{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001000574"],"host":["EGA"],"description":["EGA study EGAS00001000574"],"dataset_title":["Sardinia FACS pilot project"],"repository":["EGA"],"category":["restricted"],"pubmed_abstract":["The complex network of specialized cells and molecules in the immune system has evolved to defend against pathogens, but inadvertent immune system attacks on \"self\" result in autoimmune disease. Both genetic regulation of immune cell levels and their relationships with autoimmunity are largely undetermined. Here, we report genetic contributions to quantitative levels of 95 cell types encompassing 272 immune traits, in a cohort of 1,629 individuals from four clustered Sardinian villages. We first estimated trait heritability, showing that it can be substantial, accounting for up to 87% of the variance (mean 41%). Next, by assessing ∼8.2 million variants that we identified and confirmed in an extended set of 2,870 individuals, 23 independent variants at 13 loci associated with at least one trait. Notably, variants at three loci (HLA, IL2RA, and SH2B3/ATXN2) overlap with known autoimmune disease associations. These results connect specific cellular phenotypes to specific genetic variants, helping to explicate their involvement in disease."],"pubmed_title":["Genetic variants regulating immune cell levels in health and disease."],"pubmed_authors":["Orrù Valeria V, Steri Maristella M, Sole Gabriella G, Sidore Carlo C, Virdis Francesca F, Dei Mariano M, Lai Sandra S, Zoledziewska Magdalena M, Busonero Fabio F, Mulas Antonella A, Floris Matteo M, Mentzen Wieslawa I WI, Urru Silvana A M SA, Olla Stefania S, Marongiu Michele M, Piras Maria G MG, Lobina Monia M, Maschio Andrea A, Pitzalis Maristella M, Urru Maria F MF, Marcelli Marco M, Cusano Roberto R, Deidda Francesca F, Serra Valentina V, Oppo Manuela M, Pilu Rosella R, Reinier Frederic F, Berutti Riccardo R, Pireddu Luca L, Zara Ilenia I, Porcu Eleonora E, Kwong Alan A, Brennan Christine C, Tarrier Brendan B, Lyons Robert R, Kang Hyun M HM, Uzzau Sergio S, Atzeni Rossano R, Valentini Maria M, Firinu Davide D, Leoni Lidia L, Rotta Gianluca G, Naitza Silvia S, Angius Andrea A, Angius Andrea A, Congia Mauro M, Whalen Michael B MB, Jones Chris M CM, Schlessinger David D, Abecasis Gonçalo R GR, Fiorillo Edoardo E, Sanna Serena S, Cucca Francesco F"],"name_synonyms":["Dissections, other disease, human disease, leucocyte, human being, Man (Taxonomy), immune cell, Modern, familial, disorders, PMNC, PMN cell, primary structure of sequence macromolecule, human, genetic, Human, non-neoplastic, white blood cell, disease, Homo sapiens, diseases, Modern Man, Diseases, sequence, disease or disorder, condition, disorder, diseases and disorders, Homo sapiens disease, medical condition., inherited genetic, constitutitional genetic, hereditary, Man, polymorphonuclear cell"],"description_synonyms":["extent, Autoimmune Responses, d230, Unspecified disorder of immune mechanism, Immune Systems, determination, FESTA-L, FESTA-S, AUTOIMMUNE DISEASE NEC, Autoimmunities, Autoimmune Disease, number, dTAFII250, EfW1, presence, unspecified (disorder), Other specified disorders of the immune mechanism (disorder), dmTAF[[II]]230, unspecified, Other specified disorders involving the immune mechanism, dmTAF1, Taf230, IMMUNE MECHANISM DIS NOS, AW048865, autoimmunity, Low, Autoimmune, U19, Autoimmune condition, TAF250, DEFIC CELL IMMUNITY NOS, Autoimmune Response, Taf200, BM040, Other deficiency of cell-mediated immunity, me75, Complete, Whole Genome, dTAF[[II]]250, Deficiency of cell-mediated immunity, Autoimmune disease, TFIID TAF250, cel, cell, Disorders involving the immune mechanism, [X]Disorder involving the immune mechanism, Tissue, Complete Genome Sequencing, Immune System and Related Disorders, study., Taf1p, clumped, immune disorder, D17Mit170, T1, Sequencing, genetic, dTAF250, Sardinia, Immune, clustered, Whole, high density, TAF, constitutitional genetic, single-organism behavior, Autoimmunity, Autoimmune disorder, Disease, dTAF[[II]]230, TAF[[II]]250, cou, completeness, not elsewhere classified, Traits, familial, Genome Sequencing, TAF200, l(3)84Ab, BG:DS00004.13, TAFII-250, Tl3, TAF250/230, Tl2, Cell, disease or disorder of immune system, dTAF230, count in organism, TAFII250, Immunodeficiency and Immunosuppression Disorders, Lr, Complete Genome, p230, Systems, chemical analysis, Diseases, TAF[[II]]250/230, TFIID, Disorder of the immune mechanism NOS (disorder), immune system disease or disorder, Taf[[II]]250, immune system disorder, TAF[[II]]230, IMMUNDEF T-CELL DEF NOS, System, TAF[II]250, disease of immune system, CG17603, TAF[[II]], TRAITS, disorder of immune system, autoimmune diseases, immune dysfunction, immune disease, DmelCG17603, Taf250, SR3-5, Festa, Bra, Other specified disorders of the immune mechanism, inherited genetic, assay, IMMUNE MECHANISM DIS NEC, hereditary, TAF230, Immunodeficiency with predominant T-cell defect, Disorder of the immune mechanism NOS, TAF1"],"pubmed_title_synonyms":["Normalities, average, Individual Health, other disease, human disease, leucocyte, immune cell, Normality, familial, disorders, PMNC, PMN cell, Normalcy, Normalcies, genetic, non-neoplastic, white blood cell, disease, Health, diseases, Diseases, disease or disorder, condition, disorder, diseases and disorders, Homo sapiens disease, medical condition., inherited genetic, Individual, constitutitional genetic, hereditary, polymorphonuclear cell"],"pubmed_abstract_synonyms":["Autoimmune Responses, Regulations, other disease, IPP2A2, d230, IL-2 receptor subunit alpha, Immune Systems, Lnk, LNK, FESTA-L, FESTA-S, IL-2R subunit alpha, Autoimmunities, Autoimmune Disease, number, p55, dTAFII250, Progress Reports, autoimmune hypersensitivity disease, EfW1, presence, Social Controls, PHAPII, 5730420M11Rik, Il2r, dmTAF[[II]]230, Investigative, diseases, dmTAF1, Taf230, Summary Report, Associations, hypersensitivity reaction type II disease, disease or disorder, AW048865, diseases and disorders, autoimmunity, Autoimmune, Formal Social Controls, Summary Reports, Trait, TCGFR, U19, Autoimmune condition, TAF250, TAC antigen, Autoimmune Response, SET, Taf200, BM040, TNRC13, human disease, ASL13, Sca2, dTAF[[II]]250, SCA2, Autoimmune disease, TFIID TAF250, Progress Report, cel, TAF-I, cell, Accountings, ipp2a2, IDDM20, ATX2, 2pp2a, Taf1p, clumped, PMNC, Estimated, CG10574, genetic, Social, DmelCG4299, non-neoplastic, Progress, dTAF250, IGAAD, set, Immune, Field Reports, clustered, 2PP2A, DmelCG10574, taf-ibeta, dSET, dSet, disorder, IDDM10, Homo sapiens disease, Investigative Reports, TAF, constitutitional genetic, CD25, Autoimmunity, phapii, Autoimmune disorder, Disease, dTAF[[II]]230, TAF[[II]]250, immune cell, PLATEST, Formal Social Control, Traits, familial, igaad, disorders, TAF200, StF-IT-1, l(3)84Ab, IL2-RA, BG:DS00004.13, PMN cell, TAFII-250, TAF250/230, Cell, results, group, dTAF230, count in organism, TAFII250, Investigative Report, 9630045M23Rik, Social Control, I-2PP2A, p230, Systems, Research Reports, Dm I-2, Diseases, I2PP2A, TAF[[II]]250/230, TFIID, condition, AW544490, Taf[[II]]250, leucocyte, TAF[[II]]230, HLA-DR-associated protein II, ensemble, DI-2, System, I-2Dm, Field, Control, TAF[II]250, CG4299, Controls, CG17603, TAF[[II]], TRAITS, I-2PP1, IL2R, Phenotypes, white blood cell, dSET/TAF-Ibeta, disease, Report, 2610030F17Rik, DmelCG17603, TAF-IBETA, Reports, Taf250, SR3-5, Festa, medical condition., inherited genetic, regulation, TAF-Ibeta, IL2RA, Summary, AA407739, Ly-43, hereditary, Regulation, i2pp2a, Platelets, IL-2-RA, Field Report, TAF230, polymorphonuclear cell, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"A sequence-based genetic dissection of human immune cell types and implications for immune-related disease.","description":"The immune system is an intricate biological network mediating interactions with other organisms while preserving the integrity of our tissues. By mounting appropriate responses it protects us from a vast range of pathogens while inadvertent immune system attacks on self result in autoimmune diseases. The project aims to discover whether and to what extent the behaviour of the immune system is genetically regulated and to detect the relationships of diverse immune cells with autoimmunity. The project consists of the genetic analysis using up to ~8.2 Million variants, deriving from high density genotyping data and low pass whole genome sequencing, and quantitative levels of 95 cell types encompassing 272 immune traits, in a cohort of 1,629 individuals from four clustered Sardinian villages belonging to the SardiNIA/ProgeNIA study.","dates":{"updated":"2017-08-14 17:49:26"},"accession":"EGAS00001000574","cross_references":{"TAXONOMY":["9606"],"pubmed":["24074872"],"EGA":["EGAD00001000656","EGAC00001000132"]}}