Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1308570 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptome-wide association studies (TWAS) integrate genome-wide association studies (GWAS) and gene expression datasets to prioritize causal genes at GWAS loci. The NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844) has collected genetic data from thousands of HS rats to perform GWAS on numerous behavioral traits that are relevant to substance use disorders. However, GWAS loci remain difficult to interpret. In this scenario, TWAS offer an orthogonal approach to prioritize causal variants. TWAS rely on a reference gene panel in which both gene expression in relevant tissues and genetic variation has been measured from the same individuals to learn per-gene predictive models of expression variation. This dataset will be used to generate transcriptomic phenotypes from brain tissues of naïve heterogeneous stock rats for use in molecular QTL mapping, TWAS reference panels, expression prediction, and other transcriptomic applications.
2026-02-18 | GSE319591 | GEO
Project description:Submission of SARS-CoV-2 genomes isolated in Italy/Apulia
| PRJEB41697 | ENA
Project description:Transcriptome-wide association studies (TWAS) to pinpoint enhanced expression of genes involved in DNA repair attributed to viral resistance of atxr5 atxr6.
2023-10-17 | GSE235141 | GEO
Project description:To identify credible causal risk variants (CCVs) associated with different histotypes of epithelial ovarian cancer (EOC), we performed genome-wide association analysis for 470,825 genotyped and 10,163,797 imputed SNPs in 25,981 EOC cases and 105,724 controls of European origin. We identified five new histotype-specific EOC risk regions (P-value < 5 x 10-8) and confirmed previously reported associations for 27 risk regions. Conditional analyses identified an additional 11 signals independent of the primary signal at six risk regions (P-value < 10-5). Fine mapping identified 4,008 CCVs in these regions, of which 1,452 CCVs were located in ovarian cancer-related chromatin marks with significant enrichment in active enhancers, active promoters, and active regions for CCVs from each EOC histotype. Transcriptome-wide association and colocalization analyses across histotypes using tissue-specific and cross-tissue data sets identified 86 candidate susceptibility genes in known EOC risk regions and 32 genes in 23 additional genomic regions that may represent novel EOC risk loci (FDR < 0.05). Finally, by integrating genome-wide HiChIP interactome analysis with TWAS, variant effect predictor, transcription factor ChIP-seq, and motifbreakR data, we identified candidate gene-CCV interactions at each locus. This included risk loci where TWAS identified one or more candidate susceptibility genes (e.g., HOXD-AS2, HOXD8 and HOXD3 at 2q31) and other loci where no candidate gene was identified (e.g., MYC and PVT1 at 8q24) by TWAS. In summary, this study describes a functional framework and provides a greater understanding of the biological significance of risk alleles and candidate gene targets at EOC susceptibility loci identified by GWAS.
2024-03-27 | GSE255142 | GEO