Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 21 for “"eQTLs"”.
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New statistical methods in bioinformatics: for the analysis of quantitative trait loci (QTL), microarrays, and eQTLs
<p>This thesis focuses on new statistical methods in the area of bioinformatics which uses computers and statistics to solve biological problems. The first study discusses a method for detecting a quantitative trait locus (QTL) when the trait of interest has a zero-inflated Poisson (ZIP) …
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Regulation of gene expression in macrophage immune response
… of disease-associated variants. However, many eQTLs are cell type and context specific. This is particularly relevant for immune cells, whose cellular function and behaviour can be substantially altered by external cues. Furthermore, understanding mechanisms behind eQTLs is hindered by the …
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Computational personal genomics : understanding the functional effects of sequence variation
… data to identify putative causal variants in eQTLs or GWAS loci. We show that these approaches improve upon existing methods. We observe that there are genome-wide correlations in allele-specific activity, and that allele-specific activity is widespread across the autosomes. We demonstrate …
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A More Holistic Analysis of Privacy Risks in Transcriptomic Datasets
… such a risk could analyze only a fraction of eQTLs that are independent of each other due to restrictive model assumptions, leaving the full extent of this risk incompletely understood. To address this challenge, we introduce discriminative sequence model (DSM), a novel probabilistic framework …
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Quantitative genetics of gene expression during fruit fly development
… Using these expression levels I call proximal eQTLs both common and specific to a single developmental stage with a multivariate linear mixed model approach while accounting for various confounding factors. I then investigate the properties of these eQTLs, such as their location or the gene …
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Primary sclerosing cholangitis: from genetic risk to disease biology
… i.e. are expression quantitative trait loci (eQTLs). Colocalisation assesses the evidence that a single shared causal variant is responsible for driving PSC risk and gene expression via an eQTL. In order to assign dysregulated genes to PSC risk loci, I perform colocalisation with eQTLs mapped …
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Germline variants associated with alternative splicing in colonic mucosa
… were enriched within linkage blocks containing eQTLs (expression quantitative trait loci) identified from the same cohort, and eQTLs identified from GTEx sigmoid and transverse colon tissues; however the lead SNPs associated with sQTLs and eQTLs were different in 97% of cases, implying a strong …
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A genetic analysis of molecular traits in skeletal muscle
… with molecular traits such as gene expression (eQTLs) and DNA methylation (mQTLs). The Finland-United States Investigation of NIDDM (FUSION) tissue biopsy study is motivated by the desire to understand the molecular pathogenesis of Type 2 diabetes (T2D), a complex disease where the vast majority …
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Cortisol responsive gene networks in cardiovascular disease
… 0.05) as cis-expression Quantitative Trait Loci (eQTLs). We go on to describe the extra-hepatic consequences of genetic variation for plasma cortisol by linking SNPs associated with plasma cortisol to genes expressed in trans across STARNET tissues, finding the highest representation of …
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GENOMIC AND MICROBIOME ANALYSIS TO IMPROVE FILLET YIELD AND QUALITY TRAITS IN RAINBOW TROUT
… and phenotypic outcomes. A total of 6,275 cis-eQTLs were identified near promoter regions influencing gene expression. Notable candidate genes included GABRR1-like, AZIN1, and ATP6V1 for body weight; TNNI2, PDLIM3, CDK5, and CYP3A27 for tissue robustness; and GATD3A, PPP2R1BB, and USP6NL for …
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Inferring Transcriptional and Post-Transcriptional Network Structure by Exploiting Natural Sequence Variation
… by first mapping expression quantitative loci (eQTLs) for individual genes, and then looking for so-called “eQTLs hotspots”. Our method avoids the first step by integrating information across all genes, leading to a more elegant method that has increased statistical power. For yeast, we …
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Uncovering novel genes causing isolated gonadotropin releasing hormone deficiency using runs of homozygosity in outbred families
… IGD genes, Expression Quantitative Trait Loci (eQTLs) of known genes and novel regions predicted to be associated with IGD were explored. RESULTS: While there was no statistical difference between the ROH burden in cases vs. controls, there was an unexpected trend towards a greater burden in the …
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Inference of Gene Regulatory Networks with integration of prior knowledge
… the form of expression quantitative trait loci (eQTLs) perturbations. FLAP enhances FSSEM by integrating prior knowledge of gene-gene interactions into the initial network estimate, guiding the selection of relevant gene interactions in the final inferred network. We evaluated FLAP using …
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A multi-ancestry genetic analysis of type 2 diabetes
… miRNA-expression quantitative trait loci (miRNA-eQTLs). I use several strategies to link these findings to T2D, including colocalising miRNA-eQTLs with loci associated with T2D and related glycaemic traits, identifying T2D-related variants that may disrupt miRNA binding potential, and performing …
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Identification of Functional Variants in Alzheimer's Disease-Associated Genes
… cis-acting expression quantitative trait loci (eQTLs) for nearby genes. The IGAP study also identified an intergenic polymorphism near TREML2 suggestively associated with AD risk; however, due to the study design, it was not possible to uncover the underlying functional variant or to determine …
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Understanding functional mechanisms of genetic susceptibility to mycobacterial infection
… to identify expression quantitative trait loci (eQTLs), i.e., DNA polymorphism that affect gene expression. In particular, we identified an eQTL located in the TLR10-TLR1-TLR6 gene cluster. In non-infected macrophages, a group of polymorphisms in this region was associated in cis with the level …
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Combining population-scale single-cell transcriptomics with germline genetics to understand the biology of inflammatory bowel diseases
… phenotypes to test for interaction eQTLs effects and show that these can be valuable for understanding biology too. Overall, my thesis looks at diverse scRNA-seq data generated from a large cohort and harnesses that power to provide insight into IBD biology. The datasets created will …
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Novel Statistical Methods for Mediation Analysis with High-dimensional Omics Mediators
… leverages expression quantitative trait loci (eQTLs) as instrumental variables to reduce bias caused by unmeasured confounders. Extensive simulations validate that MR-based method outperforms the standard linear regression-based method in the presence of unmeasured confounders. Additionally, …
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Genetic architecture of transcript splicing in blood and phenotypic consequences
… analysis of these with the generated spliceQTLs to explore their shared genetic architecture. This reveals that many splice events and molecular phenotypes appear to be regulated by shared genetic effects, and through examples demonstrate how splicing could be modulating these downstream …
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Genetic ancestry and population health: elucidating the relative role of African genetic ancestry in cancer genomics and the broader implications for racial health disparities in cancer
… work identified 196 SNPs acting as cis- or trans-eQTLs across the various cancers, with the bulk of the interactions being tissue-specific. Only 13 of the SNPs were found as eQTL in 3 or more cancers. The associated eGenes were involved in a wide array of biological functions, with many implicated …
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