Oncotator

Oncotator annotates genomic point mutations and short nucleotide insertions/deletions (indels) with variant- and gene-centric information for cancer research.

Key Features:

• Variant and gene-centric annotations: Assigns variant- and gene-level annotations including gene names and functional classifications (e.g., missense).
• Mutation types supported: Processes genomic point mutations and short nucleotide insertions/deletions (indels).
• Cancer-specific database integration: Integrates annotations from 14 publicly available resources including the Catalogue of Somatic Mutations in Cancer (COSMIC), the Cancer Gene Census, and The Cancer Genome Atlas (TCGA).
• Comprehensive cancer-relevant annotations: Incorporates cancer-specific information to contextualize the potential implications of genetic alterations in oncological contexts.
• Extensible data framework: Supports incorporation of additional data sources to expand annotation content.

Scientific Applications:

• Mutation annotation in cancer studies: Provide annotated variant and gene information to support analysis of mutations in cancer cohorts.
• Driver and functional interpretation: Aid interpretation of putative driver mutations and assessment of functional consequences using gene and mutation annotations.
• Cross-referencing with cancer genomics resources: Enable linkage of variants to COSMIC, the Cancer Gene Census, and TCGA for studies of mutation prevalence and significance.

Methodology:

Integrates annotation data from 14 publicly available resources, including COSMIC, the Cancer Gene Census, and TCGA, to assign variant- and gene-centric annotations such as gene names and functional classifications to genomic point mutations and short indels.