Enabling precision medicine via standard communication of HTS provenance, analysis, and results

Authors

• Gil Alterovitz, Harvard Medical School
• Dennis Dean, Seven Bridges
• Carole Globe, University of Manchester
• Michael R. Crusoe, Common Workflow Language Project
• Stiam Soiland-Reyes, University of Manchester
• Amanda Bell, George Washington University
• Anais Hayes, George Washington University
• Anita Suresh, Foundation for Innovative New Diagnostics
• Anjan Purkkayastha, George Washington University
• Charles H. King, George Washington University
• Dan Taylor, Internet 2
• Elaine Johanson, US Food and Drug Administration
• Elaine E. Thompson, US Food and Drug Administration
• Eric Donaldson, US Food and Drug Administration
• Hiroki Morizono, Children’s National Medical Center
• Hsinyi Tsang, National Cancer Institute
• Jeet K. Vora, George Washington University
• Jeremy Goecks, Oregon Health & Science University
• Jianchao Yao, MRL IT, Merck & Co.
• Jonas S. Almeida, SUNY Stony Brook
• Jonathon Keeney, George Washington University
• KanakaDurga Addepalli, Attain, McClean
• Konstantinos Krampis, CUNY Hunter CollegeFollow
• Krista M. Smith, George Washington University
• Lydia Guo, Wellesley College
• Mark Walderhaug, George Washington University
• Marco Schito, Critical Path Institute
• Matthew Ezewudo, Critical Path Institute
• Nuria Guimera, DDL Diagnostic Laboratory
• Paul Walsh, University College Dublin
• Robel Kahsay, George Washington University
• Srikanth Gottipati, OTSUKA Pharmaceutical Development & Commercialization
• Timothy C. Rodwell, Foundation for Innovative New Diagnostics
• Toby Bloom, New York Genome Center
• Yuching Lai, DDL Diagnostic Laboratory
• Vahan Simonyan, George Washington University
• Raja Mazumder, George Washington University

Document Type

Article

Publication Date

12-31-2018

Abstract

A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development.” With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews.

Comments

This article was originally published in PLOS Biology, available at https://doi.org/10.1371/journal.pbio.3000099.

This is an open access article, free of all copyright,and may be freely reproduced,distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.The work is made available under the Creative Commons CC0 public domain dedication.