Abstract
Manually curated variant knowledgebases and their associated knowledge models are serving an increasingly important role in distributing and interpreting variants in cancer. These knowledgebases vary in their level of public accessibility, and the complexity of the models used to capture clinical knowledge. CIViC (Clinical Interpretation of Variants in Cancer - www.civicdb.org) is a fully open, free-to-use cancer variant interpretation knowledgebase that incorporates highly detailed curation of evidence obtained from peer-reviewed publications and meeting abstracts, and currently holds over 6300 Evidence Items for over 2300 variants derived from over 400 genes. CIViC has seen increased adoption by, and also undertaken collaboration with, a wide range of users and organizations involved in research. To enhance CIViC’s clinical value, regular submission to the ClinVar database and pursuit of other regulatory approvals is necessary. For this reason, a formal peer reviewed curation guideline and discussion of the underlying principles of curation is needed. We present here the CIViC knowledge model, standard operating procedures (SOP) for variant curation, and detailed examples to support community-driven curation of cancer variants.
Highlights
Expansion of pan-cancer sequencing efforts in research and clinical settings has led to a rapid increase in the number of variants that require clinical annotation [1,2,3,4,5]
We previously reported the release of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase [12] with only informal online documentation to guide curation
The Supporting Evidence grid allows users to associate Evidence Items with Assertions. This collection of Evidence Items should cover the important clinically relevant findings for the CIViC Variant in the context of Conclusions While an earlier publication has introduced the CIViC database [12], no publication has yet offered a comprehensive documentation and standard operating procedures (SOP) of the complex curation practice developed over 4 years of work by the CIViC community worldwide
Summary
Expansion of pan-cancer sequencing efforts in research and clinical settings has led to a rapid increase in the number of variants that require clinical annotation [1,2,3,4,5]. Manual entry is required (e.g., not automatically linked based on representative coordinates) to permit entries for complex or Categorical CIViC Variants and to support alternate transcripts and reference build versions (Additional file 1: Figure S8).
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