Summary Statistics GWAS SSNS
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ABSTRACT:
PROVIDER: EGAD00010002316 | EGA |
REPOSITORIES: EGA
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Project description:Column 1 “rsidâ€Â: SNP identifier
Column 2 “chromosomeâ€Â: name of chromosome on which the SNP is located
Column 3: “positionâ€Â: base pair position on the chromosome
Column 4 “minor_test_alleleâ€Â: the base that constitutes the minor allele
Column 5 “major_alleleâ€Â: the base that constitutes the major allele
Column 6 “mafâ€Â: the frequency of the minor allele, indicated as a fraction of 1
Column 7 “allele_freq_casesâ€Â: the minor allele frequency in cases
Column 8 “allele_freq_controlsâ€Â: the minor allele frequency in controls
Column 9 “regression_pvalueâ€Â: the p-value for the difference in allele frequency between cases and controls
Column 10 “odds_ratioâ€Â: the odds ratio, as calculated using logistic regression under an additive model with adjustment for the first ten principal components of ancestry
| EGAD00001008782 | EGA
Project description:Our fine-mapping of 76 non-MHC loci associated with risk for rheumatoid arthritis (RA, 11,475 cases, 15,870 controls) has recently identified rs117701653, a non-coding single nucleotide polymorphism (SNP) in the CTLA4/CD28/ICOS locus, as the variant most likely to modulate RA risk within this region, with the minor allele (C) showing disease protection compared to the major allele (A). Notably, this SNP exhibits allele-specific protein binding, further supporting its regulatory nature, including greater binding of proteins from Jurkat T cell nuclear extract to the protective allele (C) than to the risk allele (A) by electrophoretic mobility shift assay (EMSA). To identify this protein or protein complex, we applied an efficient DNA pulldown technique, flanking restriction enhanced pulldown (FREP), using nuclear extract from Jurkat T cells, bait DNA corresponding to the (C) allele of rs117701653, competitor DNA fragment, and irrelevant DNA sequence as a negative control. Mass spectrometry analysis of peptides released from FREP identified 43 proteins. Our strongest candidate was structural maintenance of chromosomes flexible hinge domain-containing protein 1 (SMCHD1), which exhibited specific binding to the (C) allele of rs117701653. We confirmed the allelic affinity of SMCHD1 using multiple orthogonal approaches, including FREP and western blotting, EMSA with anti-SMCHD1 antibodies, and CHIP-qPCR with CRISPR-modified Jurkat clones bearing different genotype at rs117701653. In this study, we identified SMCHD1, a chromatin regulator that binds allelically to the rs117701653 allele (C) associated with protection against RA risk.
2024-05-23 | PXD048977 | Pride
Project description:One of our new major finding among the genes that contributes to MS susceptibility is ICSBP1. The so called disease modifying therapies like interferon-beta (IFN-β), possibly acting on the peripheral T-cells, reduce the disease activity and the clinical progression, with a MRI-detectable effect in preventing lesion burden and cerebral atrophy development in RR-MS. It suggests a critical role of peripheral blood mononuclear cells (PBMCs) immune response and modulation in developing inflammation in the brain. We tested the hypothesis that the genetic effect of the susceptible allele ICSBP1 can impact the gene expression profile of molecules belonging to the interferon pathway. We therefore interrogated the PBMC for changes in gene expression profile. We correlate those changes with the minor allele frequency for ICSBP1, performing independent quantitative trait analysis for each treatment category. Expression Quantitative Trait Loci Association with a p value < 0.05 have been used in follow up analysis. The regression coefficient of the Quantitative trait association represents the degree of correlation between the gene expression for each interrogated target gene and the minor allele frequency of the SNP for our gene of interest. This coefficient has been used as input in the subsequent Gene Set Enrichment Analysis performed in a pre-ranked approach. The resulting GSEA-SNP method rests on the assumption that SNPs underlying a disease phenotype might affect genes constituting a signaling pathway or genes with a common regulation. Therefore, GSEA-SNP can facilitate the identification of pathways or of underlying biological mechanisms. We used microarrays to capture gene expression profile of untreated subjects and of subjects under disease modyfing treatment (Interferon Beta and Glatiramer Acetate), in order to correlate gene expression and genotype data and in order to identify sets of genes specifically regulated in the different treatment categories.
2009-08-01 | GSE16214 | GEO
Project description:Bipolar disorder (BD) has an estimated heritability of about 80%. Different pathways and candidate genes may contribute to the pathogenesis of BD, but definite mechanisms are yet unresolved. In a previous study, we identified the single nucleotide polymorphism (SNP) rs4500567, located in the upstream region of Tetraspanin 8 (TSPAN8), to be associated with bipolar disorder (BD). The SNP´s minor allele results in a predicted binding site for the transcription factor Nuclear Factor Interleukin 3, regulated (NFIL3); luciferase assays confirmed allele-specific TSPAN8 expression levels.
2018-06-26 | GSE65459 | GEO
Project description:One of our new major finding among the genes that contributes to MS susceptibility is ICSBP1. The so called disease modifying therapies like interferon-beta (IFN-β), possibly acting on the peripheral T-cells, reduce the disease activity and the clinical progression, with a MRI-detectable effect in preventing lesion burden and cerebral atrophy development in RR-MS. It suggests a critical role of peripheral blood mononuclear cells (PBMCs) immune response and modulation in developing inflammation in the brain. We tested the hypothesis that the genetic effect of the susceptible allele ICSBP1 can impact the gene expression profile of molecules belonging to the interferon pathway. We therefore interrogated the PBMC for changes in gene expression profile. We correlate those changes with the minor allele frequency for ICSBP1, performing independent quantitative trait analysis for each treatment category. Expression Quantitative Trait Loci Association with a p value < 0.05 have been used in follow up analysis. The regression coefficient of the Quantitative trait association represents the degree of correlation between the gene expression for each interrogated target gene and the minor allele frequency of the SNP for our gene of interest. This coefficient has been used as input in the subsequent Gene Set Enrichment Analysis performed in a pre-ranked approach. The resulting GSEA-SNP method rests on the assumption that SNPs underlying a disease phenotype might affect genes constituting a signaling pathway or genes with a common regulation. Therefore, GSEA-SNP can facilitate the identification of pathways or of underlying biological mechanisms. We used microarrays to capture gene expression profile of untreated subjects and of subjects under disease modyfing treatment (Interferon Beta and Glatiramer Acetate), in order to correlate gene expression and genotype data and in order to identify sets of genes specifically regulated in the different treatment categories. Experiment Overall Design: Between July 2002 and October 2007, PBMC samples were collected from relapsing-remitting MS subjects and CIS subjects as part of the Comprehensive Longitudinal Investigation of MS at the Brigham & Womenâs Hospital (CLIMB study). We then selected the first time point for each subject with multiple measurements based on an at least three months of treatment criteria. We thereafter analyzed the data for each treament category.
2009-08-09 | E-GEOD-16214 | biostudies-arrayexpress
Project description:Anopheles gambiae mosquitoes of the M form N'gousso laboratory colony were antibiotic treated and subsequently orally infected with the Db11-GFP fluorescent strain of Serratia marcescens. Bacteria-fed mosquitoes were separated 2 days post infection based on the presence in the mosquito gut of a dye contained in the sugar solution. Mosquitoes were dissected 5 days post infection and the level of S. marcescens infection was determined through microscopic observation of mosquito guts under a fluorescence microscope. Highly infected mosquitoes, with an extensive presence of fluorescent S. marcescens throughout their gut and non-infected mosquitoes, with no sign of fluorescence traced in their gut, were further used for SNP genotyping. Genomic DNA from pools of 15 highly infected and 15 non-infected mosquitoes, in equimolar amounts, was hybridized in a customized Affymetrix 400k SNP genotyping arrays, interrogating genetic variation at ~400,000 variable positions in the An. gambiae genome, as determined by a previous sequencing effort of M/S An. gambiae molecular forms. Allele calls in both array hybridizations were used to determine the minor allele frequency difference for each individual SNP between the two phenotypic pools, which were subsequently used to determine loci associated with the outcome of S. marcescens infection.
2013-11-30 | E-MEXP-3951 | biostudies-arrayexpress
Project description:Copy number analysis of human GBM samples were performed, and a high frequency of deletions of the PTPRD gene on chromosome 9p23-24.1 were identified. Keywords: SNP microarray, glioblastoma multiforme, copy number, amplification, deletion
2009-01-05 | GSE13021 | GEO
Project description:Background: Adults with at least one copy of the minor allele in the rs6967330 SNP (AA/AG) in the rhinovirus (RV) receptor Cadherin related family member 3 gene (CDHR3), have a higher risk for CRS than those with two copies of the major allele (GG). Objective: To determine if the rs6967330 SNP increased the risk for acute exacerbations of chronic rhinosinusitis (AECRS) in adults and identify if their nasal cells showed a distinct pathophysiologic process activated by RV infection. Methods: We recruited adults with CRS (AG/AA,n=17; GG,n=37) and at baseline collected sinonasal outcome tests (SNOT-22), objective endoscopy scores, and nasal brushings for cells and RV viral detection. Subjects were contacted every two weeks for AECRS over one year, and if symptomatic this data was re-collected. To determine the effect of the rs6967330 SNP, air-liquid-interface (ALI) cultures were derived from nasal samples (AG/AA,n=19; GG,n=19). Cytokines and RNA transcriptome responses were measured 48 hours-post viral challenge with RV-A, RV-B, and RV-C. Results: During AECRS, adults with the AA/AG allele had 1.6x higher SNOT-22 scores, 2x higher endoscopic scores, and were 4x more likely to have RV infections during AECRS than those with the GG allele. (AA/AG) ALI cultures had significantly greater virus replication of RV-A (2.4x) and RV-C (3.5x) but not RV-B, higher levels of inflammatory cytokines, and significantly increased interferon-related pathways compared to (GG) ALI cultures. Conclusions: The minor allele in the rs6967330 SNP increases the risk for AECRS disease severity and is associated with an aberrant interferon-mediated inflammatory response to both RV-A and RV-C infections.
2024-09-12 | GSE270312 | GEO
Project description:Purpose: The purpose of this study was to evaluate SNP genotyping methodology as a means to detect chromosomal abnormalities previously diagnosed by G-band karyotype or fluorescence in situ hybridization (FISH) analysis and to determine the frequency of sub-microscopic (cryptic) chromosomal alterations in these subjects. Methods: We used the Illumina HumanHap Beadchip platform to genotype 40 individuals having previously detected chromosomal anomalies (by G-banded and/or FISH analysis). The resulting data were analyzed for signal intensity (log R ratio) and allelic composition (B allele frequency). Results: SNP array analysis detected 100% of previously identified cytogenetic abnormalities. Changes or clarifications of the ISCN karyotype designation assigned by conventional cytogenetic and/or FISH analysis were made in 82 % of the cases (32 of 39). Nine of the 39 cases (23%) involved a reassignment of an abnormal band while an additional 9 of the 39 (23%) resulted in a clarification of a sub-band assignment. In 8 more of the 39 cases (21%) the previously reported alterations were confirmed, however the SNP analysis also identified related cryptic alterations. SNP analysis not only confirmed FISH-detected abnormalities but also more precisely mapped the breakpoints of 6/6 patients. Investigations into the origin of de novo abnormalities in 15 trio families established that 12 /15 occurred on the paternal chromosome. Conclusions: SNP genotyping array analysis, confirmed all previously detected structural chromosomal abnormalities and provided additional, clinically-relevant genomic information in 82% of these alterations.
2011-02-22 | GSE20623 | GEO
Project description:Effective anti-cancer immunity is associated with the presence of T cells directed at potentially immunogenic tumor neoantigens arising from tumor-specific mutation. We confirmed the expression of reported MC38 neoantigens (Nature 515: 572, 2014). MC38 cells in our laboratory had the same point mutation at amino acid position 299 in Adpgk (ASMTN[R/M]ELM), but did not have a point mutation at amino acid position 42 in Reps1 (AQL[P/A]NDVVL). The allele frequency of mutated Adpgk (ASMTNMELM) was 30%.
2019-02-13 | GSE126280 | GEO