Important discoveries in the field of asthma were made using eQTL mapping in lymphoblastoid cell lines [10]. In this study, we used lung tissue to map lung eQTLs, which is likely the most relevant tissue to study the genetics of lung diseases like asthma. Ideally one would want to relate SNPs to gene expression and to disease phenotype using tissue or cells from individuals affected by the disease of interest [44]. In this study, only a small percentage of the subjects had self-reported asthma. It should be noted that eQTL mapping in liver tissues was successful to identify new susceptibility genes for type 1 diabetes, coronary artery disease and blood lipid levels [19], [20], [45]. These discoveries were made regardless of the medical condition of patients from whom the liver tissues were explanted. Similarly, lung tissue from any source (normal or diseased) is a valid approach to identify the genetic variants that influence gene expression irrespective of disease status. The heterogeneous nature of the tissue we profiled with varying environmental exposures (e.g. smoking) and disease status (e.g. lung cancer) would
