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Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [CRISPR guide-seq]

ABSTRACT: Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [CRISPR guide-seq]

PROVIDER: PRJNA563074 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10050400.fastq.gz	Fastqsanger.gz
	SRR10050500.fastq.gz	Fastqsanger.gz
	SRR10050600.fastq.gz	Fastqsanger.gz
	SRR10050700.fastq.gz	Fastqsanger.gz
	SRR10050800.fastq.gz	Fastqsanger.gz

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Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits

Project description:Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits

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Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [MPRA]

Project description:Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [MPRA]

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Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [CRISPR guide-seq]

Project description:Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we used seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in three disease-relevant immune cell types, based on a set of features related to regulatory potential. Trait/disease-associated variants were enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 had at least one variant meeting one or both of these criteria, with 3 of these haplotypes having a single prioritized variant. 5 of the 9 prioritized variants were further supported by genetic fine-mapping in our and other studies. Our work provides evidence for the efficacy and limitations of strategies for prioritizing disease- and trait-associated genetic variants.

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Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [ATAC-seq]

Project description:Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [ATAC-seq]

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Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [MPRA]

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Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [ATAC-seq]

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Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-02-11 | GSE136703 | GEO

Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs.

Project description:BackgroundShort tandem repeats (STRs) were recently found to have significant impacts on gene expression and diseases in humans, but their roles on gene expression and complex traits in pigs remain unexplored. This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.ResultsWe identified 5203 and 5868 significantly expression STRs (eSTRs, FDR < 1%) in the F6 and F7 populations, respectively, most of which could be reciprocally validated (π1 = 0.92). The eSTRs explained 27.5% of the cis-heritability of gene expression traits on average. We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs, respectively, which were significantly enriched in intron, ATAC peak, compartment A and H3K4me3 regions. We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs, which colocalized with epigenetic markers such as H3K27ac and ATAC peaks. These included eSTR of the CLPB, PGLS, PSMD6 and DHDH genes, which are linked with genome-wide association study (GWAS) SNPs for blood-related traits, leg conformation, growth-related traits, and meat quality traits, respectively.ConclusionsThis study provides insights into the effects of STRs on gene expression traits. The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.

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Quantitative Versus Qualitative Fecal Immunochemical Tests (FIT) to Prioritize Urgency of Colonoscopy Referral

Project description:The main aim of this study is to determine whether there is a difference in time to diagnosis of advanced colorectal neoplasms using quantitative Fecal Immunochemical Tests (FIT) to prioritize referral for colonoscopy (intervention) compared to usual care (qualitative FIT and appointment-based referral).

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Project description:We evaluate whether human induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) cells can be used to prioritize and functionally characterize causal variants at age-related macular degeneration (AMD) risk loci. We generated iPSC-RPE from six subjects and show that they have morphological and molecular characteristics similar to native RPE. We generated RNA-seq, ATAC-seq, and H3K27ac ChIP-seq data and observe high similarity in gene expression and enriched transcription factor motif profiles between iPSC-RPE and human fetal-RPE. We performed fine-mapping of AMD risk loci by integrating molecular data from the iPSC-RPE, adult retina, and adult RPE, which identified rs943080 as the probable causal variant at VEGFA. We show that rs943080 is associated with altered chromatin accessibility of a distal ATAC-seq peak, decreased overall gene expression of VEGFA, and allele specific expression of a non-coding transcript. These results provide insight into the mechanism underlying the association of the VEGFA locus with AMD. Raw data requires controlled access and is deposited at dbGaP http://www.ncbi.nlm.nih.gov/gap/?term=phs000924

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