Enabling precision medicine via standard communication of HTS provenance, analysis, and results
| Autor: | Jonas S. Almeida, Lydia Guo, Vahan Simonyan, Dan Taylor, Matthew Ezewudo, Hsinyi S. Tsang, Robel Kahsay, Anais Hayes, Jonathon Keeney, Elaine E. Thompson, Krista Smith, KanakaDurga Addepalli, Konstantinos Krampis, Gil Alterovitz, Anita Suresh, Raja Mazumder, Jeet Vora, Eric F. Donaldson, Amanda Bell, Carole Goble, Charles Hadley King, Yuching Lai, Michael R. Crusoe, Srikanth Gottipati, Stian Soiland-Reyes, Nuria Guimera, Hiroki Morizono, Paul Walsh, Marco Schito, Elaine Johanson, Jianchao Yao, Dennis A. Dean, Jeremy Goecks, Mark Walderhaug, Anjan Purkayastha, Toby Bloom, Timothy C. Rodwell |
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| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Science and Technology Workforce Standardization Computer science Interoperability Careers in Research Workflow Database and Informatics Methods Software 0302 clinical medicine Documentation Community Page BioCompute Objects Medicine and Health Sciences Precision Medicine Biology (General) 0303 health sciences Genome General Neuroscience Communication High-Throughput Nucleotide Sequencing high-throughput sequencing Genomics Research Assessment Genomic Databases Reproducibility HL7 3. Good health Professions Open standard 030220 oncology & carcinogenesis NGS HTS General Agricultural and Biological Sciences Bioinformatics Science Policy QH301-705.5 FHIR Biology CWL Research and Analysis Methods General Biochemistry Genetics and Molecular Biology Domain (software engineering) World Wide Web 03 medical and health sciences Genomic Medicine Genetics Animals Humans research objects 030304 developmental biology Clinical Genetics General Immunology and Microbiology business.industry regulatory review Personalized Medicine Computational Biology Reproducibility of Results Biology and Life Sciences Usability Sequence Analysis DNA Genome Analysis Precision medicine Data science GAG4H Clinical trial 030104 developmental biology Biological Databases People and Places Scientists Population Groupings Software engineering business |
| Zdroj: | Alterovitz, G, Dean, D, Goble, C, Crusoe, M R, Soiland-Reyes, S, Bell, A, Hayes, A, Suresh, A, Purkayastha, A, King, C H S, Taylor, D, Johanson, E, Thompson, E E, Donaldson, E, Morizono, H, Tsang, H, Vora, J K, Goecks, J, Yao, J, Almeida, J S, Keeney, J, Addepalli, K, Krampis, K, Smith, K M, Guo, L, Walderhaug, M, Schito, M, Ezewudo, M, Guimera, N, Walsh, P, Kahsay, R, Gottipati, S, Rodwell, T C, 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 PLOS Biology PLoS Biology, Vol 16, Iss 12, p e3000099 (2018) PLoS Biology |
| DOI: | 10.1371/journal.pbio.3000099 |
| Popis: | 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. This Community Page article presents a communication standard for the provenance of high-throughput sequencing data; a BioCompute Object (BCO) can serve as a history of what was computed, be used as part of a validation process, or provide clarity and transparency of an experimental process to collaborators. |
| Databáze: | OpenAIRE |
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