Genome-wide association study and meta-analysis in multiple populations identifies new loci for peanut allergy and establishes C11orf30/EMSY as a genetic risk factor for food allergy.


BACKGROUND: Peanut allergy (PA) is a complex disease with both environmental and genetic risk factors. Previously, PA loci were identified in filaggrin (FLG) and HLA in candidate gene studies, and loci in HLA were identified in a genome-wide association study and meta-analysis. OBJECTIVE: We sought to investigate genetic susceptibility to PA. METHODS: Eight hundred fifty cases and 926 hyper-control subjects and more than 7.8 million genotyped and imputed single nucleotide polymorphisms (SNPs) were analyzed in a genome-wide association study to identify susceptibility variants for PA in the Canadian population. A meta-analysis of 2 phenotypes (PA and food allergy) was conducted by using 7 studies from the Canadian, American (n?=?2), Australian, German, and Dutch (n?=?2) populations. RESULTS: An SNP near integrin a6 (ITGA6) reached genome-wide significance with PA (P?=?1.80?×?10-8), whereas SNPs associated with Src kinase-associated phosphoprotein 1 (SKAP1), matrix metallopeptidase 12 (MMP12)/MMP13, catenin a3 (CTNNA3), rho GTPase-activating protein 24 (ARHGAP24), angiopoietin 4 (ANGPT4), chromosome 11 open reading frame (C11orf30/EMSY), and exocyst complex component 4 (EXOC4) reached a threshold suggestive of association (P?=?1.49?×?10-6). In the meta-analysis of PA, loci in or near ITGA6, ANGPT4, MMP12/MMP13, C11orf30, and EXOC4 were significant (P?=?1.49?×?10-6). When a phenotype of any food allergy was used for meta-analysis, the C11orf30 locus reached genome-wide significance (P?=?7.50?×?10-11), whereas SNPs associated with ITGA6, ANGPT4, MMP12/MMP13, and EXOC4 and additional C11orf30 SNPs were suggestive (P?=?1.49?×?10-6). Functional annotation indicated that SKAP1 regulates expression of CBX1, which colocalizes with the EMSY protein coded by C11orf30. CONCLUSION: This study identifies multiple novel loci as risk factors for PA and food allergy and establishes C11orf30 as a risk locus for both PA and food allergy. Multiple genes (C11orf30/EMSY, SKAP1, and CTNNA3) identified by this study are involved in epigenetic regulation of gene expression.

Authors Asai, Yuka; Eslami, Aida; van Ginkel, C Dorien; Akhabir, Loubna; Wan, Ming; Ellis, George; Ben-Shoshan, Moshe; Martino, David; Ferreira, Manuel A; Allen, Katrina; Mazer, Bruce; de Groot, Hans; de Jong, Nicolette W; Gerth van Wijk, Roy N; Dubois, Anthony E J; Chin, Rick; Cheuk, Stephen; Hoffman, Joshua; Jorgensen, Eric; Witte, John S; Melles, Ronald B; Hong, Xiumei; Wang, Xiaobin; Hui, Jennie; Musk, Arthur W Bill; Hunter, Michael; James, Alan L; Koppelman, Gerard H; Sandford, Andrew J; Clarke, Ann E; Daley, Denise
Journal The Journal of allergy and clinical immunology
Pages 991-1001
Volume 141
Date 1/10/2017
Grant ID
Funding Body Allergy, Genes, and Environment Network of Centres of Excellence (AllerGen NCE)