Utilizing the CIViC curation interface and leveraging the expertise of the ClinGen Somatic WG, we will develop a procedure for submitting somatic variant interpretations from the ClinGen Somatic WG to ClinVar in an automated way. The interface will allow for iterative assembly and revision of ClinGen interpretation assertions, which we will periodically synchronize with the ClinVar submission interface as submissions are entered and accepted by the ClinGen Somatic WG. To enable this process, we have developed a civic2clinvar utility (https://github.com/griffithlab/civic2clinvar) that extracts designated assertions and converts them into the ClinVar submission format. We will extend this functionality by adding submission tracking into the CIViC data action cycle, allowing us to precisely track when and in what state a variant or assertion was submitted to ClinVar. Doing so will allow CIViC to automatically identify when accepted changes to a variant are made and need to be updated in the ClinVar system, and generate appropriately referenced update forms for submission to ClinVar. In order to fulfill our goal of submitting 3-star interpretations to ClinVar, establishing a standard operating procedure for this process is required. The CIViC data model tracks the provenance of all data within CIViC. This will be used to limit or filter the assertions approved by the ClinGen Somatic WG for submission to ClinVar. Not only can we limit to the content of specific users, but the Organizations feature will allow us to identify curators from ClinGen versus other curators. As this process develops, additional features may be needed to finalize a ClinVar submission, particularly to maintain the stringency required of 3-star variants in ClinVar. For this reason, we anticipate development of the assertions feature to be ongoing with additional functionality added to the CIViC interface. Once this functionality is developed, this will facilitate the submission of other assertions in CIViC, with the submission process modified appropriately for the ClinVar review status criteria.
Utilizing the CIViC curation interface and leveraging the expertise of the ClinGen Somatic WG, we will develop a procedure for submitting somatic variant interpretations from the ClinGen Somatic WG to ClinVar in an automated way. The interface will allow for iterative assembly and revision of ClinGen interpretation assertions, which we will periodically synchronize with the ClinVar submission interface as submissions are entered and accepted by the ClinGen Somatic WG. To enable this process, we have developed a civic2clinvar utility (https://github.com/griffithlab/civic2clinvar) that extracts designated assertions and converts them into the ClinVar submission format. We will extend this functionality by adding submission tracking into the CIViC data action cycle, allowing us to precisely track when and in what state a variant or assertion was submitted to ClinVar. Doing so will allow CIViC to automatically identify when accepted changes to a variant are made and need to be updated in the ClinVar system, and generate appropriately referenced update forms for submission to ClinVar. In order to fulfill our goal of submitting 3-star interpretations to ClinVar, establishing a standard operating procedure for this process is required. The CIViC data model tracks the provenance of all data within CIViC. This will be used to limit or filter the assertions approved by the ClinGen Somatic WG for submission to ClinVar. Not only can we limit to the content of specific users, but the Organizations feature will allow us to identify curators from ClinGen versus other curators. As this process develops, additional features may be needed to finalize a ClinVar submission, particularly to maintain the stringency required of 3-star variants in ClinVar. For this reason, we anticipate development of the assertions feature to be ongoing with additional functionality added to the CIViC interface. Once this functionality is developed, this will facilitate the submission of other assertions in CIViC, with the submission process modified appropriately for the ClinVar review status criteria.