To investigate the association between the sentinel variants and mRNA expression, we used three different eQTL datasets: (i) Microarray eQTL study: The lung tissues for eQTL analyses were from patients who underwent lung surgery at three academic sites, Laval University, University of British Columbia (UBC), and University of Groningen. Whole-genome gene expression profiling in the lung was performed on a custom Affymetrix array (GPL10379). Microarray pre-processing and quality controls were described previously. Genotyping was carried on the Illumina Human 1M-Duo BeadChip array. Genotypes and gene expression levels were available for 409, 287 and 342 patients at Laval, UBC, and Groningen, respectively. (ii) NCI RNAseq eQTL study: RNA was extracted from lung tissue samples within the Environment and Genetics in Lung cancer Etiology (EAGLE) study. RNAseq was carried out on 90 lung tissue sampled from an area distant from the tumor (defined here as “non-malignant lung tissue”) to minimize the potential for local cancer field effects. Transcriptome sequencing of 90 non-tumor samples was performed on the Illumina HiSeq2000/2500 platform with 100-bp paired-end reads. Genotyping was undertaken using Illumina bead arrays as
