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

Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida & 17 others Jonathon Keeney, Kanaka Durga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish (US)
Article numbere3000099
JournalPLoS Biology
Volume16
Issue number12
DOIs
StatePublished - Dec 1 2018

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Precision Medicine
communication (human)
provenance
Medicine
medicine
Communication
Throughput
genomics
Workflow
Pathogens
United States Food and Drug Administration
Bioinformatics
Computational methods
Computational Biology
Routine Diagnostic Tests
Interoperability
bioinformatics
Documentation
diagnostic techniques
clinical trials

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Alterovitz, G., Dean, D., Goble, C., Crusoe, M. R., Soiland-Reyes, S., Bell, A., ... Mazumder, R. (2018). Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biology, 16(12), [e3000099]. https://doi.org/10.1371/journal.pbio.3000099

Enabling precision medicine via standard communication of HTS provenance, analysis, and results. / Alterovitz, Gil; Dean, Dennis; Goble, Carole; Crusoe, Michael R.; Soiland-Reyes, Stian; Bell, Amanda; Hayes, Anais; Suresh, Anita; Purkayastha, 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, Kanaka Durga; 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; Mazumder, Raja.

In: PLoS Biology, Vol. 16, No. 12, e3000099, 01.12.2018.

Research output: Contribution to journalArticle

Alterovitz, G, Dean, D, Goble, C, Crusoe, MR, Soiland-Reyes, S, Bell, A, Hayes, A, Suresh, A, Purkayastha, A, King, CH, Taylor, D, Johanson, E, Thompson, EE, Donaldson, E, Morizono, H, Tsang, H, Vora, JK, Goecks, J, Yao, J, Almeida, JS, Keeney, J, Addepalli, KD, Krampis, K, Smith, KM, Guo, L, Walderhaug, M, Schito, M, Ezewudo, M, Guimera, N, Walsh, P, Kahsay, R, Gottipati, S, Rodwell, TC, Bloom, T, Lai, Y, Simonyan, V & Mazumder, R 2018, 'Enabling precision medicine via standard communication of HTS provenance, analysis, and results', PLoS Biology, vol. 16, no. 12, e3000099. https://doi.org/10.1371/journal.pbio.3000099
Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A et al. Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biology. 2018 Dec 1;16(12). e3000099. https://doi.org/10.1371/journal.pbio.3000099
Alterovitz, Gil ; Dean, Dennis ; Goble, Carole ; Crusoe, Michael R. ; Soiland-Reyes, Stian ; Bell, Amanda ; Hayes, Anais ; Suresh, Anita ; Purkayastha, 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, Kanaka Durga ; 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 ; Mazumder, Raja. / Enabling precision medicine via standard communication of HTS provenance, analysis, and results. In: PLoS Biology. 2018 ; Vol. 16, No. 12.
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