EGAD00000000115
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00000000115 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Total RNA-seq of blasts derived 100 adult T-ALL cases, 211 AML cases and 13 mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, CD34+ HSPCs derived from 9 healthy donors are used as a control. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011054, EGAD00001007646, EGAD00001007581 (datasets).
2023-08-31 | E-MTAB-13121 | biostudies-arrayexpress
Project description:The EGA hosts the summary genotype results of the GWAS in 856 patients with Dupuytren's disease and 2,836 population based controls from 'LifeLines' cohort study
| EGAS00000000043 | EGA
Project description:Recent GWAS have identified several susceptibility loci for NHL. Despite these successes, much of the heritable variation in NHL risk remains to be explained. Common copy-number variants are important genomic sources of variability, and hence a potential source to explain part of this missing heritability. In this study, we carried out a CNV analysis using GWAS data from 681 NHL cases and 749 controls to explore the relationship between common structural variation and lymphoma susceptibility. Here we found a novel association with diffuse large B-cell lymphoma (DLBCL) risk involving a partial duplication of the C-terminus region of the LOC283177 long non-coding RNA that was further validated by quantitative PCR. For chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), known somatic deletions were identified on chromosomes 13q14, 11q22-23, 14q32 and 22q11.22. Our study shows that GWAS data can be used to identify germline CNVs associated with disease risk for DLBCL and somatic CNVs for CLL/SLL. We performed a genome-wide CNV analysis of 681 NHL cases and 749 controls from the San Francisco Bay Area, genotyped using the Illumina HumanCNV370-Duo BeadChip array. Signal intensity data in the form of log R ratio (LRR) and B allele frequency (BAF) values were obtained directly from the Beadstudio software. Quality control filtering was used to exclude unreliable samples, resulting in a final dataset of 619 NHL cases (205 FL, 242 DLBCL, 172 CLL/SLL) and 730 controls.
2014-09-23 | E-GEOD-58718 | biostudies-arrayexpress
Project description:CTCF ChIP-seq of 39 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011059 (dataset).
2023-08-31 | E-MTAB-13117 | biostudies-arrayexpress
Project description:Fixed effect meta-analysis summary statistics combining GWAS of maternal preeclampsia cases and controls from Central Asia (Kazakhstan and Uzbekistan).
| EGAD00010001985 | EGA
Project description:H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011060 (dataset).
2023-08-31 | E-MTAB-13119 | biostudies-arrayexpress
Project description:This series consists of summary data generated from a genome-wide association study (GWAS) investigating inherited genetic risk to childhood acute lymphoblastic leukemia (ALL). The GWAS comprised 784 cases recruited to the Medical Research Council UK ALL-2003 and ALL-97/99 trials and 7,385 controls. The data describe SNPtest association statistics from the case-control analysis.
| EGAS00001002809 | EGA
Project description:Fixed effect meta-analysis summary statistics combining GWAS of fetal (baby) preeclampsia cases and controls from Central Asia (Kazakhstan and Uzbekistan).
| EGAD00010001987 | EGA
Project description:Background: Functional enrichment analysis of genome-wide association study (GWAS)-summary statistics has suggested that immune cell-types, and especially CD4+ T-cells, play an important role in asthma pathogenesis. Despite this, CD4+ T-cells are under-represented in asthma transcriptome studies. Objective: To identify differences in gene expression between asthmatics and healthy controls in CD4+ T-cells. Methods: CD4+ T-cells were isolated within 2 hours from collection from peripheral blood from people with well-established asthma (n=33) and healthy controls (n=12). 3'-RNA-Seq was used to generate gene expression data. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify sets of co-expressed genes (modules). The asthma-associated modules were tested for enrichment of GWAS-identified asthma genes and gene ontology (GO) biological processes. For the genes in the asthma-associated modules, integration of eQTL and GWAS summary statistics (colocalisation), and protein-protein interaction (PPI) data was used to identify master regulators. Results: After quality control, 43 samples were available for the analysis. WGCNA identified three modules associated with asthma, which are strongly enriched for GWAS-identified asthma genes, antigen processing/presentation and immune response to viral infections. Colocalisation analysis of eQTL and GWAS summary statistics, together with PPI data, identified PTPRC as a master regulator of asthma gene-expression profiles in CD4+ T-cells. Conclusion: Unstimulated CD4+ T-cells from peripheral blood from asthmatics have different expression profiles, compared to healthy controls, for sets of genes involved in immune response to viral infections and antigen processing/presentation . Integration of genetic and protein-protein interaction data identified PTPRC as a master regulator of genes in asthma.
2023-12-27 | GSE217904 | GEO
Project description:Fixed effect meta-analysis summary statistics combining GWAS of maternal preeclampsia cases and controls from Europe (UK, Iceland, Norway, Denmark and Finland).
| EGAD00010001984 | EGA