Elsevier

Genomics

Volume 102, Issue 4, October 2013, Pages 278-287
Genomics

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

https://doi.org/10.1016/j.ygeno.2013.07.006Get rights and content
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Highlights

  • 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.

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.

Abbreviations

BC
breast cancer
SNP
single nucleotide polymorphism
mRNA
messenger RNA
FDR
false discovery rate
IPA
ingenuity pathway analysis
HLA
human leukocyte antigen
MHC
major histocompatibility
UTR
untranslated region
chr
chromosome
LD
linkage disequilibrium

Keywords

Breast cancer
Treatment
eQTL
Gene expression
SNP
Radiotherapy
Breast cancer survivors

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