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.
journal_name
Hum Immunoljournal_title
Human immunologyauthors
Song GG,Lee YHdoi
10.1016/j.humimm.2012.11.003subject
Has Abstractpub_date
2013-02-01 00:00:00pages
256-60issue
2eissn
0198-8859issn
1879-1166pii
S0198-8859(12)00610-6journal_volume
74pub_type
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