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 35 for “"Single Nucleotide Variants"”.
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Dynamic DNA Nanotechnology for Probing Single Nucleotide Variants and DNA Modifications
… that attempt to conquer the challenge of single-nucleotide-variants (SNVs) detection. Even though a powerful toolbox including the toehold-exchange reaction, the dynamic ‘sink’ design, and the polymerase chain reaction (PCR) has been built, it still faces practical problems. For example, …
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Elucidating the mechanistic impact of single nucleotide variants in model organisms
… and protein folding. Understanding the impact of variants on such processes has key implications in therapeutics, drug development, and more. This thesis aims to utilise computational predictors to shed light on how cellular mechanisms are altered in the context of genetic variation and better …
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Förster Resonance Energy Transfer-Based Quantification of D-2-Hydroxyglutarate & Locked Nucleic Acid Loop-Mediated Isothermal Amplification Mediated Detection of IDH1-R132 Single Nucleotide Variants in Glioma
… panel identifies the specific <em>IDH1</em>-R132 single nucleotide variant (SNV) present. The biosensor’s robust function in biological fluids suggests its powerful utility in liquid biopsies and monitoring remission vs. recurrence, while the genotyping panel aids in the genetic detection of …
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cis-Regulation in the Mammalian Rod Photoreceptor
… regulatory activity of thousands of CREs in a single experiment. In this method I insert unique barcodes in the 3'UTR of a reporter gene and multiplex expression measurements with RNA sequencing. Using this technique in explanted retinas, I determined the impact of single nucleotide variants in …
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Avaliação de genes auto inflamatórios em crianças com Síndrome Inflamatória Multissistêmica Pediátrica (SIM-P) associada à infecção pelo SARS-CoV-2
… response against SARS-CoV-2. Ain: Identify variants in genes involved in primary auto inflammatory conditions that may be implicated in MIS-C. Methods: Cells and clinical/laboratory information were collected from 21 pediatric patients with MIS-C recruited from three public hospitals in the …
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Transcription Factor-Centric Approaches to Identify Regulatory Driver Mutations in Cancer
… for predicting the quantitative effects of single nucleotide variants on transcription factor (TF) binding. Unlike most of the previous work on driver identification, our method does not require the driver mutations to be highly recurrent; instead, we assess the mutations’ significance by …
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Improving Dbnsfp
… studies (WES). Genome research has focused on single nucleotide variants (SNVs). Since indels are as important as SNVs, especially indels in coding regions are often candidates of disease-causing variants, thus, it is necessary to expand the focus to include indel mutations.</p> <p>The goal of …
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Mitochondrial Contributions to Schizophrenia Symptom Severity: A GWAS Approach in a South African Population
… General Linear Models to assess mitochondrial single nucleotide variants (SNVs), cumulative mitochondrial gene burdens, and epistatic interactions between mitochondrial SNVs and nuclear-encoded mitochondrial genes (NEMtGs) against Positive and Negative Syndrome Scale (PANSS) scores. Although no …
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FUNCTIONAL ROLE OF NON-CODING REGULATORY VARIANTS IN NEUROBLASTOMA
… evidence suggests that non-coding somatic variants in cancer can contribute to disease, mainly by residing in functional regulatory regions and ultimately affecting gene expression networks. However, their interpretation is challenging. In our recent work, whole-genome sequencing (WGS) data …
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Strain-resolved transcriptomics: exploring functional heterogeneity of the gut microbiota in health and disease
… trees for over 250 bacterial species using the single nucleotide variants within essential housekeeping genes, enabling the identification of bacterial strains. Next, we devised a statistical approach to assign mRNA reads to these strains, leveraging the natural genetic variation that is present …
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Somatic Mutation Detection in Leukemia-Derived Circulating DNA: Utility in Monitoring Clonal Dynamics and Disease Response in Pediatric Acute Lymphoblastic Leukemia
… captured all the clinically relevant somatic single nucleotide variants (SNVs) detected by whole exome sequencing (WES) in bone marrow (BM) biopsy samples at diagnosis. Moreover, we were able to show the ability of Ct-DNA analysis to track the change in the mutant allele fraction (MAF) across …
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Identification and Characterization of APOBEC1 mRNA Editing Targets: A Transcriptomics Approach
… sequence from that encoded by the genome through nucleotide insertion, deletion or modification. The Apolipoprotein B mRNA Editing Catalytic polypeptide 1 (APOBEC1) cytidine deaminase is an mRNA editing enzyme that modifies a specific cytidine in the apolipoprotein B (apoB) transcripts of small …
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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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Inferring tumour evolution from single-cell and multi-sample data
… for inferring trees of tumour evolution from single-cell and multi-sample sequencing data. Recent advances in single-cell sequencing technologies have promised to reveal tumour heterogeneity at a much higher resolution, but single-cell sequencing data is inherently noisy, making it unsuitable …
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The Intra-Tumour Heterogeneity Landscape of Human Cancers
… and a method to infer subclones from single nucleotide variants (DPClust). Both are extensively validated on simulated and on real data, and I describe a rigorous quality control procedure. The methods are then applied to a single sample to showcase what can be learned about the life …
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Developing Methods for Enhanced Measurement of DNA Single-Strand Breaks and Somatic Variants
… demonstrate DENT-seq, a method that identifies single-strand breaks with single-nucleotide resolution. Single-strand breaks are the most common form of DNA damage, occurring at rates of ~10,000 per cell per day, but have to date been understudied due to lack of an unbiased, high-resolution …
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Network based analysis of genetic disease associations
… increasingly the prevailing view is that common variants, the target of GWAS, are not solely responsible for susceptibility to common diseases and a substantial portion of human disease risk will be found among rare variants. Relatively new, such variants have not been subject to purifying …
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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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CRISPR AS A TOOL FOR TARGET DISCOVERY AND TECHNOLOGICAL INNOVATION: HIGH-THROUGHPUT CBE SCREENING TO EVALUATE M6A MODIFICATION PATHWAY IN CANCER PROLIFERATION AND DRUG RESISTANCE, AND INNOVATIVE PRIME EDITING STRATEGIES FOR DISEASE MODELLING AND THERAPY
… effectors. In details, we assessed the effect of single nucleotide variants (SNVs) in CRC proliferation, highlighting domains of m6A effectors that are critical for promoting, or downregulating, tumor growth. In AML, the proliferative effect of m6A-effectors mutagenesis was determined upon METTL3 …
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Reconstructing Mutational Lineages In Breast Cancer By Multi-Patient-Targeted Single Cell Dna Sequencing
… known regarding the timing and impact of single nucleotide variants (SNVs) contributing to these early transformative genomic events. Paramount to novel treatment options is understanding the underlying biology of initiation in the early stages of TNBC development, where inferring clonal …
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