Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus

[1]  Scott R. Presnell,et al.  Endotype of Allergic Asthma with Airway Obstruction in Urban Children. , 2021, The Journal of allergy and clinical immunology.

[2]  D. Nicolae,et al.  Chromosome 17q12-21 Variants are Associated with Multiple Wheezing Phenotypes in Childhood. , 2021, American journal of respiratory and critical care medicine.

[3]  D. Nicolae,et al.  Altered transcriptional and chromatin responses to rhinovirus in bronchial epithelial cells from adults with asthma , 2020, Communications Biology.

[4]  E. Burchard,et al.  A genome-wide association study of severe asthma exacerbations in Latino children and adolescents , 2020, European Respiratory Journal.

[5]  E. Silverman,et al.  Sex-specific associations with DNA methylation in lung tissue demonstrate smoking interactions , 2020, Epigenetics.

[6]  R. Krishnan,et al.  Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma , 2020, Genome Medicine.

[7]  S. Sørensen,et al.  Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age. , 2020, The Journal of allergy and clinical immunology.

[8]  Brent F. Olson,et al.  Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic association and gene expression study. , 2020, The Lancet. Respiratory medicine.

[9]  G. Canino,et al.  Expression quantitative trait methylation analysis reveals methylomic associations with gene expression in childhood asthma , 2020, bioRxiv.

[10]  Bjarni V. Halldórsson,et al.  Eighty-eight variants highlight the role of T cell regulation and airway remodeling in asthma pathogenesis , 2020, Nature Communications.

[11]  Ivana V. Yang,et al.  Nasal DNA methylation profiling of asthma and rhinitis. , 2020, The Journal of allergy and clinical immunology.

[12]  G. Canino,et al.  SNPs identified by GWAS affect asthma risk through DNA methylation and expression of cis-genes in airway epithelium , 2019, European Respiratory Journal.

[13]  Christopher D. Brown,et al.  The GTEx Consortium atlas of genetic regulatory effects across human tissues , 2019, Science.

[14]  L. Liang,et al.  The nasal methylome as a biomarker of asthma and airway inflammation in children , 2019, Nature Communications.

[15]  C. Pariante,et al.  Glucocorticoid Exposure During Hippocampal Neurogenesis Primes Future Stress Response by Inducing Changes in DNA Methylation: Glucocorticoids induce DNAm changes during neurogenesis , 2019 .

[16]  D. Nicolae,et al.  Shared and distinct genetic risk factors for childhood-onset and adult-onset asthma: genome-wide and transcriptome-wide studies. , 2019, The Lancet. Respiratory medicine.

[17]  D. Weeks,et al.  DNA methylation in nasal epithelium, atopy, and atopic asthma in children: a genome-wide study. , 2019, The Lancet. Respiratory medicine.

[18]  Manuel A. R. Ferreira,et al.  Genetic Architectures of Childhood- and Adult-Onset Asthma Are Partly Distinct. , 2019, American journal of human genetics.

[19]  Matthew C. Altman,et al.  Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus , 2019, Genome Medicine.

[20]  Yan V. Sun,et al.  Novel DNA methylation sites associated with cigarette smoking among African Americans , 2019, Epigenetics.

[21]  E. Birney,et al.  GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals , 2019, Nature Genetics.

[22]  Timothy J. Hohman,et al.  Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk , 2019, Nature Genetics.

[23]  L. Wain,et al.  Moderate-to-severe asthma in individuals of European ancestry: a genome-wide association study , 2019, The Lancet. Respiratory medicine.

[24]  David A. Knowles,et al.  Landscape of stimulation-responsive chromatin across diverse human immune cells , 2018, Nature Genetics.

[25]  Tanya M. Teslovich,et al.  Biobank-driven genomic discovery yields new insight into atrial fibrillation biology , 2018, Nature Genetics.

[26]  G. Koppelman,et al.  Nasal epithelium as a proxy for bronchial epithelium for smoking-induced gene expression and expression Quantitative Trait Loci. , 2018, The Journal of allergy and clinical immunology.

[27]  A. Chen-Plotkin,et al.  The Post-GWAS Era: From Association to Function. , 2018, American journal of human genetics.

[28]  Girija Syamlal,et al.  Prevalence of Asthma, Asthma Attacks, and Emergency Department Visits for Asthma Among Working Adults — National Health Interview Survey, 2011–2016 , 2018, MMWR. Morbidity and mortality weekly report.

[29]  Cathy M. Bailey,et al.  Vital Signs: Asthma in Children — United States, 2001–2016 , 2018, MMWR. Morbidity and mortality weekly report.

[30]  W. Busse.  The atopic march: Fact or folklore? , 2018, Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology.

[31]  D. Nicolae,et al.  A decade of research on the 17q12-21 asthma locus: Piecing together the puzzle , 2018, The Journal of allergy and clinical immunology.

[32]  Manuel A. R. Ferreira,et al.  Multiancestry association study identifies new asthma risk loci that colocalize with immune cell enhancer marks , 2017, Nature Genetics.

[33]  Ian J. Deary,et al.  Association analysis in over 329,000 individuals identifies 116 independent variants influencing neuroticism , 2017, Nature Genetics.

[34]  Manuel A. R. Ferreira,et al.  Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology , 2017, Nature Genetics.

[35]  Nicola J. Rinaldi,et al.  Genetic effects on gene expression across human tissues , 2017, Nature.

[36]  Wen Zhang,et al.  A Bayesian Framework for Multiple Trait Colocalization from Summary Association Statistics , 2017, bioRxiv.

[37]  S. Ziegler,et al.  The atopic march: current insights into skin barrier dysfunction and epithelial cell‐derived cytokines , 2017, Immunological reviews.

[38]  Wei Wu,et al.  Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease , 2017, American journal of respiratory and critical care medicine.

[39]  Brent S. Pedersen,et al.  The nasal methylome and childhood atopic asthma , 2017, The Journal of allergy and clinical immunology.

[40]  Joseph K. Pickrell,et al.  Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations , 2017, bioRxiv.

[41]  Agnes S. Sundaresan,et al.  Nasal and sinus symptoms and chronic rhinosinusitis in a population‐based sample , 2017, Allergy.

[42]  M. Stephens,et al.  Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions , 2016, Nature Genetics.

[43]  Yoav Gilad,et al.  DNA methylation in lung cells is associated with asthma endotypes and genetic risk. , 2016, JCI insight.

[44]  X. Wen,et al.  Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization , 2016, bioRxiv.

[45]  S. Greenberg.  Update on Human Rhinovirus and Coronavirus Infections , 2016, Seminars in Respiratory and Critical Care Medicine.

[46]  M. Ege,et al.  The Early Development of Wheeze. Environmental Determinants and Genetic Susceptibility at 17q21. , 2016, American journal of respiratory and critical care medicine.

[47]  K. Bønnelykke,et al.  Leveraging gene-environment interactions and endotypes for asthma gene discovery. , 2016, The Journal of allergy and clinical immunology.

[48]  C. Ober.  Asthma Genetics in the Post-GWAS Era. , 2016, Annals of the American Thoracic Society.

[49]  D. Nicolae,et al.  Genome-Wide Methylation Study Identifies an IL-13-induced Epigenetic Signature in Asthmatic Airways. , 2016, American journal of respiratory and critical care medicine.

[50]  M. Obeidat,et al.  Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases. , 2016, American journal of respiratory cell and molecular biology.

[51]  Matthew Stephens,et al.  False discovery rates: a new deal , 2016, bioRxiv.

[52]  W. Busse,et al.  eQTL of bronchial epithelial cells and bronchial alveolar lavage deciphers GWAS‐identified asthma genes , 2015, Allergy.

[53]  Yakir A Reshef,et al.  Partitioning heritability by functional annotation using genome-wide association summary statistics , 2015, Nature Genetics.

[54]  Alexander Dobin,et al.  Mapping RNA‐seq Reads with STAR , 2015, Current protocols in bioinformatics.

[55]  Emmanouil T. Dermitzakis,et al.  Fast and efficient QTL mapper for thousands of molecular phenotypes , 2015, bioRxiv.

[56]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[57]  Timothy J. Peters,et al.  De novo identification of differentially methylated regions in the human genome , 2015, Epigenetics & Chromatin.

[58]  Peter L Molloy,et al.  De novo identification of differentially methylated regions in the human genome , 2015, Epigenetics & Chromatin.

[59]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[60]  Christopher F. Baum,et al.  IVREG2: Stata module for extended instrumental variables/2SLS and GMM estimation , 2015 .

[61]  J. Denburg,et al.  Thymic stromal lymphopoietin (TSLP) secretion from human nasal epithelium is a function of TSLP genotype , 2014, Mucosal Immunology.

[62]  Ivana V. Yang,et al.  An Epigenome-Wide Association Study of Total Serum Immunoglobulin E Concentration , 2014, Nature.

[63]  Ross M. Fraser,et al.  Defining the role of common variation in the genomic and biological architecture of adult human height , 2014, Nature Genetics.

[64]  John D. Blischak,et al.  Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels , 2014, bioRxiv.

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

[66]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[67]  Y. Luo,et al.  Promoter demethylation contributes to TSLP overexpression in skin lesions of patients with atopic dermatitis , 2014, Clinical and experimental dermatology.

[68]  C. Wallace,et al.  Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics , 2013, PLoS genetics.

[69]  E. Chuang,et al.  Prenatal smoke exposure, DNA methylation, and childhood atopic dermatitis , 2013, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[70]  Hans Bisgaard,et al.  Rhinovirus wheezing illness and genetic risk of childhood-onset asthma. , 2013, The New England journal of medicine.

[71]  André Aleman,et al.  The biological and psychological basis of neuroticism: Current status and future directions , 2013, Neuroscience & Biobehavioral Reviews.

[72]  J. Greenbaum,et al.  Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data , 2013, PloS one.

[73]  W. Leonard,et al.  TSLP: A Key Regulator of Asthma Pathogenesis. , 2012, Drug discovery today. Disease mechanisms.

[74]  G. Abecasis,et al.  Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. , 2012, American journal of human genetics.

[75]  David C. Nickle,et al.  Lung eQTLs to Help Reveal the Molecular Underpinnings of Asthma , 2012, PLoS genetics.

[76]  Shane J. Neph,et al.  Systematic Localization of Common Disease-Associated Variation in Regulatory DNA , 2012, Science.

[77]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[78]  A. Oshlack,et al.  SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips , 2012, Genome Biology.

[79]  H. Goossens,et al.  EPOS 2012: European position paper on rhinosinusitis and nasal polyps 2012. A summary for otorhinolaryngologists. , 2012, Rhinology.

[80]  H. Goossens,et al.  EPOS 2012: European position paper on rhinosinusitis and nasal polyps 2012. A summary for otorhinolaryngologists , 2012, Rhinology journal.

[81]  John C. Marioni,et al.  Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection , 2012, Proceedings of the National Academy of Sciences.

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

[83]  J. Marchini,et al.  Genotype Imputation with Thousands of Genomes , 2011, G3: Genes | Genomes | Genetics.

[84]  S. Greenberg,et al.  Update on Rhinovirus and Coronavirus Infections , 2011, Seminars in respiratory and critical care medicine.

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

[86]  P. Mattila,et al.  Allergy as an epithelial barrier disease , 2011, Clinical and translational allergy.

[87]  R. Depue,et al.  Neurogenetic and experiential processes underlying major personality traits: Implications for modelling personality disorders , 2011, International review of psychiatry.

[88]  D. Reich,et al.  Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays , 2011, Genetic epidemiology.

[89]  George Davey Smith,et al.  Mendelian Randomization for Strengthening Causal Inference in Observational Studies , 2010, Perspectives on psychological science : a journal of the Association for Psychological Science.

[90]  N. Cox,et al.  Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS , 2010, PLoS genetics.

[91]  I. Heijink,et al.  Epidermal growth factor receptor signalling contributes to house dust mite-induced epithelial barrier dysfunction , 2010, European Respiratory Journal.

[92]  F Kauffmann,et al.  17q21 variants modify the association between early respiratory infections and asthma , 2009, European Respiratory Journal.

[93]  T. Stürmer,et al.  Neuroticism, extraversion, stressful life events and asthma: a cohort study of middle‐aged adults , 2009, Allergy.

[94]  J. Bousquet,et al.  Effect of 17q21 variants and smoking exposure in early-onset asthma. , 2008, The New England journal of medicine.

[95]  M. McCarthy,et al.  Genome-wide association studies: potential next steps on a genetic journey. , 2008, Human molecular genetics.

[96]  F. Perera,et al.  Combined inhaled diesel exhaust particles and allergen exposure alter methylation of T helper genes and IgE production in vivo. , 2008, Toxicological sciences : an official journal of the Society of Toxicology.

[97]  Gonçalo R. Abecasis,et al.  Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma , 2007, Nature.

[98]  D. Robinson,et al.  Thymic Stromal Lymphopoietin Expression Is Increased in Asthmatic Airways and Correlates with Expression of Th2-Attracting Chemokines and Disease Severity1 , 2005, The Journal of Immunology.

[99]  S. Johnston,et al.  Asthmatic bronchial epithelial cells have a deficient innate immune response to infection with rhinovirus , 2005, The Journal of experimental medicine.

[100]  J. Kaprio,et al.  Asthma in relation to personality traits, life satisfaction, and stress: a prospective study among 11 000 adults , 2001, Allergy.

[101]  S. Mostafavi,et al.  Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation , 2017, The Journal of allergy and clinical immunology.

[102]  Alberto Maffey,et al.  [Rhinovirus wheezing illness and genetic risk of childhood-onset asthma]. , 2013, Archivos argentinos de pediatria.

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

[104]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[105]  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 .