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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E1. Asai Y, Greenwood C, Hull PR, Alizadehfar R, Ben-Shoshan M, Brown SJ, et al. Filaggrin gene mutation associations with peanut allergy persist despite variations in peanut allergy diagnostic criteria or asthma status. J Allergy Clin Immunol 2013; 132:239-42.
E2. James AL, Knuiman MW, Divitini ML, Hui J, Hunter M, Palmer LJ, et al. Changes in the prevalence of asthma in adults since 1966: the Busselton health study. Eur Respir J 2010; 35:273-8.
E3. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81:559-75.
E4. Delaneau O, Marchini J, Genomes Project C, Genomes Project C. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun 2014; 5:3934.
E5. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009; 5:e1000529.
E6. Hong X, Hao K, Ladd-Acosta C, Hansen KD, Tsai HJ, Liu X, et al. Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children. Nat Commun 2015; 6:6304. E7. Martino DJ, Ashley S, Koplin J, Ellis J, Saffery R,
Dharmage SC, et al. Genome-wide association
study of peanut allergy reproduces association with amino acid polymorphisms in HLA-DRB1. Clin Exp Allergy 2016.
E8. Banda Y, Kvale MN, Hoffmann TJ, Hesselson SE, Ranatunga D, Tang H, et al. Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics 2015; 200:1285-95. E9. Hoffmann TJ, Kvale MN, Hesselson SE, Zhan Y,
Aquino C, Cao Y, et al. Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics 2011; 98:79-89.
E10.Kvale MN, Hesselson S, Hoffmann TJ, Cao Y, Chan D, Connell S, et al. Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics 2015; 200:1051-60. E11. van der Valk JP, Gerth van Wijk R, Dubois AE,
de Groot H, Reitsma M, Vlieg-Boerstra B, et al. Multicentre Double-Blind Placebo-Controlled Food Challenge Study in Children Sensitised to Cashew Nut. PLoS One 2016; 11:e0151055. E12. van Ginkel CD, Flokstra-de Blok BM, Kollen
BJ, Kukler J, Koppelman GH, Dubois AE. Loss-of-function variants of the filaggrin gene are associated with clinical reactivity to foods. Allergy 2015; 70:461-4.
CHAPTER 11
CANADIAN GENOME-WIDE ASSOCIATION
STUDY AND META ANALYSIS CONFIRM HLA AS
A RISK FACTOR FOR PEANUT ALLERGY
YUKA ASAI, MD, MSC*, AIDA ESLAMI, PHD*, C. DORIENE VAN GINKEL, BSC,
LOUBNA AKHABIR, PHD, MING WAN, MSC, DAVID YIN, GEORGE ELLIS, BASC,
MOSHE BEN-SHOSHAN, MD, MSC,INGO MARENHOLZ, PHD, DAVID MARTINO,
MD, PHD, MANUEL A. FERREIRA, PHD, KATRINA ALLEN, MD, PHD, BRUCE
MAZER, MD, HANS DE GROOT, MD, PHD, NICOLETTE W. DE JONG, PHD, ROY
GERTH VAN WIJK, MD, PHD, ANTHONY E. J. DUBOIS, MD, PHD, SARAH
GROSCHE, MS, SARAH ASHLEY, PHD, FRANZ RÜSCHENDORF, PHD, BIRGIT KALB,
MD, KIRSTEN BEYER, MD, MARKUS M. NÖTHEN, MD, YOUNG-AE LEE, MD, RICK
CHIN, MSC, STEPHEN CHEUK, MD, JOSHUA HOFFMAN, PHD, 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^,DENISE DALEY, PHD^
*These authors contributed equally to this work as joint first authors. ^These authors contributed equally to this work as joint senior authors.
242
TO THE EDITOR
Previously, we identified the HLA region as a risk factor for peanut allergy (PA); this observation is supported further by 2 independent genome-wide association studies
(GWASs).1,2 The HLA class II genes (including HLA-DR, HLA-DQ, and HLA-DP) encode molecules
involved in presentation of extracellular antigens, such as peanut allergens, to T lymphocytes, which in turn mediates B-cell antibody production. We used the Canadian Peanut Allergy
Registry (CanPAR) and the Busselton Health Study3 to conduct the largest GWAS for PA to
date. Here we report analysis of the HLA region and a meta-analysis with data from 6 additional studies, which confirms and narrows the region of interest to HLA-DQB1 and establishes independence from asthma loci.
In the CanPAR GWAS more than 7.8 million single nucleotide polymorphisms (SNPs; 1,388,588 genotyped and 6,441,607 imputed) and 1776 subjects (850 cases and 926 control subjects) passed quality control. Detailed methods, including PA inclusion criteria (see Table E1 in this article’s Online Repository at www. jacionline.org), quality control, and imputation, were published previously (see Figs E1 and E2 in this article’s Online Repository at
www.jacionline.org).4
FIGURE 1. Manhattan plot of genotyped and imputed SNPs on chromosome 6. Manhattan
plot: Genotyped and imputed SNPs in 850 PA cases and 926 hypercontrol subjects. 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 3 1028), and the dashed line
indicates the suggestive association significance threshold (P < 1.49 3 1026). Imputed SNPs with
P values of less than 1.49 3 1026 are presented in gray.
In addition to the CanPAR GWAS, 6 additional studies were included in a meta-analysis of the
HLA region: 2 American studies (the Chicago Food Allergy study [n 5 2,197; 316 PA cases])1
and the Genetic Epidemiology Research on Aging (GERA) cohort (n 5 29,053; 5108
self-reported food allergy]),5 the Australian HealthNuts study (n 5 221; 73 PA cases),2 and the
German Understanding Food Allergy study (n 5 2,592; 205 PA cases).2 Genotyping for HLA
SNPs was conducted in Dutch subjects from 2 studies: IDEAL and GENEVA (n 5 1,512; 138 PA
cases). Both the IDEAL and GENEVA studies include cases of general food allergy.6 See Table
E2 in this article’s Online Repository at www.jacionline.org for study and phenotype
descriptions.4
Fixed- and random-effects models evaluate heterogeneity and require point estimates. Because the Chicago Food Allergy and Understanding Food Allergy studies provided P value and sample sizes only, for meta-analyses, P values were obtained by using the Stouffer weighted z score. We conducted stratified analyses on genotyped SNPs to evaluate associations with reaction severity (mild, moderate, or severe; see Tables E3 and E4 in this article’s Online Repository at www.jacionline.org), specificity to PA, and asthma comorbidity. Asthma history in conjunction with PA reaction severity was also examined because these features are known to be correlated. Patients with PA self-identified as ever having asthma, and patients with PA with no asthma were analyzed separately against control subjects for 6 asthma SNPs identified from the GWAS catalog (see https:// www.ebi.ac.uk/gwas/).
Eighty-five SNPs located in HLA on chromosome 6, in the region of HLA-DQB1, reached genome-wide significance (Fig 1 and see Fig E3 in this article’s Online Repository at www. jacionline.org) in the CanPAR GWAS. The most significant SNP was rs1049213, which is located
in the 39 untranslated region of HLA-DQB1 (P 5 1.82 3 10211, see Table E5 in this article’s Online
Repository at www.jacionline.org). Meta-analysis identified rs1063347 (P 5 3.67 3 10223, see
Chap
ter 11
TO THE EDITOR
Previously, we identified the HLA region as a risk factor for peanut allergy (PA); this observation is supported further by 2 independent genome-wide association studies
(GWASs).1,2 The HLA class II genes (including HLA-DR, HLA-DQ, and HLA-DP) encode molecules
involved in presentation of extracellular antigens, such as peanut allergens, to T lymphocytes, which in turn mediates B-cell antibody production. We used the Canadian Peanut Allergy
Registry (CanPAR) and the Busselton Health Study3 to conduct the largest GWAS for PA to
date. Here we report analysis of the HLA region and a meta-analysis with data from 6 additional studies, which confirms and narrows the region of interest to HLA-DQB1 and establishes independence from asthma loci.
In the CanPAR GWAS more than 7.8 million single nucleotide polymorphisms (SNPs; 1,388,588 genotyped and 6,441,607 imputed) and 1776 subjects (850 cases and 926 control subjects) passed quality control. Detailed methods, including PA inclusion criteria (see Table E1 in this article’s Online Repository at www. jacionline.org), quality control, and imputation, were published previously (see Figs E1 and E2 in this article’s Online Repository at
www.jacionline.org).4
FIGURE 1. Manhattan plot of genotyped and imputed SNPs on chromosome 6. Manhattan
plot: Genotyped and imputed SNPs in 850 PA cases and 926 hypercontrol subjects. 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 3 1028), and the dashed line
indicates the suggestive association significance threshold (P < 1.49 3 1026). Imputed SNPs with
P values of less than 1.49 3 1026 are presented in gray.
In addition to the CanPAR GWAS, 6 additional studies were included in a meta-analysis of the
HLA region: 2 American studies (the Chicago Food Allergy study [n 5 2,197; 316 PA cases])1
and the Genetic Epidemiology Research on Aging (GERA) cohort (n 5 29,053; 5108
self-reported food allergy]),5 the Australian HealthNuts study (n 5 221; 73 PA cases),2 and the
German Understanding Food Allergy study (n 5 2,592; 205 PA cases).2 Genotyping for HLA
SNPs was conducted in Dutch subjects from 2 studies: IDEAL and GENEVA (n 5 1,512; 138 PA
cases). Both the IDEAL and GENEVA studies include cases of general food allergy.6 See Table
E2 in this article’s Online Repository at www.jacionline.org for study and phenotype
descriptions.4
Fixed- and random-effects models evaluate heterogeneity and require point estimates. Because the Chicago Food Allergy and Understanding Food Allergy studies provided P value and sample sizes only, for meta-analyses, P values were obtained by using the Stouffer weighted z score. We conducted stratified analyses on genotyped SNPs to evaluate associations with reaction severity (mild, moderate, or severe; see Tables E3 and E4 in this article’s Online Repository at www.jacionline.org), specificity to PA, and asthma comorbidity. Asthma history in conjunction with PA reaction severity was also examined because these features are known to be correlated. Patients with PA self-identified as ever having asthma, and patients with PA with no asthma were analyzed separately against control subjects for 6 asthma SNPs identified from the GWAS catalog (see https:// www.ebi.ac.uk/gwas/).
Eighty-five SNPs located in HLA on chromosome 6, in the region of HLA-DQB1, reached genome-wide significance (Fig 1 and see Fig E3 in this article’s Online Repository at www. jacionline.org) in the CanPAR GWAS. The most significant SNP was rs1049213, which is located
in the 39 untranslated region of HLA-DQB1 (P 5 1.82 3 10211, see Table E5 in this article’s Online
Repository at www.jacionline.org). Meta-analysis identified rs1063347 (P 5 3.67 3 10223, see
244
imputed (rs1049213) and genotyped (rs3134976) SNPs increased to a P value of 10221 in the
meta-analysis (see Table E5).
The stratified analysis demonstrated a trend for increased odds ratios (ORs) with increasing reaction severity (see Table E6 in this article’s Online Repository at www.jacionline.org) and with PA alone versus PA and other food allergy (see Table E7 in this article’s Online Repository at www.jacionline.org). Those with a mild reaction history without other food allergy had a statistically significant increase in ORs for SNPs in HLA (rs17612852, rs9275596, and rs1612904), despite a small number of cases; this was not observed in patients with moderate or severe PA.
To evaluate the independence of PA GWAS associations from asthma comorbidity, Canadian patients with PA were stratified by the presence or absence of self-reported asthma and changes in effect sizes, and P values were evaluated. There was a higher proportion of asthmatic patients in the severe PA group compared with all cases (76% vs 64%, P 5 .003). There was no difference in ORs for HLA SNPs in asthmatic and nonasthmatic patients with PA (Table I). This is of interest because asthma comorbidity increases PA severity and the presence of PA increases asthma morbidity and mortality.
Examination of the HLA region associated with PA in the GWAS catalog (http://www.ebi.ac.uk/gwas/) identified 8 asthma SNPs in the same region as the PA locus; of these, 6 were genotyped in CanPAR and are interspersed in the same region as our meta-analysis (see Fig E3). We found no difference in ORs between asthmatic and nonasthmatic patients with PA and no genome-wide significant associations with PA in the CanPAR sample (see Table E8 in this article’s Online Repository at www.jacionline.org).
The Genotype-Tissue Expression (gtexportal.org)7 and Gene Expression Omnibus
(ncbi.nlm.nih.gov/geo)8 databases were interrogated for expression quantitative trait loci
(eQTLs) in the HLA region. Results were then narrowed to the esophageal mucosa (P < 1.0 3
1026), which identified a number of genes regulated by SNPs in this region (see Fig E3).
In this study we have confirmed HLA as a PA susceptibility locus. The relationship of PA to HLA-DQB1 is likely independent of asthma because association results stratified by asthma (Table I) demonstrate no significant changes and no asthma GWAS SNPs are significant in CanPAR (see Table E8). Although confounding by asthma might never be controlled fully, the indepen-dence of PA associations from asthma suggests a lack of pleiotropy at this locus (see Fig E3). The presence of genetic risk factors for multiple atopic conditions within HLA, all at genome-wide significance, and our results demonstrating that HLA-DQB1 SNPs identified in CanPAR are independent of asthma and numerous eQTLs identified in the region suggest that this region is associated with the cause of several allergic phenotypes. The HLA class II region has been associated with various allergic diseases. However, these earlier studies and the data presented here suggest that the HLA variants underlying these phenotypes are specific to each trait. This might reflect differences in the efficiency of antigen presentation as a result of the alternate alleles at each locus. The numerous eQTLs identified in the region suggest a potential
underlying mechanism for association with PA. Further discussion is provided in the Methods and Discussion sections in this article’s Online Repository at www.jacionline.org.
CONCLUSION
We conclude that variants in HLA-DQB1 are associated with PA, but the relationship to general food allergy is difficult to assess because PA was an ascertainment criterion for CanPAR. The importance of phenotyping is evident by the sizable changes in P values when a large cohort
of self-reported patients with food allergy, who might have a high rate of misclassification,9
was added to the meta-analysis. Inclusion of the GERA study increased the sample size but might not have increased the power because of self-reported phenotypes. The strengths of this GWAS include the sample size and clinical data available, allowing for subanalyses that indicate the relationship between PA and HLA is independent of asthma. Association results are further supported by evidence that this is a regulatory region, as demonstrated by the numerous eQTLs.
ACKNOWLEDGMENTS
We wish to thank the subjects and parents who participated in this study and in the CanPAR registry. We acknowledge Basia Rogula, who assisted in quality control; JinCheol Choi, who assisted with figure development; Jessica Que, who assisted with SNP annotation; Reza Alizadehfar, Edmund Chan, Whitney Steber, Chynace Van Lambalgen, Heather Waldhauser, Greg Shand, Elizabeth Turnbull, Popi Panaritis, and Peter Hull, who assisted in data/DNA collection for CanPAR; and Peter Pare for his valuable comments.
Chap
ter 11
imputed (rs1049213) and genotyped (rs3134976) SNPs increased to a P value of 10221 in the
meta-analysis (see Table E5).
The stratified analysis demonstrated a trend for increased odds ratios (ORs) with increasing reaction severity (see Table E6 in this article’s Online Repository at www.jacionline.org) and with PA alone versus PA and other food allergy (see Table E7 in this article’s Online Repository at www.jacionline.org). Those with a mild reaction history without other food allergy had a statistically significant increase in ORs for SNPs in HLA (rs17612852, rs9275596, and rs1612904), despite a small number of cases; this was not observed in patients with moderate or severe PA.
To evaluate the independence of PA GWAS associations from asthma comorbidity, Canadian patients with PA were stratified by the presence or absence of self-reported asthma and changes in effect sizes, and P values were evaluated. There was a higher proportion of asthmatic patients in the severe PA group compared with all cases (76% vs 64%, P 5 .003). There was no difference in ORs for HLA SNPs in asthmatic and nonasthmatic patients with PA (Table I). This is of interest because asthma comorbidity increases PA severity and the presence of PA increases asthma morbidity and mortality.
Examination of the HLA region associated with PA in the GWAS catalog (http://www.ebi.ac.uk/gwas/) identified 8 asthma SNPs in the same region as the PA locus; of these, 6 were genotyped in CanPAR and are interspersed in the same region as our meta-analysis (see Fig E3). We found no difference in ORs between asthmatic and nonasthmatic patients with PA and no genome-wide significant associations with PA in the CanPAR sample (see Table E8 in this article’s Online Repository at www.jacionline.org).
The Genotype-Tissue Expression (gtexportal.org)7 and Gene Expression Omnibus
(ncbi.nlm.nih.gov/geo)8 databases were interrogated for expression quantitative trait loci
(eQTLs) in the HLA region. Results were then narrowed to the esophageal mucosa (P < 1.0 3
1026), which identified a number of genes regulated by SNPs in this region (see Fig E3).
In this study we have confirmed HLA as a PA susceptibility locus. The relationship of PA to HLA-DQB1 is likely independent of asthma because association results stratified by asthma (Table I) demonstrate no significant changes and no asthma GWAS SNPs are significant in CanPAR (see Table E8). Although confounding by asthma might never be controlled fully, the indepen-dence of PA associations from asthma suggests a lack of pleiotropy at this locus (see Fig E3). The presence of genetic risk factors for multiple atopic conditions within HLA, all at genome-wide significance, and our results demonstrating that HLA-DQB1 SNPs identified in CanPAR are independent of asthma and numerous eQTLs identified in the region suggest that this region is associated with the cause of several allergic phenotypes. The HLA class II region has been associated with various allergic diseases. However, these earlier studies and the data presented here suggest that the HLA variants underlying these phenotypes are specific to each trait. This might reflect differences in the efficiency of antigen presentation as a result of the alternate alleles at each locus. The numerous eQTLs identified in the region suggest a potential
underlying mechanism for association with PA. Further discussion is provided in the Methods and Discussion sections in this article’s Online Repository at www.jacionline.org.
CONCLUSION
We conclude that variants in HLA-DQB1 are associated with PA, but the relationship to general food allergy is difficult to assess because PA was an ascertainment criterion for CanPAR. The importance of phenotyping is evident by the sizable changes in P values when a large cohort
of self-reported patients with food allergy, who might have a high rate of misclassification,9
was added to the meta-analysis. Inclusion of the GERA study increased the sample size but might not have increased the power because of self-reported phenotypes. The strengths of this GWAS include the sample size and clinical data available, allowing for subanalyses that indicate the relationship between PA and HLA is independent of asthma. Association results are further supported by evidence that this is a regulatory region, as demonstrated by the numerous eQTLs.
ACKNOWLEDGMENTS
We wish to thank the subjects and parents who participated in this study and in the CanPAR registry. We acknowledge Basia Rogula, who assisted in quality control; JinCheol Choi, who assisted with figure development; Jessica Que, who assisted with SNP annotation; Reza Alizadehfar, Edmund Chan, Whitney Steber, Chynace Van Lambalgen, Heather Waldhauser, Greg Shand, Elizabeth Turnbull, Popi Panaritis, and Peter Hull, who assisted in data/DNA collection for CanPAR; and Peter Pare for his valuable comments.
246 SUPPORT
Supported by the Allergy, Genes, and Environment Network of Centres of Excellence (AllerGen NCE), Canadian Institutes of Health Research, Canadian Research Chairs Program (salary award to D.D.), Natural Sciences and Engineering Research Council and Michael Smith Foundation for Health Research/AllerGen NCE postdoctoral research fellowship awards (to A.E.), Division of Experimental Medicine Entrance Fellowship (to Y.A.), Montreal Children’s Hospital Foundation, McGill University Health Centre Foundation, Canadian Dermatology Foundation, Canadian Allergy, Asthma and Immunology Foundation, Canadian Society of Allergy and Clinical Immunology, the National Institutes of Health (grant no. CA112355 awarded to J.S.W. and RC2 AG036607 awarded to C. A. Schaefer and N. J. Risch), HealthWay, National Health and Medical Research Council (Australia), Australian Research Council, US Department of Defense (grant no. W81XWH-10-1-0487), and a Clinical Exchange Program fellowship of the Experimental and Clinical Research Center of Max-Delbruck-Center and Charite Medical School. C.D.v.G., A.E.J.D., and G.H.K. received an unrestricted grant from the Nutricia Research Foundation to complete the Dutch GENEVA cohort. The Dutch IDEAL cohort of N.W.d.J., H.d.G., R.G.v.W., and A.E.J.D. was supported by the Dutch Technology Foundation STW, which is part of the Netherlands Organisation for Scientific Research (NOW) and funded in part by the Ministry of Economic Affairs (project number 11868) and Food Allergy Foundation, Siemens Healthcare Diagnostics, HAL Allergy, Intersnack the Netherlands B.V., ALK-Albello B.V., and the Netherlands Anaphylaxis Network. Funding sources had no role in study design, collection, analysis and interpretation of data or in the decision to submit or writing of the report. The Genotype-Tissue Expression Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by the National Cancer Institute; National Human Genome Research Institute; National Heart, Lung, and Blood Institute; National Institute of Drug Abuse; National Institute of Mental Health; and National Institute of Neurological Disorders and Stroke. The data used for the analyses described in this manuscript were obtained from the Genotype-Tissue Expression Project Portal on January 1, 2017, to February 28, 2017.
REFERENCES
1. Hong X, Hao K, Ladd-Acosta C, Hansen KD, Tsai HJ, Liu X, et al. Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children. Nat Commun 2015;6:6304. 2. Martino DJ, Ashley S, Koplin J, Ellis J, Saffery
R, Dharmage SC, et al. Genome-wide association study of peanut allergy reproduces association with amino acid polymorphisms in HLA-DRB1. Clin Exp Allergy 2017;47:217-23.
3. James AL, Knuiman MW, Divitini ML, Hui J, Hunter M, Palmer LJ, et al. Changes in the prevalence of asthma in adults since 1966: the Busselton health study. Eur Respir J 2010;35:273-8.
4. Asai Y, Eslami A, van Ginkel CD, Akhabir L, Wan M, Ellis G, et al. 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 al-lergy. J Allergy Clin Immunol 2017 [Epub ahead of print].
5. Hoffmann TJ, Kvale MN, Hesselson SE, Zhan Y, Aquino C, Cao Y, et al. Next gen-eration genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics 2011;98:79-89.
6. van Ginkel CD, Flokstra-de Blok BM, Kollen BJ, Kukler J, Koppelman GH, Du-bois AE. Loss-of-function variants of the filaggrin gene are associated with clinical reactivity to foods. Allergy 2015;70:461-4.
7. GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet 2013;45:580-5.
8. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002; 30:207-10. 9. Rona RJ, Keil T, Summers C, Gislason D,
Zuidmeer L, Sodergren E, et al. The
prevalence of food allergy: a meta-analysis. J Allergy Clin Immunol 2007;120: 638-46.
Chap
ter 11
SUPPORT
Supported by the Allergy, Genes, and Environment Network of Centres of Excellence (AllerGen NCE), Canadian Institutes of Health Research, Canadian Research Chairs Program (salary award to D.D.), Natural Sciences and Engineering Research Council and Michael Smith Foundation for Health Research/AllerGen NCE postdoctoral research fellowship awards (to A.E.), Division of Experimental Medicine Entrance Fellowship (to Y.A.), Montreal Children’s Hospital Foundation, McGill University Health Centre Foundation, Canadian Dermatology Foundation, Canadian Allergy, Asthma and Immunology Foundation, Canadian Society of Allergy and Clinical Immunology, the National Institutes of Health (grant no. CA112355 awarded to J.S.W. and RC2 AG036607 awarded to C. A. Schaefer and N. J. Risch), HealthWay, National Health and Medical Research Council (Australia), Australian Research Council, US Department of Defense (grant no. W81XWH-10-1-0487), and a Clinical Exchange Program fellowship of the Experimental and Clinical Research Center of Max-Delbruck-Center and Charite Medical School. C.D.v.G., A.E.J.D., and G.H.K. received an unrestricted grant from the Nutricia Research Foundation to complete the Dutch GENEVA cohort. The Dutch IDEAL cohort of N.W.d.J., H.d.G., R.G.v.W., and A.E.J.D. was supported by the Dutch Technology Foundation STW, which is part of the Netherlands Organisation for Scientific Research (NOW) and funded in part by the Ministry of Economic Affairs (project number 11868) and Food Allergy Foundation, Siemens Healthcare Diagnostics, HAL Allergy, Intersnack the Netherlands B.V., ALK-Albello B.V., and the Netherlands Anaphylaxis Network. Funding sources had no role in study design, collection, analysis and interpretation of data or in the decision to submit or writing of the report. The Genotype-Tissue Expression Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by the National Cancer Institute; National Human Genome Research Institute; National Heart, Lung, and Blood Institute; National Institute of Drug Abuse; National Institute of Mental Health; and National Institute of Neurological Disorders and Stroke. The data used for the analyses described in this manuscript were obtained from the Genotype-Tissue Expression Project Portal on January 1, 2017, to February 28, 2017.
REFERENCES
1. Hong X, Hao K, Ladd-Acosta C, Hansen KD, Tsai HJ, Liu X, et al. Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children. Nat Commun 2015;6:6304. 2. Martino DJ, Ashley S, Koplin J, Ellis J, Saffery
R, Dharmage SC, et al. Genome-wide association study of peanut allergy reproduces association with amino acid polymorphisms in HLA-DRB1. Clin Exp Allergy 2017;47:217-23.
3. James AL, Knuiman MW, Divitini ML, Hui J, Hunter M, Palmer LJ, et al. Changes in the prevalence of asthma in adults since 1966: the Busselton health study. Eur Respir J 2010;35:273-8.
4. Asai Y, Eslami A, van Ginkel CD, Akhabir L, Wan M, Ellis G, et al. 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 al-lergy. J Allergy Clin Immunol 2017 [Epub ahead of print].
5. Hoffmann TJ, Kvale MN, Hesselson SE, Zhan Y, Aquino C, Cao Y, et al. Next gen-eration genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics 2011;98:79-89.
6. van Ginkel CD, Flokstra-de Blok BM, Kollen BJ, Kukler J, Koppelman GH, Du-bois AE. Loss-of-function variants of the filaggrin gene are associated with clinical reactivity to foods. Allergy 2015;70:461-4.
7. GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet 2013;45:580-5.
8. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002; 30:207-10. 9. Rona RJ, Keil T, Summers C, Gislason D,
Zuidmeer L, Sodergren E, et al. The
prevalence of food allergy: a meta-analysis. J Allergy Clin Immunol 2007;120: 638-46.
248
Online repository material for
CANADIAN GENOME-WIDE ASSOCIATION STUDY AND
META-ANALYSIS CONFIRM HLA AS A RISK FACTOR FOR PEANUT
ALLERGY
METHODS
Genome-wide association study (GWAS): Inclusion criteria for the PA cases (Table E1), definition of hypercontrols, description of study populations (Table E2), quality control measures for sample and SNP inclusion (Figure E1, E2), imputation and meta-analysis are
detailed in previous publications .E1, 2
DISCUSSION
The results of this study are consistent with data that show a relationship between the HLA
region and other allergic conditions, such as allergic rhinitis,E3 serum total IgE,E4 and drug
allergies.E5 The HLA class II region in particular has been associated with various allergic
diseasesE4, 6 as well as total serum IgE.E6-8 However, these earlier studies and the data
presented here suggest that, although the HLA locus is associated with several traits, the individual variants underlying these phenotypes are specific to each trait. This may reflect differences in the efficiency of antigen presentation as a result of the alternate alleles of each variant. Similar findings have been identified in other loci related to allergic disease. For
example, FCER1A, IL13/IL4. and STAT6 have all been associated with serum IgE levelsE4, 9, 10
but different SNPs at these loci were associated with clinical outcomes such as asthma. E10 As
a further complication, different variants have been associated with total serum IgE
dependent on the asthma status of the individual.E9
REFERENCES
E1. Asai Y, Greenwood C, Hull PR, Alizadehfar R, Ben-Shoshan M, Brown SJ, et al. Filaggrin gene mutation associations with peanut allergy persist despite variations in peanut allergy diagnostic criteria or asthma status. J Allergy Clin Immunol 2013; 132:239-42. E2. Asai Y, Eslami A, van Ginkel CD, Akhabir L,
Wan M, Ellis G, et al. 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. J Allergy Clin Immunol 2017. E3. Nilsson D, Henmyr V, Hallden C, Sall T, Kull I,
Wickman M, et al. Replication of genomewide associations with allergic sensitization and allergic rhinitis. Allergy 2014; 69:1506-14.
E4. Potaczek DP, Kabesch M. Current concepts of IgE regulation and impact of genetic determinants. Clin Exp Allergy 2012; 42:852-71.
E5. Illing PT, Mifsud NA, Purcell AW. Allotype specific interactions of drugs and HLA molecules in hypersensitivity reactions. Curr Opin Immunol 2016; 42:31-40.
E6. Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, et al. A large-scale, consortium-based genomewide association study of asthma. N Engl J Med 2010; 363:1211-21.
E7. Levin AM, Mathias RA, Huang L, Roth LA, Daley D, Myers RA, et al. A meta-analysis of genome-wide association studies for serum total IgE in diverse study populations. J Allergy Clin Immunol 2013; 131:1176-84. E8. Granada M, Wilk JB, Tuzova M, Strachan DP,
Weidinger S, Albrecht E, et al. A genome-wide association study of plasma total IgE concentrations in the Framingham Heart Study. J Allergy Clin Immunol 2012; 129:840-5.e21.
E9. Potaczek DP, Michel S, Sharma V, Zeilinger S, Vogelberg C, von Berg A, et al. Different FCER1A polymorphisms influence IgE levels in
asthmatics and non-asthmatics. Pediatr Allergy Immunol 2013; 24:441-9.
E10. Sharma V, Michel S, Gaertner V, Franke A, Vogelberg C, von Berg A, et al. Fine-mapping of IgE-associated loci 1q23, 5q31, and 12q13 using 1000 Genomes Project data. Allergy 2014; 69:1077-84.
Chap
ter 11
Online repository material for
CANADIAN GENOME-WIDE ASSOCIATION STUDY AND
META-ANALYSIS CONFIRM HLA AS A RISK FACTOR FOR PEANUT
ALLERGY
METHODS
Genome-wide association study (GWAS): Inclusion criteria for the PA cases (Table E1), definition of hypercontrols, description of study populations (Table E2), quality control measures for sample and SNP inclusion (Figure E1, E2), imputation and meta-analysis are
detailed in previous publications .E1, 2
DISCUSSION
The results of this study are consistent with data that show a relationship between the HLA
region and other allergic conditions, such as allergic rhinitis,E3 serum total IgE,E4 and drug
allergies.E5 The HLA class II region in particular has been associated with various allergic
diseasesE4, 6 as well as total serum IgE.E6-8 However, these earlier studies and the data
presented here suggest that, although the HLA locus is associated with several traits, the individual variants underlying these phenotypes are specific to each trait. This may reflect differences in the efficiency of antigen presentation as a result of the alternate alleles of each variant. Similar findings have been identified in other loci related to allergic disease. For
example, FCER1A, IL13/IL4. and STAT6 have all been associated with serum IgE levelsE4, 9, 10
but different SNPs at these loci were associated with clinical outcomes such as asthma. E10 As
a further complication, different variants have been associated with total serum IgE
dependent on the asthma status of the individual.E9
REFERENCES
E1. Asai Y, Greenwood C, Hull PR, Alizadehfar R, Ben-Shoshan M, Brown SJ, et al. Filaggrin gene mutation associations with peanut allergy persist despite variations in peanut allergy diagnostic criteria or asthma status. J Allergy Clin Immunol 2013; 132:239-42. E2. Asai Y, Eslami A, van Ginkel CD, Akhabir L,
Wan M, Ellis G, et al. 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. J Allergy Clin Immunol 2017. E3. Nilsson D, Henmyr V, Hallden C, Sall T, Kull I,
Wickman M, et al. Replication of genomewide associations with allergic sensitization and allergic rhinitis. Allergy 2014; 69:1506-14.
E4. Potaczek DP, Kabesch M. Current concepts of IgE regulation and impact of genetic determinants. Clin Exp Allergy 2012; 42:852-71.
E5. Illing PT, Mifsud NA, Purcell AW. Allotype specific interactions of drugs and HLA molecules in hypersensitivity reactions. Curr Opin Immunol 2016; 42:31-40.
E6. Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, et al. A large-scale, consortium-based genomewide association study of asthma. N Engl J Med 2010; 363:1211-21.
E7. Levin AM, Mathias RA, Huang L, Roth LA, Daley D, Myers RA, et al. A meta-analysis of genome-wide association studies for serum total IgE in diverse study populations. J Allergy Clin Immunol 2013; 131:1176-84. E8. Granada M, Wilk JB, Tuzova M, Strachan DP,
Weidinger S, Albrecht E, et al. A genome-wide association study of plasma total IgE concentrations in the Framingham Heart Study. J Allergy Clin Immunol 2012; 129:840-5.e21.
E9. Potaczek DP, Michel S, Sharma V, Zeilinger S, Vogelberg C, von Berg A, et al. Different FCER1A polymorphisms influence IgE levels in
asthmatics and non-asthmatics. Pediatr Allergy Immunol 2013; 24:441-9.
E10. Sharma V, Michel S, Gaertner V, Franke A, Vogelberg C, von Berg A, et al. Fine-mapping of IgE-associated loci 1q23, 5q31, and 12q13 using 1000 Genomes Project data. Allergy 2014; 69:1077-84.
250
FIGURE E1: Flowchart of exclusion criteria of single nucleotide polymorphisms
Chap
ter 11
FIGURE E1: Flowchart of exclusion criteria of single nucleotide polymorphisms
252
FIGURE E3: HLA ideogram covers the region from 32,411,646 to 33,048,661. Trait column
indicates that the SNP is either associated in the current peanut allergy GWAS or has been associated with a related trait: asthma, allergic asthma, dermatitis, Total IgE, specific IgE, lung function or food allergy in the GWAS catalog (http://www.ebi.ac.uk/gwas). The gene column provides the gene location or nearest gene for each SNP. EQTL were identified using the Gene Expression Omnibus database (GEO; https://www.ncbi.nlm.nih.gov/geo/). SNPs are identified as
an eQTL for the genes listed in the “EQTL” column in esophageal mucosa with a p-value<1.00x10
-6. Number in brackets represents the number of peanut allergy SNPs between the listed SNPs.
The Canadian peanut allergy SNPs in LD (r2 > 0.8) are excluded unless they are listed in Table 1.
Shaded areas represent SNPs from Table 1 Red text represents Canadian peanut allergy SNPs Black text represents NHGRI GWAS Catalog SNPs
Abbreviations: IgE: Immunoglobulin E, AHR: airway hyper-responsiveness, EQTL: expression quantitative trait loci, NHGRI: National Human Genome Research Institute
History Skin prick test to peanut Peanut-specific IgE # of subjects (N=850)
1 Oral food challenge 27
2 A convincing history of an allergic
reaction* AND ≥ 3 mm AND ≥ 0.35 kU/L 314
3 A convincing history of an allergic
reaction* AND ≥ 3 mm 354
4 A convincing history of an allergic
reaction* AND ≥ 0.35 kU/L 45
5 Uncertain history of an allergic reaction& AND ≥ 3 mm AND ≥ 15 kU/L 46
6 No history of a reaction^ AND ≥ 3 mm AND ≥ 15 kU/L 64
TABLE E1:
Case definition of peanut allergy in the Canadian Peanut Allergy Registry. *Convincing history
includes: 2 mild symptoms or signs, OR 1 moderate or 1 severe symptom or sign, AND occurring
within 120 minutes after known peanut contact or ingestion; & Uncertain history includes: 1 mild
symptom or sign occurring within 120 minutes after known peanut contact or ingestion, OR 1
moderate or 1 severe symptom or sign but lacking information on time or mode of peanut
contact; ^No history of a reaction; individuals were advised to avoid peanut due to testing
AND/OR a peanut-allergic sibling, OR have no history of peanut exposure.
Chap
ter 11
FIGURE E3: HLA ideogram covers the region from 32,411,646 to 33,048,661. Trait column
indicates that the SNP is either associated in the current peanut allergy GWAS or has been associated with a related trait: asthma, allergic asthma, dermatitis, Total IgE, specific IgE, lung function or food allergy in the GWAS catalog (http://www.ebi.ac.uk/gwas). The gene column provides the gene location or nearest gene for each SNP. EQTL were identified using the Gene Expression Omnibus database (GEO; https://www.ncbi.nlm.nih.gov/geo/). SNPs are identified as
an eQTL for the genes listed in the “EQTL” column in esophageal mucosa with a p-value<1.00x10
-6. Number in brackets represents the number of peanut allergy SNPs between the listed SNPs.
The Canadian peanut allergy SNPs in LD (r2 > 0.8) are excluded unless they are listed in Table 1.
Shaded areas represent SNPs from Table 1 Red text represents Canadian peanut allergy SNPs Black text represents NHGRI GWAS Catalog SNPs
Abbreviations: IgE: Immunoglobulin E, AHR: airway hyper-responsiveness, EQTL: expression quantitative trait loci, NHGRI: National Human Genome Research Institute
History Skin prick test to peanut Peanut-specific IgE # of subjects (N=850)
1 Oral food challenge 27
2 A convincing history of an allergic
reaction* AND ≥ 3 mm AND ≥ 0.35 kU/L 314
3 A convincing history of an allergic
reaction* AND ≥ 3 mm 354
4 A convincing history of an allergic
reaction* AND ≥ 0.35 kU/L 45
5 Uncertain history of an allergic reaction& AND ≥ 3 mm AND ≥ 15 kU/L 46
6 No history of a reaction^ AND ≥ 3 mm AND ≥ 15 kU/L 64
TABLE E1:
Case definition of peanut allergy in the Canadian Peanut Allergy Registry. *Convincing history
includes: 2 mild symptoms or signs, OR 1 moderate or 1 severe symptom or sign, AND occurring
within 120 minutes after known peanut contact or ingestion; & Uncertain history includes: 1 mild
symptom or sign occurring within 120 minutes after known peanut contact or ingestion, OR 1
moderate or 1 severe symptom or sign but lacking information on time or mode of peanut
contact; ^No history of a reaction; individuals were advised to avoid peanut due to testing
AND/OR a peanut-allergic sibling, OR have no history of peanut exposure.
254 Loc at ion Ca se s Con tr ol s Age Ge no ty pi ng chi p Ca na di an (N =1 97 4) PA (N =987) , s ee Ta bl e E 1 f or in clu sio n cr ite ria . S elf -re po rt ed F A a nd P A ( N= 63 6) N= 987, n on -a to pi c, n o h isto ry o f as th m a, ai rw ay h yp er -re sp on siv en es s, at op y, e cze m a, alle rg ic rh in itis o r F A (A us tr al ia , Bus se lto n He al th St udy ) Ca se s: ra ng e = 1-63 ye ar s, m ea n ( SD ) = 1 2 ( 6) y ea rs Contr ol s: r an ge = 6 -93 ye ar s, m ea n ( SD ) = 4 9 ( 25 ) y ea rs Ill um in a Om ni 2. 5M+ Ex om e 8v 1. 1 Am eri ca n (Ch ica go F ood St udy ) E6 (N =2 , 197) PA (N =316) , c on vi nc in g hi st or y of cl in ica l a lle rg ic re ac tion on in ge st ion to pe an ut a nd e vi de nc e of se ns iti za tio n to p ea nu t (pe anut -s pe cif ic IgE ³0. 10k U/ L a nd /o r a po siti ve S PT ³ 3 mm) N= 144 no n-alle rg ic, n on -se ns iti ze d c on tr ol s a nd 1, 737 co nt ro ls of unc er ta in phe no ty pe s Ra ng e: 0 -21 ye ar s Ill um in a Hu m an Om ni 1-Q ua d Be adC hi p Am eri ca n GE RA co ho rt (G en et ic Ep id em io lo gy Re se ar ch on Agi ng) E8 -10 To ta l c oh or t m em be rs : N= 103, 067 Da ta u se d f or th e a na ly sis is a nes ted ca se co nt ro l Ca se s: Se lf-re por te d food alle rg y in m ed ica l c ha rt : (N =5 10 8) Co nt ro ls: w ith ou t s elf -re po rt ed fo od al le rg y N= 23, 945 Ra ng e: 1 8 - > 10 0 ye ar s, m ean 6 3 ye ar s Af fy m etr ix A xi om w ith 674, 517 SN Ps Au st ral ian (H ea lth N uts St ud y) (N =2 21 ) E7 PA (N =7 3), + or al ch al len ge to p ea nu t o r p ar en t r ep or t o f cle ar h isto ry o f i m m ed ia te re ac tio n i n t he p as t 2 m on th s (N =3 ) N= 14 8 S PT n eg ati ve to e gg w hi te , pe anut , s es am e, shr im p, co w’ s m ilk, ca sh ew, a lm on d, ha ze ln ut , s oy a nd w he at , w ith neg at iv e or al ch al len ge to pe an ut Ra ng e = 1 1-15 m on th s Ca se s: m ea n (S D) = 1 2. 8 (0 .8 ) m on th s Co ntr ol s: m ea n ( SD ) = 12. 6 (0. 7) m on th s Ill um in a Om ni 2 .5 +8 Ge rm an (U nde rs ta ndi ng Food a lle rg y) E7 PA (N =2 05 ), + DB PC FC o r a hi st or y o f a se ve re a lle rg ic re ac tio n to p ea nu ts p lu s sp ec ifi c s en siti za tio n to pe an ut p ro te in (> 0. 35 k Ul -1). 2, 38 7 c on tr ol s u nr el ate d indi vi dua ls fro m the G er m an po pu la tio n ba se d He in z N ix do rf Re ca ll St udy E1 2 Ca se s: ch ild re n Cont ro ls: a dul ts ag ed 4 5-75 ye ar s Hum anO m ni Ex pr es sE xo m e-8 v1. 2 (C as es ) Hum anO m ni Ex pr es s-12 v1 .1 pl us H um anE xo m e-12 v1 or Hum anO m ni 1M -4 v1 pl us H um an Ex om e-12 v1 . ( Con tr ol s) D ut ch (IDE AL an d GE NE VA st ud ie s) PA (N =138) : + DB PC FC to pe an ut FA in g en er al (N =36 0) : +D BP CFC to a ny fo od; pe anut (N =138) , c as he w (N =132) , co w ’s m ilk (N =6 7) , h az el nu t (N =5 5) , h en s e gg (N =5 8) , w al nu t ( N= 21 ), soy (N =1 1) , al m ond (N =1 ), buc kw he at (N =1 ), se sa m e se ed (N =3 ), pi ne n ut (N =2 ) a nd b ra zil n ut (N =1 ). S om e s ub je cts h av e a +D BP CFC fo r m ul tipl e fo ods ; th er e w er e n o + DB PCF C to lupi n, m ac ada m ia , pi st ac hi o, w he at ) Co nt ro ls fo r P A (N =10 4) : -DB PC FC to p ea nu t Con tr ol s f or F A: -D BP CF C t o a ny food (N =1 52 ) i nc lu di ng : pea nu t(N =1 04 ), ca sh ew (N =3 5), co w ’s m ilk (N =7 1) , h az el nu t (N =4 4) , h en s e gg (N =5 0) , w al nu t (N =1 1) , S oy (N =1 9) , a lm ond (N =1 2) , w he at (N =8 ), lupi n se ed (N =5 ), se sa m e se ed (N =1 ), pi st ac hi o (N =8 ), m ac ad am ia (N =2 ) So m e su bje ct s h av e a -D BP CF C fo r m ul tip le fo od s ID EA L: ra ng e = 2 -7 y ears , m ed ia n = 9 .0 y ea rs GENE VA : pa re nt -c hi ld tr io s, a ge u nk no w n Co m pe tit iv e all ele -sp ec ific P CR u sin g KAS Pa r ge no ty pi ng che m ist ry , unde r co ntr ac t b y L GC Ge no m ic ( LG C, Te ddi ng to n, U K) . TA BL E E2: Sum m ar y of cas e and co nt ro l gr oups . PA : pe anut al le rgy ; F A: fo od al le rgy , D BP CF C: do ub le -b lin d, p lac ebo -c ont ro lle d fo od chal le nge , S PT : s ki n pr ick te st , + : p os itiv e, -: ne gat iv e
Chap ter 11 Loc at ion Ca se s Con tr ol s Age Ge no ty pi ng chi p Ca na di an (N =1 97 4) PA (N =987) , s ee Ta bl e E 1 f or in clu sio n cr ite ria . S elf -re po rt ed F A a nd P A ( N= 63 6) N= 987, n on -a to pi c, n o h isto ry o f as th m a, ai rw ay h yp er -re sp on siv en es s, at op y, e cze m a, alle rg ic rh in itis o r F A (A us tr al ia , Bus se lto n He al th St udy ) Ca se s: ra ng e = 1-63 ye ar s, m ea n ( SD ) = 1 2 ( 6) y ea rs Contr ol s: r an ge = 6 -93 ye ar s, m ea n ( SD ) = 4 9 ( 25 ) y ea rs Ill um in a Om ni 2. 5M+ Ex om e 8v 1. 1 Am eri ca n (Ch ica go F ood St udy ) E6 (N =2 , 197) PA (N =316) , c on vi nc in g hi st or y of cl in ica l a lle rg ic re ac tion on in ge st ion to pe an ut a nd e vi de nc e of se ns iti za tio n to p ea nu t (pe anut -s pe cif ic IgE ³0. 10k U/ L a nd /o r a po siti ve S PT ³ 3 mm) N= 144 no n-alle rg ic, n on -se ns iti ze d c on tr ol s a nd 1, 737 co nt ro ls of unc er ta in phe no ty pe s Ra ng e: 0 -21 ye ar s Ill um in a Hu m an Om ni 1-Q ua d Be adC hi p Am eri ca n GE RA co ho rt (G en et ic Ep id em io lo gy Re se ar ch on Agi ng) E8 -10 To ta l c oh or t m em be rs : N= 103, 067 Da ta u se d f or th e a na ly sis is a nes ted ca se co nt ro l Ca se s: Se lf-re por te d food alle rg y in m ed ica l c ha rt : (N =5 10 8) Co nt ro ls: w ith ou t s elf -re po rt ed fo od al le rg y N= 23, 945 Ra ng e: 1 8 - > 10 0 ye ar s, m ean 6 3 ye ar s Af fy m etr ix A xi om w ith 674, 517 SN Ps Au st ral ian (H ea lth N uts St ud y) (N =2 21 ) E7 PA (N =7 3), + or al ch al len ge to p ea nu t o r p ar en t r ep or t o f cle ar h isto ry o f i m m ed ia te re ac tio n i n t he p as t 2 m on th s (N =3 ) N= 14 8 S PT n eg ati ve to e gg w hi te , pe anut , s es am e, shr im p, co w’ s m ilk, ca sh ew, a lm on d, ha ze ln ut , s oy a nd w he at , w ith neg at iv e or al ch al len ge to pe an ut Ra ng e = 1 1-15 m on th s Ca se s: m ea n (S D) = 1 2. 8 (0 .8 ) m on th s Co ntr ol s: m ea n ( SD ) = 12. 6 (0. 7) m on th s Ill um in a Om ni 2 .5 +8 Ge rm an (U nde rs ta ndi ng Food a lle rg y) E7 PA (N =2 05 ), + DB PC FC o r a hi st or y o f a se ve re a lle rg ic re ac tio n to p ea nu ts p lu s sp ec ifi c s en siti za tio n to pe an ut p ro te in (> 0. 35 k Ul -1). 2, 38 7 c on tr ol s u nr el ate d indi vi dua ls fro m the G er m an po pu la tio n ba se d He in z N ix do rf Re ca ll St udy E1 2 Ca se s: ch ild re n Cont ro ls: a dul ts ag ed 4 5-75 ye ar s Hum anO m ni Ex pr es sE xo m e-8 v1. 2 (C as es ) Hum anO m ni Ex pr es s-12 v1 .1 pl us H um anE xo m e-12 v1 or Hum anO m ni 1M -4 v1 pl us H um an Ex om e-12 v1 . ( Con tr ol s) D ut ch (IDE AL an d GE NE VA st ud ie s) PA (N =138) : + DB PC FC to pe an ut FA in g en er al (N =36 0) : +D BP CFC to a ny fo od; pe anut (N =138) , c as he w (N =132) , co w ’s m ilk (N =6 7) , h az el nu t (N =5 5) , h en s e gg (N =5 8) , w al nu t ( N= 21 ), soy (N =1 1) , al m ond (N =1 ), buc kw he at (N =1 ), se sa m e se ed (N =3 ), pi ne n ut (N =2 ) a nd b ra zil n ut (N =1 ). S om e s ub je cts h av e a +D BP CFC fo r m ul tipl e fo ods ; th er e w er e n o + DB PCF C to lupi n, m ac ada m ia , pi st ac hi o, w he at ) Co nt ro ls fo r P A (N =10 4) : -DB PC FC to p ea nu t Con tr ol s f or F A: -D BP CF C t o a ny food (N =1 52 ) i nc lu di ng : pea nu t(N =1 04 ), ca sh ew (N =3 5), co w ’s m ilk (N =7 1) , h az el nu t (N =4 4) , h en s e gg (N =5 0) , w al nu t (N =1 1) , S oy (N =1 9) , a lm ond (N =1 2) , w he at (N =8 ), lupi n se ed (N =5 ), se sa m e se ed (N =1 ), pi st ac hi o (N =8 ), m ac ad am ia (N =2 ) So m e su bje ct s h av e a -D BP CF C fo r m ul tip le fo od s ID EA L: ra ng e = 2 -7 y ears , m ed ia n = 9 .0 y ea rs GENE VA : pa re nt -c hi ld tr io s, a ge u nk no w n Co m pe tit iv e all ele -sp ec ific P CR u sin g KAS Pa r ge no ty pi ng che m ist ry , unde r co ntr ac t b y L GC Ge no m ic ( LG C, Te ddi ng to n, U K) . TA BL E E2: Sum m ar y of cas e and co nt ro l gr oups . PA : pe anut al le rgy ; F A: fo od al le rgy , D BP CF C: do ub le -b lin d, p lac ebo -c ont ro lle d fo od chal le nge , S PT : s ki n pr ick te st , + : p os itiv e, -: ne gat iv e
256
Reaction severity Symptoms/Signs
Mild Pruritus, itchy throat, urticaria, flushing, rhinoconjunctivitis
Moderate Angioedema, coughing, stridor, tight throat, voice change, nausea, abdominal pain, vomiting, difficulty breathing
Severe Wheezing, cyanosis, circulatory collapse
TABLE E3: Definitions of mild, moderate and severe reaction. Reaction severity was determined by the severity of the most severe reaction
Symptom severity N (% of 850)
Food allergy other than peanut allergy
Yes: Total = 636, No: Total = 214 N (% of 850) Self-reported asthma Yes: Total = 545 N (% of 850) No: Total = 305 N (% of 850) Mild: 111 (13.1) Yes No 81 (9.5) 30 (3.5) 45 (5.3) 10 (1.2) 36 (4.2) 20 (2.4) Moderate: 473 (55.6) Yes No 341 (40.1) 132 (15.5) 221 (26.0) 70 (8.2) 120 (14.1) 62 (7.3) Severe: 201 (23.6) Yes No 151 (17.8) 50 (5.9) 118 (13.9) 34 (4.0) 33 (3.9) 16 (1.9) No reaction history*: 65 (7.6) Yes No 63 (7.4) 2 (0.2) 46 (5.4) 1 (0.1) 17 (2.0) 1 (0.1) TABLE E4: Mild, moderate and severe reactions, self-reported asthma and presence of other
food allergies in peanut-allergic cases (N=850)* no reported reaction; may not have been exposed to peanut TA B LE E 5: HL A m et a-ana ly sis re sul ts fo r t he m os t s igni fic ant S NP s i n the C ana di an PA , A m er ic an, A us tr al ian Du tc h and Ge rm an GW AS st udi es , or de re d by the pe anut a lle rgy m et a-an al ysi s p -v al ue . ¥ P an el A : pe an ut al le rgy , p ane l B : f oo d al le rgy ¥ D ue to di ffe re nc es in ge no ty pi ng pl at fo rm s a nd im put at io n re fe re nc e pa ne ls, it w as no t po ss ibl e to e va lua te a ll SN Ps in al l s tudi es . Th e m os t s ig ni fic an t H LA S NP in th e C an PA R G W AS (r s1 04 92 13 ) w as n ot a va ila bl e in the U FA o r D ut ch st udi es * U se d f or b ot h - p ea nu t a lle rg y ( PA ) a nd fo od a lle rg y ( FA ) m et a-an al ys es a P-va lue fr om C ana di an pe an ut a lle rg y st udy (N =1 ,7 76 ), b P-va lue fr om A m er ica n pe anut a lle rg y st udy (N =2 ,1 97 ), c P-va lue fr om Aus tr al ia n pe anut a lle rg y st udy (N =2 21 ), d P-va lue fr om G er m an pe anut a lle rg y st udy (N =2 ,5 92 ) e P-va lue fr om D ut ch pe an ut a lle rg y ca se -c ont ro l s tudy , c or re ct ed fo r a to pi c de rm at iti s ( AD ), As thm a (A s) a nd rhi no co nj unc tiv iti s (R C) ; num be r o f i ndi vi dua ls fo r S NP s e1, e2, a nd e3: 227, 21 9, a nd 226. fP-va lue fr om D ut ch pe anut a lle rg y fa m ily st udy , n um be r o f i nfo rm at iv e fa m ili es fo r S NP s f1, f2, a nd f3: 13 3, 134, a nd 1 30 g P-va lue fr om S to uffe r’s w ei ght ed z-sc or e m et a-ana ly sis m et ho d fo r pe anut a lle rg y h P-va lu e from A m er ica n food a lle rg y st ud y (N =2, 197) iP-va lu e f ro m D ut ch fo od a lle rg y c as e-co nt ro l s tudy , c or re ct ed fo r A D, A s a nd RC ; num be r o f i ndi vi dua ls fo r S NP s i1, i2, a nd i3: 483, 476, a nd 47 9 jP-va lue fr om D ut ch fo od al le rg y fa m ily st udy , num be r o f i nfo rm at iv e fa m ili es fo r S NP s j1, j2, a nd j3: 238, 24 2, a nd 230 k P-va lu e from G ER A fo od a lle rg y st ud y (N =29, 053) lP-va lue fr om S to uffe r’s w ei ght ed z-sc or e m et a-an al ys is m et ho d f or fo od a lle rg y m P-va lue fr om S to uffe r’s w ei ght ed z-sc or e m et a-an aly sis m et ho d fo r fo od al le rg y w itho ut G ER A st udy a To p S NP fo r P A m et a-an al ys is (C an ad ian – Im put ed) b To p S NP fo r F A m et a-ana ly sis w itho ut G ER A (C ana di an – Im put ed) g T op Ca na di an SN P – Im put ed d Ame ric an - Ta bl e 1 e Top Ca na di an SN P - G eno ty pe d f Au st ral ian - Ta bl e 1 h T op S NP fo r F A m et a-an al ysi s w ith GE RA �(A m eric an - Su ppl em ent ar y Ta bl e 2) � k Ame ric an - Suppl em ent ar y Ta bl e 2# µ H iro ta e t a l As th ma SN P∫ # Sec ond to p im put ed SN P (the fi rs t t op im put ed SN P is no t i n 10 00 G eno m es P ha se 3 ) ∫ As thm a SNP fr om th e NH GR I G W AS C at al og in LD w ith rs 71 92 (r 2 =0. 45)
Chap
ter 11
Reaction severity Symptoms/Signs
Mild Pruritus, itchy throat, urticaria, flushing, rhinoconjunctivitis
Moderate Angioedema, coughing, stridor, tight throat, voice change, nausea, abdominal pain, vomiting, difficulty breathing
Severe Wheezing, cyanosis, circulatory collapse
TABLE E3: Definitions of mild, moderate and severe reaction. Reaction severity was determined by the severity of the most severe reaction
Symptom severity N (% of 850)
Food allergy other than peanut allergy
Yes: Total = 636, No: Total = 214 N (% of 850) Self-reported asthma Yes: Total = 545 N (% of 850) No: Total = 305 N (% of 850) Mild: 111 (13.1) Yes No 81 (9.5) 30 (3.5) 45 (5.3) 10 (1.2) 36 (4.2) 20 (2.4) Moderate: 473 (55.6) Yes No 341 (40.1) 132 (15.5) 221 (26.0) 70 (8.2) 120 (14.1) 62 (7.3) Severe: 201 (23.6) Yes No 151 (17.8) 50 (5.9) 118 (13.9) 34 (4.0) 33 (3.9) 16 (1.9) No reaction history*: 65 (7.6) Yes No 63 (7.4) 2 (0.2) 46 (5.4) 1 (0.1) 17 (2.0) 1 (0.1) TABLE E4: Mild, moderate and severe reactions, self-reported asthma and presence of other
food allergies in peanut-allergic cases (N=850)* no reported reaction; may not have been exposed to peanut TA B LE E 5: HL A m et a-ana ly sis re sul ts fo r t he m os t s igni fic ant S NP s i n the C ana di an PA , A m er ic an, A us tr al ian Du tc h and Ge rm an GW AS st udi es , or de re d by the pe anut a lle rgy m et a-an al ysi s p -v al ue . ¥ P an el A : pe an ut al le rgy , p ane l B : f oo d al le rgy ¥ D ue to di ffe re nc es in ge no ty pi ng pl at fo rm s a nd im put at io n re fe re nc e pa ne ls, it w as no t po ss ibl e to e va lua te a ll SN Ps in al l s tudi es . Th e m os t s ig ni fic an t H LA S NP in th e C an PA R G W AS (r s1 04 92 13 ) w as n ot a va ila bl e in the U FA o r D ut ch st udi es * U se d f or b ot h - p ea nu t a lle rg y ( PA ) a nd fo od a lle rg y ( FA ) m et a-an al ys es a P-va lue fr om C ana di an pe an ut a lle rg y st udy (N =1 ,7 76 ), b P-va lue fr om A m er ica n pe anut a lle rg y st udy (N =2 ,1 97 ), c P-va lue fr om Aus tr al ia n pe anut a lle rg y st udy (N =2 21 ), d P-va lue fr om G er m an pe anut a lle rg y st udy (N =2 ,5 92 ) e P-va lue fr om D ut ch pe an ut a lle rg y ca se -c ont ro l s tudy , c or re ct ed fo r a to pi c de rm at iti s ( AD ), As thm a (A s) a nd rhi no co nj unc tiv iti s (R C) ; num be r o f i ndi vi dua ls fo r S NP s e1, e2, a nd e3: 227, 21 9, a nd 226. fP-va lue fr om D ut ch pe anut a lle rg y fa m ily st udy , n um be r o f i nfo rm at iv e fa m ili es fo r S NP s f1, f2, a nd f3: 13 3, 134, a nd 1 30 g P-va lue fr om S to uffe r’s w ei ght ed z-sc or e m et a-ana ly sis m et ho d fo r pe anut a lle rg y h P-va lu e from A m er ica n food a lle rg y st ud y (N =2, 197) iP-va lu e f ro m D ut ch fo od a lle rg y c as e-co nt ro l s tudy , c or re ct ed fo r A D, A s a nd RC ; num be r o f i ndi vi dua ls fo r S NP s i1, i2, a nd i3: 483, 476, a nd 47 9 jP-va lue fr om D ut ch fo od al le rg y fa m ily st udy , num be r o f i nfo rm at iv e fa m ili es fo r S NP s j1, j2, a nd j3: 238, 24 2, a nd 230 k P-va lu e from G ER A fo od a lle rg y st ud y (N =29, 053) lP-va lue fr om S to uffe r’s w ei ght ed z-sc or e m et a-an al ys is m et ho d f or fo od a lle rg y m P-va lue fr om S to uffe r’s w ei ght ed z-sc or e m et a-an aly sis m et ho d fo r fo od al le rg y w itho ut G ER A st udy a To p S NP fo r P A m et a-an al ys is (C an ad ian – Im put ed) b To p S NP fo r F A m et a-ana ly sis w itho ut G ER A (C ana di an – Im put ed) g T op Ca na di an SN P – Im put ed d Ame ric an - Ta bl e 1 e Top Ca na di an SN P - G eno ty pe d f Au st ral ian - Ta bl e 1 h T op S NP fo r F A m et a-an al ysi s w ith GE RA �(A m eric an - Su ppl em ent ar y Ta bl e 2) � k Ame ric an - Suppl em ent ar y Ta bl e 2# µ H iro ta e t a l As th ma SN P∫ # Sec ond to p im put ed SN P (the fi rs t t op im put ed SN P is no t i n 10 00 G eno m es P ha se 3 ) ∫ As thm a SNP fr om th e NH GR I G W AS C at al og in LD w ith rs 71 92 (r 2 =0. 45)
258 TA B LE E5 P A N EL A SN P P ea nu t a lle rg y Ge ne /N ea re st G en e P - Ca na di an* a P - Am eri ca n b P -Au st ral ian * c P - Ge rm an * d P - D ut ch Ca se -c on tr ol st udy e P - D ut ch Fa m ily st udy f Pm et a_P A g rs 1063347 a 3. 61x 10 -10 4. 40x 10 -10 6. 91x 10 -3 1. 59x 10 -5 NA NA 3. 67x 10 -23 HLA -DQ B1 rs 3134975 b 1. 28x 10 -10 4. 40x 10 -8 1. 69x 10 -3 3. 24x 10 -6 NA NA 7. 01x 10 -23 (1 8k b) HLA -D Q B1| (5 7k b) HLA -DQ A2 rs 1049213 g 1. 82x 10 -11 1. 60x 10 -9 1. 08x 10 -3 NA NA NA 2. 30x 10 -21 HLA -DQ B1 rs 9275596 d 1. 04x 10 -7 6. 80x 10 -10 NA 2. 97x 10 -6 0. 08 e1 0. 12 f1 1. 15x 10 -21 (4 7k b) HLA -D Q B1| (2 8k b) HLA -DQ A2 rs 3134976 e 2. 15x 10 -10 8. 70x 10 -9 NA 1. 26x 10 -5 NA NA 6. 86x 10 -21 (1 8k b) HLA -DQ B1 |( 57 kb )H LA -DQ A2 rs 2858305 f 1. 95x 10 -5 3. 10x 10 -8 2. 72x 10 -4 8. 42x 10 -6 NA NA 2. 25x 10 -18 (3 6k b) HLA -DQ B1 |( 39 kb )H LA -DQ A2 rs 2858309 f 1. 95x 10 -5 2. 70x 10 -8 3. 61x 10 -4 8. 48x 10 -6 NA NA 2. 26x 10 -18 (3 4k b) HLA -DQ B1 |( 40 kb )H LA -DQ A2 rs 2856717 f 1. 95x 10 -5 3. 10x 10 -8 3. 28x 10 -4 8. 42x 10 -6 NA NA 2. 43x 10 -18 (3 6k b) HLA -DQ B1 |( 39 kb )H LA -DQ A2 rs 2858320 h 1. 49x 10 -5 4. 10x 10 -8 2. 28x 10 -3 4. 14x 10 -6 NA NA 2. 48x 10 -18 (2 7k b) HLA -DQ B1 |( 48 kb )H LA -DQ A2 rs 7192 d 6. 80x 10 -6 5. 50x 10 -8 NA 2. 16x 10 -5 6. 00x 10 -3 e2 0. 02 f2 1. 94x 10 -18 HLA -DR A rs 9275227 k 3. 18x 10 -4 3. 40x 10 -10 2. 06x 10 -2 5. 02x 10 -4 NA NA 1. 43x 10 -15 (2 6k b) HLA -DQ B1 |( 49 kb )H LA -DQ A2 rs 2858332 f 4. 91x 10 -5 1. 37x 10 -4 3. 48x 10 -4 9. 05x 10 -5 NA NA 2. 63x 10 -13 (4 7k b) HLA -DQ B1 |( 28 kb )H LA -DQ A2 rs 3129890 µ 0. 46 1. 65x 10 -3 NA 0. 55 NA NA 9. 73x 10 -3 (1 kb )H LA -DR A| (7 1k b) HLA -DR B5 rs 154975 f 0. 65 0. 74 1. 30x 10 -4 0. 32 0. 99 e3 0. 69 1 f3 0. 08 (2 9k b) LO C10029 4145 |( 2k b) HLA -D MB TA B LE E5 P A N EL B SN P B Food a lle rg y P - A m eri can h P - D ut ch Ca se -c on tr ol st udy i P - D ut ch Fa m ily st udy j P - G ERA k Pm eta F A l Pm eta F A (w ith ou t GE RA ) m rs 1063347 a 0. 04 NA NA 0. 95 8. 52x 10 -4 5. 07x 10 -14 rs 3134975 b 0. 02 NA NA 0. 82 2. 23x 10 -4 1. 12x 10 -15 rs 1049213 g 0. 07 NA NA 0. 90 0. 02 1. 26x 10 -10 rs 9275596 d 6. 15x 10 -3 0. 87 i1 0. 21 j1 0. 07 1. 33x 10 -6 6. 49x 10 -13 rs 3134976 e 0. 03 NA NA 0. 91 1. 14x 10 -3 2. 13x 10 -13 rs 2858305 f 0. 01 NA NA 0. 26 4. 72x 10 -5 2. 11x 10 -12 rs 2858309 f 0. 01 NA NA 0. 27 5. 06x 10 -5 2. 34x 10 -12 rs 2856717 f 0. 01 NA NA 0. 31 6. 95x 10 -5 2. 25x 10 -12 rs 2858320 h 1. 14x 10 -3 NA NA NA 8. 51x 10 -14 8. 51x 10 -14 rs 7192 d 0. 02 0. 47 i2 0. 04 j2 0. 01 9. 13x 10 -7 1. 30x 10 -9 rs 9275227 k 1. 37x 10 -3 NA NA NA 4. 62x 10 -10 4. 62x 10 -10 rs 2858332 f 0. 03 NA NA 0. 18 6. 37x 10 -5 1. 69x 10 -10 rs 3129890 µ 0. 61 NA NA 0. 19 0. 10 0. 29 rs 154975 f 0. 84 0. 72 i3 0. 44 j3 0. 34 0. 10 0. 07
Chap ter 11 259 TA B LE E5 P A N EL A SN P P ea nu t a lle rg y Ge ne /N ea re st G en e P - Ca na di an* a P - Am eri ca n b P -Au st ral ian * c P - Ge rm an * d P - D ut ch Ca se -c on tr ol st udy e P - D ut ch Fa m ily st udy f Pm et a_P A g rs 1063347 a 3. 61x 10 -10 4. 40x 10 -10 6. 91x 10 -3 1. 59x 10 -5 NA NA 3. 67x 10 -23 HLA -DQ B1 rs 3134975 b 1. 28x 10 -10 4. 40x 10 -8 1. 69x 10 -3 3. 24x 10 -6 NA NA 7. 01x 10 -23 (1 8k b) HLA -D Q B1| (5 7k b) HLA -DQ A2 rs 1049213 g 1. 82x 10 -11 1. 60x 10 -9 1. 08x 10 -3 NA NA NA 2. 30x 10 -21 HLA -DQ B1 rs 9275596 d 1. 04x 10 -7 6. 80x 10 -10 NA 2. 97x 10 -6 0. 08 e1 0. 12 f1 1. 15x 10 -21 (4 7k b) HLA -D Q B1| (2 8k b) HLA -DQ A2 rs 3134976 e 2. 15x 10 -10 8. 70x 10 -9 NA 1. 26x 10 -5 NA NA 6. 86x 10 -21 (1 8k b) HLA -DQ B1 |( 57 kb )H LA -DQ A2 rs 2858305 f 1. 95x 10 -5 3. 10x 10 -8 2. 72x 10 -4 8. 42x 10 -6 NA NA 2. 25x 10 -18 (3 6k b) HLA -DQ B1 |( 39 kb )H LA -DQ A2 rs 2858309 f 1. 95x 10 -5 2. 70x 10 -8 3. 61x 10 -4 8. 48x 10 -6 NA NA 2. 26x 10 -18 (3 4k b) HLA -DQ B1 |( 40 kb )H LA -DQ A2 rs 2856717 f 1. 95x 10 -5 3. 10x 10 -8 3. 28x 10 -4 8. 42x 10 -6 NA NA 2. 43x 10 -18 (3 6k b) HLA -DQ B1 |( 39 kb )H LA -DQ A2 rs 2858320 h 1. 49x 10 -5 4. 10x 10 -8 2. 28x 10 -3 4. 14x 10 -6 NA NA 2. 48x 10 -18 (2 7k b) HLA -DQ B1 |( 48 kb )H LA -DQ A2 rs 7192 d 6. 80x 10 -6 5. 50x 10 -8 NA 2. 16x 10 -5 6. 00x 10 -3 e2 0. 02 f2 1. 94x 10 -18 HLA -DR A rs 9275227 k 3. 18x 10 -4 3. 40x 10 -10 2. 06x 10 -2 5. 02x 10 -4 NA NA 1. 43x 10 -15 (2 6k b) HLA -DQ B1 |( 49 kb )H LA -DQ A2 rs 2858332 f 4. 91x 10 -5 1. 37x 10 -4 3. 48x 10 -4 9. 05x 10 -5 NA NA 2. 63x 10 -13 (4 7k b) HLA -DQ B1 |( 28 kb )H LA -DQ A2 rs 3129890 µ 0. 46 1. 65x 10 -3 NA 0. 55 NA NA 9. 73x 10 -3 (1 kb )H LA -DR A| (7 1k b) HLA -DR B5 rs 154975 f 0. 65 0. 74 1. 30x 10 -4 0. 32 0. 99 e3 0. 69 1 f3 0. 08 (2 9k b) LO C10029 4145 |( 2k b) HLA -D MB TA B LE E5 P A N EL B SN P B Food a lle rg y P - A m eri can h P - D ut ch Ca se -c on tr ol st udy i P - D ut ch Fa m ily st udy j P - G ERA k Pm eta F A l Pm eta F A (w ith ou t GE RA ) m rs 1063347 a 0. 04 NA NA 0. 95 8. 52x 10 -4 5. 07x 10 -14 rs 3134975 b 0. 02 NA NA 0. 82 2. 23x 10 -4 1. 12x 10 -15 rs 1049213 g 0. 07 NA NA 0. 90 0. 02 1. 26x 10 -10 rs 9275596 d 6. 15x 10 -3 0. 87 i1 0. 21 j1 0. 07 1. 33x 10 -6 6. 49x 10 -13 rs 3134976 e 0. 03 NA NA 0. 91 1. 14x 10 -3 2. 13x 10 -13 rs 2858305 f 0. 01 NA NA 0. 26 4. 72x 10 -5 2. 11x 10 -12 rs 2858309 f 0. 01 NA NA 0. 27 5. 06x 10 -5 2. 34x 10 -12 rs 2856717 f 0. 01 NA NA 0. 31 6. 95x 10 -5 2. 25x 10 -12 rs 2858320 h 1. 14x 10 -3 NA NA NA 8. 51x 10 -14 8. 51x 10 -14 rs 7192 d 0. 02 0. 47 i2 0. 04 j2 0. 01 9. 13x 10 -7 1. 30x 10 -9 rs 9275227 k 1. 37x 10 -3 NA NA NA 4. 62x 10 -10 4. 62x 10 -10 rs 2858332 f 0. 03 NA NA 0. 18 6. 37x 10 -5 1. 69x 10 -10 rs 3129890 µ 0. 61 NA NA 0. 19 0. 10 0. 29 rs 154975 f 0. 84 0. 72 i3 0. 44 j3 0. 34 0. 10 0. 07
