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

Genomics. 2013 Oct;102(4):278-87. doi: 10.1016/j.ygeno.2013.07.006. Epub 2013 Jul 21.

Abstract

Introduction: We 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.

Methods: eQTL 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.

Results: A 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.

Conclusions: The results suggest that the immune system has a different constitution in BC survivors compared to healthy women.

Keywords: BC; Breast cancer; Breast cancer survivors; FDR; Gene expression; HLA; IPA; LD; MHC; Radiotherapy; SNP; Treatment; UTR; breast cancer; chr; chromosome; eQTL; false discovery rate; human leukocyte antigen; ingenuity pathway analysis; linkage disequilibrium; mRNA; major histocompatibility; messenger RNA; single nucleotide polymorphism; untranslated region.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / genetics*
  • Case-Control Studies
  • Chromosome Mapping
  • Cohort Studies
  • Female
  • Gene Expression*
  • Genes, MHC Class I*
  • Genes, MHC Class II*
  • Genetic Predisposition to Disease
  • Genetic Variation
  • Genome-Wide Association Study*
  • Humans
  • Linear Models
  • Middle Aged
  • Polymorphism, Single Nucleotide*
  • Survivors*