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 11 of 11 for “"Variant discovery"”.
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Optimizing analysis pipelines for improved variant discovery
… genomic features such as indels, Copy Number Variants (CNVs), or microsatellite repeats. Here is the development of accuracy measurements in read alignment and variation calls, allowing the optimization of sequencing pipelines at all stages. The underlying hypothesis, then, is that different …
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A new filtering method for improving the quality of variant discovery
Variants identified by current genomic analysis pipelines contain many incorrectly called variants. These can be potentially eliminated by applying state-of-the-art filtering tools, such as Variant Quality Score Recalibration (VQSR) or Hard Filtering (HF). However, these methods are very …
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Improved prediction and optimal sequencing strategies for genomic variant discovery via Bayesian nonparametrics
… have already conducted a pilot study to reveal variants in a genome and are contemplating a follow-up study. Spending additional resources has the potential to reveal new variations in the genome, and thereby new genetic insights. Therefore, practitioners are interested in (i) predicting how …
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Statistical methods for variant discovery and functional genomic analysis using next-generation sequencing data
… novel statistical methods to identify sequence variants, find transcription factor (TF) binding patterns, and decode the relationship between TF and gene expression levels. Accurate and reliable identification of sequence variants, including single nucleotide polymorphisms (SNPs) and …
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NOVEL APPROACHES IN GENETIC VARIANT DISCOVERY AND CLASSIFICATION TACKLING UNSOLVED PROBLEMS IN CANCER CLINICAL GENOMICS
Accurate interpretation of germline and somatic variants plays a pivotal role in clinical practice, providing the foundation for the correct diagnosis and targeted therapy in personalized medicine. However, variant classification is a complex process that requires the integration of multiple, often …
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Whole genomic structural variant calling in soybean: Analysis on 481 different soybean lines
… 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 …
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Structural variant calling by assembly in whole human genomes: Applications in hypoplastic left heart syndrome
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 …
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Examining bacterial variation with genome graphs and Nanopore sequencing
… first chapter, we present algorithms for de novo variant discovery within such genome graphs and evaluate their performance with empirical data. The remaining chapters address a question relating to a critical bacterial pathogen: can Nanopore sequencing of Mycobacterium tuberculosis provide …
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Construction and analysis of the miscanthus genespace
… crops. Both genomes create a challenge for variant discovery and genotyping because of their abundant repeats and the presence of a genome scale duplication with little subsequent divergence. In addition, the Miscanthus genome has high heterozygosity due to its self-incompatible breeding …
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Genetics of Cerebral Small Vessel Disease
… We next adopt a candidate gene approach to rare variant discovery using high throughput sequencing (HTS) techniques in two forms: 1) a multi-gene sequencing panel to examine the presence of rare variants in a cohort of 993 presumed-sporadic, early-onset SVD stroke patients, and 2) whole genome …
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Genetic determinants underlying rare diseases identified using next-generation sequencing technologies
… families and the health care system. Gene discovery is the starting point in understanding the molecular mechanisms underlying these diseases. The advent of next-generation sequencing has accelerated discovery of disease-causing genetic variants and is showing numerous benefits for research …