Pathway analysis of genome-wide association study on asthma

Abstract

Objective: The aims of this study were to identify the candidate causal single nucleotide polymorphisms (SNPs) and candidate causal mechanisms of asthma and to generate SNP to gene to pathway hypotheses. Methods: SNPs that met a threshold of p <= 0.001 in a genome-wide association study (GWAS) dataset of asthma, which included 292,443 SNPs in 473 asthma cases and 1892 controls, were used in the present study. Identify candidate causal SNPs and pathway (ICSNPathway) analysis was applied to this dataset. Results: ICSNPathway analysis identified four candidate causal SNPs, four genes, and 21 candidate causal pathways, which in total provided four hypothetical biologic mechanisms: (1) rs7192 (nonsynonymous coding) to HLA-DRA to 21 pathways, such as, the role of eosinophils in the chemokine network of allergy, Th1/Th2 differentiation, and asthma (nominal p <= 0.001, FDR p <= 0.01); (2) rs20541 (nonsynonymous coding) to IL13 to asthma and cytokines and inflammatory response (nominal p < 0.001, FDR p <= 0.008); (3) rs1058808 (frameshift coding) to ERBB2 to transmembrane receptor activity (nominal p = 0.001, FDR p = 0.01); (4) rs17350764 (nonsynonymous coding (deleterious)) to OR52J3 to transmembrane receptor activity (nominal p = 0.001, FDR p = 0.01). Conclusion: By applying ICSNPathway analysis to asthma GWAS data, we found four candidate causal SNPs, four genes involving HLA-DRA and IL-13, and four hypotheses, which may contribute to asthma susceptibility. (C) 2012 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.