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.
Alterovitz, Gil; Dean, Dennis; Globe, Carole; Crusoe, Michael R.; Soiland-Reyes, Stiam; Bell, Amanda; Hayes, Anais; Suresh, Anita; Purkkayastha, Anjan; King, Charles H.; Taylor, Dan; Johanson, Elaine; Thompson, Elaine E.; Donaldson, Eric; Morizono, Hiroki; Tsang, Hsinyi; Vora, Jeet K.; Goecks, Jeremy; Yao, Jianchao; Almeida, Jonas S.; Keeney, Jonathon; Addepalli, KanakaDurga; Krampis, Konstantinos; Smith, Krista M.; Guo, Lydia; Walderhaug, Mark; Schito, Marco; Ezewudo, Matthew; Guimera, Nuria; Walsh, Paul; Kahsay, Robel; Gottipati, Srikanth; Rodwell, Timothy C.; Bloom, Toby; Lai, Yuching; Simonyan, Vahan; and Mazumder, Raja, "Enabling precision medicine via standard communication of HTS provenance, analysis, and results" (2018). CUNY Academic Works.