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The immune system is highly diverse, but characterization of its genetic architecture has lagged behind the vast progress made by genome-wide association studies (GWASs) of emergent diseases. Our GWAS for 54 functionally relevant phenotypes of the adaptive immune system in 489 healthy individuals identifies eight genome-wide significant associations explaining 6%-20% of variance. Coding and splicing variants in PTPRC and COMMD10 are involved in memory T cell differentiation. Genetic variation controlling disease-relevant T helper cell subsets includes RICTOR and STON2 associated with Th2 and Th17, respectively, and the interferon-lambda locus controlling regulatory T cell proliferation. Early and memory B cell differentiation stages are associated with variation in LARP1B and SP4. Finally, the latrophilin family member ADGRL2 correlates with baseline pro-inflammatory interleukin-6 levels. Suggestive associations reveal mechanisms of autoimmune disease associations, in particular related to pro-inflammatory cytokine production. Pinpointing these key human immune regulators offers attractive therapeutic perspectives.
Pubmed ID: 30332657
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Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.
View all literature mentionsAn international leader in genetics, genomics and structural biology, and research institute of the Nuffield Department of Medicine at the University of Oxford, whose objective is to extend our understanding on how genetic inheritance makes us who we are in order to gain a clearer insight into mechanisms of health and disease. Looking across all three billion letters of the human genetic code, they aim to pinpoint variant spellings and discover how they increase or decrease an individual's risk of falling ill. They collaborate with research teams across the world on a number of large-scale studies in these areas.
View all literature mentionsHaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.
View all literature mentionsCommercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
View all literature mentionsSoftware application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software)
View all literature mentionsSoftware program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software)
View all literature mentionsA computer program for phasing observed genotypes and imputing missing genotypes.
View all literature mentionsFramework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.
View all literature mentionsCollection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.
View all literature mentionsSoftware for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.
View all literature mentionsAn Organization portal, Antibody supplier, Service resource,
View all literature mentionsSoftware application designed to facilitate viewing of local association results together with useful information about a locus, such as the location and orientation of the genes it includes, linkage disequilibrium coefficients and local estimates of recombination rates. It was developed by popular demand, as a result of many questions we have had about How did you make the figures in your talk? or How did you make the figures for your GWAS paper? (entry from Genetic Analysis Software)
View all literature mentionsVisualize and analyze data generated by all of Illumina''s platforms.
View all literature mentionsSoftware analysis tool that enables data analysis of multiplex experiments and advanced applications and assay strategies for Droplet Digital PCR (ddPCR). For use with data files generated on QX100 or QX200 Droplet Reader using QuantSoft Standard Edition Software versions 1.4 or later.
View all literature mentionsThis monoclonal targets CD38
View all literature mentionsThis monoclonal targets IFN gamma
View all literature mentionsThis monoclonal targets HLA-DR
View all literature mentionsThis monoclonal targets CD27
View all literature mentionsThis monoclonal targets IL-17A
View all literature mentionsThis monoclonal targets GM-CSF
View all literature mentionsThis monoclonal targets FOXP3
View all literature mentionsThis monoclonal targets IgE
View all literature mentionsThis monoclonal targets CD14
View all literature mentionsThis monoclonal targets CD197
View all literature mentionsThis monoclonal targets CD4
View all literature mentionsThis monoclonal targets CD24
View all literature mentionsThis monoclonal targets CD11c
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View all literature mentionsThis monoclonal targets CD45RA
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View all literature mentionsThis monoclonal targets CD127
View all literature mentionsThis monoclonal targets CD123
View all literature mentionsThis monoclonal targets TCR gamma/delta
View all literature mentionsThis monoclonal targets CD56
View all literature mentionsThis monoclonal targets IL-21
View all literature mentionsThis monoclonal targets IgD
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets IL-4
View all literature mentionsThis monoclonal targets CD185
View all literature mentionsThis monoclonal targets CD14
View all literature mentionsThis monoclonal targets IgM
View all literature mentionsThis monoclonal targets IL-2
View all literature mentionsThis monoclonal targets CD8a
View all literature mentionsThis monoclonal targets CD24
View all literature mentionsThis monoclonal targets CD27
View all literature mentionsThis monoclonal targets IgM
View all literature mentionsThis monoclonal targets TCR V alpha 24 J alpha 18
View all literature mentionsThis monoclonal targets CD31 (PECAM-1)
View all literature mentionsThis monoclonal targets CD38
View all literature mentionsThis monoclonal targets CD24
View all literature mentionsThis monoclonal targets FOXP3
View all literature mentionsThis monoclonal targets CD27
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets CD127
View all literature mentionsThis monoclonal targets GM-CSF
View all literature mentionsThis monoclonal targets CD197
View all literature mentionsThis monoclonal targets CD56
View all literature mentionsThis monoclonal targets IgE
View all literature mentionsThis monoclonal targets CD3
View all literature mentionsThis monoclonal targets IL-17A
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets IL-4
View all literature mentionsThis monoclonal targets CD11c
View all literature mentionsThis monoclonal targets CD8a
View all literature mentionsThis monoclonal targets IgM
View all literature mentionsThis monoclonal targets CD123
View all literature mentionsThis monoclonal targets CD27
View all literature mentionsThis monoclonal targets HLA-DR
View all literature mentionsThis monoclonal targets CD24
View all literature mentionsThis monoclonal targets CD185
View all literature mentionsThis monoclonal targets CD14
View all literature mentionsThis monoclonal targets CD45RA
View all literature mentionsThis monoclonal targets IL-21
View all literature mentionsThis monoclonal targets IgM
View all literature mentionsThis monoclonal targets CD4
View all literature mentionsThis monoclonal targets TCR V alpha 24 J alpha 18
View all literature mentionsThis monoclonal targets CD31 (PECAM-1)
View all literature mentionsThis monoclonal targets IgD
View all literature mentionsThis monoclonal targets IFN gamma
View all literature mentionsThis monoclonal targets CD14
View all literature mentionsThis monoclonal targets TCR gamma/delta
View all literature mentionsThis monoclonal targets CD38
View all literature mentionsThis monoclonal targets CD38
View all literature mentionsThis monoclonal targets IL-2
View all literature mentions