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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 24 for “"structural variant"”.

  1. Whole genomic structural variant calling in soybean: Analysis on 481 different soybean lines

    Istanto, Dave DeandreUniversity of Illinois at Urbana-Champaign2020

    … protein source and rotation crop. Often, soybean variant discovery is conducted 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 …

    uiuc Repository record

  2. 1q21.1 syndrome: A perspective on Structural Variant detection & the evolutionary profile of associated protein domains

    España Bonilla, PaulaUniversitat Oberta de Catalunya (UOC)2021

    … estudio es diseñar un pipeline de detección de variantes estructurales a partir de secuenciación con long reads. El proyecto incluye la simulación de genomas con diversas variantes estructurales y la simulación de reads de secuenciación que permitan validar la aplicación de este pipeline. El …

    catalunya Repository record

  3. Structural variant calling by assembly in whole human genomes: Applications in hypoplastic left heart syndrome

    Kendzior, MatthewUniversity of Illinois at Urbana-Champaign2020

    Variant discovery in medical research typically involves alignment of short sequencing reads to the 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 …

    uiuc Repository record

  4. Variation-aware algorithms for cancer genome analysis

    Dawson, Eric ThomasUniversity of Cambridge2020

    … is rarely used during read alignment and variant calling because of a lack 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 …

    cambridge Repository record

  5. Function Study of Atrial Fibrillation-Linked Connexin Mutants and Heterotypic Docking Compatibility of Cardiac Connexins

    Ye, Willy GThe University of Western Ontario2015

    … GJs were not functional, unless a designed Cx40 structural variant (D55N) was used, suggesting these heterotypic GJs are unlikely to mediate coupling in the native heart.

    uwo Repository record

  6. Statistical analysis of short template switch mutations in human genomes

    Walker, ConorUniversity of Cambridge2021

    … nearby in three-dimensional space. These variants are routinely captured at kilobase-to-megabase scales in studies of genetic variation by using methods for structural variant calling. However, the genomic and evolutionary consequences of replication-based rearrangements remain poorly …

    cambridge Repository record

  7. Genomic changes underlying disease resistance and high protein QTL

    Fliege, Christina ElizabethUniversity of Illinois at Urbana-Champaign2020

    … 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 …

    uiuc Repository record

  8. The reconstitution of the histone octamer

    Greyling, H JDepartment of Molecular and Cell Biology1987

    … of hybrid histone octamers containing a structural variant of a specific histone. These studies were undertaken to study the effect on histone-histone interactions in hybrid octamers of which erythrocyte H2B was substituted for by sea urchin sperm H2B(l) or erythrocyte H3 and H4 were …

    cape-town Repository record

  9. Construction and analysis of the pangenome of Cucurbita moschata to uncover variants associated with virus resistance

    Mafireyi, GodwinStellenbosch : Stellenbosch University2026

    … as input. The pangenome was then used to perform variant analysis, both short variants and structural variant (SV) analysis to identify genomic diversity among these lines. For trait mapping, BSAseq was carried out using DNA extracted from highly resistant F2 (second filial generation) individuals …

    stellenbosch Repository record

  10. Establishing the feasibility of using ctDNA for molecular profiling in DLBCL

    Cutmore, Natasha HelenUniversity of Cambridge2024

    … was to develop and validate a custom somatic variant calling and annotation pipeline for use on DLBCL FFPE biopsy and plasma ctDNA samples. This was conducted in the context of a prospective observational clinical trial, DIRECT. After establishing the variant calling pipeline, the next aim of …

    cambridge Repository record

  11. Driver genes, mutational signatures and the timing of mutations in oesophageal adenocarcinoma

    Weaver, JamesUniversity of Cambridge2020

    … of cancer. By studying single nucleotide variants from 43 tumours I was able to identify the signatures of 7 mutational processes acting on the OAC genome. These include ageing, enzymatic DNA damage (by the APOBEC enzymes) and homologous recombination deficiency. Two novel signatures …

    cambridge Repository record

  12. Discovery and characterisation of the novel, pathological GNB3 mutation (D153del/ Gβ<sub>3D</sub>), in the retinopathy globe enlarged (rge) chicken

    Tummala, HemanthUniversity of Abertay Dundee2008

    The common human GNB3 825C>T variant, which is present in 50% of the world’s chromosomes, has previously been shown to predispose individuals to hypertension, cardiac and neural disorders. This variant causes the production of a stable and gain of function protein Gβ<sub>3S</sub>- This thesis …

    abertay Repository record

  13. The Contribution of Structural Variants to 2,095 Molecular Phenotypes in 12,354 European Ancestry Individuals

    Howell, BrittanyUniversity of Cambridge2022

    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 …

    cambridge Repository record

  14. Genetic and Epigenetic Interactions in in vivo and in vitro Reprogramming

    Young, Margaret Ashley2013

    … We found an average of 414 somatic nucleotide variants: SNVs) per iPS clone, with variant allele frequencies suggesting that the mutations occurred at or before reprogramming. In one experiment, four independent iPS clones contained 164 identical variants: 6 protein-coding SNVs, 157 non-coding …

    wustl Repository record

  15. Genomics and ecology of rapid adaptation: the expansion and evolution of the invasive common myna (<i>Acridotheres tristis</i>) and common starling (<i>Sturnus vulgaris</i>) in New Zealand

    Atsawawaranunt, KamolphatResearchSpace@Auckland2024

    … an alpha-amylase gene, a non-coding RNA, and a structural variant containing a transposable element. Variants were fixed or close-to-fixed in invasive populations but polymorphic in native populations. Genes in the alpha-amylase family have been associated with adaptation to high-starch diets in …

    auckland-ms Repository record

  16. Crystallization and melting behavior of an aromatic semicrystalline polyimide, LaRC CPI-2

    Brandom, Donald KeithVirginia Tech1996

    … - second generation). This aromatic polyimide, a structural variant of the well known LaRC CPI, is synthesized froml 1,4-bis( 4-aminophenoxy-4' -benzoyl)benzene (1,4-BABB) and 4,4' -oxydiphthalic dianhydride (ODPA). The multiple melting behavior at ca. 334°C and 364°C, characteristic of this …

    vt Repository record

  17. Towards a Pangenome Perspective on the Lake Malawi Cichlid Radiation

    Quah, FuUniversity of Cambridge2024

    … has the limitation of ignoring larger scale structural variation that has great potential to cause alterations to phenotype. To better address this question, I adopt a pangenomic approach by constructing a multiassembly graph of the haplochromine cichlids in Lake Malawi, making use of newly …

    cambridge Repository record

  18. Bioinformatics pipeline development for analyses of data generated by target capture-based Next-Generation Sequencing, to characterise mutations and the utility of using off-target sequences to detect genomic imbalances in Multiple Myeloma patients.

    Coysh, AlixResearchSpace@Auckland2023

    … by available methods, especially regarding structural variant (SV)/copy number alteration (CNA) detection. This study aimed to exemplify target-capture Next-Generation Sequencing data utility in bioinformatics-mediated sequence variant/SV/CNA detection, using a 1,138-gene cancer gene panel …

    auckland-ms Repository record

  19. Sequencing in Isolation: Next-generation sequencing studies in founder populations

    Gilly, Arthur LeonardUniversity of Cambridge2019

    Although common variants are routinely assayed in populations, rare mutations and copy-number variants are understudied contributors to the aetiology of complex traits. Isolated populations hold the promise of increased power gains in detecting associations in rare and low-frequency variants that …

    cambridge Repository record

  20. Reconstructing Chromothriptic Chromosomes in Oesophageal Adenocarcinomas

    Ijaz, JannatUniversity of Cambridge2021

    … how the genome is regulated. Complex regions of structural variation between alleles in cancer genomes coupled with subclonal variants means haplotype-aware de novo assemblies are essential for contiguous cancer genome assemblies. Our method takes haplotype blocks and assigns PacBio circular …

    cambridge Repository record

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