eQTL analyses were conducted in two studies: 123 normal breast tissue and 254
breast tumours from women in the Norwegian Breast Cancer Study (NBCS); all women
were of Caucasian origin. The 123 normal breast tissue is a cohort of expression
data from normal breasts biopsy (
n=74), reduction plastic surgery
(
n=37) and adjacent normal (
n=12) (adjacent to tumour).
Correlations between the two most likely causative SNPs (rs4442975 and
rs6721996) and expression levels of nearby genes (500 kb upstream and
downstream of the SNPs) were assessed using a linear regression model in which
an additive effect on expression level was assumed for each copy of the rare
allele. Calculations were carried out using the eMap library in R (
www.bios.unc.edu/~weisun/software/eMap).
The second eQTL analysis was based on 135 adjacent normal breast samples from
women of Caucasian origin in the METABRIC study27 (
link). Matched gene
expression (Illumina HT-12 v3 microarray) and germline SNP data that were either
genotyped (Affymetrix
SNP 6.0) or imputed (1000 Genomes Project, March 2012 data
using IMPUTE version 2.0) were used. Statistical methods were identical to the
NBCS analysis.
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