A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
| Autor: | Susan M. Mockus, Deborah I. Ritter, David Tamborero, Obi L. Griffith, Jeremy Goecks, Gordana Raca, Damian T. Rieke, Georgia Mayfield, Nuria Lopez-Bigas, Jianjiong Gao, Kilannin Krysiak, Melissa A. Haendel, Ryan P Duren, Olivier Elemento, Kyle Ellrott, Jordi Deu-Pons, Adam A. Margolin, Brian Walsh, Tero Aittokallio, Michael Baudis, Rodrigo Dienstmann, Subha Madhavan, Julie A. McMurry, Sara E. Patterson, Ethan Cerami, Ozman Ugur Sezerman, Robert R. Freimuth, Beth A. Pitel, Nikolaus Schultz, Lynn M. Schriml, Alex H. Wagner, Jeremy L. Warner, Mark Lawler, Jacques S. Beckmann, Dmitriy Sonkin, Catherine Del Vecchio Fitz, Xuan Shirley Li, Debyani Chakravarty, Malachi Griffith |
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| Přispěvatelé: | Acibadem University Dspace, Variant Interpretation for Cancer Consortium, Institut Català de la Salut, [Wagner AH, Krysiak K] Washington University School of Medicine, St. Louis, MO, USA. [Walsh B, Mayfield G] Oregon Health and Science University, Portland, OR, USA. [Tamborero D] Pompeu Fabra University, Barcelona, Spain. Karolinska Institute, Solna, Sweden. [Sonkin D] National Cancer Institute, Rockville, MD, USA. [Dienstmann R] Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain, Vall d'Hebron Barcelona Hospital Campus |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Matching (statistics)
Knowledge Bases MEDLINE Computational biology Biology 03 medical and health sciences 0302 clinical medicine Information Science::Computing Methodologies::Algorithms::Artificial Intelligence::Knowledge Bases [INFORMATION SCIENCE] terapéutica::medicina de precisión [TÉCNICAS Y EQUIPOS ANALÍTICOS DIAGNÓSTICOS Y TERAPÉUTICOS] SDG 3 - Good Health and Well-being Neoplasms fenómenos genéticos::variación genética [FENÓMENOS Y PROCESOS] Genetics research Databases Genetic medicine Genetics Humans Relevance (information retrieval) Medicina personalitzada Precision Medicine Ciencias de la información::metodologías computacionales::algoritmos::inteligencia artificial::bases del conocimiento [CIENCIA DE LA INFORMACIÓN] 030304 developmental biology Cancer Structure (mathematical logic) 0303 health sciences Intel·ligència artificial - Aplicacions a la medicina Interpretation (philosophy) Diploidy Genetic Variation/genetics Genomics/methods Neoplasms/genetics Precision Medicine/methods Genetic Variation Genomics medicine.disease 3. Good health Genetic Phenomena::Genetic Variation [PHENOMENA AND PROCESSES] Genòmica Precision oncology 030220 oncology & carcinogenesis Meta-analysis Therapeutics::Precision Medicine [ANALYTICAL DIAGNOSTIC AND THERAPEUTIC TECHNIQUES AND EQUIPMENT] Analysis |
| Zdroj: | Variant Interpretation for Cancer Consortium 2020, ' A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer ', Nature Genetics, vol. 52, no. 4, pp. 448-457 . https://doi.org/10.1038/s41588-020-0603-8 Nature Genetics Nature genetics, vol. 52, no. 4, pp. 448-457 Scientia |
| DOI: | 10.1038/s41588-020-0603-8 |
| Popis: | Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. We developed a framework for harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations. We demonstrated large gains in overlap between resources across variants, diseases and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 57% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide a freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases. This analysis presents a harmonized meta-knowledgebase to facilitate clinical interpretation of somatic genomic variants in cancer. This community-based project highlights the need for cooperative efforts to curate clinical interpretations of somatic variants for robust practice of precision oncology. |
| Databáze: | OpenAIRE |
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