A consortium led by the George Washington University (GW) has been refunded for their BioCompute Object Specification Project, thanks to a $2.2 million, five-year grant from the U.S. Food and Drug Administration (FDA). The BioCompute Object Specification Project, which was launched in fall 2017, provides much-needed standards for communicating high-throughput sequencing (HTS) computations and data analysis, known as BioCompute Objects (BCOs).
This community-driven project works to streamline data and workflow exchange between the FDA, researchers, pharmaceutical companies, and bioinformatics technology developers. Over the last several years, the consortium organized regular open meetings, including a yearly workshop to allow participants to expand, refine, and prioritize the need for standard reporting while also discussing their own stakeholder-specific requirements for a standard. After these workshops, the BioCompute Object Specification Document was published - one in 2017 and another updated document in 2018 - to communicate best practices. Included in the GW-led consortium are experts from DNAnexus, Galaxy Project, Seven Bridges, and more.
"In order to help drive personalized medicine, we need to find a better way to compare and build on genomic data that could yield insights into cancer, ancestry, microbiome dynamics, metagenomics, and more. This is where the BioCompute Object Specification Project comes in," said Raja Mazumder, PhD, the project's principal investigator and professor of biochemistry and molecular medicine at the GW School of Medicine and Health Sciences.
The standard is currently being evaluated by the Institute of Electrical and Electronics Engineers Standards Association to become an officially recognized standard. Because establishing and maintaining HTS standards for validating data, computation and interoperability is critical to the FDA's regulatory mission, the consortium aims to create an accompanying database (BioComputeDB). This will include development of mechanisms to transfer BCOs, updates to the technical specification documentation, and hosting regular informational sessions for FDA personnel on the creation and use of BCOs.
"I think our proposed database and mechanism to transfer BCOs has the potential to streamline the submission process," said Jonathon Keeney, PhD, a co-investigator on the project and assistant research professor of biochemistry and molecular medicine at the GW School of Medicine and Health Sciences. "We plan to work with FDA personnel very closely to make sure that the project supports their mission, and that it meets the needs of other community members as well."
The BioCompute project has also coordinated an "App-a-thon" Challenge on the PrecisionFDA platform that engaged the bioinformatics community to build BCOs and apps related to them, and has also recently launched a public private partnership that will further develop tools and feedback, and will extend the reach of the project to include more groups across different areas.