eQTL analysis

Data from BC tumours and adjacent normal breast tissue were accessed from The Cancer Genome Atlas⁷⁴ (TCGA). Germline SNP genotypes (Affymetrix 6.0 arrays) from individuals of European ancestry were processed and imputed to the 1000 Genomes reference panel (October 2014)³⁵. Tumour tissue copy number was estimated from the Affymetrix 6.0 and called using the GISTIC2 algorithm⁷⁵. Complete genotype, RNA-seq and copy number data were available for 679 genetically European patients (78 with adjacent normal tissue). Further, RNA-seq for normal breast tissue and imputed germline genotype data were available from 80 females from the GTEx Consortium⁷⁶. Genes with a median expression level of 0 RPKM across samples were removed, and RPKM values of each gene were log2 transformed. Expression values of samples were quantile normalized. Genetic variants were evaluated for association with the expression of genes located within ±2 Mb of the lead variant at each risk region using linear regression models, adjusting for ESR1 expression. Tumour tissue was also adjusted for copy number variation⁷⁷. eQTL analyses were performed using the MatrixEQTL program in R⁷⁸.