EGAGenomicsMultiomicsEoin McKinneyhttps://ega-archive.org/dacs/EGAC00001000338EGAEGA DAC EGAC00001000338EGAefm30@cam.ac.ukGenome-wide association studies (GWAS) have transformed our understanding of the genetics of complex traits such as autoimmune diseases, but how risk variants contribute to pathogenesis remains largely unknown. Identifying genetic variants that affect gene expression (expression quantitative trait loci, or eQTLs) is crucial to addressing this. eQTLs vary between tissues and following in vitro cellular activation, but have not been examined in the context of human inflammatory diseases. We performed eQTL mapping in five primary immune cell types from patients with active inflammatory bowel disease (n = 91), anti-neutrophil cytoplasmic antibody-associated vasculitis (n = 46) and healthy controls (n = 43), revealing eQTLs present only in the context of active inflammatory disease. Moreover, we show that following treatment a proportion of these eQTLs disappear. Through joint analysis of expression data from multiple cell types, we reveal that previous estimates of eQTL immune cell-type specificity are likely to have been exaggerated. Finally, by analysing gene expression data from multiple cell types, we find eQTLs not previously identified by database mining at 34 inflammatory bowel disease-associated loci. In summary, this parallel eQTL analysis in multiple leucocyte subsets from patients with active disease provides new insights into the genetic basis of immune-mediated diseases.Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease.Peters James E JE, Lyons Paul A PA, Lee James C JC, Richard Arianne C AC, Fortune Mary D MD, Newcombe Paul J PJ, Richardson Sylvia S, Smith Kenneth G C KGIndividual Health, other disease, dTAF[[II]]230, TAF[[II]]250, d230, disorders, TAF200, l(3)84Ab, dTAFII250, BG:DS00004.13, Normalcy, TAFII-250, TAF250/230, EfW1, Normalcies, Cell, dTAF230, dmTAF[[II]]230, TAFII250, Genogroup, diseases, dmTAF1, Taf230, Associations, p230, Diseases, TAF[[II]]250/230, disease or disorder, TFIID, condition, diseases and disorders, Individual, TAF250, Normalities, Taf[[II]]250, average, Taf200, human disease, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, Normality, cell, Taf1p, TAF[II]250, CG17603, TAF[[II]], Genotypes, non-neoplastic, Phenotypes, dTAF250, Genogroups, disease, Health, DmelCG17603, Taf250, SR3-5, disorder, Homo sapiens disease, medical condition., TAF, TAF230, TAF1Autoimmunity, Normalities, average, Individual Health, Autoimmune disorder, Disease, leucocyte, immune cell, Autoimmune disease, Normality, Autoimmune Disease, PMNC, PMN cell, Normalcy, autoimmune hypersensitivity disease, white blood cell, Health, Diseases, hypersensitivity reaction type II disease, autoimmunity, Individual, Autoimmune, Autoimmune condition, polymorphonuclear cell, Normalcies.Genome-Wide Association, ANCA-Associated Vasculitide, MGC130048, joints, Unspecified disorder of immune mechanism, determination, Whole Genome Association Study, positive regulation by symbiont of host non-apoptotic programmed cell death, A4, Quantitative, Other specified disorders of the immune mechanism (disorder), Relative, dmTAF[[II]]230, Readability, unspecified, Other specified disorders involving the immune mechanism, diseases, anatomical structure inflammation, Joint, Inflammatory bowel disease, pathogenesis, AW048865, diseases and disorders, AAV, Autoimmune, treatment, gamma sarcoglycan, GWA Study, DEFIC CELL IMMUNITY NOS, human disease, Deficiency of cell-mediated immunity, Gene Expressions, Man (Taxonomy), Autoimmune disease, stimulation by symbiont of host programmed cell death, TFIID TAF250, IBD, cel, proportionality to, Moods, [X]Disorder involving the immune mechanism, Tissue, Vasculitide, Immune System and Related Disorders, PMNC, Genome-Wide Association Studies, genetic, Inflammatory Bowel Diseases, inflammatory disease, disease management, Therapies, gamma-sarcoglycan, Homo sapiens disease, associated, Therapy, joint, dTAF[[II]]230, ANCA-Associated Vasculitides, Modern, familial, SG-gamma, TAF200, PMN cell, TAFII-250, TAF250/230, Genome-Wide, Quantitative Trait, TAFII250, Immunodeficiency and Immunosuppression Disorders, Genome Wide Association Study, Quantitative Trait Locus, Relative Risks, Diseases, modulation by symbiont of host system process, sarcoglycan, Whole Genome Association Analysis, ANCA Associated Vasculitis, activation, immune system disorder, Risk, Pauci-Immune Vasculitides, proportionality, rate, CG17603, gamma (35kDa dystrophin-associated glycoprotein), TAF[[II]], Treatments, human, immune dysfunction, disease, white blood cell, DMDA, Patient, Taf250, Festa, SR3-5, 35kD dystrophin-associated glycoprotein, activation by symbiont of host programmed cell death, autoimmune bowel disorder, medical condition., inherited genetic, Association Study, inflammation of anatomical structure, IMMUNE MECHANISM DIS NEC, TAF230, polymorphonuclear cell, antineutrophil cytoplasmic antibody-associated vasculitis, Disorder of the immune mechanism NOS, other disease, Pauci Immune Vasculitis, d230, human being, SGCG_HUMAN, FESTA-L, FESTA-S, Genome Wide Association Analysis, regulation by symbiont of host system process, AUTOIMMUNE DISEASE NEC, Autoimmune Disease, Gene, dTAFII250, Trait Loci, Inflammatory Bowel Disease, EfW1, TYPE, unspecified (disorder), Human, DAGA4, GWA Studies, Homo sapiens, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, dmTAF1, Taf230, heredity, Pauci-Immune, inflammatory bowel disease, 35DAG, Studies, disease or disorder, IMMUNE MECHANISM DIS NOS, Mood, MAM, gamma-SG, SCG3, Man, U19, TAF250, BM040, proportion, Taf200, Other deficiency of cell-mediated immunity, dTAF[[II]]250, ANCA Associated Vasculitides, cell, Disorders involving the immune mechanism, GWA, Pauci-Immune Vasculitis, Vasculitis, Trait Locus, Taf1p, causes, immune disorder, Expressions, Genome Wide Association Scan, non-neoplastic, Study, dTAF250, Clients, Loci, causality, articular joint, disorder, Expression, Quantitative Trait Loci Genes, Inflammatory, TAF, constitutitional genetic, Disease, TAF[[II]]250, activation by organism of non-apoptotic programmed cell death in other organism, immune cell, Bowel Diseases, hemolysin activity, Anti Neutrophil Cytoplasmic Antibody Associated Vasculitis, 35 kDa dystrophin-associated glycoprotein, Traits, not elsewhere classified, Affects, ANCA-associated vasculitis, disorders, l(3)84Ab, medical condition, BG:DS00004.13, Client, Cell, SGCG, disease or disorder of immune system, LGMD2C, dTAF230, p230, chemical analysis, TAF[[II]]250/230, condition, TFIID, Disorder of the immune mechanism NOS (disorder), Data Base, Relative Risk, immune system disease or disorder, Taf[[II]]250, inflammatory disorder, leucocyte, articulation, TAF[[II]]230, DMDA1, IMMUNDEF T-CELL DEF NOS, ANCA-Associated, Risks, INFLAMM BOWEL DIS, TAF[II]250, Understanding, disease of immune system, ANCA-Associated Vasculitis, TRAITS, Locus, disorder of immune system, Genome Wide Association Studies, autoimmune diseases, immune disease, DmelCG17603, Therapeutic, Modern Man, SCARMD2, quotient, Association Studies, Other specified disorders of the immune mechanism, Vasculitides, Treatment, assay, hereditary, Immunodeficiency with predominant T-cell defect, TAF1falseLeucocyte eQTLs in autoimmune disease and healthData Access Committee EGAC00001000338EGAC00001000338960627015630EGAS00001001251EGAD00010000748