domingo, 6 de enero de 2019

Enabling precision medicine via standard communication of HTS provenance, analysis, and results. - PubMed - NCBI

2018 Dec 31;16(12):e3000099. doi: 10.1371/journal.pbio.3000099. [Epub ahead of print]

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

Alterovitz G1,2,3, Dean D4, Goble C5, Crusoe MR6, Soiland-Reyes S5, Bell A7, Hayes A7, Suresh A8, Purkayastha A7,9, King CH7,10, Taylor D11, Johanson E12, Thompson EE12, Donaldson E12, Morizono H13,14, Tsang H15,16, Vora JK7, Goecks J17, Yao J18, Almeida JS19, Keeney J7, Addepalli K16, Krampis K20,21, Smith KM10, Guo L22, Walderhaug M10, Schito M23, Ezewudo M23, Guimera N24, Walsh P25, Kahsay R7, Gottipati S26, Rodwell TC8, Bloom T27, Lai Y24, Simonyan V10, Mazumder R7,10.

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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.