Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children

Xiumei Hong1,*, Ke Hao2,*, Christine Ladd-Acosta3,*, Kasper D. Hansen4,5, Hui-Ju Tsai6,7,8, Xin Liu6,9, Xin Xu10, Timothy A. Thornton11, Deanna Caruso1, Corinne A. Keet3,12, Yifei Sun4, Guoying Wang1, Wei Luo2,13, Rajesh Kumar14, Ramsay Fuleihan14, Anne Marie Singh15, Jennifer S. Kim14,16, Rachel E. Story14,17, Ruchi S. Gupta6, Peisong Gao18, Zhu Chen1, Sheila O. Walker1, Tami R. Bartell6, Terri H. Beaty3, M. Daniele Fallin19, Robert Schleimer20, Patrick G. Holt21, Kari Christine Nadeau22, Robert A. Wood12, Jacqueline A. Pongracic14, Daniel E. Weeks23 & Xiaobin Wang1,24

[1]  T. Spector,et al.  The Presence of Methylation Quantitative Trait Loci Indicates a Direct Genetic Influence on the Level of DNA Methylation in Adipose Tissue , 2013, PloS one.

[2]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[3]  D. Venkataraman,et al.  Filaggrin loss-of-function mutations are associated with food allergy in childhood and adolescence. , 2014, The Journal of allergy and clinical immunology.

[4]  Peter Kraft,et al.  Quality control and quality assurance in genotypic data for genome‐wide association studies , 2010, Genetic epidemiology.

[5]  Buhm Han,et al.  Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens , 2013, PloS one.

[6]  C. Greenwood,et al.  Filaggrin gene mutation associations with peanut allergy persist despite variations in peanut allergy diagnostic criteria or asthma status , 2013, The Journal of allergy and clinical immunology.

[7]  Christian Gieger,et al.  META-ANALYSIS OF GENOME-WIDE ASSOCIATION STUDIES IDENTIFIES THREE NEW RISK LOCI FOR ATOPIC DERMATITIS , 2011, Nature Genetics.

[8]  David A Holdford,et al.  Estimating the economic burden of food-induced allergic reactions and anaphylaxis in the United States. , 2011, The Journal of allergy and clinical immunology.

[9]  W. Shreffler,et al.  Lack of association of HLA class II alleles with peanut allergy. , 2006, Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology.

[10]  Andrew E. Jaffe,et al.  Bioinformatics Applications Note Gene Expression the Sva Package for Removing Batch Effects and Other Unwanted Variation in High-throughput Experiments , 2022 .

[11]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[12]  Carol Byrd-Bredbenner,et al.  Guidelines for the diagnosis and management of food allergy in the United States: report of the NIAID-sponsored expert panel. , 2010, The Journal of allergy and clinical immunology.

[13]  Ryan D. Hernandez,et al.  Meta-analysis of Genome-wide Association Studies of Asthma In Ethnically Diverse North American Populations , 2011, Nature Genetics.

[14]  R. Guigó,et al.  Transcriptome genetics using second generation sequencing in a Caucasian population , 2010, Nature.

[15]  Eric E Schadt,et al.  Disentangling molecular relationships with a causal inference test , 2009, BMC Genetics.

[16]  Yan Wang,et al.  Genome-wide association study identifies two new susceptibility loci for atopic dermatitis in the Chinese Han population , 2011, Nature Genetics.

[17]  S. Dreskin,et al.  Association of genetic variants of CD14 with peanut allergy and elevated IgE levels in peanut allergic individuals. , 2011, Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology.

[18]  Luigi Ferrucci,et al.  GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease. , 2014, American journal of human genetics.

[19]  Florence Demenais,et al.  A large-scale, consortium-based genomewide association study of asthma. , 2010, The New England journal of medicine.

[20]  O. Delaneau,et al.  Supplementary Information for ‘ Improved whole chromosome phasing for disease and population genetic studies ’ , 2012 .

[21]  T. Thornton,et al.  XM: Association Testing on the X‐Chromosome in Case‐Control Samples With Related Individuals , 2012, Genetic epidemiology.

[22]  Denise Daley,et al.  Genome-wide gene expression in a patient with 15q13.3 homozygous microdeletion syndrome , 2013, European Journal of Human Genetics.

[23]  C. Wijmenga,et al.  Loss-of-function variants in the filaggrin gene are a significant risk factor for peanut allergy , 2011, The Journal of allergy and clinical immunology.

[24]  S. Dreskin,et al.  Peanut-allergic subjects and their peanut-tolerant siblings have large differences in peanut-specific IgG that are independent of HLA class II. , 2010, Clinical immunology.

[25]  Martin J. Aryee,et al.  Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in Rheumatoid Arthritis , 2013, Nature Biotechnology.

[26]  Xiao Zhang,et al.  Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis , 2010, BMC Bioinformatics.

[27]  T. Thornton,et al.  Case-control association testing with related individuals: a more powerful quasi-likelihood score test. , 2007, American journal of human genetics.

[28]  Scott H Sicherer,et al.  Clinical reviews in allergy and immunology , 2022 .

[29]  A. Cummings,et al.  The psychosocial impact of food allergy and food hypersensitivity in children, adolescents and their families: a review , 2010, Allergy.

[30]  D. Ikle,et al.  Comparative performance of five commercial prick skin test devices. , 1993, The Journal of allergy and clinical immunology.

[31]  Yusuke Nakamura,et al.  Genome-wide association study identifies eight new susceptibility loci for atopic dermatitis in the Japanese population , 2012, Nature Genetics.

[32]  Yusuke Nakamura,et al.  Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population , 2011, Nature Genetics.

[33]  M. Stephens,et al.  High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation , 2008, PLoS genetics.

[34]  M. Rescigno Dendritic cells in oral tolerance in the gut , 2011, Cellular microbiology.

[35]  S. Sicherer,et al.  Development of a questionnaire to measure quality of life in families with a child with food allergy. , 2004, The Journal of allergy and clinical immunology.

[36]  U. Şahin,et al.  Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices , 1999, Nature Biotechnology.

[37]  David Martino,et al.  Epigenome-wide association study reveals longitudinally stable DNA methylation differences in CD4+ T cells from children with IgE-mediated food allergy , 2014, Epigenetics.

[38]  D. Reich,et al.  Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.

[39]  Xiumei Hong,et al.  Early life precursors, epigenetics, and the development of food allergy , 2012, Seminars in Immunopathology.

[40]  B. Gelb,et al.  Genetics of peanut allergy: a twin study. , 2000, The Journal of allergy and clinical immunology.

[41]  R. Irizarry,et al.  Accounting for cellular heterogeneity is critical in epigenome-wide association studies , 2014, Genome Biology.

[42]  Chuong B. Do,et al.  A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci , 2013, Nature Genetics.

[43]  Rafael A. Irizarry,et al.  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays , 2014, Bioinform..

[44]  P. Donnelly,et al.  A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies , 2009, PLoS genetics.

[45]  G. Wang,et al.  IgE, but not IgG4, antibodies to Ara h 2 distinguish peanut allergy from asymptomatic peanut sensitization , 2012, Allergy.

[46]  David M. Simcha,et al.  Tackling the widespread and critical impact of batch effects in high-throughput data , 2010, Nature Reviews Genetics.

[47]  Bin Zhang,et al.  A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. , 2011, Genome research.

[48]  David Levine,et al.  GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies , 2012, Bioinform..

[49]  D. Balding,et al.  Epigenome-wide association studies for common human diseases , 2011, Nature Reviews Genetics.

[50]  J. Kere,et al.  Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility , 2012, PloS one.

[51]  S. Turner,et al.  HLA class II DRB1, DQB1 and DPB1 genotypic associations with peanut allergy: evidence from a family‐based and case‐control study , 1998, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[52]  Alexander T. Dilthey,et al.  HLA*IMP - an integrated framework for imputing classical HLA alleles from SNP genotypes , 2011, Bioinform..

[53]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

[54]  Böhm,et al.  Identification of HLA‐DR and ‐DQ alleles conferring susceptibility to pollen allergy and pollen associated food allergy , 1998, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[55]  A. Fanous,et al.  Molecular validation of the schizophrenia spectrum. , 2014, Schizophrenia bulletin.

[56]  B. Baldo,et al.  A family study of allergy: segregation with HLA but not with T-cell receptor genes. , 1996, The Journal of allergy and clinical immunology.

[57]  Ruchi Gupta,et al.  The economic impact of childhood food allergy in the United States. , 2013, JAMA pediatrics.

[58]  Kari Stefansson,et al.  Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization , 2013, Nature Genetics.

[59]  Devin C. Koestler,et al.  DNA methylation arrays as surrogate measures of cell mixture distribution , 2012, BMC Bioinformatics.

[60]  Egidio Barbi,et al.  IgE-mediated food allergy in children , 2013, The Lancet.

[61]  W. Ollier,et al.  Polymorphism in the STAT6 gene encodes risk for nut allergy , 2002, Genes and Immunity.

[62]  H. Tsai,et al.  Familial aggregation of food allergy and sensitization to food allergens: a family‐based study , 2009, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[63]  A. Delvig,et al.  Diversity in MHC class II antigen presentation , 2002, Immunology.