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.
Results
Showing 1 to 20 of 55 for “"indels"”.
-
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 …
-
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 …
-
Identifying and Analyzing Indel Variants in the Human Genome Using Computational Approaches
… most abundant variant type in the human genome, indels have not been studied as much as the single nucleotide polymorphism (SNP). With the advance of next-generation sequencing technology, many indel calling tools have been developed. However, performance comparison of commonly used tools has …
-
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 …
-
Predicting the Functional Effects of Human Short Variations Using Hidden Markov Models
… (SNPs), short insertions and deletions (indels), and large structural variations such as large duplications and deletions. Of great research interest is the functional effects of these variants. Although many programs have been developed to predict the effect of SNPs, few can be used to …
-
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 …
-
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 …
-
Expression and Function of the Chloroplast-encoded Gene matK
… for matK in some plant species that buffers indels (insertions and deletions) in the open reading frame (ORF) that are not in multiples of three in the gene sequence. Usually, indels not in multiples of three result in frame shifts that destroy the reading frame. Our results indicate that an …
-
Structural determinants of mutability across cancer genomes
… and transcription strand asymmetries at indels systematically for the first time. As a result, mutational processes that are causally implicated in strand asymmetries at indels were identified and analysed. These included mismatch repair and transcription-coupled nucleotide excision …
-
Functional Analysis of Genomic Variation and Impact on Molecular and Higher Order Phenotypes
… (SNPs), 0.94 million intersections/deletions (indels), and 20,000 structural variants. We systematically scanned massive databases of molecular phenotypes and ~4,000 classical phenotypes to detect linked functional consequences of sequence variants. In majority of cases we successfully …
-
Statistical methods for variant discovery and functional genomic analysis using next-generation sequencing data
… (SNPs) and insertion-deletion polymorphisms (INDELs), plays a fundamental role in NGS applications. Existing methods for calling these variants often make simplified assumption of positional independence and fail to leverage the dependence of genotypes at nearby loci induced by linkage …
-
Cas9-induced on-target genomic damage
… followed the time dynamics of Cas9-induced small indels as a function of reagent delivery methods, established an assay for quantification of Cas9-induced genomic lesions that are not small indels ("complex lesions") and used this assay to isolate and genotype complex lesions, many of which would …
-
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 …
-
Genome-graph based genotyping with applications to highly variable genes in P. falciparum
… state-of-the-art: jointly studying small (SNPs, indels) and large (indels >50bp) variation, and accessing variation on multiple references. I validate these methods using different datasets, ultimately genotyping SNPs on diverged haplotypes in two highly variable Pf genes, including one gene from …
-
The evolution of mRNA splicing in mammals
… I also present evidence implicating genomic indels in exon creation and splicing variation.
-
Structural variant calling by assembly in whole human genomes: Applications in hypoplastic left heart syndrome
… 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 from short-read alignments, and thus many software applications aimed at detecting …
-
The ecology, life history, and phylogeny of the marine thecate heterotrophic dinoflagellates Protoperidinium and Diplopsalidaceae (Dinophyceae)
… single base pair insertion/deletions (indels), and/or large indels. Phylogenetic analysis of all clones gave strong support for monophyly of the polymorphic copies of each species, and recovered the same species tree as an analysis using just one sequence per species. Analysis of LSU …
-
Characterising the evolutionary dynamics of hypermutated tumours using single-cell sequencing
… in an elevated rate of point mutations and indels, called hypermutation, which leads to a high burden of neoantigens and increased tumour immunogenicity. As a result, hypermutated cancers show the highest response rates to immune checkpoint blockade (ICB), a type of immunotherapy that has …
-
Complete computational sequence characterization of mobile element variations in the human genome using meta-personal genome data
… single nucleotide polymorphisms (SNPs) and small indels, comparatively 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 …
-
Integrated Multimodal Genomic Analyses Reveal Novel Mechanisms of Glucocorticoid Resistance in Acute Lymphoblastic Leukemia
… expression, DNA methylation, SNPs, CNAs and SNVs/Indels) in primary human acute lymphoblastic leuke</p>
Page 1 of 3