CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

Abstract

CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and predisposing relevance of inherited and somatic variants of all types. CIViC is committed to open-source code, open-access content, public application programming interfaces (APIs) and provenance of supporting evidence to allow for the transparent creation of current and accurate variant interpretations for use in cancer precision medicine.

Figure 1

Contribution of CIViC to the precision cancer treatment cycle. The diagram summarizes how research, clinical treatment and CIViC knowledge curation are interrelated. The CIViC knowledgebase aims to develop clinical interpretations for raw cancer variant observations stored in large variant databases (gray). Each CIViC variant interpretation is based on published evidence and leverages complementary knowledge bases and ontologies wherever possible (yellow). The precision medicine clinical treatment cycle (blue) and research cycle (green) both involve sampling, sequencing, analysis, interpretation, intervention, evaluation and publication. These cycles start with hypothesis generation, followed by research projects or clinical trials, and dissemination of their findings. Examples of how each stage specifically relates to or benefits from the CIViC resource are represented by ‘persona’ icons for the four types of CIViC stakeholders: research scientists (green), clinical scientists (blue), patient advocates (orange) and developers (red). Each is accompanied by a brief description of a possible research, clinical, outreach or software development action. In the center of the diagram, key features of the CIViC interface and data model are summarized (purple). These include the roles and permissions of CIViC users, especially consumers of the content, curators and editors. Members of the CIViC community participate by adding, editing, discussing and approving individual evidence records and summaries that support the clinical interpretation of cancer variants. Anyone willing to log in may assume the role of curator, but contributions must be reviewed by expert editors before acceptance.