A platform for oncogenomic reporting and interpretation
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Published:2022-02-09
Issue:1
Volume:13
Page:
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ISSN:2041-1723
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Container-title:Nature Communications
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language:en
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Short-container-title:Nat Commun
Author:
Reisle CaralynORCID, Williamson Laura M., Pleasance Erin, Davies Anna, Pellegrini Brayden, Bleile Dustin W., Mungall Karen L., Chuah Eric, Jones Martin R.ORCID, Ma Yussanne, Lewis Eleanor, Beckie Isaac, Pham David, Matiello Pletz Raphael, Muhammadzadeh Amir, Pierce Brandon M., Li Jacky, Stevenson Ross, Wong Hansen, Bailey Lance, Reisle Abbey, Douglas Matthew, Bonakdar MelikaORCID, Nelson Jessica M. T., Grisdale Cameron J.ORCID, Krzywinski Martin, Fisic Ana, Mitchell Teresa, Renouf Daniel J., Yip StephenORCID, Laskin Janessa, Marra Marco A.ORCID, Jones Steven J. M.ORCID
Abstract
AbstractManual interpretation of variants remains rate limiting in precision oncology. The increasing scale and complexity of molecular data generated from comprehensive sequencing of cancer samples requires advanced interpretative platforms as precision oncology expands beyond individual patients to entire populations. To address this unmet need, we introduce a Platform for Oncogenomic Reporting and Interpretation (PORI), comprising an analytic framework that facilitates the interpretation and reporting of somatic variants in cancer. PORI integrates reporting and graph knowledge base tools combined with support for manual curation at the reporting stage. PORI represents an open-source platform alternative to commercial reporting solutions suitable for comprehensive genomic data sets in precision oncology. We demonstrate the utility of PORI by matching 9,961 pan-cancer genome atlas tumours to the graph knowledge base, calculating therapeutically informative alterations, and making available reports describing select individual samples.
Funder
Genome British Columbia Canada Foundation for Innovation Ministry of Technology, Innovation and Citizens' Services | British Columbia Knowledge Development Fund Canada Research Chairs Genome Canada
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary
Reference70 articles.
1. Good, B. M., Ainscough, B. J., McMichael, J. F., Su, A. I. & Griffith, O. L. Organizing knowledge to enable personalization of medicine in cancer. Genome Biol. 15, 438 (2014). 2. Mardis, E. R. The 1,000 genome, the 100,000 analysis? Genome Med 2, 84 (2010). 3. Chakravarty, D. et al. OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol 2017, PO.17.00011 (2017). 4. Griffith, M. et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat. Genet. 49, 170–174 (2017). 5. Tamborero, D. et al. Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations. Genome Med 10, 25 (2018).
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