CancerImmunityQTL

CancerImmunityQTL maps how germline genetic variants influence tumor immune cell infiltration and identifies immunity quantitative trait loci (immunQTLs) across human cancers.

Key Features:

• Data source: Uses genotype data from The Cancer Genome Atlas (TCGA).
• Immune quantification: Quantifies immune cell fractions using CIBERSORT.
• Scope: Analyzes immune infiltration and immunQTLs across 33 cancer types.
• ImmunQTL discovery: Identified a total of 913 immunQTLs affecting immune cell infiltration.
• Survival associations: Detected five immunQTLs significantly associated with patient overall survival.
• GWAS integration: Intersects immunQTLs with genome-wide association study (GWAS) data and reports 527 immunQTLs overlapping known GWAS linkage disequilibrium regions.
• Biological focus: Focuses on germline genetic determinants of the tumor microenvironment and immune infiltration.

Scientific Applications:

• Germline mapping: Mapping germline variants that influence tumor-infiltrating immune cell composition.
• Biomarker discovery: Prioritizing genetic variants for potential biomarkers of immunotherapy response or prognosis.
• GWAS interpretation: Linking GWAS loci to immune phenotypes in cancer by overlapping immunQTLs with GWAS LD regions.

Methodology:

Uses TCGA genotype data, quantifies immune cell fractions with CIBERSORT, identifies immunity quantitative trait loci (immunQTLs) across 33 cancer types, tests associations with overall survival, and intersects immunQTLs with GWAS linkage disequilibrium regions.