Combining omics data to identify genes associated with allergic rhinitis.
Allergic rhinitis is a common chronic disorder characterized by immunoglobulin E-mediated inflammation. To identify new genes associated with this trait, we performed genome- and epigenome-wide association studies and linked marginally significant CpGs located in genes or its promoter and SNPs located 1 Mb from the CpGs, by identifyingcismethylation quantitative trait loci (mQTL). This approach relies on functional cellular aspects rather than stringent statistical correction. We were able to identify one gene with significantcis-mQTL for allergic rhinitis, caudal-type homeobox 1 (CDX1). We also identified 11 genes with marginally significantcis-mQTLs (p< 0.05) including one with both allergic rhinitis with or without asthma (RNF39). Moreover, most SNPs identified were not located closest to the gene they were linked to throughcis-mQTLs counting the one linked toCDX1located in a gene previously associated with asthma and atopic dermatitis. By combining omics data, we were able to identify new genes associated with allergic rhinitis and better assess the genes linked to associated SNPs.
Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Montréal, Québec H3A 1A5 Canada.|Département des sciences fondamentales, Université du Québec à Chicoutimi, 555 boulevard de l'Université, Saguenay, Québec G7H 2B1 Canada.
Andréanne
A
Morin
Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, 2725 chemin Sainte-Foy, Québec, Québec G1V 4G5 Canada.
Michel
M
Laviolette
Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Montréal, Québec H3A 1A5 Canada.
Tomi
T
Pastinen
Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, 2725 chemin Sainte-Foy, Québec, Québec G1V 4G5 Canada.
Louis-Philippe
LP
Boulet
Département des sciences fondamentales, Université du Québec à Chicoutimi, 555 boulevard de l'Université, Saguenay, Québec G7H 2B1 Canada.
Catherine
C
Laprise
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001249:Asthma / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D018899:CpG Islands; D044127:Epigenesis, Genetic; D005260:Female; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study / Q000379:methods; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D017874:Immediate-Early Proteins / Q000235:genetics*; D007223:Infant; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D065631:Rhinitis, Allergic / Q000235:genetics*; D055815:Young Adult
C491273:CDX1 protein, human; D018398:Homeodomain Proteins; D017874:Immediate-Early Proteins; C444639:RNF39 protein, human
Allergic rhinitis; Asthma; EWAS; GWAS; Omics; mQTLs