iVar

iVar manages variant annotation, classification, and versioned tracking for genomic datasets derived from Next Generation Sequencing (NGS), accepting Variant Call Format (VCF) and text annotation files to keep variant interpretations current with emerging evidence.

Key Features:

• Centralized variant management: Consolidates variants from multiple sequencing-derived datasets into a unified management system for consistent annotation and classification.
• Input flexibility: Accepts Variant Call Format (VCF) files and text annotation files as inputs for integration and downstream processing.
• Annotation versioning and history: Supports periodic re-uploading of annotation updates and links successive annotations to variants as historical attributes.
• Data optimization: Processes input data to optimize organization and minimize redundancies within the variant database.
• Change-tracking search: Provides customizable search capabilities to track changes in pathogenicity-related data of variants over time.
• Patient identification for recontact: Identifies all database patients carrying specific variants to support downstream recontacting based on reinterpretation.

Scientific Applications:

• Genomic research: Management and versioned annotation of medium-throughput NGS-derived datasets to support longitudinal variant interpretation studies.
• Clinical diagnostics and reinterpretation: Maintenance of up-to-date variant classifications and tracking of pathogenicity changes to inform clinical reinterpretation and patient recontacting.

Methodology:

Integration and optimization of genomic data from VCF and text annotation files with support for periodic annotation updates linked as historical attributes; architecture demonstrated on 4,171 VCF files and 1,463 annotation files, resulting in a database of 4,166 samples and 22,569 unique variants.