Lung expression quantitative trait loci (eQTL) were calculated from 1,111 human subjects who underwent lung surgery at three academic sites, Laval University, University of British Columbia (UBC), and University of Groningen, henceforth referred to as Laval, UBC, and Groningen, respectively. This lung eQTL dataset has been described previously22,60. Briefly, 66.7% to 91.2% of the individuals in this study were current or former smokers and 24.2% to 35.3% had moderate to severe COPD (GOLD spirometry grade 2 to 4). Whole-genome gene expression profiling in the lung was performed on a custom Affymetrix array (GPL10379). Microarray pre-processing and quality controls were described previously22,61,62. Probe sequences were mapped to the human genome (hg19) using Bowtie63 and probes not mapping to a coding region or having a common SNP (MAF ≥ 5%) in their sequence were removed. Expression data were adjusted for age, sex, and smoking status using residuals obtained with the robust fitting of linear models function (rlm) in the R statistical package MASS. Residual values deviating from the median by more than three standard deviations were filtered as outliers. Genotyping was carried on the Illumina Human 1M-Duo BeadChip array.
