BRCA1 and autoimmune disease: Up-regulated genes in BRCA1/2 associated tumors were significantly enriched in immune related pathways (Q < 0.05) including autoimmune diseases, infection response and antigen processing and presentation (Fig. 5E) even though there were no clear differences in immune cell infiltration in BRCA1/2 tumors compared to non-BRCA1/2 tumors (consesusTME scores P-value = 0.97) (Additional File 2, Supplementary Fig. 1).