VariantAlert

VariantAlert monitors and automatically updates genetic variant annotations to support continuous reinterpretation of variants based on changes in external annotation resources.

Key Features:

• Automated Daily Re-annotation: Performs daily re-annotations of submitted genetic variants using external resources accessed via APIs.
• Integration with Multiple Databases: Aggregates annotations from MyVariant.info, gnomAD, COSMIC (Catalogue of Somatic Mutations in Cancer), ClinVar, CIViC, and other external resources.
• Continuous Monitoring: Continuously monitors submitted variant lists for annotation changes to support reinterpretation workflows.
• Change Detection: Detects specific annotation changes such as allele frequency adjustments in gnomAD, new entries in COSMIC, and ClinVar classification changes.
• User Notification System: Notifies users by email when annotation changes are detected for monitored variants.
• Annotation Storage: Stores updated annotations for subsequent retrieval and review.

Scientific Applications:

• Oncology: Supports monitoring of somatic and cancer-associated variants by tracking COSMIC and related annotation updates.
• Personalized Medicine: Enables timely reevaluation of variant significance as allele frequencies and clinical classifications are updated.
• Genomic Research: Facilitates longitudinal studies that require up-to-date variant annotations from multiple public resources.
• Clinical Genetics and Diagnostics: Assists clinical laboratories and clinicians in maintaining current variant interpretations informed by ClinVar, CIViC, and other databases.

Methodology:

Daily re-annotation using external resources accessed via APIs (e.g., MyVariant.info); integration with gnomAD, COSMIC, ClinVar, and CIViC; detection of annotation changes such as allele frequency adjustments and ClinVar classification changes; email notification of detected changes; storage of updated annotations.