evidenced by the expected lack of genome-wide significant findings in a GWAS meta-analysis comparing smoker cases vs. smoker controls from independent datasets. Lastly, GAWMerge recovered known COPD-associated findings from Hobbs et al28. including CHRNA3 on chromosome 15, FAM13A on chromosome 4, CYP2A6 on chromosome 19, TGFB2 on chromosome 1, and HHIP on chromosome 4. The key aspects of the protocol that provide these unbiased findings are (1) phasing the array and WGS data independently using only the intersection of variants across technologies and (2) including the empirical R2 and R2 difference filters to remove poorly imputed and differently imputed variants.
