Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors

Germline genetic variants modulate human immune response. We present analytical pipelines for assessing the contribution of hosts’ genetic background to the immune landscape of solid tumors using harmonized data from more than 9,000 patients in The Cancer Genome Atlas (TCGA). These include protocols for heritability, genome-wide association studies (GWAS), colocalization, and rare variant analyses. These workflows are developed around the structure of TCGA but can be adapted to explore other repositories or in the context of cancer immunotherapy. For complete details on the use and execution of this protocol, please refer to Sayaman et al. (2021). [Display omitted] •Pipelines for assessing the contribution of germline genetics on tumor immune contexture•Workflow for data download, processing, assembly, curation, and annotation•Protocols for heritability, GWAS, colocalization, and rare variant analysis•Visualization tools for exploration of the results by iAtlas and PheWeb Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Germline genetic variants modulate human immune response. We present analytical pipelines for assessing the contribution of hosts’ genetic background to the immune landscape of solid tumors using harmonized data from more than 9,000 patients in The Cancer Genome Atlas (TCGA). These include protocols for heritability, genome-wide association studies (GWAS), colocalization, and rare variants analysis. These workflows are developed around the structure of TCGA but can be adapted to explore other repositories or in the context of cancer immunotherapy.