CusVarDB

CusVarDB generates sample-specific variant protein databases from NGS datasets to enable identification of coding variants expressed at the protein level for proteogenomics and cancer neo-antigen analysis.

Key Features:

• Variant Calling for Genome, RNA-Seq and ExomeSeq: Supports variant calling on Genome, RNA-Seq, and ExomeSeq NGS datasets to detect genetic variations.
• Sample-Specific Variant Protein Database Generation: Produces customized protein databases that incorporate called coding variants for individual samples.
• Genomic–Proteomic Integration: Integrates genomic variant calls with proteomic data analysis to link coding variants to expressed proteins.
• Mass Spectrometry Integration: Facilitates identification of variant peptides by incorporating mass spectrometry proteomic data into the database generation workflow.

Scientific Applications:

• Neo-antigen discovery: Identifies coding variants expressed at the protein level that can generate neo-antigens presented by the major histocompatibility complex (MHC).
• Cancer proteogenomics: Enables characterization of the mutational landscape and protein-level expression of coding variants in cancer samples, including triple-negative breast cancer.
• Immunotherapy biomarker evaluation: Supports assessment of neo-antigen load relevant to immunotherapy response.

Methodology:

Integrates a variant calling pipeline with proteomic data analysis to generate sample-specific variant protein databases from NGS datasets; validated on triple-negative breast cancer cell lines (BT474, MDMAB157, MFM223, HCC38) where it identified variant peptides.