Internet2 Community Collaboration in Precision Medicine Result in BioCompute Framework
For genomics scientists and researchers, the production and sharing of big data is key to understanding the human genome sequence. Lower costs and greater accessibility to high-throughput sequencing resulted in a proliferation of data. Yet the recording and reporting of this data is varied and fragmented, impeding the advancement of genomic data analysis techniques.
Thanks to a partnership between the U.S. Food and Drug Administration and George Washington University, a group of researchers across higher education, the federal government, and industry collaborated with colleagues in Europe on describing a standardized communication method for researchers performing high-throughput sequencing called BioCompute.
High-throughput sequencing has outpaced the development of much-needed infrastructure around its use. The collaboration helped establish a framework for community-based standards development and harmonization of high-throughput sequencing computations and data formats. This enables standardized reporting of genomic sequence data provenance, helping to promote interoperability and simplify the verification of bioinformatics protocols. The standard is freely accessible as a GitHub organization.
"There was a shared commitment by everyone involved in this project to help create standards on how to organize big data for genomics and bioinformatics research," said Dan Taylor, co-contributor to the BioCompute project and director at Internet2. "The availability of robust and reproducible data analysis is key to supporting researchers, and the BioCompute standards aim to help improve communication, repeatability, and reproducibility of future high-throughput genomic sequencing findings."
The Internet2 member institutions involved in the project include Cornell University, George Washington University, Harvard University, National Institutes of Health, Oregon Health & Science University, OTSUKA Pharmaceutical Development & Commercialization, Inc., Stony Brook University, and the US Food and Drug Administration.
“Enabling precision medicine via standard communication of HTS provenance, analysis, and results” was published in PLOS Biology. A total of 36 researchers collaborated on this paper.