title: 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).
  
  
  CONCLUSIONS
  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.
authors.affiliation: Division of Rheumatology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea.
authors.forename: Gwan Gyu
authors.initials: GG
authors.lastname: Song
authors.forename: Young Ho
authors.initials: YH
authors.lastname: Lee
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D001249:Asthma / Q000235:genetics* / Q000378:metabolism; D002648:Child; D005260:Female; D055106:Genome-Wide Association Study; D059805:HLA-DR alpha-Chains / Q000235:genetics; D006801:Humans; D018793:Interleukin-13 / Q000235:genetics; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics*; D055815:Young Adult
chemical_list: D059805:HLA-DR alpha-Chains; D018793:Interleukin-13; D018719:Erb-b2 Receptor Tyrosine Kinases