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 302 for “"whole genome sequencing"”.
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Estimating telomere length from whole genome sequencing data
… and Parabam, as well as their applications to whole genome sequencing (WGS) data. Telomerecat is a tool for estimating telomere length from WGS data. The strength of Telomerecat lies in its applicability. This applicability is due to a number of advantages over previous attempts to estimate …
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Advancing RNA Virus Discovery and Biology with Whole Genome Sequencing
… to define these mechanisms is the lack of whole genome sequences for many of these viruses. To address this specific gap, I developed a versatile amplicon-based whole-genome sequencing (WGS) approach to identify viral genomes of hantaviruses and severe acute respiratory syndrome coronavirus …
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COMPREHENSIVE WHOLE GENOME SEQUENCING UNRAVELS THE COMPLEX GENOMIC LANDSCAPE OF NEUROBLASTOMA
… spectrum of clinical outcomes. Although the genome of this tumor has been extensively studied through the last decades, a comprehensive analysis of NBL mutational landscape – which may expain its complexity – is still lacking. Moreover, while the role of germline variants in the …
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Identification of Familial Wilms Tumor Predisposition Genes Using Whole Genome Sequencing
… penetrance, estimated to be 30%.</p> <p>Whole genome sequencing of eleven individuals in three Wilms tumor families was performed to identify the gene(s) responsible for genetic predisposition to Wilms tumor in these families, and to increase our understanding of a genetically …
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Whole genome sequencing to characterize Cutthroat Trout populations across the Continental Divide
… markers representing only a small portion of the genome, such as with ND2 mitochondrial DNA haplotypes, microsatellites, and amplified fragment length polymorphisms (AFLPs), and have not included a comprehensive nuclear DNA assessment from all extant lineages of Cutthroat Trout found in Colorado. …
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Insights into the genomic histories of diverse human populations using whole-genome sequencing analysis.
… 54 human populations which are part of the Human Genome Diversity Project (HGDP-CEPH) panel. Using whole-genome sequences previously produced at the Wellcome Sanger Institute, I generated a comprehensive catalogue of structural variation identifying a total of 126,018 variants, of which 78% are …
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Enhancing Early Detection of Oesophageal Squamous Cell Carcinoma Through Shallow Whole-Genome Sequencing and Non-Endoscopic Sponge Sampling
… this thesis, I explored the potential of shallow whole-genome sequencing (sWGS) to detect genome-wide copy number alterations (CNAs) in cells collected using a non-endoscopic sponge pan-oesophageal sampling device (Cytosponge) for the early detection of OSCC and its precursor lesions, oesophageal …
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Whole genome sequencing approach to identifying genetic risk factors underlying anterior cruciate ligament injuries in a twin family study
… and extrinsic risk factors. Variation in the genome is now considered a key intrinsic risk factor, but the majority of currently implicated loci have been identified through case-control genetic association studies, which are limited by a candidate gene approach and insufficient statistical …
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Understanding the Effects of Genetic Variation on Osmo-adaptation Dynamics Across S. cerevisiae using Bulk Segregant Analysis and Whole Genome Sequencing
<p>Adapting to environmental changes (i.e. an increase in osmolarity) is critical for cell survival. How cells respond and adapt to osmotic stress has been well-studied in the model eukaryote Saccharomyces cerevisiae. Although the molecular and systems properties of osmo-adaptation have been well …
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The Search for Regulatory Mutations in Gitelman Syndrome
<p>The development of whole exome and whole genome sequencing technologies has allowed geneticists to gradually uncover a wide spectrum of rare, deleterious mutations with large effect sizes, which are responsible for Mendelian diseases. Roughly 70% of human genes are single copy and have orthologs …
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Probabilistic modelling of somatic alterations in bulk tissue and single cells using repeat DNA
… which large-scale structural alterations of the genome accumulate at an increased rate. An important class of structural alterations are somatic copy number alterations (SCNAs). SCNAs have been shown to be major drivers of oncogenesis and are associated with prognosis and response to therapies. …
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Computational methods for the detection of somatic structural variants in cancer genomes using long-read sequencing
… for the analysis of somatic SVs using long-read whole genome sequencing data from tumours and matched normal samples. SAVANA employs machine learning to distinguish true somatic SVs from germline events and noise. Additionally, I establish best practices for benchmarking SV detection using …
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Heavy metal inducible antimicrobial activity of streptomyces spp. isolated from the Leadhills and Wanlockhead lead mines in Scotland, Uk
… the rise of multidrug resistant infections. Whole genome sequencing and genome mining have revealed that Streptomyces spp. possess a range of biosynthetic gene clusters for secondary metabolites, however many of them are silent and cryptic under conventional laboratory conditions. It has also …
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Do bacteria implicated in Ventilator-Associated Pneumonia adapt to antibiotic exposure?
… including co-infection and limited growth media. Whole genome sequencing data was collected to identify genetic mutations correlated to such growth. The findings included in this thesis indicates that the P. aeruginosa clinical strain was able to adapt to all antibiotics prescribed, including the …
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Characterization of two component systems of Acinetobacter baumannii.
… of putative two component systems encoded in the genome of A. baumannii that await detailed characterization. Differential expressions of six different TCSs was observed in two clinical isolates of A. baumannii AB030 and AB031, and whole-genome sequencing of both clinical isolates was performed. …
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Phenotypic and genotypic characterisation of invasive Streptococcus pneumoniae expressing atypical capsular types
… characterization was conducted by analysing whole-genome sequencing data to reveal the in-silico serotype, multi-locus sequence type profiles, virulence factors, and antibiotic-resistance genes present, including whole genome sequencing-inferred minimum inhibitory concentration where …
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Genetic and Epigenetic Interactions in in vivo and in vitro Reprogramming
… "dysregulation" in these cases is unknown. Whole genome sequencing of 45 de novo AML genomes showed that recurrent mutations in the HOX gene clusters are not responsible for the phenotype. Expression array data from 190 AML cases revealed that while translocations have unique HOX expression …
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Sequencing in Isolation: Next-generation sequencing studies in founder populations
… imputation reference panels and very low-depth whole-genome sequencing have been proposed as ways to boost power in next-generation association studies while keeping sequencing costs low. The aim of this work is to leverage the wealth of sequencing data generated as part of the HELIC project to …
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Genomic Instability and Gene Dosage Obscures Clues to Virulence Mechanisms of F. tularensis species
… and was considered as a possible vaccine strain. Whole genome sequencing was performed to identify genetic differences between the virulent, avirulent and protective strains using both Roche/454 and Illumina next-generation sequencing technologies. Additionally, RNASeq analysis was performed to …
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