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 59 for “"structural variants"”.
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Engineering structural variants with prime editing
… coding genes and the systematic exploration of structural variants.
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Decoding the Little Skate Retina: Structural Variants and Developmental Dynamics
… (Lannoy et. al, 1998) providing context and structural information that will be useful in this investigation. Finally, to attempt overexpression experiments in the little skate at critical timepoints of developmental processes, it is important to have cell cycle dynamic information in the …
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Decoding the Little Skate Retina: Structural Variants and Developmental Dynamics
… (Lannoy et. al, 1998) providing context and structural information that will be useful in this investigation. Finally, to attempt overexpression experiments in the little skate at critical timepoints of developmental processes, it is important to have cell cycle dynamic information in the …
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The Contribution of Structural Variants to 2,095 Molecular Phenotypes in 12,354 European Ancestry Individuals
Structural Variants (SVs) are large scale rearrangements of the genome resulting in linear and spatial changes which can profoundly affect the function of the genome. SVs contribute the majority of nucleotide variation among human genomes by number of basepairs and have been linked to various …
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Computational methods for the detection of somatic structural variants in cancer genomes using long-read sequencing
Accurate detection of somatic structural variants (SVs) is critical for informing the diagnosis and treatment of human cancers. In this thesis, I present SAVANA, a computational method for the analysis of somatic SVs using long-read whole genome sequencing data from tumours and matched normal …
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Defining the functional response of Mycobacterium sp. infected macrophages to structural variants of Interferon gamma (IFN-y)
… by an incomplete understanding of how subtle structural variation influences its conformational organisation and stability. In biological systems, IFN-γ exists not as a single uniform molecular entity but as a structurally heterogeneous population arising from post-translational modification, …
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Structural variant calling by assembly in whole human genomes: Applications in hypoplastic left heart syndrome
… human reference genome. SNPs and small indels (variants less than 50 nucleotides) are the most common types of variants detected from alignments. Structural variation can be more difficult to detect from short-read alignments, and thus many software applications aimed at detecting structural …
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Complete computational sequence characterization of mobile element variations in the human genome using meta-personal genome data
… fewer methods have been developed for finding structural variants (SVs) and in particular mobile elements insertions (MEIs). Moreover, almost all these methods can detect only the breakpoints of an occurred SV, sometimes with approximation, and do not provide complete sequences representing the …
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Whole genomic structural variant calling in soybean: Analysis on 481 different soybean lines
… using alignment methods and largely yields short variants such as SNP(s) and short indel(s). We conducted variant discovery on 481 soybean lines using both alignment and assembly methods. We used the Sentieon Haplotyper algorithm for our alignment-based variant calling and Cortex-var for our …
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Variation-aware algorithms for cancer genome analysis
… of algorithms for doing so. Rediscovering these variants wastes significant computational time and negatively impacts the sensitivity of detection, motivating the development of new solutions. The variants in malignant cells can arise from a number of genetic and environmental sources. In the …
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Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes
… study functions of thousands of normal sequence variants and spontaneous mutations that segregate in intercross and backcross progeny generated by mating completely sequenced parental lines. To evaluate this new reverse genetic method we resequenced the genome of one of the oldest inbred strains …
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Genomic changes underlying disease resistance and high protein QTL
… for SCN resistance in cqSCN-006 and cqSCN-007. Structural variation causes high protein phenotype in cqProt-003 In addition to the G. soja genotype PI 468916 having resistance to SCN, it also contains genes for increased protein production. Three genes have been annotated in the genetically …
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Exploring the genetic landscape in cutaneous T-cell lymphoma with short- and long-read sequencing
… In general, there are recurrent copy-number variants and rare, single nucleotide variants that ultimately cluster in a limited number of pathways, including JAK-STAT- and T-cell receptor signaling. Currently, there is a lack of knowledge about the genetic changes in early and treatment-naïve …
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Chromatin Architecture Aberrations Contribute and Acute Lymphoblastic Leukemia Relapse
… of the chromatin fiber. The majority of genetic variants target non-coding regions of the genome and many genes affected by genetic and epigenetic variants have important roles in chromatin remodelling and maintenance. Thus, understanding the origins of cancer progression requires investigating …
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Enhancing genomic data quality through deep learning methods
… arrays capture only a subset of common variants while rare and structural variants remain underrepresented. Without complete genomes, predictive models cannot reach their full potential. This thesis traces a research trajectory that began with phenotype prediction and expanded to …
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Structural and Functional Analysis of HIV-1 Nef Activation of PAK-2
… 2 (PAK-2). Previous work has characterized the structural plasticity of Nef with regard to PAK-2 activation. Residues 89 and 191 were identified to be components of an effector domain required for Nef mediating PAK-2 activation with lesser contributions from position 85 and 188. H89 and F191 are …
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Investigation of the Molecular Interaction Between Pyr mRNA and the Bacillus Subtilis Attenuation Regulatory Protein, PyrR
… shift experiments using progressively shorter variants of BL2 mRNA determined that the minimal RNA necessary for tight PyrR binding was 28 nt long. The stoichiometry of the PyrR-pyr mRNA interaction was determined to be equimolar using a gel mobility shift titration assay. The effects of 31 …
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Study of the rate and spectrum of spontaneous mutations
… large microsatellite loci.</p><p>We observe that structural variants in C. elegans and S. cerevisiae, which are ∼1000 fold larger than base substitution rates on a per nucleotide basis, occur on the same order of magnitude as base substitutions. The rate and direction of structural gains and …
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A GPU program to compute SNP-SNP interactions in genome-wide association studies
… a novel approach to optimize the detection of structural variants using a new short read alignment program is presented. Pairwise interaction effects of the Single Nucleotide Polymorphisms (SNPs) have proven to uncover the underlying complex disease traits. Computing the disease risk based on …
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