The ClinGen Variant Curation Interface (VCI) to support direct submission and tracking of submissions to ClinVar
Clinical Genetics and Therapeutics
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Primary Categories:
- General Education
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Secondary Categories:
- General Education
Introduction:
The NIH-funded Clinical Genome Resource Consortium (ClinGen) has developed a suite of tools that support variant classification. Several of these tools focus on the application of evidence criteria and classification of variants based on the ACMG/AMP sequence variant classification guidelines and the dissemination of those classifications to the global community. Among these tools is the Variant Curation Interface (VCI: https://curation.clinicalgenome.org), an open-source variant classification platform that supports the FDA-recognized human variant curation process by ClinGen Variant Curation Expert Panels (VCEPs).
Methods:
ClinGen’s variant classification activity continues to expand with an increasing number of genetic variants curated across a greater number of genes by teams of curators (known as affiliations in the VCI). The variant curation workflow is intended to support dissemination of variant curations into two repositories: the ClinGen Evidence Repository (ERepo: https://erepo.genome.network/evrepo/ui) for approved ClinGen VCEPs, and ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) for all users. As of late 2024, ClinGen VCEPs have submitted over 8000 curations to these two repositories. Support for dissemination of curations into the ERepo from the VCI is through an Application Programming Interface (API) - driven process via the ClinGen Data Exchange. In contrast, to date ClinVar submission from the VCI has required curators to download the needed variant information from the VCI onto a spreadsheet and then submit to ClinVar with manual tracking of the submissions.
Results:
To facilitate ClinVar submission with the increasing growth in ClinGen curations, we have developed the data model and user workflow in the VCI to support affiliations submitting variant curations and classifications to ClinVar using an API.
Conclusion:
These features will streamline workflows for both ClinGen VCEPs and non-ClinGen VCI users, and further the ClinGen goal of creating scalable curation workflows to support the clinical genomics community.
The NIH-funded Clinical Genome Resource Consortium (ClinGen) has developed a suite of tools that support variant classification. Several of these tools focus on the application of evidence criteria and classification of variants based on the ACMG/AMP sequence variant classification guidelines and the dissemination of those classifications to the global community. Among these tools is the Variant Curation Interface (VCI: https://curation.clinicalgenome.org), an open-source variant classification platform that supports the FDA-recognized human variant curation process by ClinGen Variant Curation Expert Panels (VCEPs).
Methods:
ClinGen’s variant classification activity continues to expand with an increasing number of genetic variants curated across a greater number of genes by teams of curators (known as affiliations in the VCI). The variant curation workflow is intended to support dissemination of variant curations into two repositories: the ClinGen Evidence Repository (ERepo: https://erepo.genome.network/evrepo/ui) for approved ClinGen VCEPs, and ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) for all users. As of late 2024, ClinGen VCEPs have submitted over 8000 curations to these two repositories. Support for dissemination of curations into the ERepo from the VCI is through an Application Programming Interface (API) - driven process via the ClinGen Data Exchange. In contrast, to date ClinVar submission from the VCI has required curators to download the needed variant information from the VCI onto a spreadsheet and then submit to ClinVar with manual tracking of the submissions.
Results:
To facilitate ClinVar submission with the increasing growth in ClinGen curations, we have developed the data model and user workflow in the VCI to support affiliations submitting variant curations and classifications to ClinVar using an API.
Conclusion:
These features will streamline workflows for both ClinGen VCEPs and non-ClinGen VCI users, and further the ClinGen goal of creating scalable curation workflows to support the clinical genomics community.