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 34 for “"Indel"”.
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Identifying and Analyzing Indel Variants in the Human Genome Using Computational Approaches
Insertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. Despite this importance and being the second most abundant variant type in the human genome, indels have not been studied as much as the single nucleotide …
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Characterization of virus strain- and pig age-dependence of porcine epidemic diarrhea virus: Implications for vaccine development
… have been circulating in U.S. swine herds: non-S INDEL and S INDEL PEDVs. While two commercially available vaccines (one killed PEDV vaccine and one RNA particle PEDV vaccine) exist in the U.S., their efficacy is limited in naïve pigs. Therefore, a safe and efficacious PEDV vaccine is still needed …
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Improving Dbnsfp
… 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 my project is to provide an automatic …
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Evaluation of insertion / deletion polymorphisms (INDELs) applied to forensic casework in Malaysia
… Insertion/deletion polymorphisms (INDELs) are relatively new class of a DNA marker used in forensic casework; used most commonly as a supplementary method to STR (Short Tandem Repeat) based typing. INDELs, like SNPs (Single Nucleotide Polymorphisms), are particularly useful for the …
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Structural determinants of mutability across cancer genomes
… regions. A detailed characterisation of indel mutagenesis was performed across the different cancer types. The analysis indicated the roles of different non-B DNA motif categories as well as sequence homologies in indel mutagenesis. In particular, sequence characteristics of a subset of …
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Application of autosomal INDELs as a forensic tool in Qatar
… marker, insertion deletion polymorphisms (INDELs), offer an effective way to analyze challenged DNA sample (degraded and inhibited ones). INDELs have short amplicons, low mutation rates, no stutter peaks and are analyzed using the same equipment and protocols as STR polymorphisms. In this …
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Incidence of aminoglycoside-induced hearing loss in HIV positive and HIV negative multidrug-resistant tuberculosis patients
… (A1555G, C1494T, T1095C, T1291C, A827G and 961 indel C) in a cohort of MDR-TB patients; To determine whether HIV positive MDR-TB patients are more likely to develop aminoglycoside-induced hearing loss than HIV negative MDR-TB patients; To provide clinical guidelines to the medical fraternity on …
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Characterising fitness landscapes of protein evolution by next-generation sequencing
… shows that short insertions and deletions (InDels) also play a key role. Beyond rare targeted studies of specific InDels, high-throughput data on fitness landscape for mutations other than substitutions are lacking entirely. In my PhD, I worked towards experimentally describing the fitness …
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Mechanisms of Genome Buffering and Cell Fate Coordination in Adult Tissue Homeostasis
… buffer the proteome against insertion/deletion (INDEL)-type genetic mutations. Wnt-mediated signaling is essential for embryogenesis and the maintenance of adult tissues. Lipidation of Wnt proteins by the acyltransferase Porcupine (Porcn) is crucial for secretory pathway exiting. Using chemically …
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Risk prediction with genomic data
… and deletions in the genomic sequence (INDEL) together with SNPs as a feature for prediction. A substantial improvement in the prediction accuracy is achieved using the latter approach. The success of the approach of using NSG data shows that it contains valuable information which the …
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The direct injection of CRISPR/Cas9 system into porcine zygotes for genetically modified pig production
… of mutated pigs was that insertion or deletion (indel) mutations did not always introduce a premature stop codon because it did not interfere with the codon read. As a result of these triplet indel(s) mutations, a hypomorphic phenotype was presented; consequently, the mutated gene was partially …
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Avaliação da relação entre polimorfismos dos genes beta-defensina e mbl2 e a predisposição à infecção pela Leishmania infantum chagasi em cães de Serra Talhada, Pernambuco
… OR = 37.36 (1.55 – 903.16)). Para MBL2 apenas um indel foi encontrado e não apresentou associação significativa com L. infantum, obtendo um valor de p<0,21, possivelmente por apresentar um baixo número de indivíduos infectados e polimorfismos nas sequencias obtidas.
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Whole genomic structural variant calling in soybean: Analysis on 481 different soybean lines
… 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 assembly-based variant discovery and …
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The impact of cytotoxic chemotherapy on somatic mutation in normal human cells
… (DBS), and small insertions and deletions (indels). Treatment of normal human cells with chemotherapy drugs and environmental agents *in vitro* demonstrated mutational signatures associated with a wide range of agents. Alkylating and platinum-based agents were the most mutagenic classes of …
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Cancer risk prediction with next generation sequencing data using machine learning
… Polymorphism (SNP) and Insertion Deletion (INDEL) are identified and are filtered using SAMtools as well as with Genome Analyzer Tool Kit (GATK). Subsequently, the variants are encoded and feature selection is performed with the Pearson correlation coefficient (PCC) and the chi-square 2-df …
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Cas9-induced on-target genomic damage
… Cas9 delivery format influences the dynamics of indel introduction. Finally, many studies of on-target activity were conducted in cancerous cell lines, which do not accurately model the mutagenesis of normal cells in the therapeutic context. In my thesis, I have investigated on-target lesions …
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In Vitro Evolution of Antibody Affinity using Libraries with Insertions and Deletions
… and a small percentage of insertions/deletions (indels). Although the percentage of indels in affinity matured antibodies is low, probably due to the low rate incorporation of in-frame indels throughout the course of the SHM diversification process, it is likely that the antibody fold can …
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Probabilistic Model-Based Approach to Evolutionary Analysis of Non-Coding Sequences
… the locations of insertions and deletions (indels) in a multiple alignment. Its performance is found to be better than that obtained by a parsimony-based method. We study the evolution of sequences involved in the regulation of body patterning in the Drosophila embryo, reporting statistical …
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Interrogation of CRISPR-Cas targeting specificity for mammalian genome engineering
… cleavage by Cas9 as well as relative rates of indel, chromosomal rearrangement, and translocation accompanying NHEJ repair. However, insert capture is largely limited to use in model cell lines and is fundamentally limited in sensitivity due to labeling of low frequency errors in DSB repair. To …
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Rethinking phylogenetics using Caryophyllales (angiosperms), matK gene and trnK intron as experimental platform
… Ephedra based on the presense of a 38 base pair indel in several species that otherwise result in pre-mature stop codons, and present 20 RNA edited sites in two Zamiaceae and three Pinaceae species.
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