Дисертації з теми "Next Generation Sequencin"
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Espach, Yolandi. "The detection of mycoviral sequences in grapevine using next-generation sequencing." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/80025.
Повний текст джерелаENGLISH ABSTRACT: Metagenomic studies that make use of next-generation sequencing (NGS) generate large amounts of sequence data, representing the genomes of multiple organisms of which no prior knowledge is necessarily available. In this study, a metagenomic NGS approach was used to detect multiple novel mycoviral sequences in grapevine phloem tissue. Individual sequencing libraries of doublestranded RNA (dsRNA) from two grapevine leafroll diseased (GLD) and three shiraz diseased (SD) vines were sequenced using an Illumina HiScanSQ instrument. Over 3.2 million reads were generated from each of the samples and these reads were trimmed and filtered for quality before being de novo assembled into longer contigs. The assembled contigs were subjected to BLAST (Basic Local Alignment Search Tool) analyses against the NCBI (National Centre for Biotechnology Information) database and classified according to database sequences with which they had the highest identity. Twenty-six putative mycovirus species were identified, belonging to the families Chrysoviridae, Endornaviridae, Narnaviridae, Partitiviridae and Totiviridae. Two of the identified mycoviruses, namely grapevine-associated chrysovirus (GaCV) and grapevine-associated mycovirus 1 (GaMV-1) have previously been identified in grapevine while the rest appeared to be novel mycoviruses not present in the NCBI database. Primers were designed from the de novo assembled mycoviral sequences and used to screen the grapevine dsRNA used for sequencing as well as endophytic fungi isolated from the five sample vines. Only two mycoviruses, related to sclerotinia sclerotiorum partitivirus S and chalara elegans endornavirus 1 (CeEV-1), could be detected in grapevine dsRNA and in fungus isolates. In order to validate the presence of mycoviruses in grapevine phloem tissue, two additional sequencing runs, using an Illumina HiScanSQ and an Applied Biosystems (ABI) SOLiD 5500xl instrument respectively, were performed. These runs generated more and higher quality sequence data than the first sequencing run. Twenty-two of the putative mycoviral sequences initially detected were detected in the subsequent sequence datasets, as well as an additional 29 species not identified in the first HiScanSQ sequence datasets. The samples harboured diverse mycovirus populations, with as many as 19 putative species identified in a single vine. This indicates that the complete virome of diseased grapevines will include a high number of mycoviruses. Additionally, the complete genome of a novel endornavirus, for which we propose the name grapevine endophyte endornavirus (GEEV), was assembled from one of the second HiScanSQ sequence datasets. This is the first complete genome of a mycovirus detected in grapevine. Grapevine endophyte endornavirus has the highest sequence similarity to CeEV-1 and is the same virus that was previously detected in fungus isolates using the mycovirus primers. The virus was detected in two fungus isolates, namely Stemphylium sp. and Aureobasidium pullulans, which is of interest since mycoviruses are not known to be naturally associated with two distinctly different fungus genera. Mycoviral sequence data generated in this study can be used to further investigate the diversity and the effect of mycoviruses in grapevine.
AFRIKAANSE OPSOMMING: Metagenomiese studies, wat gebruik maak van volgende-generasie volgordebepalingstegnologie, het die vermoë om die genetiese samestelling van veelvoudige onbekende organismes te bepaal deurdat dit groot hoeveelhede data genereer. Die bogenoemde tegniek was in hierdie studie aangewend om aantal nuwe mikovirusse in die floëem weefsel van wingerd te identifiseer. Dubbelstring-RNS was gesuiwer vanuit twee druiwestokke met rolbladsiekte en drie met shirazsiekte en Illumina HiScanSQ instrument is gebruik om meer as 3.2 miljoen volgorde fragmente te genereer van elk van die monsters. Lae-kwaliteit volgordes was verwyder en die oorblywende kort volgorde fragmente was saamgestel om langer konstrukte te vorm wat met behulp van BLAST soektogte teen die NCBI databasis geïdentifiseer kon word. Ses-en-twintig mikovirus spesies, wat aan die families Chrysoviridae, Endornaviridae, Narnaviridae, Partitiviridae en Totiviridae behoort, was geïdentifiseer. Twee van die geïdentifiseerde mikovirusse, naamlik grapevine-associated chrysovirus (GaCV) en grapevine-associated mycovirus 1 (GaMV-1), was voorheen al in wingerd gekry terwyl die res nuwe mikovirusse is wat tans nie in die NCBI databasis voorkom nie. Inleiers was ontwerp vanaf die saamgestelde mikovirus basisvolgordes en gebruik om wingerd dubbelstring-RNS sowel as swamme wat vanuit die wingerd geïsoleer is te toets vir die teenwoordigheid van hierdie mikovirusse. Slegs twee mikovirusse, wat onderskeidelik verwant is aan sclerotinia sclerotiorum partitivirus S en chalara elegans endornavirus 1 (CeEV-1), kon deur middel van die inleiers in wingerd en swam isolate geïdentifiseer word. Twee addisionele volgordebepalingsreaksies, wat gebruik gemaak het van die Illumina HiScanSQ en ABI SOLiD 5500xl volgordebepalingsplatforms, was gebruik om die teenwoordigheid van mikovirusse in wingerd te bevestig. Groter hoeveelheid volgorde fragmente was geprodusser wat ook van hoër gehalte was as dié van die eerste volgordebepalingsreaksie. Twee-en-twintig mikovirus spesies kon weer geïdentifiseer word, sowel as 29 spesies wat nie in die eerste HiScanSQ basisvolgorde datastelle gevind was nie. Die wingerdstokke wat in hierdie studie ondersoek was, het hoë diversiteit van mikovirusse bevat aangesien daar tot 19 mikovirus spesies in enkele wingerdstok geïdentifiseer was. Dit is aanduiding dat volledige virus profiele van siek wingerdstokke aantal mikovirusse sal insluit. Die vollengte genoomvolgorde van voorheen onbekende endornavirus was saamgestel vanuit een van die tweede HiScanSQ volgorde datastelle. Dit is die eerste mikovirus wat in wingerd gevind word waarvan die volledige genoomvolgorde bepaal is en ons stel die naam grapevine endophyte endornavirus (GEEV) voor vir hierdie virus. Grapevine endophyte endornavirus is die naaste verwant aan CeEV-1 en is dieselfde virus wat voorheen in wingerd dubbelstring-RNS en swam isolate gevind was deur middel van die mikovirus inleiers. Swam isolate waarin GEEV gevind is, was geïdentifiseer as Stemphylium sp. en Aureobasidium pullulans. Dit is van belang dat GEEV in twee swam isolate gevind is wat aan verskillende genusse behoort aangesien hierdie verskynsel nog nie voorheen in die natuur gevind is nie. Mikovirus nukleiensuurvolgordes wat in hierdie studie bepaal was kan gebruik word in toekomstige studies om die verskeidenheid en impak van mikovirusse in wingerd verder te ondersoek.
National Research Foundation (NRF)
Stellenbosch University
TROVÃO, Nídia Isabel Sequeira. "Evaluation of next generation sequency protocols for VIH complete genome sequencing." Master's thesis, Instituto de Higiene e Medicina Tropical, 2011. http://hdl.handle.net/10362/51111.
Повний текст джерелаHuman immunodeficiency virus (HIV) is a retrovirus that gave rise to a worldwide epidemic after its successful zoonotic transmission in the first half of the twentieth century. Current therapy, referred to as Highly Active AntiRetroviral Therapy (HAART), can significantly delay disease progression. However, despite more than 25 years of intensive research there is still no cure available. All available antiretroviral drugs are faced with the insurmountable challenge posed by the high evolutionary potential of HIV. This implies that regardless the administered drug cocktail, drug resistance can and will develop. To manage these negative effects, patients should be screened on a regular basis in order to detect the development of drug resistance in an early phase, so the therapy regimen can be timely adjusted. Importantly, both drug resistant variants that have evolved de novo or were acquired through transmission can negatively impact on therapy outcome. Thus, also therapy-naive patients should be screened before therapy onset. This screening usually involves genotyping of the viral population through the direct sequencing of the RT-PCR products. Unfortunately, this approach does not allow the reliable detection of viral variants present in less then at about 20%-25% of the population. The association of such minor variants harboring drug resistance mutations with therapy failure fueled investigations to exploit the recently developed Roche® 454 NGS platform in an attempt to gain a more accurate in-depth view of the viral population. These inquiries are characterized by two major drawbacks: their focus on limited genomic regions and the need for large amounts of input material characteristic for the proprietary Roche® 454 fragmentation approach. As part of a larger project on the comparison of currently available sample preprocessing protocols for complete genome sequencing of clinical HIV plasma and PBMC samples, and the identification of the most suitable viral reservoir for resistance testing in newly infected patients as a secondary objective, this thesis focuses on the corresponding practical aspects of pre-processing prior to sequence data generation. Specifically, all wet-lab procedures for both the sequence-specific and random priming amplification strategies were carried out. For the former, we generated 6 overlapping amplicons to cover the entire HIV-1 genome. After equimolar pooling of all amplicons for each sample, we performed two enzymatic fragmentation methods. These will be compared to conventional mechanical 454 shearing. The successful sequencing of one sample and the completion of all sample pre-processing procedures is promising for further applications but a comprehensive evaluation of the sequence data to be generated is necessary to make an informed choice among the different approaches.
Sundquist, Andreas. "Algorithms for next-generation sequencing /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
Повний текст джерелаEspírito, Ana Cláudia Pereira. "Saccharomycotin transcriptomics by next-generation sequencing." Master's thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/15677.
Повний текст джерелаThe non-standard decoding of the CUG codon in Candida cylindracea raises a number of questions about the evolutionary process of this organism and other species Candida clade for which the codon is ambiguous. In order to find some answers we studied the transcriptome of C. cylindracea, comparing its behavior with that of Saccharomyces cerevisiae (standard decoder) and Candida albicans (ambiguous decoder). The transcriptome characterization was performed using RNA-seq. This approach has several advantages over microarrays and its application is booming. TopHat and Cufflinks were the software used to build the protocol that allowed for gene quantification. About 95% of the reads were mapped on the genome. 3693 genes were analyzed, of which 1338 had a non-standard start codon (TTG/CTG) and the percentage of expressed genes was 99.4%. Most genes have intermediate levels of expression, some have little or no expression and a minority is highly expressed. The distribution profile of the CUG between the three species is different, but it can be significantly associated to gene expression levels: genes with fewer CUGs are the most highly expressed. However, CUG content is not related to the conservation level: more and less conserved genes have, on average, an equal number of CUGs. The most conserved genes are the most expressed. The lipase genes corroborate the results obtained for most genes of C. cylindracea since they are very rich in CUGs and nothing conserved. The reduced amount of CUG codons that was observed in highly expressed genes may be due, possibly, to an insufficient number of tRNA genes to cope with more CUGs without compromising translational efficiency. From the enrichment analysis, it was confirmed that the most conserved genes are associated with basic functions such as translation, pathogenesis and metabolism. From this set, genes with more or less CUGs seem to have different functions. The key issues on the evolutionary phenomenon remain unclear. However, the results are consistent with previous observations and shows a variety of conclusions that in future analyzes should be taken into consideration, since it was the first time that such a study was conducted.
A descodificação não-standard do codão CUG na Candida cylindracea levanta uma série de questões sobre o processo evolutivo deste organismo e de outras espécies do subtipo Candida para as quais o codão é ambíguo. No sentido de encontrar algumas respostas procedeu-se ao estudo do transcriptoma de C. cylindracea, comparando o seu comportamento com o de Saccharomyces cerevisiae (descodificador standard) e de Candida albicans (descodificador ambíguo). A caracterização do transcriptoma foi realizada a partir de RNA-seq. Esta metodologia apresenta várias vantagens em relação aos microarrays e a sua aplicação encontra-se em franca expansão. TopHat e Cufflinks foram os softwares utilizados na construção do protocolo que permitiu efectuar a quantificação génica. Cerca de 95% das reads alinharam contra o genoma. Foram analisados 3693 genes, 1338 dos quais com codão start não-standard (TTG/CTG) e a percentagem de genoma expresso foi de 99,4%. Maioritarimente, os genes têm níveis de expressão intermédios, alguns apresentam pouca ou nenhuma expressão e uma minoria é altamente expressa. O perfil de distribuição do codão CUG entre as três espécies é muito diferente, mas pode associar-se significativamente aos níveis de expressão: os genes com menos CUGs são os mais altamente expressos. Porém, o conteúdo em CUG não se relaciona com o nível de conservação: genes mais e menos conservados têm, em média, igual número de CUGs. Os genes mais conservados são os mais expressos. Os genes de lipases corroboram os resultados obtidos para os genes de C. cylindracea em geral, sendo muito ricos em CUGs e nada conservados. A quantidade reduzida de codões CUG que se observa em genes altamente expressos pode dever-se, eventualmente, a um número insuficiente de genes de tRNA para fazer face a mais CUGs sem comprometer a eficiência da tradução. A partir da análise de enriquecimento foi possível confirmar que os genes mais conservados estão associados a funções básicas como tradução, patogénese e metabolismo. Dentro destes, os genes com mais e menos CUGs parecem ter funções diferentes. As questões-chave sobre o fenómeno evolutivo permanecem por esclarecer. No entanto, os resultados são compatíveis com as observações anteriores e são apresentadas várias conclusões que em futuras análises devem ser tidas em consideração, já que foi a primeira vez que um estudo deste tipo foi realizado.
Kumar, Sujai. "Next-generation nematode genomes." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7609.
Повний текст джерелаQiao, Dandi. "Statistical Approaches for Next-Generation Sequencing Data." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10689.
Повний текст джерелаIceton, Gregg. "Next generation sequencing for the water industry." Thesis, University of Newcastle upon Tyne, 2018. http://hdl.handle.net/10443/4187.
Повний текст джерелаOdelgard, Anna. "Coverage Analysis in Clinical Next-Generation Sequencing." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-379228.
Повний текст джерелаClifford, Harry William. "Next generation sequencing in disease-relevant tissues." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:cf2eb0ac-62dd-41c7-896d-35f11f416b82.
Повний текст джерелаPyon, Yoon Soo. "Variant Detection Using Next Generation Sequencing Data." Case Western Reserve University School of Graduate Studies / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=case1347053645.
Повний текст джерелаSala, Claudia. "Ecological modelling for next generation sequencing data." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2013. http://amslaurea.unibo.it/6279/.
Повний текст джерелаRoyall, Ariel. "Next-generation Sequencing Methods for Complex Communities." Thesis, University of Oregon, 2017. http://hdl.handle.net/1794/22682.
Повний текст джерелаRandel, Melissa. "New Technology Development for Next-Generation Sequencing." Thesis, University of Oregon, 2017. http://hdl.handle.net/1794/22704.
Повний текст джерелаBERETTA, STEFANO. "Algorithms for next generation sequencing data analysis." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2013. http://hdl.handle.net/10281/42355.
Повний текст джерелаSuren, Haktan. "Sequence capture as a tool to understand the genomic basis for adaptation in angiosperm and gymnosperm trees." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/86383.
Повний текст джерелаPh. D.
Tork, Bassam A. "VIRAL QUASISPECIES RECONSTRUCTION USING NEXT GENERATION SEQUENCING READS." Digital Archive @ GSU, 2013. http://digitalarchive.gsu.edu/cs_diss/77.
Повний текст джерелаBusby, Michele Anne. "Measuring Gene Expression With Next Generation Sequencing Technology." Thesis, Boston College, 2012. http://hdl.handle.net/2345/3145.
Повний текст джерелаWhile a PhD student in Dr. Gabor Marth's laboratory, I have had primary responsibility for two projects focused on using RNA-Seq to measure differential gene expression. In the first project we used RNA-Seq to identify differentially expressed genes in four yeast species and I analyzed the findings in terms of the evolution of gene expression. In this experiment, gene expression was measured using two biological replicates of each species of yeast. While we had several interesting biological findings, during the analysis we dealt with several statistical issues that were caused by the experiment's low number of replicates. The cost of sequencing has decreased rapidly since this experiment's design and many of these statistical issues can now practically be avoided by sequencing a greater number of samples. However, there is little guidance in the literature as to how to intelligently design an RNA-Seq experiment in terms of the number of replicates that are required and how deeply each replicate must be sequenced. My second project, therefore, was to develop Scotty, a web-based program that allows users to perform power analysis for RNA-Seq experiments. The yeast project resulted in a highly accessed first author publication in BMC Genomics in 2011. I have structured my dissertation as follows: The first chapter, entitled General Issues in RNA-Seq, is intended to synthesize the themes and issues of RNA-Seq statistical analysis that were common to both papers. In this section, I have discussed the main findings from the two papers as they relate to analyzing RNA-Seq data. Like the Scotty application, this section is designed to be "used" by wet-lab biologists who have a limited background in statistics. While some background in statistics would be required to fully understand the following chapters, the essence of this background can be gained by reading this first chapter. The second and third chapters contain the two papers that resulted from the two RNA-Seq projects. Each chapter contains both the original manuscript and original supplementary methods and data section. Finally, I include brief summaries of my contributions to the two papers on which I was a middle author. The first was a functional analysis of the genomic regions affected by mobile element insertions as a part of Chip Stewart's paper with the 1000 Genome Consortium. This paper was published in Plos Genetics. The second was a cluster analysis of microarray gene expression in Toxoplasma gondii, which was included as part of Alexander Lorestani et al.'s paper, Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1. This paper is currently under review. The yeast project was a collaborative effort between Jesse Gray, Michael Springer, and Allen Costa at Harvard Medical School, Jeffery Chuang here at Boston College, and members of the Marth lab. Jesse Gray conceived of the project. While I wrote the draft for the manuscript, many people, particularly Gabor Marth, provided substantial guidance on the actual text. I conceived of and implemented Scotty and wrote its manuscript with only editorial assistance from my co-authors. I produced all figures for the two manuscripts. Chip Stewart provided extensive guidance and mentorship to me on all aspects of my statistical analyses for both projects
Thesis (PhD) — Boston College, 2012
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
Laver, Thomas William. "Evaluating metagenomic quantifications from next-generation sequencing data." Thesis, University of Exeter, 2014. http://hdl.handle.net/10871/17439.
Повний текст джерелаLjungström, Viktor. "Exploring next-generation sequencing in chronic lymphocytic leukemia." Doctoral thesis, Uppsala universitet, Experimentell och klinisk onkologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-302026.
Повний текст джерелаCui, Hongzhu. "In Silico Edgetic Profiling and Network Analysis of Human Genetic Variants, with an Application to Disease Module Detection." Digital WPI, 2020. https://digitalcommons.wpi.edu/etd-dissertations/596.
Повний текст джерелаNafisinia, Michael. "Gene Discovery for Genetic Disorders using Next Generation Sequencing and Functional Genomics." Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/16867.
Повний текст джерелаDAL, MOLIN MATTEO. "Identification and validation of DNA sequence variants in cancer predisposition genes by next generation sequencing approaches." Doctoral thesis, Università degli studi di Pavia, 2022. https://hdl.handle.net/11571/1468217.
Повний текст джерелаDAL, MOLIN MATTEO. "Identification and validation of DNA sequence variants in cancer predisposition genes by next generation sequencing approaches." Doctoral thesis, Università degli studi di Pavia, 2022. https://hdl.handle.net/11571/1468215.
Повний текст джерелаKislyuk, Andrey O. "Algorithm development for next generation sequencing-based metagenome analysis." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/42779.
Повний текст джерелаDupuis, Sandoval Fabien. "Exploring optimal snoRNA profiling using Next Generation Sequencing methods." Mémoire, Université de Sherbrooke, 2018. http://hdl.handle.net/11143/11931.
Повний текст джерелаDes avancées récentes dans le domaine du séquençage de prochaine génération ont ouvert une panoplie de façons de générer des données. Toutefois, chaque nouvelle méthode dévelopée est souvent appropriée à la caractérisation d’un seul type de phénomène ou de molécules. L’objectif de cette analyse est d’identifier la manière la plus appropriée de générer et traiter les données pour étudier les petits ARNs nucléolaires, snoRNAs. Récemment, ceux-ci ont été révélés comme des acteurs dans une variété de fonctions alternatives comme l’épissage alternatif, la résistance au choc oxidatif et l’état de la chromatine. Il est donc impératif de trouver une méthode qui puisse traiter une large quantité de données contenant les snoRNAs et leurs intéracteurs pour découvrir les rôles encore inexplorés des snoRNAs. Dans cette optique, un nouveau protocole a été élaboré. Cette nouvelle suite d’analyses s’appuie sur une reverse transcriptase isolée d’un intron de groupe II bactérien qui affiche une meilleure représentation des petits ARNs structurés comme les tRNAs et les snoRNAs. En effet, quand les données générées à travers la méthode de préparation des libraries pour petits ARNs standard est comparée à celle basée sur la reverse transcriptase bactérienne, cette dernière donne une meilleure représentation du compte des espèces. Ces avancées sont aussi présentes dans la méthode d’analyse informatique. La suite d’outils a été modifiée afin de permettre une meilleure détection des petits ARN non-codants. Ces modifications permettent de récupérer des millions de lectures par ensemble de données ce qui augmente le pouvoir prédictif de l’analyse.
Forster, Michael [Verfasser]. "Translating Next-Generation-Sequencing into Precision Medicine / Michael Forster." Kiel : Universitätsbibliothek Kiel, 2019. http://d-nb.info/1182989748/34.
Повний текст джерелаWang, Yi, and 王毅. "Binning and annotation for metagenomic next-generation sequencing reads." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/208040.
Повний текст джерелаpublished_or_final_version
Computer Science
Doctoral
Doctor of Philosophy
Bowen, Margot Elizabeth. "Applying Next Generation Sequencing to Skeletal Development and Disease." Thesis, Harvard University, 2013. http://dissertations.umi.com/gsas.harvard:11233.
Повний текст джерелаBrown, J. R. "Next generation sequencing to understand norovirus in immunocompromised children." Thesis, University College London (University of London), 2017. http://discovery.ucl.ac.uk/1558811/.
Повний текст джерелаWasylenko, Theresa Anne. "Understanding Huntington's Disease pathogenesis using next generation sequencing analyses." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/103260.
Повний текст джерелаCataloged from PDF version of thesis. "February 2015."
Includes bibliographical references (pages 215-240).
Huntington's disease is one of nine expanded (CAG) repeat disorders. The expansion in Huntington's disease lies in the first exon of the huntingtin (HTT) gene and is pathogenic when (CAG)>/= 40 . Individuals with Huntington's disease develop motor, cognitive, and psychiatric symptoms in adulthood. These symptoms progress for approximately 15 years at which time they become fatal. The clinical manifestation of HD largely results from the extreme degeneration of neurons in the striatum and cortex. The HTT gene encodes the huntingtin (HTT) protein. Over the years, researchers have developed a rich understanding of the consequences of loss of wildtype HTT function, gain of toxic mutant HTT function, and mutant HTT RNA toxicity. However, the mechanisms through which pathology develops are still largely ambiguous. Given the widespread involvement of HTT in cellular processes, next generation DNA sequencing technologies offer a rich opportunity to explore genome-wide effects of the HD mutation and may help answer mechanistic questions. The application of many next generation DNA sequencing methods is a new luxury for researchers. DNA sequencing methods have undergone a rapid technical evolution which has accelerated the financial feasibility of applying DNA sequencing involved methods on a routine basis. In this thesis, two high throughput analysis techniques, RNA-Seq and ChIP-Seq, were applied to Huntington's disease models to better understand disease mechanisms, and a third high throughput analysis technique, Ribo-Seq, was optimized for future HD studies. RNA-Seq on Huntington's disease model mice and their wildtype littermates demonstrated extensive and progressive dysregulation of the transcriptome in HD striatum and cortex, with most of the affected genes having a lower steady state expression in mutant tissues. ChIP-Seq with an antibody against trimethylated- Histone3-Lysine4 (H3K4Me3) demonstrated both a general reduction of H3K4me3 levels and a unique histone profile at the promoters of HD downregulated genes. Analysis of RNA-Seq results for splicing changes showed that mutant HTT itself is mis-spliced. This mis-splicing product is translated into a small, pathogenic HTT fragment which may have considerable implications for HD therapeutic design. In addition to CNS degeneration, severe muscle dysfunction is an early clinical observation in HD and many CAG repeat expansion disorders. Proper muscle form and function is dependent on an extensive alternative splicing program. Thus RNASeq data on muscle tissue from mouse models of several CAG expansion disorders was examined for genome-wide splicing alterations. Widespread mis-splicing was detected in the muscle of both Spinocerebellar ataxia 7 and Huntington's disease mouse models and minor splicing dysregulation was detected in Spinal-bulbar muscular atrophy. Lastly, methods were developed to examine translational control and mRNA localization in the brain of Huntington's disease mice. Concurrent Ribo-Seq and RNA-Seq in diseased and wildtype animals would answer if there was altered translational control. The Ribo-Seq protocol designed in cell culture was optimized for use on brain tissue and is ready for application in HD mouse models. Analysis of the localization of mRNA transcripts to neuronal projections can be studied by combining fractionation experiments with RNA-Seq. A method to prepare high quality RNA from isolated neuronal projections was developed and is now applicable to RNA-Seq studies.
by Theresa Anne Wasylenko.
Ph. D.
Farrell, Andrew R. "Expanding the horizons of next generation sequencing with RUFUS." Thesis, Boston College, 2014. http://hdl.handle.net/2345/bc-ir:104176.
Повний текст джерелаTo help improve the analysis of forward genetic screens, we have developed an efficient and automated pipeline for mutational profiling using our reference guided tools including MOSAIK and FREEBAYES. Studies using next generation sequencing technologies currently employ either reference guided alignment or de novo assembly to analyze the massive amount of short read data produced by second generation sequencing technologies; the far more common approach being reference guided alignment due to the massive computational and sequencing costs associated with de novo assembly. The success of reference guided alignment is dependent on three factors; the accuracy of the reference, the ability of the mapper to correctly place a read, and the degree to which a variant allele differs from the reference. Reference assemblies are not perfect and none are entirely complete. Moreover, read mappers can only map reads in genomic locations that are unique enough to confidently place reads; paralogous sections, such as related gene families, cannot be characterized and are often ignored. Further, variant alleles that drastically alter the subject's DNA, such as insertions or deletions (INDELs), will not map to the reference and are either entirely missed or require further downstream analysis to characterize. Most importantly, reference guided methods are restricted to organisms for which such reference genomes have been assembled. The current alternative, de novo assembly of a genome, is prohibitively expensive for most labs requiring deep read coverage from numerous different library preparations as well as massive computing power. To address the shortcomings of current methods, while eliminating the costs intrinsic to de novo sequence assembly, we developed RUFUS, a novel, completely reference-independent variant discovery tool. RUFUS directly compares raw sequence data from two or more samples and identifies groups of reads unique to one or the other sample. RUFUS has at least the same variant detection sensitivity as mapping methods, with greatly increased specificity for SNPs and INDEL variation events. RUFUS is also capable of extremely sensitive copy number detection, without any restriction on event length. By modeling the underlying k-mer distribution, RUFUS produces a specific copy number spectrum for each individual sample. Applying a Bayesian detection method to detect changes in k-mer content between two samples, RUFUS produces copy number calls that are equally as sensitive as traditional copy number detection methods with far fewer false positives. Our data suggest that RUFUS' reference-free approach to variant discovery is able to substantially improve upon existing variant detection methods: reducing reference biases, reducing false positive variants, and detecting copy number variants with excellent sensitivity and specificity
Thesis (PhD) — Boston College, 2014
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
Innocenti, Nicolas. "Data Analysis and Next Generation Sequencing : Applications in Microbiology." Doctoral thesis, KTH, Beräkningsbiologi, CB, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-173219.
Повний текст джерелаQC 20150930
Shahbazi, Daniel. "Investigating streptococcal biodiversity in sepsis using next-generation sequencing." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-16248.
Повний текст джерелаYu, Xiaoqing. "Statistical Methods and Analyses for Next-generation Sequencing Data." Case Western Reserve University School of Graduate Studies / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=case1403708200.
Повний текст джерелаKhuder, Basil. "Human Genome and Transcriptome Analysis with Next-Generation Sequencing." University of Toledo Health Science Campus / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=mco1501886695490104.
Повний текст джерелаLee, Michael. "Next Generation Sequencing Strategies to Investigate Telomeres in Cancer." Thesis, The University of Sydney, 2019. https://hdl.handle.net/2123/21844.
Повний текст джерелаHelmuth, Johannes [Verfasser]. "Robust Normalization of Next Generation Sequencing Data / Johannes Helmuth." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1136319379/34.
Повний текст джерелаAntanaviciute, Agne. "Novel algorithm development for 'next generation' sequencing data analysis." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/20734/.
Повний текст джерелаLi, Zhiwei. "Characterising copy number polymorphisms using next generation sequencing data." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-386050.
Повний текст джерелаGiollo, Manuel. "Computational Approaches to Address the Next-Generation Sequencing Era." Doctoral thesis, Università degli studi di Padova, 2015. http://hdl.handle.net/11577/3424280.
Повний текст джерелаIn questa tesi, vengono proposti nuovi algoritmi e modelli per affrontare problemi biologici. L'informatica svolge un ruolo chiave nella proteomica e nella ricerca genetica dovuto alla gestione delle grandi moli di dati biologici. Nel contesto dello studio di proteine, ho sviluppato nuovi metodi per la predizione delle loro funzioni basati su principi di reperimento dell'informazione. Utilizzando fonti eterogenee di conoscenza, come la ricerca su grafi e la similarità di sequenze, ho progettato uno strumento chiamato INGA che può essere utilizzato per annotare interi genomi. Questo è stato valutato imparzialmente dal Critical Assessment of Function Annotation, e ha dimostrato di essere uno degli approcci più efficaci per l'inferenza di funzione. Per meglio caratterizzare le proteine dal punto di vista strutturale, ho proposto una strategia di rilevamento delle conformazioni delle proteine basata su rete di interazione di residui (RIN). Le reti RIN sono state quindi estese per gestire le fluttuazioni temporali delle coordinate atomiche. Tali grafi sono stati infine generati automaticamente da algoritmi di clustering. Un'implementazione chiamata RING MD ha evidenziato efficacemente i principali amminoacidi noti per essere funzionalmente rilevanti nell'Ubiquitina. Questi aminoacidi sono infatti molto importanti per spiegare la dinamica strutturale della proteina. Con la stessa logica, sono stati usati i grafi RIN anche per prevedere l'impatto delle mutazioni all'interno di una struttura proteica. Combinando informazioni sul nodo mutante in una rete e le sue caratteristiche, una rete neurale artificiale è stata addestrata per stimare la variazione di energia libera di Gibbs all'interno di una proteina. Cambiamenti estremi nell'energia interna potrebbe portare all'unfolding della proteina, ed eventualmente ad una malattia. D'altro canto, anche la riduzione della flessibilità proteica può ostacolare la sua funzione. Ad esempio, le fluttuazioni estreme osservate nelle proteine intrinsecamente disordinate (IDP) sono fondamentali per le loro attività. Per studiare le IDP, ho contribuito alla raccolta del più grandi dataset di regioni disordinate mai esistito. Nella seguente analisi è stato dimostrato quali sono le funzioni tipiche di queste sequenze e i processi biologici in cui sono coinvolte. Data l'importanza della loro identificazione, una valutazione globale di predittori del disordine è stata eseguita per mostrare quali sono i metodi più efficaci e le loro limitazioni. Nel contesto della genetica, mi sono concentrato sulla previsione di fenotipi. Durante il Critical Assessment of Genome Interpretation (CAGI), ho proposto nuovi approcci per l'analisi dei dati dell'esoma progettati per valutare il rischio di morbo di Crohn e di ipercolesterolemia. Queste sono spesso definite come malattie complesse, dal momento che il meccanismo alla base della loro insorgenza è ancora sconosciuto. Nel mio studio, i campioni umani con un arricchimento di mutazioni in geni critici sono stati predetti come soggetti a rischio genetico elevato. Oltre ai geni associati alla malattia, le reti di interazione proteiche sono state considerate per valutare l'accumulo di varianti in pathway biologici. Tale strategia ha dimostrato di essere tra le migliori secondo gli organizzatori del CAGI. Nel caso più semplice dei tratti mendeliani, con BOOGIE ho progettato un metodo per la predizione dei gruppi sanguigni umani basata su dati di esoma. Esso utilizza una versione specializzata dell'algoritmo nearest neighbour al fine di far corrispondere le varianti genetiche in un esoma non annotato con quelle disponibili in una base di conoscenza di riferimento. L'esempio più simile è usato per trasferire il gruppo sanguigno. Con una precisione superiore al 90%, BOOGIE è un prototipo che mostra le potenziali applicazioni della predizione genetica, e può essere facilmente esteso a qualsiasi tratto mendeliano. Riassumendo, questa tesi è una risposta parziale alla crescita esponenziale di sequenze disponibili che necessitano ulteriori esperimenti. Integrando informazioni eterogenee e la progettazione di nuovi modelli predittivi basati su apprendimento automatico, ho sviluppato nuovi strumenti per l'analisi di dati biologici e per la loro classificazione. Tutte le implementazioni sono liberamente disponibili per la comunità e potrebbero essere utili durante indagini future come in studi di malattie e nella progettazione di farmaci.
Nicchia, Elena. "Development of a new diagnostic algorithm for the study of diseases caractherized by high genetic heterogeneity." Doctoral thesis, Università degli studi di Trieste, 2015. http://hdl.handle.net/10077/10854.
Повний текст джерелаNext Generation Sequencing (NGS) technologies, such the Ion Torrent platform, could allow to simplify the diagnostic process of diseases characterized by an high genetic and phenotypic heterogeneity, because of the possibility to sequence simultaneously more genes and more patients in a single sequencing run. In order to develop a new diagnostic algorithm for rapid molecular diagnosis of these disorders, we have applied the Ion Torrent technology on two different genetically heterogeneous diseases, Fanconi anemia (FA) and inherited thrombocytopenias (IT). Since FA is a disorder better characterized than ITs, we first validated the Ion torrent technology on 30 samples (2 wild type and 28 FA), 25 of which were already analyzed with Sanger sequencing. Because of their low sequencing quality, we have excluded from this type of analysis 2 of the 28 FA samples. Then, comparing Ion Torrent and Sanger sequencing data, we have evaluated the sensitivity (95%) and the specificity (100%) of Ion Torrent technology. Moreover, in order to detect copy number variations (CNVs) in FA genes, we have improved a statistical analysis based on coverage sequencing data, confirming the presence of large intragenic deletions on FANCA in 5 patients. In summary we have characterized 25 of the 26 FA patients analyzed, identifying also 4 mutant alleles in the rare complementation group FANCL and FANCF and 10 mutations in loci different from genes causing the disease. Since we cannot exclude that new genes are involved in FA, the only patient without any mutation identified is suitable for whole exome analysis. Taking advantage from these good sequencing data, we have developed a diagnostic algorithm that combines the identification of both point mutations and CNVs. In order to verify if this new diagnostic process could be applied also to other genetically heterogeneous diseases, we have analyzed 21 IT patients, already characterized by Sanger sequencing. Among the 2225 variants identified by Ion torrent technology, using this new approach, we have select those (N=75, 56 different) potentially pathogenetic because of their frequency (MAF<0.01), or of their presence in IT mutation database o because of bioinformatics analysis. Thirty of these variants were confirmed by Sanger sequencing, 14 (12 different) of which localized in loci different from the gene causing the disease. It would be interesting to carry out functional studies on these additional variants to unravel the molecular basis of ITs. In summary we were able to characterized 17 of the 21 IT patients, including 2 patients with deletions in RBM8A (Thrombocytopenia and Absent Radii syndrome, TAR). The remaining 4 mutant alleles were not detected because of a low sequencing coverage. In conclusion, according to our data, we can consider the Ion Torrent technology and in particular the diagnostic algorithm proposed in our study, as a feasible approaches for the study of diseases characterized by high genetic and phenotypic heterogeneity. RIASSUNTO Le tecnologie di Next Generation Sequencing (NGS) consentono di analizzare più geni e più campioni contemporaneamente. In questo modo potrebbe essere possibile ridurre i tempi e i costi di analisi di tutte quelle patologie caratterizzate da elevata eterogeneità genetica e fenotipica, la cui caratterizzazione risulta essere spesso complessa e dispendiosa. Al fine di elaborare un nuovo algoritmo diagnostico che consenta la rapida elaborazione di una diagnosi molecolare di tali patologie, abbiamo deciso di validare una tra le più innovative tecnologie NGS attualmente in commercio, la metodica Ion Torrent, su due differenti malattie, entrambe caratterizzate da eterogeneità genetica. l’anemia di Fanconi (FA) e le piastrinopenie ereditarie (IT). Siccome la FA è una patologia meglio caratterizzata rispetto alle IT, durante la prima fase di questo lavoro di tesi abbiamo analizzato 30 campioni (25 dei quali già precedentemente analizzati con sequenziamento Sanger), di cui 2 wild type e 28 affetti. In seguito all’esclusione dalla nostra analisi di 2 campioni FA a causa di una bassa qualità di sequenziamento, abbiamo determinato la sensibilità (95%) e la specificità (100%) della nuova metodica confronto i dati di sequenziamento Ion Torrent e quelli Sanger a nostra disposizione. Inoltre, utilizzando i dati di copertura della sequenza, abbiamo messo a punto un’analisi statistica volta all’identificazione delle Copy Number Variation (CNV), confermando le delezioni a carico del gene FANCA presenti in 5 pazienti. Abbiamo quindi caratterizzato 25 dei 26 pazienti analizzati, identificando inoltre 2 casi con mutazioni nei rari gruppi di complementazione FANCF e FANCL e 10 mutazioni in loci differenti dai geni causativi. Poiché non escludiamo la possibilità che un nuovo gene possa essere coinvolto nella patologia, riteniamo che l’unico paziente ancora privo di diagnosi molecolare possa essere un buon candidato per lo studio dell’esoma. Infine, avvalendoci dei buoni risultati ottenuti, abbiamo elaborato un nuovo processo diagnostico con il quale identificare in modo semplice e rapido sia le mutazioni sia le CNV a carico dei 16 geni coinvolti nella FA. Nella seconda parte del nostro studio, abbiamo verificato se l’applicazione di tale algoritmo possa essere estesa anche ad altre patologie ad elevata eterogeneità genetica. Per questo motivo abbiamo analizzato 21 campioni affetti da piastrinopenie ereditarie, già precedentemente analizzati mediante sequenziamento Sanger. Grazie all’algoritmo proposto abbiamo potuto selezionare tra le 2225 varianti identificate le 75 (56 differenti) che sono risultate essere potenzialmente patogenetiche in base alla loro frequenza nella popolazione (MAF<0.01), alla loro presenza nei database di mutazione e all’analisi bioinformatica di patogenicità. Trenta (27 differenti) di queste varianti sono state confermate mediante sequenziamento Sanger, di cui in particolare 14 (12 differenti) presenti in geni diversi da quelli causativi. Alla luce di questo dato si rendono necessari studi funzionali su tali varianti al fine di comprendere i meccanismi molecolari alla base delle piastrinopenie ereditarie. Infine, utilizzando l’algoritmo proposto, è stato possibile confermare la diagnosi molecolare in 17 dei 21 pazienti IT, compresi i 2 affetti da trombocitopenia con assenza del radio (TAR) e portatori di una delezione sul cromosoma 1q21.1. I restanti 4 alleli mutati non sono stati identificati a causa di una bassa copertura di sequenziamento. In conclusione, in base ai dati raccolti sui campioni affetti da FA e IT, possiamo affermare che la tecnologia di sequenziamento Ion Torrent e l’algoritmo diagnostico da noi proposto sono degli strumenti utili per ottenere una diagnosi molecolare completa, veloce ed economica.
XXVII Ciclo
1984
Emelianova, Katie. "Using next generation sequencing to investigate the generation of diversity in the genus Begonia." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/29584.
Повний текст джерелаKhan, Azeem. "Affordable and accesible rolony template preparation for next-generation sequencing." Thesis, Boston University, 2012. https://hdl.handle.net/2144/12443.
Повний текст джерелаThe first draft of the entire human genome was released in 2000, bringing with it the potential for personalized medicine in which there would be customization of health care, with practices and decisions being specially suited to each individual patient by the use of their genetic code. However, the costs and duration of the sequencing with the available technology at that time still left genome analysis out of reach for the majority of people. Since then, there has been an ongoing challenge to lower the cost of sequencing, and to make it more accessible to the public. Newer methods of genome sequencing using circularized human DNA have now been developed that have the potential to both lower the cost and speed up the process. One such method is rolony technology in which the DNA is circularized, amplified, and then fluorescent probes are ligated to the DNA template for sequencing. The order of bases is determined by fluorescence of the ligated and bound probes. The main hurdle with this technology remains the lack of good quality sequencing templates. A good template allows for a rolony to be produced that is efficient in circularization and amplification. It has been proposed that sequence and secondary structure contribute to the quality of rolony, but the exact parameters have not yet been determined. In the work describe here, different rolony templates were chosen and studied for their sequencing potential. The hypotheses tested were whether a sequence specific secondary structure was required for circularization, whether a sequence specific secondary structure was required for Rolling Circle Amplification, and if the secondary structures assisted in folding the DNA into rolonies. It was determined through various experiments that template sequence, and the secondary structure of the template are representative of the quality of rolony produced.
Alshanbari, Huda Mohammed H. "Additive Cox proportional hazards models for next-generation sequencing data." Thesis, University of Leeds, 2017. http://etheses.whiterose.ac.uk/19739/.
Повний текст джерелаGraham, Joseph (Joseph Arthur). "An analysis of the next generation DNA sequencing technology market." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42360.
Повний текст джерелаIncludes bibliographical references (p. 57-60).
While there is no shortage of successful and failed biotechnology ventures, it is still very difficult to gage, a priori, how a new company will fare in this industry. In many cases new biotechnology ventures are driven by rapidly evolving technology and emergent customer needs, both unpredictable by nature. Also, the Biotech Industry faces increased public and federal scrutiny as companies attempt to navigate murky ethical and legal waters. This thesis will explore the ongoing development of the next generation DNA sequencing market in an effort to predict exactly which factors will play a role in determining who will ultimately succeed. This will be accomplished through an analysis incorporating a combination of historical precedents in this industry and traditional market theories. The goal is to produce a set of dimensions along which to judge the current and future participants in this market in order to determine which are most likely to succeed.
by Joseph Graham.
S.M.
Mayo, Thomas Richard. "Machine learning for epigenetics : algorithms for next generation sequencing data." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/33055.
Повний текст джерелаChen, Xi. "Bayesian Integration and Modeling for Next-generation Sequencing Data Analysis." Diss., Virginia Tech, 2016. http://hdl.handle.net/10919/71706.
Повний текст джерелаPh. D.
Thrush, Mariah A. "Analyzing Algal Diversity in Aquatic Systems Using Next Generation Sequencing." Ohio University Honors Tutorial College / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ouhonors1366807717.
Повний текст джерелаCamerlengo, Terry Luke. "Techniques for Storing and Processing Next-Generation DNA Sequencing Data." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1388502159.
Повний текст джерелаPorter, Ashleigh Fay. "Next generation sequencing to explore microbial diversity, origins and evolution." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/24919.
Повний текст джерела