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Showing 1 to 20 of 37 for “"Variant Calling"”.
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Computational methods for genomic variant calling and analysis
… markers for association with phenotypic traits. Variant calling refers to the process of detecting genetic polymorphisms based on analysis of genome sequence data output by NGS technology. The projects described here investigate these analysis methods. Chapter One reviews variant calling and its …
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Empirical accuracy bounds for next-generation sequencing variant calling workflows
… the accuracy bounds imposed on alignment-based variant calling workflows due to inherent uncertainties introduced by sequencing platforms. In this work we will use simulated data to empirically quantify the maximum performance that can be expected for alignment and variant detection accuracy in …
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Hardware acceleration of the pair HMM algorithm for DNA variant calling
Made available in DSpace on 2017-08-10T19:16:15Z (GMT). No. of bitstreams: 2 HUANG-THESIS-2017.pdf: 3198752 bytes, checksum: 355bc51ce749cb631e269cc6116f3c3f (MD5) LICENSE.txt: 4208 bytes, checksum: 29aa487d1a5b8c7beed523d9c3a35801 (MD5) Previous issue date: 2017-04-26
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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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Germline Mutation Detection In Next Generation Sequencing Data and Tp53 Mutation Carrier Probability Estimation For Li-Fraumeni Syndrome
… has been compromised by the missing true variants, especially when these variants are rare. We proposed a family-based variant calling method, FamSeq, integrating Mendelian transmission information with <em>de novo</em> mutation and sequencing data to improve the variant calling accuracy. …
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Improving quality of high-throughput sequencing reads
… analyzes the effect of sequencing errors on variant calling, which is one of the most important clinical applications for HTS data. For this, the environments for tracing the effect of sequencing errors on germline and somatic variant calling was developed. Using the environment, this …
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Navigating through the uncertainty of genotyping-by-sequencing data in polyploids
… in non-model species, including polyploids. Variant and genotype calling methods have been established for autopolyploids but for a species with a complex genome, such as sugarcane, the level of uncertainty within GBS data increases making trait mapping difficult. Furthermore, variant and …
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Statistical analysis of short template switch mutations in human genomes
… 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 …
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Applying deep learning technologies to discovery and characterization of genetic variants in animal genomes
… for research using billions of genomic variants. An incomplete understanding of error plateaued further advancement, but we can now account for known and unknown errors with genomics-specific, deep-neural networks. However, they often contain assumptions based on the human genome. Here, …
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Development of An In Silico Kir Genotyping Algorithm and Its Application to Population and Cancer Immunogenetic Analyses
<p>Gene content determination and variant calling in the complex KIR genomic region are useful for immune system function analysis, pathogenesis and disease risk factor elucidation, immunotherapy development, evolutionary investigations, and human migration modeling. Sequence-specific …
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Bioinformatics Analysis of Whole-Exome Sequencing Data for the Identification of Nuclear and Chloroplast Diversity in Barley
… improving our ability to identify genetic variants that can affect heritable phenotypes. However, sequencing whole genomes is still an expensive and time-consuming process compared to targeted sequencing. In this study, targeted exome sequencing data from a large set of diverse …
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A sequencing-based analyisis of epigenetic modifications of the mitochondrial genome
… and assess the accuracy of a protocol for variant-specific methylation identification using long-read based technology Oxford Nanopore Sequencing. Our approach circumvents mtDNA-specific confounders, while enriching for native full-length molecules over nuclear DNA. Variant calling analysis …
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Establishing the feasibility of using ctDNA for molecular profiling in DLBCL
… 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 …
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Leveraging Whole Genome Sequences to Compare Mutational Mechanism and Identify Medically Relevant Variation in African versus Non-African Descend Populations
… WGS downstream analysis are accurate, mainly the variant calling (VC). Current VC tools may produce falsepositive/negative results; such result may produce misleading conclusions in prioritisation of mutation, clinical relevancy and actionability of genes. With such many VC tools, two questions …
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Compressive algorithms for search and storage in biological data
… we also present work on filtering empirical base-calling quality scores from Next Generation Sequencing data. By using the sparsity of k-mers of sufficient length in the human genome and imposing a human prior through the use of frequent k-mers in a large corpus of human DNA reads, we are able to …
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Hardware acceleration of the SAMtools variant caller
… implementation of the SAMtools variant caller on an FPGA. It also includes a performance analysis of the algorithm and a proposed change to its software architecture to improve performance. SAMtools is normally invoked as a two-step command, where the results of samtools mpileup …
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Simultaneous SNV calling and Phylogenetic Inference for Single-cell Sequencing Data
… allelic dropout, and non-uniform coverage. Variant calling in this context is the task of identifying mutations in the genomes of individual cells while accounting for the multiple types of errors. One powerful approach for solving this task computationally is to rely on a phylogenetic …
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A Quantitative Exploration of Causes of False Positive Single Nucleotide Polymorphisms in Next-Generation Sequencing Data
… sequence, read length, choice of mapper and variant caller, mapping stringency, and filtering of SNPs by read mapping quality and read depth. The study shows that both paralogs and the choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP …
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Role of inherited DNA repair deficiencies in cancer susceptibility and evolution
… from family trios and a carefully curated variant calling pipeline, my results support the hypothesis that inherited DNA repair deficiencies impact germline mutational processes. Offspring from parents with germline DNA repair deficiencies have significantly increased burdens of pre-zygotic …
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