized Medicine Coalition (PMC). The PMC commended the FDA for an “encouraging effort” to engage the personalized medicine community as the agency decides whether and how to use curated databases for regulatory oversight of next-generation sequencing technologies. According to the FDA’s website the project is expected to “generate knowledge to inform regulatory pathways and decision-making.”

“We hope stakeholders will use it and participate in its continued development,” said Daryl Pritchard, PhD, Vice President of Science Policy at Personalized Medicine Coalition (PMC), in a PMC statement. “Keeping up with scientific advancements in personalized medicine is difficult, but FDA is addressing the challenge,” Pritchard concluded.

Pathologists, molecular PhDs, and medical laboratory scientists can use this website. To request access to precisionFDA, go to the portal’s website.

—Andrea Downing Peck

Related Information:

FDA Launches precisionFDA to Harness the Power of Scientific Collaboration

Coalition Commends FDA’s Launch of Community Platform for Evaluating Approaches to Next-Generation Sequencing Analysis

precisionFDA: A Community Approach for Submitting and Evaluating Diagnostic Tests, Powered by DNAnexus

NIST, Genome in a Bottle Release First Reference Material for Assessing Genome Sequencing
precisionFDA

FDA Unveils Next-Gen DNA Sequencing Portal: precisionFDA

Experts Predict Explosive Growth in Molecular Diagnostics and Next-Generation Gene Sequencing for Clinical Pathology Laboratories

NIST’s New Standard Genetic Reference Specimen Promises to Increase Accuracy of Clinical Pathology Laboratories Using Next-Generation Sequencing Technology

Clinical Trials Find Success with Use of Next-Generation Gene Sequencing; Could Lead to More Precise Clinical Pathology Laboratory Tests

Obama’s $215 Million Precision Medicine Initiative: Will Congress Fund It and Can It Advance Genetic Testing and the Value of Clinical Laboratory Services?