Genome-wide association study in breast cancer survivors reveals SNPs associated with gene expression of genes belonging to MHC class I and II

•eQTL analysis on a cohort of breast cancer (BC) survivors•HLA gene expression was associated with SNPs in 100 genes in BC survivors.•Comparing with healthy women, we found eQTLs that only occurred in BC survivors.•eQTLs specifically found in BC survivors were enriched for immune system genes.

IntroductionWe investigated the effect of genetic variation on gene expression in blood from a cohort of BC survivors. Further, we investigated the associations that were specific for BC survivors by performing identical analyses for a group of healthy women and comparing the results.MethodseQTL analysis was performed for 288 BC survivors (full data set). Further, using a subset of the data, eQTL analyses were performed on 288 BC survivors and on 81 healthy women separately and results were compared.ResultsA large number of associations were observed for the BC survivors, and the expression of human leukocyte antigen genes was found associated with SNPs in 100 genes. The comparison analyses with healthy women revealed associations occurring specifically in BC survivors, and the genes showed enrichment for immune system processes.ConclusionsThe results suggest that the immune system has a different constitution in BC survivors compared to healthy women.