The multifactorial nature of food allergy
van Ginkel, Cornelia Doriene
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van Ginkel, C. D. (2018). The multifactorial nature of food allergy. Rijksuniversiteit Groningen.
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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
YUKA ASAI, MD, MSC,* AIDA ESLAMI, PHD,* C. DORIENE VAN GINKEL, BSC, LOUBNA AKHABIR, PHD, MING WAN, BSC, GEORGE ELLIS, BSC, MOSHE BEN-SHOSHAN, MD, MSC,
DAVID MARTINO, PHD, MANUEL A. FERREIRA, PHD, KATRINA ALLEN, MD, PHD, BRUCE MAZER, MD, HANS DE GROOT, MD, PHD, NICOLETTE W. DE JONG, PHD, ROY N. GERTH
VAN WIJK, MD, PHD, ANTHONY E. J. DUBOIS, MD, PHD, RICK CHIN, MSC, STEPHEN CHEUK, MD, JOSHUA HOFFMAN, PHD,K ERIC JORGENSEN, PHD, JOHN S. WITTE, PHD,
RONALD B. MELLES, MD, XIUMEI HONG, MD, PHD, XIAOBIN WANG, MD, MPH, SCD, JENNIE HUI, PHD, ARTHUR W. (BILL) MUSK, FRACP, MICHAEL HUNTER, PHD, ALAN L.
JAMES, FRACP, GERARD H. KOPPELMAN, MD, PHD,
ANDREW J. SANDFORD, PHD, ANN E. CLARKE, MD, MSC+ AND DENISE DALEY, PHDB+ *These authors contributed equally to this work as joint first authors.
+These authors contributed equally to this work as joint senior authors.
190
ABSTRACT
BACKGROUNDPeanut 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 α6 (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 α3 (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.
ABBREVIATIONS
ANGPT4 Angiopoietin
4ARHGAP24 Rho GTPase–activating protein 24 CanPAR Canadian Peanut Allergy Registry CFA Chicago Food Allergy
CHCHD3 Coiled-coil-helix-coiled-coil-helix domain containing 3 C11orf30 Chromosome 11 open reading frame
CNV Copy number variant CTNNA3 Catenin α3
eQTL Expression quantitative trait locus EXOC4 Exocyst complex component 4 FLG Filaggrin
GERA Genetic Epidemiology Research on Aging GWAS Genome-wide association study
ITGA6 Integrin α6
MAF Minor allele frequency MMP Matrix metallopeptidase
OR Odds ratio
PA Peanut allergy
QC Quality control QQ Quantile-quantile
SKAP1 Src kinase–associated phosphoprotein 1 SNP Single nucleotide polymorphism UFA Understanding Food Allergy
Chap
ter 10
191
ABSTRACT
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 α6 (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 α3 (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.
ABBREVIATIONS
ANGPT4 Angiopoietin
4ARHGAP24 Rho GTPase–activating protein 24 CanPAR Canadian Peanut Allergy Registry CFA Chicago Food Allergy
CHCHD3 Coiled-coil-helix-coiled-coil-helix domain containing 3 C11orf30 Chromosome 11 open reading frame
CNV Copy number variant CTNNA3 Catenin α3
eQTL Expression quantitative trait locus EXOC4 Exocyst complex component 4 FLG Filaggrin
GERA Genetic Epidemiology Research on Aging GWAS Genome-wide association study
ITGA6 Integrin α6
MAF Minor allele frequency MMP Matrix metallopeptidase
OR Odds ratio
PA Peanut allergy
QC Quality control QQ Quantile-quantile
SKAP1 Src kinase–associated phosphoprotein 1 SNP Single nucleotide polymorphism UFA Understanding Food Allergy
192
INTRODUCTION
Peanut allergy (PA) is a main cause of anaphylaxis in North America.1,2 In Canada the
prevalence of PA is 1% overall, with a prevalence of 2.2% in children.2 The self-reported
prevalence of tree nut allergy and PA in the United States was 2.1% in children,1 whereas 3% of infants in an Australian study had a positive food challenge result to peanut.3 PA is highly
heritable, with a concordance rate of 64% in monozygotic twins compared with 7% in dizygotic twins.4 Family studies have found the risk of PA in subjects with a sibling with PA to
be significantly greater than in the general population, with odds ratios (ORs) ranging from 6.7 to 13.5.5,6
The pathogenesis of PA involves both genetics and the environment. Involvement of environmental exposures is supported by (1) findings that early oral exposure to peanut leads to development of tolerance,7,8 (2) differences in PA prevalence internationally,9-11 and
(3) the rapid increase in disease prevalence reported in some studies that cannot be explained by genetic changes.1
Previous genetic work has found risk factors for PA in the innate and adaptive immune pathways, including HLA,12-15 CD14,16 IL9,17 and filaggrin (FLG).18,19 Recently,
genome-wide association studies (GWASs) of food allergy identified associations between PA and the HLA region.20,21 We have previously identified HLA and FLG associations with PA
in a well-characterized group of Canadian patients with PA from the Canadian Peanut Allergy Registry (CanPAR).15,18,19 As a follow-up to this work, we conducted a GWAS of PA,22 along
with a meta-analysis of results from the previously published GWASs20,21 and other studies of
food allergy. HLA variants were identified as significant risk factors for PA in the CanPAR GWAS (rs1049213, P = 1.82 × 10−11) and in a meta-analysis (rs1063347, P = 3.67 × 10−23), as reported in a separate publication, in which we narrowed the locus to HLA-DQB1 and showed that its relationship to PA is independent of asthma.22 Here we present novel
non-HLA loci identified in a GWAS and meta-analysis in an additional 6 populations.
METHODS
CLINICAL CHARACTERISTICS
Inclusion criteria for CanPAR cases are found in Table E1 in this article's Online Repository at www.jacionline.org.19
GWAS
Salivary DNA was isolated from patients with PA in the CanPAR study. Hyper-control subjects were self-reported white subjects from the Busselton Health Study in Australia with no history of asthma, airway hyperresponsiveness, atopy, eczema, allergic rhinitis, or food allergy who had blood-derived DNA and assessment by using methacholine challenge and skin prick tests.23 Genotyping of 1974 subjects (987 cases and 987 control subjects) was conducted on
the Illumina Omni 2.5M+Exome 8v1.1 chip (Génome Québec Innovation Centre, Montreal, Quebec, Canada). Quality control (QC), including batch effects, single nucleotide polymorphisms (SNPs), and sample quality, are described in Fig E1 in this article's Online
Repository at www.jacionline.org. A total of more than 7.8 million SNPs (1,388,588 genotyped and 6,441,607 imputed) and 1,776 subjects (850 cases and 926 control subjects) passed QC (see Fig E2 in this article's Online Repository at www.jacionline.org). Details on imputation are presented in the Methods section in this article's Online Repository at www.jacionline.org.
Two analyses were performed (related and unrelated) because examination of alleles determined to be identical by using state and KING24 kinship coefficients identified related
cases (siblings) and control subjects (first- to third-degree relatives). PC-AiR25 and KING24
(KING1.4; http://people.virginia.edu/∼wc9c/KING/) were used to estimate principal components and kinship coefficients for the related analysis. Association analyses were conducted with Stata software,26 with sandwich estimation to model the clustering of family
genotypes with the addition of a family group identifier, 10 principal components to account for population stratification, and plate numbers to account for plate effects.
A secondary case-control study excluding related subjects was conducted with PLINK (version 1.07).27 To make the sample unrelated, 160 subjects were excluded (14 cases and 146
control subjects); the youngest subject in each family was retained. The unrelated analysis was performed with 834 cases and 781 control subjects (n = 1615; see Fig E2, B).
The analysis including related subjects is our primary analysis because it has the largest sample size and greatest power. Rank order and OR differences were evaluated between related and unrelated analyses. All subsequent analyses, including conditioning, were conducted by using the related analysis. A P value of 3.60 × 10−8 was considered the threshold
for genome-wide significance (Bonferroni correction), with 1.49 × 10−6 being suggestive
evidence for association. We chose 1.49 × 10−6 as our threshold based on significance levels
presented in 2 previously published PA GWAS studies.20,21
CONDITIONING ON HLA
After identification of multiple SNPs in the HLA region,22 we conditioned on the top genotyped
SNP (rs3134976) to investigate independence of signals from the rest of the genome and to determine the contribution of HLA associations to deviation from the expected line observed in the quantile-quantile plots (Fig 1).
Chap
ter 10
193
INTRODUCTION
Peanut allergy (PA) is a main cause of anaphylaxis in North America.1,2 In Canada the
prevalence of PA is 1% overall, with a prevalence of 2.2% in children.2 The self-reported
prevalence of tree nut allergy and PA in the United States was 2.1% in children,1 whereas 3% of infants in an Australian study had a positive food challenge result to peanut.3 PA is highly
heritable, with a concordance rate of 64% in monozygotic twins compared with 7% in dizygotic twins.4 Family studies have found the risk of PA in subjects with a sibling with PA to
be significantly greater than in the general population, with odds ratios (ORs) ranging from 6.7 to 13.5.5,6
The pathogenesis of PA involves both genetics and the environment. Involvement of environmental exposures is supported by (1) findings that early oral exposure to peanut leads to development of tolerance,7,8 (2) differences in PA prevalence internationally,9-11 and
(3) the rapid increase in disease prevalence reported in some studies that cannot be explained by genetic changes.1
Previous genetic work has found risk factors for PA in the innate and adaptive immune pathways, including HLA,12-15 CD14,16 IL9,17 and filaggrin (FLG).18,19 Recently,
genome-wide association studies (GWASs) of food allergy identified associations between PA and the HLA region.20,21 We have previously identified HLA and FLG associations with PA
in a well-characterized group of Canadian patients with PA from the Canadian Peanut Allergy Registry (CanPAR).15,18,19 As a follow-up to this work, we conducted a GWAS of PA,22 along
with a meta-analysis of results from the previously published GWASs20,21 and other studies of
food allergy. HLA variants were identified as significant risk factors for PA in the CanPAR GWAS (rs1049213, P = 1.82 × 10−11) and in a meta-analysis (rs1063347, P = 3.67 × 10−23), as reported in a separate publication, in which we narrowed the locus to HLA-DQB1 and showed that its relationship to PA is independent of asthma.22 Here we present novel
non-HLA loci identified in a GWAS and meta-analysis in an additional 6 populations.
METHODS
CLINICAL CHARACTERISTICS
Inclusion criteria for CanPAR cases are found in Table E1 in this article's Online Repository at www.jacionline.org.19
GWAS
Salivary DNA was isolated from patients with PA in the CanPAR study. Hyper-control subjects were self-reported white subjects from the Busselton Health Study in Australia with no history of asthma, airway hyperresponsiveness, atopy, eczema, allergic rhinitis, or food allergy who had blood-derived DNA and assessment by using methacholine challenge and skin prick tests.23 Genotyping of 1974 subjects (987 cases and 987 control subjects) was conducted on
the Illumina Omni 2.5M+Exome 8v1.1 chip (Génome Québec Innovation Centre, Montreal, Quebec, Canada). Quality control (QC), including batch effects, single nucleotide polymorphisms (SNPs), and sample quality, are described in Fig E1 in this article's Online
Repository at www.jacionline.org. A total of more than 7.8 million SNPs (1,388,588 genotyped and 6,441,607 imputed) and 1,776 subjects (850 cases and 926 control subjects) passed QC (see Fig E2 in this article's Online Repository at www.jacionline.org). Details on imputation are presented in the Methods section in this article's Online Repository at www.jacionline.org.
Two analyses were performed (related and unrelated) because examination of alleles determined to be identical by using state and KING24 kinship coefficients identified related
cases (siblings) and control subjects (first- to third-degree relatives). PC-AiR25 and KING24
(KING1.4; http://people.virginia.edu/∼wc9c/KING/) were used to estimate principal components and kinship coefficients for the related analysis. Association analyses were conducted with Stata software,26 with sandwich estimation to model the clustering of family
genotypes with the addition of a family group identifier, 10 principal components to account for population stratification, and plate numbers to account for plate effects.
A secondary case-control study excluding related subjects was conducted with PLINK (version 1.07).27 To make the sample unrelated, 160 subjects were excluded (14 cases and 146
control subjects); the youngest subject in each family was retained. The unrelated analysis was performed with 834 cases and 781 control subjects (n = 1615; see Fig E2, B).
The analysis including related subjects is our primary analysis because it has the largest sample size and greatest power. Rank order and OR differences were evaluated between related and unrelated analyses. All subsequent analyses, including conditioning, were conducted by using the related analysis. A P value of 3.60 × 10−8 was considered the threshold
for genome-wide significance (Bonferroni correction), with 1.49 × 10−6 being suggestive
evidence for association. We chose 1.49 × 10−6 as our threshold based on significance levels
presented in 2 previously published PA GWAS studies.20,21
CONDITIONING ON HLA
After identification of multiple SNPs in the HLA region,22 we conditioned on the top genotyped
SNP (rs3134976) to investigate independence of signals from the rest of the genome and to determine the contribution of HLA associations to deviation from the expected line observed in the quantile-quantile plots (Fig 1).
194
FIGURE 1. Quantile-quantile and Manhattan plots of related and unrelated analyses. A,
Quantile-quantile plot of the expected distribution of test statistics (x-axis) versus observed P values (y-axis) for related (left) and unrelated (right) analyses. B, Manhattan plot: SNPs in 850 patients with PA and 926 hyper-control subjects for the related (upper) and unrelated (lower) analyses. The x-axis denotes the genomic location, and the y-axis denotes the association level. The solid line indicates the threshold for genome-wide significance (P ≤ 3.60 × 10−8), and the dashed line indicates the suggestive association significance threshold (P ≤ 1.49 × 10−6). META-ANALYSIS
A meta-analysis was conducted by using 2 phenotypes (PA and food allergy), including previously published PA GWAS results 20,21 and unpublished data. The CanPAR study and 6
additional studies were included in the meta-analysis: 2 American studies (the Chicago Food Allergy [CFA] study [n = 2,197; 316 PA cases]20 and the Genetic Epidemiology Research on
Aging [GERA] cohort [n = 29,053; 5,108 self-reported food allergy]),28 the Australian
HealthNuts study (n = 221; 73 patients with PA),21 and the German Understanding Food
Allergy (UFA) study (n = 2,592; 205 patients with PA),21 which contributed 21 previously
published SNPs. Genotyping for SNPs was conducted in 2 Dutch studies: IDEAL and GENEVA (n = 512; 138 patients with PA). Both IDEAL and GENEVA include cases with general food allergy.29 See Table E2 in this article's Online Repository at www.jacionline.org for full study
and phenotype descriptions. The meta-analysis for PA included 1,582 patients with PA and 5,446 control subjects, with more than half of the patients and control subjects coming from the CanPAR study. Because the GERA cohort used self-reported food allergy phenotypes with no additional diagnostic testing or history, the meta-analysis was completed both with and without GERA data to evaluate the sensitivity of the meta-analysis results to stringent food allergy phenotyping. The meta-analysis for food allergy included 7,267 patients with food allergy and 29,084 control subjects, with inclusion of GERA data.
Fixed- and random-effects models evaluate heterogeneity but require point estimates and SEs. Because the CFA study provided P values and sample sizes only, for meta-analyses, P values were obtained by using the Stouffer weighted z score, which requires consistency in the direction of effects (for accurate P value estimation), and we were able to confirm that the direction of effect is the same for the CFA study because the investigators provided us with the case/control allele frequencies, which are consistent with the CanPAR associations.
IDENTIFICATION OF EXPRESSION QUANTITATIVE TRAIT LOCI
The Genotype-Tissue Expression (gtexportal.org)30 database was queried for novel regions.
RESULTS
GWASSNPs in HLA22 and an imputed SNP on chromosome 2 close to integrin α6 (ITGA6;
rs115218289, P = 1.80 × 10−8; Fig 1 and Table I and see Table E3 in this article's Online
Repository at www.jacionline.org) reached genome-wide significance. Several SNPs with suggestive evidence for association were detected in novel loci (Table I and see Table E3),
Chap
ter 10
195
FIGURE 1. Quantile-quantile and Manhattan plots of related and unrelated analyses. A,
Quantile-quantile plot of the expected distribution of test statistics (x-axis) versus observed P values (y-axis) for related (left) and unrelated (right) analyses. B, Manhattan plot: SNPs in 850 patients with PA and 926 hyper-control subjects for the related (upper) and unrelated (lower) analyses. The x-axis denotes the genomic location, and the y-axis denotes the association level. The solid line indicates the threshold for genome-wide significance (P ≤ 3.60 × 10−8), and the dashed line indicates the suggestive association significance threshold (P ≤ 1.49 × 10−6). META-ANALYSIS
A meta-analysis was conducted by using 2 phenotypes (PA and food allergy), including previously published PA GWAS results 20,21 and unpublished data. The CanPAR study and 6
additional studies were included in the meta-analysis: 2 American studies (the Chicago Food Allergy [CFA] study [n = 2,197; 316 PA cases]20 and the Genetic Epidemiology Research on
Aging [GERA] cohort [n = 29,053; 5,108 self-reported food allergy]),28 the Australian
HealthNuts study (n = 221; 73 patients with PA),21 and the German Understanding Food
Allergy (UFA) study (n = 2,592; 205 patients with PA),21 which contributed 21 previously
published SNPs. Genotyping for SNPs was conducted in 2 Dutch studies: IDEAL and GENEVA (n = 512; 138 patients with PA). Both IDEAL and GENEVA include cases with general food allergy.29 See Table E2 in this article's Online Repository at www.jacionline.org for full study
and phenotype descriptions. The meta-analysis for PA included 1,582 patients with PA and 5,446 control subjects, with more than half of the patients and control subjects coming from the CanPAR study. Because the GERA cohort used self-reported food allergy phenotypes with no additional diagnostic testing or history, the meta-analysis was completed both with and without GERA data to evaluate the sensitivity of the meta-analysis results to stringent food allergy phenotyping. The meta-analysis for food allergy included 7,267 patients with food allergy and 29,084 control subjects, with inclusion of GERA data.
Fixed- and random-effects models evaluate heterogeneity but require point estimates and SEs. Because the CFA study provided P values and sample sizes only, for meta-analyses, P values were obtained by using the Stouffer weighted z score, which requires consistency in the direction of effects (for accurate P value estimation), and we were able to confirm that the direction of effect is the same for the CFA study because the investigators provided us with the case/control allele frequencies, which are consistent with the CanPAR associations.
IDENTIFICATION OF EXPRESSION QUANTITATIVE TRAIT LOCI
The Genotype-Tissue Expression (gtexportal.org)30 database was queried for novel regions.
RESULTS
GWASSNPs in HLA22 and an imputed SNP on chromosome 2 close to integrin α6 (ITGA6;
rs115218289, P = 1.80 × 10−8; Fig 1 and Table I and see Table E3 in this article's Online
Repository at www.jacionline.org) reached genome-wide significance. Several SNPs with suggestive evidence for association were detected in novel loci (Table I and see Table E3),
196
including multiple SNPs located in Src kinase–associated phosphoprotein 1 (SKAP1; chromosome 17), 1 located between matrix metallopeptidase 12 (MMP12) and MMP13 (rs144897250, chromosome 11; P = 2.90 × 10−7), multiple SNPs within catenin α3 (CTNNA3;
chromosome 10), rs744597 near rho GTPase–activating protein 24 (ARHGAP24; chromosome 4, P = 3.98 × 10−7), rs523865 in angiopoietin 4 (ANGPT4; chromosome 20, P = 4.42 × 10−7),
multiple SNPs near the chromosome 11 open reading frame (C11orf30; chromosome 11, also known as EMSY), and rs78048444, which is located in a region between coiled-coil-helix-coiled-coil-helix domain containing 3 (CHCHD3) and exocyst complex component 4 (EXOC4; chromosome 7, P = 5.44 × 10−7).
No significant difference in ORs for SNPs was noted between the unrelated and related analyses (Table I). For 2 imputed SNPs (rs115218289 and rs144897250) with low (approximately 2%) minor allele frequency (MAF), there were differences in the rank order between the related and unrelated analyses (see Table E3 in this article's Online Repository at www.jacionline.org), likely because of the low MAF.
CONDITIONING
After conditioning on the top genotyped HLA SNP (rs3134976, Fig 2), deviation observed in the quantile-quantile plot was largely resolved (Figs 1, A, and 2, A); residual deviation is primarily due to the number of SNPs supporting SKAP1, CTNNA3, and C11orf30/EMSY associations. Conditioning identified 16 additional SNPs near SKAP1 and CTNNA3 (rs139902172, see Table E4 in this article's Online Repository at www.jacionline.org).
META-ANALYSIS FOR PA
We identified 85 SNPs in common between the CanPAR study and 1 or more of the previously reported PA GWASs.20,21 The top novel SNP identified in the meta-analysis for PA was
rs115218289, which was located near ITGA6 and did not reach genome-wide significance but met the threshold suggestive for significance (P = 9.16 × 10−8; Table II and see Table E5 and
full results in Table E6 in this article's Online Repository at www.jacionline.org). Loci in ANGPT4 (rs523865, P = 1.54 × 10−7) and intragenic SNPs (rs144897250, P = 2.94 × 10−7) near
MMP12/MMP13, C11orf30 (rs7936434, P = 3.13 × 10−7), and EXOC4 (rs78048444,
P = 3.73 × 10−7) were suggestive of significance (P ≤ 1.49 × 10−6) in a meta-analysis for the PA
phenotype.
META-ANALYSIS OF FOOD ALLERGY
By using the phenotype of “any food allergy” in all 6 populations, both with and without GERA data, the top SNP identified in meta-analysis was rs7936434 near C11orf30 (P = 1.98 × 10−8 and P = 7.50 × 10−11 with and without GERA data, respectively; Table II and see Table E5). The
SNPs associated with ITGA6, ANGPT4, and MMP12/MMP13 were suggestive of significance (P ≤ 1.49 × 10−6) in a meta-analysis for food allergy but only if GERA data were not included
(Table II and see Table E5). SNPs in EXOC4, ARHGAP24, SKAP1, and CTNNA3 were not suggestive of significance for food allergy.
IDENTIFICATION OF EXPRESSION QUANTITATIVE TRAIT LOCI
Many SNPs identified near SKAP1 by the CanPAR study were expression quantitative trait loci (eQTLs) regulating expression of 2 genes, sorting nexin 1 (SNX11) and chromobox protein homolog 1 (CBX1), in numerous tissues (sun-exposed skin, whole blood, transformed fibroblasts, testis, colon, and thyroid). Results are presented for tissues relevant to PA and food allergy (sun-exposed skin, whole blood, and transformed fibroblasts) with a P value of less than 1.0 × 10−6 (Table III and see Table E7 in this article's Online Repository at
www.jacionline.org). Little is known about SNX11; it belongs to a family of retrograde transport molecules,31 and its protein is involved in targeting cell-surface molecules to the
lysosome.32 CBX1 is a member of the highly conserved heterochromatin protein family that
binds to histones through methylated lysine residues, mediating gene silencing and alternative splicing.33,34 It is believed that CBX1 can play an important role in epigenetic
Chap
ter 10
197
including multiple SNPs located in Src kinase–associated phosphoprotein 1 (SKAP1; chromosome 17), 1 located between matrix metallopeptidase 12 (MMP12) and MMP13 (rs144897250, chromosome 11; P = 2.90 × 10−7), multiple SNPs within catenin α3 (CTNNA3;
chromosome 10), rs744597 near rho GTPase–activating protein 24 (ARHGAP24; chromosome 4, P = 3.98 × 10−7), rs523865 in angiopoietin 4 (ANGPT4; chromosome 20, P = 4.42 × 10−7),
multiple SNPs near the chromosome 11 open reading frame (C11orf30; chromosome 11, also known as EMSY), and rs78048444, which is located in a region between coiled-coil-helix-coiled-coil-helix domain containing 3 (CHCHD3) and exocyst complex component 4 (EXOC4; chromosome 7, P = 5.44 × 10−7).
No significant difference in ORs for SNPs was noted between the unrelated and related analyses (Table I). For 2 imputed SNPs (rs115218289 and rs144897250) with low (approximately 2%) minor allele frequency (MAF), there were differences in the rank order between the related and unrelated analyses (see Table E3 in this article's Online Repository at www.jacionline.org), likely because of the low MAF.
CONDITIONING
After conditioning on the top genotyped HLA SNP (rs3134976, Fig 2), deviation observed in the quantile-quantile plot was largely resolved (Figs 1, A, and 2, A); residual deviation is primarily due to the number of SNPs supporting SKAP1, CTNNA3, and C11orf30/EMSY associations. Conditioning identified 16 additional SNPs near SKAP1 and CTNNA3 (rs139902172, see Table E4 in this article's Online Repository at www.jacionline.org).
META-ANALYSIS FOR PA
We identified 85 SNPs in common between the CanPAR study and 1 or more of the previously reported PA GWASs.20,21 The top novel SNP identified in the meta-analysis for PA was
rs115218289, which was located near ITGA6 and did not reach genome-wide significance but met the threshold suggestive for significance (P = 9.16 × 10−8; Table II and see Table E5 and
full results in Table E6 in this article's Online Repository at www.jacionline.org). Loci in ANGPT4 (rs523865, P = 1.54 × 10−7) and intragenic SNPs (rs144897250, P = 2.94 × 10−7) near
MMP12/MMP13, C11orf30 (rs7936434, P = 3.13 × 10−7), and EXOC4 (rs78048444,
P = 3.73 × 10−7) were suggestive of significance (P ≤ 1.49 × 10−6) in a meta-analysis for the PA
phenotype.
META-ANALYSIS OF FOOD ALLERGY
By using the phenotype of “any food allergy” in all 6 populations, both with and without GERA data, the top SNP identified in meta-analysis was rs7936434 near C11orf30 (P = 1.98 × 10−8 and P = 7.50 × 10−11 with and without GERA data, respectively; Table II and see Table E5). The
SNPs associated with ITGA6, ANGPT4, and MMP12/MMP13 were suggestive of significance (P ≤ 1.49 × 10−6) in a meta-analysis for food allergy but only if GERA data were not included
(Table II and see Table E5). SNPs in EXOC4, ARHGAP24, SKAP1, and CTNNA3 were not suggestive of significance for food allergy.
IDENTIFICATION OF EXPRESSION QUANTITATIVE TRAIT LOCI
Many SNPs identified near SKAP1 by the CanPAR study were expression quantitative trait loci (eQTLs) regulating expression of 2 genes, sorting nexin 1 (SNX11) and chromobox protein homolog 1 (CBX1), in numerous tissues (sun-exposed skin, whole blood, transformed fibroblasts, testis, colon, and thyroid). Results are presented for tissues relevant to PA and food allergy (sun-exposed skin, whole blood, and transformed fibroblasts) with a P value of less than 1.0 × 10−6 (Table III and see Table E7 in this article's Online Repository at
www.jacionline.org). Little is known about SNX11; it belongs to a family of retrograde transport molecules,31 and its protein is involved in targeting cell-surface molecules to the
lysosome.32 CBX1 is a member of the highly conserved heterochromatin protein family that
binds to histones through methylated lysine residues, mediating gene silencing and alternative splicing.33,34 It is believed that CBX1 can play an important role in epigenetic
198 SN P Ch rom os om e Pos iti on Al le le M AF So ur ce o f SN Ps Re la te d a na lys is ( 85 0 c as es a nd 92 6 co nt ro l s ubj ect s) Un re lat ed a nal ysi s ( 83 4 case s and 7 81 co nt ro l s ub je ct s) P va lu e† Gen e/ nea res t g en OR LC I UC I P va lu e OR LC I UC I P va lu e rs 115218289 2 173265750 A/ C 0. 02 Im pu te d 0. 18 0. 10 0. 32 1. 80 × 10 −8 0. 20 0. 09 0. 46 1. 39 × 10 −4 8. 04 × 10 −1 (2 98 k b) DL X2 | (2 6 kb) IT GA 6 rs 72827854 17 46460525 T/C 0. 09 Im pu te d 2. 16 1. 61 2. 90 2. 60 × 10 −7 2. 08 1. 50 2. 87 9. 00 × 10 −6 8. 58 × 10 −1 SK AP 1 rs 144897250 11 102750264 A/ C 0. 02 Im pu te d 6. 20 3. 09 12. 45 2. 90 × 10 −7 6. 72 2. 72 16. 64 3. 79 × 10 −5 8. 90 × 10 −1 (5 k b) MMP 12 | (6 3 kb) M MP 13 rs 7475217 10 68444013 T/C 0. 38 Ge no typ ed 1. 64 1. 35 1. 98 3. 58 × 10 −7 1. 56 1. 28 1. 90 9. 19 × 10 −6 7. 37 × 10 −1 CT NNA 3 rs 744597 4 86337028 A/ G 0. 40 Ge no typ ed 0. 61 0. 50 0. 74 3. 98 × 10 −7 0. 63 0. 52 0. 77 3. 91 × 10 −6 8. 01 × 10 −1 AR HG AP 24 rs 523865 20 894881 C/ T 0. 23 Ge no typ ed 0. 57 0. 46 0. 71 4. 42 × 10 −7 0. 57 0. 45 0. 71 1. 19 × 10 −6 9. 49 × 10 −1 AN GP T4 rs 7936434 11 76293805 C/ G 0. 49 Im pu te d 1. 58 1. 32 1. 90 5. 17 × 10 −7 1. 58 1. 31 1. 91 2. 73 × 10 −6 9. 85 × 10 −1 (3 0 kb )C 11O RF 30 |( 43 kb) LO C1 01 92 88 13 rs 78048444 7 132832218 C/ T 0. 02 Ge no typ ed 0. 22 0. 12 0. 39 5. 44 × 10 −7 0. 23 0. 11 0. 46 4. 57 × 10 −5 9. 35 × 10 −1 (6 5 kb )C HC HD 3 |( 10 6 kb) EXO C4 rs 56151068 17 46381431 T/C 0. 10 Im pu te d 2. 06 1. 54 2. 76 9. 58 × 10 −7 1. 97 1. 44 2. 70 2. 34 × 10 −5 8. 39 × 10 −1 SK AP 1; LO C1019271 48 rs 139462954 17 46523678 A/ AC 0. 09 Im pu te d 2. 06 1. 54 2. 76 1. 23 × 10 −6 1. 97 1. 43 2. 71 2. 92 × 10 −5 8. 37 × 10 −1 LO C1 01 92 71 66 TA BL E I. M os t s igni fic an t S NP s f ro m 1 0 ge no m ic re gi ons ide nt ifi ed in the C anP AR G W AS li st ed by o rde r o f s igni fic anc e ∗ A lle le , M in or al le le /m aj or a lle le ; L CI , l ow er 9 5% C I; U CI , u pp er 9 5% C I. ∗ T he ne ar es t ge ne w as us ed to de te rm ine ge no m ic lo ca tio n. † Co m par ing re lat ed and unr el at ed an al ys es OR s
FIGURE 2. Quantile-quantile and Manhattan plots of related and unrelated analyses
conditioned on the top HLA SNP (rs3134976). A, Quantile-quantile plot of the expected distribution of test statistics (x-axis) versus observed P values (y-axis) for related analysis conditioned on rs3134976. SNPs in complete linkage with rs3134976 were excluded. B, Manhattan plot: SNPs in 850 patients with PA and 926 hyper-control subjects for the related analysis conditioned on rs3134976. The x-axis denotes genomic location, and the y-axis denotes association level. The solid line indicates the threshold for genome-wide significance (P ≤ 3.60 × 10−8), and the dashed line indicates the suggestive association significance threshold (P ≤ 1.49 × 10−6).
Chap ter 10 199 SN P Ch rom os om e Pos iti on Al le le M AF So ur ce o f SN Ps Re la te d a na lys is ( 85 0 c as es a nd 92 6 co nt ro l s ubj ect s) Un re lat ed a nal ysi s ( 83 4 case s and 7 81 co nt ro l s ub je ct s) P va lu e† Gen e/ nea res t g en OR LC I UC I P va lu e OR LC I UC I P va lu e rs 115218289 2 173265750 A/ C 0. 02 Im pu te d 0. 18 0. 10 0. 32 1. 80 × 10 −8 0. 20 0. 09 0. 46 1. 39 × 10 −4 8. 04 × 10 −1 (2 98 k b) DL X2 | (2 6 kb) IT GA 6 rs 72827854 17 46460525 T/C 0. 09 Im pu te d 2. 16 1. 61 2. 90 2. 60 × 10 −7 2. 08 1. 50 2. 87 9. 00 × 10 −6 8. 58 × 10 −1 SK AP 1 rs 144897250 11 102750264 A/ C 0. 02 Im pu te d 6. 20 3. 09 12. 45 2. 90 × 10 −7 6. 72 2. 72 16. 64 3. 79 × 10 −5 8. 90 × 10 −1 (5 k b) MMP 12 | (6 3 kb) M MP 13 rs 7475217 10 68444013 T/C 0. 38 Ge no typ ed 1. 64 1. 35 1. 98 3. 58 × 10 −7 1. 56 1. 28 1. 90 9. 19 × 10 −6 7. 37 × 10 −1 CT NNA 3 rs 744597 4 86337028 A/ G 0. 40 Ge no typ ed 0. 61 0. 50 0. 74 3. 98 × 10 −7 0. 63 0. 52 0. 77 3. 91 × 10 −6 8. 01 × 10 −1 AR HG AP 24 rs 523865 20 894881 C/ T 0. 23 Ge no typ ed 0. 57 0. 46 0. 71 4. 42 × 10 −7 0. 57 0. 45 0. 71 1. 19 × 10 −6 9. 49 × 10 −1 AN GP T4 rs 7936434 11 76293805 C/ G 0. 49 Im pu te d 1. 58 1. 32 1. 90 5. 17 × 10 −7 1. 58 1. 31 1. 91 2. 73 × 10 −6 9. 85 × 10 −1 (3 0 kb )C 11O RF 30 |( 43 kb) LO C1 01 92 88 13 rs 78048444 7 132832218 C/ T 0. 02 Ge no typ ed 0. 22 0. 12 0. 39 5. 44 × 10 −7 0. 23 0. 11 0. 46 4. 57 × 10 −5 9. 35 × 10 −1 (6 5 kb )C HC HD 3 |( 10 6 kb) EXO C4 rs 56151068 17 46381431 T/C 0. 10 Im pu te d 2. 06 1. 54 2. 76 9. 58 × 10 −7 1. 97 1. 44 2. 70 2. 34 × 10 −5 8. 39 × 10 −1 SK AP 1; LO C1019271 48 rs 139462954 17 46523678 A/ AC 0. 09 Im pu te d 2. 06 1. 54 2. 76 1. 23 × 10 −6 1. 97 1. 43 2. 71 2. 92 × 10 −5 8. 37 × 10 −1 LO C1 01 92 71 66 TA BL E I. M os t s igni fic an t S NP s f ro m 1 0 ge no m ic re gi ons ide nt ifi ed in the C anP AR G W AS li st ed by o rde r o f s igni fic anc e ∗ A lle le , M in or al le le /m aj or a lle le ; L CI , l ow er 9 5% C I; U CI , u pp er 9 5% C I. ∗ T he ne ar es t ge ne w as us ed to de te rm ine ge no m ic lo ca tio n. † Co m par ing re lat ed and unr el at ed an al ys es OR s
FIGURE 2. Quantile-quantile and Manhattan plots of related and unrelated analyses
conditioned on the top HLA SNP (rs3134976). A, Quantile-quantile plot of the expected distribution of test statistics (x-axis) versus observed P values (y-axis) for related analysis conditioned on rs3134976. SNPs in complete linkage with rs3134976 were excluded. B, Manhattan plot: SNPs in 850 patients with PA and 926 hyper-control subjects for the related analysis conditioned on rs3134976. The x-axis denotes genomic location, and the y-axis denotes association level. The solid line indicates the threshold for genome-wide significance (P ≤ 3.60 × 10−8), and the dashed line indicates the suggestive association significance threshold (P ≤ 1.49 × 10−6).
200 SNP ∗ Ch r Al lel e PA Fo od al le rg y Ge ne /n ea re st ge ne P- CanP AR † a P-CFA b P- Heal thN ut s† c P- UFA †d P- IDEAL /G EN E VA , ca se -co nt ro l e P-Dut ch GE NE VA , fa m ily ba se d f Pm et a_P A g P-CFA h P- IDEAL /G EN E VA , ca se -co nt ro l i P- GENE VA , fa m ily st udy j P-GE RA k Pm eta l Pm et a (w ith ou t GERA ) m rs 1152182 89 ‡ 2 A/C 1. 80 × 10 −8 NA 6. 77 × 10 −1 NA 7. 18 × 1 0 −1 3. 54 × 10 −1 9. 16 × 10 −8 NA 1. 84 × 1 0 −1 1. 90 × 10 −1 5. 25 × 10 −1 2. 91 × 10 −2 2. 38 × 10 −8 (298 kb ) DL X2 | (26 kb )IT GA 6 rs 523865 § 20 C/T 4. 42 × 10 −7 NA NA NA 8. 33 × 1 0 −1 1. 63 × 10 −2 1. 54 × 10 −7 NA 2. 03 × 1 0 −1 2. 60 × 10 −2 2. 66 × 10 −1 9. 29 × 10 −3 4. 09 × 10 −8 AN GP T4 rs 1448972 50 ‡ 11 A/C 2. 90 × 10 −7 NA 3. 84 × 10 −1 NA NA NA 2. 94 × 10 −7 NA NA NA 5. 89 × 10 −1 6. 83 × 10 −2 2. 94 × 10 −7 (5 k b) MMP1 2| (63 kb ) MMP1 3 rs 7936434 ‡ 11 C/G 5. 17 × 10 −7 3. 66 × 10 −2 1. 43 × 10 −1 NA NA NA 3. 13 × 10 −7 5. 89 × 10 −5 NA NA 4. 13 × 10 −4 1. 98 × 10 −8 7. 50 × 10 −1 1 (30 kb) C11O RF 30 | (43 kb) L O C1 01 92 88 13 rs 7804844 4§ 7 C/T 5. 44 × 10 −7 NA 2. 13 × 10 −1 NA 6. 46 × 1 0 −1 3. 54 × 10 −1 3. 73 × 10 −7 NA 8. 29 × 1 0 −1 7. 87 × 10 −1 6. 97 × 10 −1 8. 88 × 10 −2 2. 53 × 10 −6 (65 kb ) CHC HD 3| (106 kb ) EX O C4 rs 744597§ 4 A/ G 3. 98 × 1 0 −7 1. 15 × 1 0 −1 5. 57 × 10 − 1 NA 8. 20 × 10 −2 9. 62 × 1 0 −1 1. 63 × 10 −6 5. 19 × 1 0 −1 1. 13 × 10 −1 2. 69 × 1 0 −1 3. 63 × 1 0 −1 1. 29 × 1 0 −2 1. 42 × 1 0 −5 AR HGA P2 4 rs 72827854 ‡ 17 T/C 2. 60 × 1 0 −7 1. 36 × 1 0 −1 3. 55 × 10 − 1 NA NA NA 3. 43 × 10 −6 5. 83 × 1 0 −1 NA NA 7. 69 × 1 0 −1 9. 27 × 1 0 −2 7. 47 × 1 0 −5 SK AP 1 rs 55765969 ‡ 17 T/C 1. 23 × 1 0 −6 1. 97 × 1 0 −1 2. 81 × 10 − 1 NA NA NA 1. 45 × 10 −5 6. 59 × 1 0 −1 NA NA 3. 77 × 1 0 −1 3. 18 × 1 0 −2 1. 97 × 1 0 −4 LO C1 01 92 71 66 rs 56151068 ‡ 17 T/C 9. 58 × 1 0 −7 2. 51 × 1 0 −1 3. 57 × 10 − 1 NA NA NA 2. 33 × 10 −5 7. 33 × 1 0 −1 NA NA 4. 45 × 1 0 −1 4. 45 × 1 0 −2 2. 66 × 1 0 −4 SK AP 1; LO C1 01 92 71 48 rs 71193762 ‡ 10 A/ G 3. 77 × 1 0 −7 8. 63 × 1 0 −1 3. 62 × 10 − 1 NA NA NA 2. 73 × 10 −4 6. 87 × 1 0 −1 NA NA 7. 06 × 1 0 −1 8. 83 × 1 0 −2 1. 41 × 1 0 −4 CT NNA 3 TA BL E II. M eta -ana ly sis o f C anadi an , A m er ican, A us tr al ian, G er m an , and Dut ch po pu lat io ns fo r as so ci at io n w ith PA and fo od al le rgy phe no ty pe s. Bo ldf ac e ro w s i nd ic at e s ug ge st ive si gn ifi ca nc e ( P ≤ 1 .4 9 × 1 0− 6) in p at ie nt s w ith P A. C hr = c hr om os om e. a = P va lu e f ro m C an PA R ( n = 1 ,7 76) . b = P val ue fr om the C hi cag o Fo od Al le rgy S tudy (n = 2, 19 7) . c = P val ue fr om the A us tr al ian He al thN ut s s tudy (n = 22 1) . d= P v al ue fr om the G er m an Un de rs ta nd in g of F oo d Al le rg y st ud y (n = 2, 592) . e = Nu m be r o f s ub je ct s = 2 26, 229, 227, a nd 217 fo r r s1 152 182 89, rs 52 386 5, rs 78 048 444, a nd rs 74 45 97 , r es pe ct ive ly , c or re ct ed fo r a to pi c d er m at iti s, A st hm a, a nd rh in oc on ju nc tivi tis . f = P v al ue fr om the D ut ch GE NE VA fam ily st udy ; num be r of in fo rm at iv e fa m ili es = 20, 112, 21, a nd 11 2 fo r r s11 521 828 9, rs 523 865, rs 7804 844 4, a nd rs 74 459 7, re sp ec tiv el y. g = P va lu e fro m th e St ou ffe r w ei gh te d z s co re m et a-an al ys is m et ho d f or P A. h = P v al ue fr om th e Chi cago F oo d Al le rgy S tudy (n = 2, 19 7) . i = P val ue fr om the D ut ch ID EA L and GEN EV A ca se -c on tr ol s tu di es ; n um be r of s ub je ct s fo r SN Ps = 47 9, 487, 4 82, a nd 466 fo r rs 11 521 8289, r s5 23 865, r s780 484 44, a nd r s744 597, re sp ec tiv el y, c or re ct ed fo r a to pi c de rm at iti s, As th m a, a nd rhi no co nj un ct iv iti s. j= P v al ue fr om the D ut ch GE NE VA s tudy ; num be r o f i nf or m at iv e fa m ili es fo r SN Ps = 26, 196, 37, a nd 214 fo r rs 11 5218 289, r s523 865, r s780 484 44, a nd r s74459 7, r es pe ct iv el y. k = P va lu e fro m th e GE RA food al le rgy s tudy (n = 29 ,0 53 ). l = P v al ue fr om th e S to uf fe r w ei gh te d z s co re m et a-ana ly sis m et ho d fo r f oo d al le rgy . m = P val ue fr om the S to uf fe r w ei gh te d z s co re m et a-anal ys is m et ho d fo r f oo d al le rgy w itho ut the G ER A co ho rt . ∗ S NPs in th is ta bl e w er e se le ct ed to re pr es en t e ac h of th e 10 ge no m ic re gi ons ide nt ifi ed in the C anP AR G W AS (s ee T abl e E4 fo r f ul l r es ul ts ). † Us ed fo r bo th PA and fo od al le rgy (F A) . ‡ Im pu te d SN P fro m CanP AR . § Ge no ty pe d SN P fro m C anP AR .
Chap ter 10 201 SNP ∗ Ch r Al lel e PA Fo od al le rg y Ge ne /n ea re st ge ne P- CanP AR † a P-CFA b P- Heal thN ut s† c P- UFA †d P- IDEAL /G EN E VA , ca se -co nt ro l e P-Dut ch GE NE VA , fa m ily ba se d f Pm et a_P A g P-CFA h P- IDEAL /G EN E VA , ca se -co nt ro l i P- GENE VA , fa m ily st udy j P-GE RA k Pm eta l Pm et a (w ith ou t GERA ) m rs 1152182 89 ‡ 2 A/C 1. 80 × 10 −8 NA 6. 77 × 10 −1 NA 7. 18 × 1 0 −1 3. 54 × 10 −1 9. 16 × 10 −8 NA 1. 84 × 1 0 −1 1. 90 × 10 −1 5. 25 × 10 −1 2. 91 × 10 −2 2. 38 × 10 −8 (298 kb ) DL X2 | (26 kb )IT GA 6 rs 523865 § 20 C/T 4. 42 × 10 −7 NA NA NA 8. 33 × 1 0 −1 1. 63 × 10 −2 1. 54 × 10 −7 NA 2. 03 × 1 0 −1 2. 60 × 10 −2 2. 66 × 10 −1 9. 29 × 10 −3 4. 09 × 10 −8 AN GP T4 rs 1448972 50 ‡ 11 A/C 2. 90 × 10 −7 NA 3. 84 × 10 −1 NA NA NA 2. 94 × 10 −7 NA NA NA 5. 89 × 10 −1 6. 83 × 10 −2 2. 94 × 10 −7 (5 k b) MMP1 2| (63 kb ) MMP1 3 rs 7936434 ‡ 11 C/G 5. 17 × 10 −7 3. 66 × 10 −2 1. 43 × 10 −1 NA NA NA 3. 13 × 10 −7 5. 89 × 10 −5 NA NA 4. 13 × 10 −4 1. 98 × 10 −8 7. 50 × 10 −1 1 (30 kb) C11O RF 30 | (43 kb) L O C1 01 92 88 13 rs 7804844 4§ 7 C/T 5. 44 × 10 −7 NA 2. 13 × 10 −1 NA 6. 46 × 1 0 −1 3. 54 × 10 −1 3. 73 × 10 −7 NA 8. 29 × 1 0 −1 7. 87 × 10 −1 6. 97 × 10 −1 8. 88 × 10 −2 2. 53 × 10 −6 (65 kb ) CHC HD 3| (106 kb ) EX O C4 rs 744597§ 4 A/ G 3. 98 × 1 0 −7 1. 15 × 1 0 −1 5. 57 × 10 − 1 NA 8. 20 × 10 −2 9. 62 × 1 0 −1 1. 63 × 10 −6 5. 19 × 1 0 −1 1. 13 × 10 −1 2. 69 × 1 0 −1 3. 63 × 1 0 −1 1. 29 × 1 0 −2 1. 42 × 1 0 −5 AR HGA P2 4 rs 72827854 ‡ 17 T/C 2. 60 × 1 0 −7 1. 36 × 1 0 −1 3. 55 × 10 − 1 NA NA NA 3. 43 × 10 −6 5. 83 × 1 0 −1 NA NA 7. 69 × 1 0 −1 9. 27 × 1 0 −2 7. 47 × 1 0 −5 SK AP 1 rs 55765969 ‡ 17 T/C 1. 23 × 1 0 −6 1. 97 × 1 0 −1 2. 81 × 10 − 1 NA NA NA 1. 45 × 10 −5 6. 59 × 1 0 −1 NA NA 3. 77 × 1 0 −1 3. 18 × 1 0 −2 1. 97 × 1 0 −4 LO C1 01 92 71 66 rs 56151068 ‡ 17 T/C 9. 58 × 1 0 −7 2. 51 × 1 0 −1 3. 57 × 10 − 1 NA NA NA 2. 33 × 10 −5 7. 33 × 1 0 −1 NA NA 4. 45 × 1 0 −1 4. 45 × 1 0 −2 2. 66 × 1 0 −4 SK AP 1; LO C1 01 92 71 48 rs 71193762 ‡ 10 A/ G 3. 77 × 1 0 −7 8. 63 × 1 0 −1 3. 62 × 10 − 1 NA NA NA 2. 73 × 10 −4 6. 87 × 1 0 −1 NA NA 7. 06 × 1 0 −1 8. 83 × 1 0 −2 1. 41 × 1 0 −4 CT NNA 3 TA BL E II. M eta -ana ly sis o f C anadi an , A m er ican, A us tr al ian, G er m an , and Dut ch po pu lat io ns fo r as so ci at io n w ith PA and fo od al le rgy phe no ty pe s. Bo ldf ac e ro w s i nd ic at e s ug ge st ive si gn ifi ca nc e ( P ≤ 1 .4 9 × 1 0− 6) in p at ie nt s w ith P A. C hr = c hr om os om e. a = P va lu e f ro m C an PA R ( n = 1 ,7 76) . b = P val ue fr om the C hi cag o Fo od Al le rgy S tudy (n = 2, 19 7) . c = P val ue fr om the A us tr al ian He al thN ut s s tudy (n = 22 1) . d= P v al ue fr om the G er m an Un de rs ta nd in g of F oo d Al le rg y st ud y (n = 2, 592) . e = Nu m be r o f s ub je ct s = 2 26, 229, 227, a nd 217 fo r r s1 152 182 89, rs 52 386 5, rs 78 048 444, a nd rs 74 45 97 , r es pe ct ive ly , c or re ct ed fo r a to pi c d er m at iti s, A st hm a, a nd rh in oc on ju nc tivi tis . f = P v al ue fr om the D ut ch GE NE VA fam ily st udy ; num be r of in fo rm at iv e fa m ili es = 20, 112, 21, a nd 11 2 fo r r s11 521 828 9, rs 523 865, rs 7804 844 4, a nd rs 74 459 7, re sp ec tiv el y. g = P va lu e fro m th e St ou ffe r w ei gh te d z s co re m et a-an al ys is m et ho d f or P A. h = P v al ue fr om th e Chi cago F oo d Al le rgy S tudy (n = 2, 19 7) . i = P val ue fr om the D ut ch ID EA L and GEN EV A ca se -c on tr ol s tu di es ; n um be r of s ub je ct s fo r SN Ps = 47 9, 487, 4 82, a nd 466 fo r rs 11 521 8289, r s5 23 865, r s780 484 44, a nd r s744 597, re sp ec tiv el y, c or re ct ed fo r a to pi c de rm at iti s, As th m a, a nd rhi no co nj un ct iv iti s. j= P v al ue fr om the D ut ch GE NE VA s tudy ; num be r o f i nf or m at iv e fa m ili es fo r SN Ps = 26, 196, 37, a nd 214 fo r rs 11 5218 289, r s523 865, r s780 484 44, a nd r s74459 7, r es pe ct iv el y. k = P va lu e fro m th e GE RA food al le rgy s tudy (n = 29 ,0 53 ). l = P v al ue fr om th e S to uf fe r w ei gh te d z s co re m et a-ana ly sis m et ho d fo r f oo d al le rgy . m = P val ue fr om the S to uf fe r w ei gh te d z s co re m et a-anal ys is m et ho d fo r f oo d al le rgy w itho ut the G ER A co ho rt . ∗ S NPs in th is ta bl e w er e se le ct ed to re pr es en t e ac h of th e 10 ge no m ic re gi ons ide nt ifi ed in the C anP AR G W AS (s ee T abl e E4 fo r f ul l r es ul ts ). † Us ed fo r bo th PA and fo od al le rgy (F A) . ‡ Im pu te d SN P fro m CanP AR . § Ge no ty pe d SN P fro m C anP AR .
