OncoGEMINI

OncoGEMINI enables identification and analysis of biologically and clinically relevant tumor variants from multi-sample and longitudinal tumor sequencing data.

Key Features:

• GEMINI-compatible database: Uses a GEMINI-compatible database generated from annotated Variant Call Format (VCF) files to leverage existing genomic annotations.
• Filtering capabilities: Provides filtering of tumor variants based on included genomic annotations and allele frequency signatures.
• Handling tumor heterogeneity: Facilitates identification and tracing of mutations within diverse subclonal populations across samples.
• Longitudinal analysis: Stores tumor sampling timepoints in a searchable database to observe changes in variant allele frequencies over time.
• External annotation integration: Integrates CIViC and DGIdb annotations to associate mutations with cancer interpretation and potential therapeutic targets.

Scientific Applications:

• Mutation prioritization: Prioritizes mutations likely contributing to tumor evolution using annotations and allele frequency dynamics.
• Therapeutic target identification: Identifies potential therapeutic targets within heterogeneous tumors by querying CIViC and DGIdb annotations.
• Longitudinal variant tracing: Traces trajectories of somatic and inherited variations across biopsies and timepoints to monitor clonal dynamics.

Methodology:

Generates a GEMINI-compatible database from annotated Variant Call Format (VCF) files; creates a searchable database including tumor sampling timepoints; applies filters based on genomic annotations and allele frequency signatures; and integrates CIViC and DGIdb annotations.