In Stage 1 of the analysis, we used Metal56,57 version 2011-03-25 to perform a fixed-effects meta-analysis of genome-wide data from 22 studies and four additional COPD cohorts genotyped on an Illumina HumanExome v1.2 platform with custom content; this content included a set of COPD candidate genes and regions identified from prior COPD GWAS efforts13. We adjusted for inflation using genomic control correction in each study. We included study populations with subjects of non-European ancestry in the overall analysis, and additionally examined results limited to study populations of European ancestry. To identify variants to test for association in Stage 2 in the UK BiLEVE study, we selected top results (P < 5×10−6) from the Stage 1 meta-analysis. We selected one lead variant from the chromosome 15q25, FAM13, and HHIP regions, as all of these have been described in multiple COPD GWASs13,16,17,21. For the remainder of the regions, we performed linkage disequilibrium pruning using the PLINK1.9 –clump procedure with an r2 of 0.5, additionally examining these SNPs for the number of cohorts with passing quality control at each variant and including SNPs
