Introduction to CIViC Curation
With the recent advent of rapid and affordable tumor genome sequencing, interpreting the clinical significance of cancer variants from the wealth of existing and rapidly evolving medical literature has become a major bottleneck to realizing the potential of precision cancer medicine.
Associating cancer variants with concrete clinical actions by manual curation of high quality evidence is a great challenge. Creating useful interpretations requires integrating complex information from diverse sources ranging from preclinical lab experiments to clinical trial results. Creating and maintaining such interpretations will require the concerted effort of many experts at a large scale.
CIViC curators are a community of such experts dedicated to creating and maintaining a knowledgebase clinical interpretations for cancer variants.
Although curators are not required to have any specific training, background or skill set, curator-generated content can only be “Accepted” once it is reviewed by a CIViC Editor. Editors are experts in cancer genomics, oncology, pathology and other relevant fields. This gate-keeper model allows significant contributions from curators with any level of experience while maintaining the quality of an expert-driven resource. Curators can be promoted to Editors once they have demonstrated sufficient understanding of the CIViC data model and requirements for cancer variant interpretation.
CIViC curation involves documenting the published evidence for the clinical relevance of cancer variants. This includes creation of structured CIViC evidence statements for cancer variants, curation of variant coordinates, integration of multiple evidence statements into CIViC assertions, and creation of molecular profile-, variant- and gene-level summaries.
However, even small contributions can make a big impact on how up-to-date and comprehensive the CIViC resource is. Examples of small curation activities include: commenting on existing entries, identifying additional literature sources, improving the wording of a variant interpretation, adding variant IDs or aliases, etc.
Create an account. Creating an account requires only that you have login credentials for one of our supported Open Authorization (OAuth) providers (currently Google, ORCiD, or GitHub).
For a primer on the fundamentals of cancer variant interpretation, we suggest that new users start by reading the CIViC paper, several recently published Standards and Guidelines that CIViC adheres to wherever possible, and other recommended reading as described below.
Required reading for curators
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.
ACMG/AMP - Standards and guidelines for the interpretation of sequence variants.
ClinGen - Somatic cancer variant curation and harmonization through consensus minimum variant level data (MVLD).
AMP/ASCO/CAP - Standards and guidelines for the interpretation and reporting of sequence variants in cancer.
Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).
Other recommended reading
Standardized decision support in next generation sequencing reports of somatic cancer variants
Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards
Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource
Organizing knowledge to enable personalization of medicine in cancer
For further information on curation with the CIViC platform we provide General Curation Practices, and documentation for Curating Molecular Profiles, Curating Variants, Curating Genes, Curating Evidence, Curating Assertions, and Suggesting Sources. For examples and ideas on how to get started, visit our Curation Ideas and Monitoring Curation Activity pages. Finally, if you are interested in Becoming An Editor we provide details on the criteria for promotion.
- General Curation Practices
- Curating Variants
- Curating Genes
- Curating Molecular Profiles
- Curating Evidence
- General Evidence Item Curation Practices
- Predictive Evidence
- Predictive Evidence Curation Practices
- Diagnostic Evidence
- Diagnostic Evidence Curation Practices
- Prognostic Evidence
- Prognostic Evidence Curation Practices
- Predisposing Evidence
- Predisposing Evidence Curation Practices
- Oncogenic Evidence Type
- Oncogenic Evidence Curation Practices
- Functional Evidence Type
- Functional Evidence Curation Practices
- Curation Scenarios
- Curating Evidence from Clinical Trials
- Complex Molecular Profiles in comparison to Categorical (Bucket) MPs
- Curating Assertions
- Curating and Suggesting Sources
- Prioritizing Curation Effort
- Example Curation Activities
- Becoming an Editor