Journal Article

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

Schultz, Nikolaus, Krysiak, Kilannin, Madhavan, Subha, Walsh, Brian, McMurry, Julie, Freimuth, Robert R., Aittokallio, Tero, Ellrott, Kyle, Mayfield, Georgia, Patterson, Sara, Pitel, Beth A., Wagner, Alex H., Rieke, Damian T., Mockus, Susan, Elemento, Olivier, Baudis, Michael, Schriml, Lynn M., Warner, Jeremy L., Li, Xuan Shirley, Dienstmann, Rodrigo, Griffith, Obi L., Tamborero, David, Margolin, Adam A., Ritter, Deborah I., Beckmann, Jacques S., Goecks, Jeremy, Griffith, Malachi, Chakravarty, Debyani, Sezerman, Ozman U., del Vecchio Fitz, Catherine, Lopez-Bigas, Nuria, Deu-Pons, Jordi, Raca, Gordana, Duren, Ryan P., Haendel, Melissa, Lawler, Mark, Sonkin, Dmitriy, Gao, Jianjiong, Cerami, Ethan

2020

Overview

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.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/67 / 692/308/2056 / Agriculture / Analysis / Animal Genetics and Genomics / Biomarkers / Biomedical and Life Sciences / Biomedicine / Cancer / Cancer Research / Databases, Genetic / Diploidy / Gene Function / Genetic Variation - genetics / Genomics / Genomics - methods / Human Genetics / Humans / Kinases / Knowledge Bases / Knowledge bases (artificial intelligence) / Neoplasms - genetics / Oncology / Ontology / Precision medicine / Precision Medicine - methods