TY - JOUR
T1 - Enabling precision medicine via standard communication of HTS provenance, analysis, and results
AU - Alterovitz, Gil
AU - Dean, Dennis
AU - Goble, Carole
AU - Crusoe, Michael R.
AU - Soiland-Reyes, Stian
AU - Bell, Amanda
AU - Hayes, Anais
AU - Suresh, Anita
AU - Purkayastha, Anjan
AU - King, Charles H.
AU - Taylor, Dan
AU - Johanson, Elaine
AU - Thompson, Elaine E.
AU - Donaldson, Eric
AU - Morizono, Hiroki
AU - Tsang, Hsinyi
AU - Vora, Jeet K.
AU - Goecks, Jeremy
AU - Yao, Jianchao
AU - Almeida, Jonas S.
AU - Keeney, Jonathon
AU - Addepalli, Kanaka Durga
AU - Krampis, Konstantinos
AU - Smith, Krista M.
AU - Guo, Lydia
AU - Walderhaug, Mark
AU - Schito, Marco
AU - Ezewudo, Matthew
AU - Guimera, Nuria
AU - Walsh, Paul
AU - Kahsay, Robel
AU - Gottipati, Srikanth
AU - Rodwell, Timothy C.
AU - Bloom, Toby
AU - Lai, Yuching
AU - Simonyan, Vahan
AU - Mazumder, Raja
N1 - Publisher Copyright:
© 2018, Public Library of Science. All rights reserved. https://creativecommons.org/publicdomain/zero/1.0/.
PY - 2018/12
Y1 - 2018/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85059522295&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85059522295&partnerID=8YFLogxK
U2 - 10.1371/journal.pbio.3000099
DO - 10.1371/journal.pbio.3000099
M3 - Article
C2 - 30596645
AN - SCOPUS:85059522295
SN - 1544-9173
VL - 16
JO - PLoS Biology
JF - PLoS Biology
IS - 12
M1 - e3000099
ER -