Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer

Figure 1

Project design, data processing, and analysis workflow for integrative analysis combining germline with somatic mutation information in TNBC and non-TNBC using gene expression data as the intermediate phenotype. RNA-seq read count data and somatic information were downloaded from the TCGA via the GDC. Germline mutation information was manually curated from GWAS studies and supplemented with information from the GWAS catalogue. LIMMA (R) package was used for the discovery of differentially expressed (DE) mutated and nonmutated genes. Ingenuity Pathway Analysis (IPA) was used for the discovery of molecular networks and biological pathways enriched for germline and somatic mutations.