Pharmacogenomics: novel loci identification via integrating gene differential analysis and eQTL analysis. Human molecular genetics Qiu, W., Rogers, A. J., Damask, A., Raby, B. A., Klanderman, B. J., Duan, Q. L., Tyagi, S., Niu, S., Anderson, C., Cahir-McFarland, E., Mariani, T. J., Carey, V., Tantisira, K. G. 2014; 23 (18): 5017-5024


Nearly one-half of asthmatic patients do not respond to the most commonly prescribed controller therapy, inhaled corticosteroids (ICS). We conducted an expression quantitative trait loci (eQTL) analysis using more than 300 expression microarrays (from 117 lymphoblastoid cell lines) in corticosteroid (dexamethasone) treated and untreated cells derived from asthmatic subjects in the Childhood Asthma Management Program (CAMP) clinical trial. We then tested the associations of eQTL with longitudinal change in airway responsiveness to methacholine (LnPC20) on ICS. We identified 2,484 cis-eQTL affecting 767 genes following dexamethasone treatment. A significant over-representation of lnPC20-associated cis-eQTL (190 SNPs) among differentially expressed genes (OR=1.76, 95% CI: 1.35-2.29) was noted in CAMP Caucasians. Forty-six of these 190 clinical associations were replicated in CAMP African Americans, including 7 SNPs near 6 genes meeting criteria for genome-wide significance (p<2x10(-7)). Notably, the majority of genome-wide findings would not have been uncovered via analysis of untreated samples. These results indicate that identifying eQTL after relevant environmental perturbation enables identification of true pharmacogenetic variants.

View details for DOI 10.1093/hmg/ddu191

View details for PubMedID 24770851