PeCaX

PeCaX annotates and visualizes somatic genomic variants to support interpretation of tumor profiles and identification of therapeutic options by integrating clinical variant annotations, functional and drug-target annotations, and gene–drug networks.

Key Features:

• Somatic variant processing: Processes somatic variants provided in VCF (Variant Call Format) files.
• Clinical variant annotation integration: Integrates clinical variant annotations with variant data.
• Functional and drug-target annotation: Incorporates functional annotation and drug target annotation for implicated genes and variants.
• Gene–drug and biological network integration: Combines annotations within gene–drug networks and the context of biological networks.
• Visual analytics: Produces visual representations of gene–drug interactions and clinical variant annotations.
• Variant interpretation and navigation: Enables annotation, navigation, and interpretation of somatic genomic variants.

Scientific Applications:

• Molecular tumor board support: Aids molecular tumor boards in interpreting tumor genomic profiles for personalized oncology decisions.
• Therapeutic option identification: Assists in identifying potential treatment options based on integrated variant and gene–drug information.
• Genomic data interpretation: Enhances interpretation of somatic genomic variants in cancer through integrated annotations and network context.
• Hypothesis generation: Facilitates generation of new hypotheses by linking variant effects to functional annotations and drug targets within networks.

Methodology:

Processes somatic variants from VCF files, performs clinical, functional, and drug-target annotation, integrates these annotations with gene–drug and biological networks, and generates visual representations of gene–drug interactions and clinical variant annotations.