Дисертації з теми "Whole genome sequences (WGS)"
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Haimel, Matthias. "Development of computational approaches for whole-genome sequence variation and deep phenotyping." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/283563.
Повний текст джерелаGordon, Nicola. "Whole genome sequencing (WGS) as a unified platform for outbreak identification and resistance prediction in Staphylococcus aureus." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:7d705b89-c5ed-4103-98fb-3f8637e88d32.
Повний текст джерелаKozma, Radoslav. "Inferring demographic history and speciation of grouse using whole genome sequences." Doctoral thesis, Uppsala universitet, Zooekologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-299926.
Повний текст джерелаJakt, Lars Martin. "Isolation of mouse Hoxb-3 protein binding sequences : a whole genome approach /." Thesis, Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B21185505.
Повний текст джерелаKhoo, Choon-Kiat. "Chicken genome variations and selection : from sequences to consequences." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28934.
Повний текст джерелаGladstein, Ariella. "Inference of Recent Demographic History of Population Isolates Using Genome-Wide High Density SNP Arrays and Whole Genome Sequences." Thesis, The University of Arizona, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10839026.
Повний текст джерелаIn this dissertation I addressed the problem of SNP array bias when finding runs of ho- mozygosity. I demonstrated the pitfalls of using uninformed methods for finding runs of homozygosity and provide better alternatives, including a more reliable algorithm for identi- fying runs of homozygosity than the most commonly used program. I then provide a review of Ashkenazi population genetics. Next, I developed software to efficiently run millions of whole chromosome simulations, which is publicly available through GitHub, DockerHub, and on the CyVerse Discovery Environment. I applied my computational method to use Approximate Bayesian Computation to test models of Ashkenazi Jewish demographic his- tory. I found that the Ashkenazi Jews are comprised of genetically distinct subgroups from Eastern and Western Europe, as a result of massive population growth in the Eastern Ashkenazi Jews, but not in the Western Ashkenazi Jews. I further confirmed that the Ashkenazi Jews do not primarily originate from Khazaria. Finally, I created a correction for SNP array ascertainment bias in the median and total length of runs of homozygosity, and applied this correction to world-wide human populations. However, I found that ascertainment bias plays a minor role compared to SNP array bias in human populations.
Alosaimi, Shatha Mobarak. "Leveraging Whole Genome Sequences to Compare Mutational Mechanism and Identify Medically Relevant Variation in African versus Non-African Descend Populations." Master's thesis, Faculty of Health Sciences, 2020. http://hdl.handle.net/11427/32191.
Повний текст джерелаWiredu, Boakye Dominic. "Life in the nucleus : the genomic basis of energy exploitation by intranuclear Microsporidia." Thesis, University of Exeter, 2016. http://hdl.handle.net/10871/26108.
Повний текст джерелаJäger, Sarah Christina [Verfasser]. "Hybrid Assembly of Whole Genome Shotgun Sequences of Two Sugar Beet (Beta vulgaris L.) Translocation Lines Carrying the Beet Cyst Nematode Resistance Gene Hs1-2 and Functional Analysis of Candidate Genes / Sarah Christina Jäger." Kiel : Universitätsbibliothek Kiel, 2013. http://d-nb.info/1054661898/34.
Повний текст джерелаFont, Porterias Neus 1994. "Genomic insights into an underrepresented population : the Romani." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2022. http://hdl.handle.net/10803/673740.
Повний текст джерелаThe Romani people are the largest transnational minority ethnic group in Europe. They have a South Asian origin and during their diaspora to Europe, they experienced multiple founder effects and gene flow events. In this thesis, the analysis of genome-wide array data shows that Romani groups share a common South Asian, Middle Eastern and Balkan ancestry, while Iberian and Baltic groups experienced additional admixture with the surrounding non-Roma European populations. After characterising their genetic landscape, the study of whole-exome sequences from Spanish Romani suggests that non-Roma gene flow has counteracted the increase in mutational load caused by the founder effects. In addition, clinically relevant variants are traced back to both European and South Asian ancestral haplotypes consistent with the extensive gene flow. Thus, the present work represents a step forward to comprehensively depict the Romani demographic history and emphasises the need to study other underrepresented and historically excluded populations to fully capture human variation.
Burkert, Christian Martin. "Cis-regulation and genetic control of gene expression in neuroblastoma." Doctoral thesis, Humboldt-Universität zu Berlin, 2021. http://dx.doi.org/10.18452/23008.
Повний текст джерелаGene regulation controls phenotypes in health and disease. In cancer, the interplay between germline variation, genetic aberrations and epigenetic factors modulate gene expression in cis. The childhood cancer neuroblastoma originates from progenitor cells of the sympathetic nervous system. It is characterized by a sparsity of recurrent exonic mutations but frequent somatic copy-number alterations, including gene amplifications on extrachromosomal circular DNA. So far, little is known on how local genetic and epigenetic factors regulate genes in neuroblastoma to establish disease phenotypes. I here combine allele-specific analysis of whole genomes, transcriptomes and circular DNA from neuroblastoma patients to characterize genetic and cis-regulatory effects, and prioritize germline regulatory variants by cis-QTLs mapping and chromatin profiles. The results show that somatic copy-number dosage dominates local genetic effects and regulates pathways involved in telomere maintenance, genomic stability and neuronal processes. Gene amplifications show strong dosage effects and are frequently located on large but not small extrachromosomal circular DNAs. My analysis implicates 11q loss in the upregulation of histone variants H3.3 and H2A in tumors with alternative lengthening of telomeres and cooperative effects of somatic rearrangements and somatic copy-number gains in the upregulation of TERT. Both 17p copy-number imbalances and associated downregulation of neuronal genes as well as upregulation of the imprinted gene RTL1 by copy-number-independent allelic dosage effects is associated with an unfavorable prognosis. cis-QTL analysis confirms the previously reported regulation of the LMO1 gene by a super-enhancer risk polymorphism and characterizes the regulatory potential of additional GWAS risk loci. My work highlights the importance of dosage effects in neuroblastoma and provides a detailed map of regulatory variation active in this disease.
Ma, Yue. "An anchor-based model for global multiple alignment of whole genome sequences /." 2005.
Знайти повний текст джерелаKidsley, Amanda Kate. "Application of whole genome sequencing to Australia-wide collections of extraintestinal pathogenic Escherichia coli from companion animals and commensal E. coli from pigs." Thesis, 2020. https://hdl.handle.net/2440/132886.
Повний текст джерелаThesis (Ph.D.) -- University of Adelaide, School of Animal and Veterinary Sciences, 2021
Sagert, Jason. "Characterization of Listeria monocytogenes plasmids that were newly identified in whole-genome sequences of listeriosis outbreak isolates." 2014. http://hdl.handle.net/1993/23160.
Повний текст джерелаNg, K. C. S., J. C. S. Ngabonziza, P. Lempens, Jong B. C. de, Leth F. van, and Conor J. Meehan. "Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data." 2019. http://hdl.handle.net/10454/17491.
Повний текст джерелаBackground: Mycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicinresistant (RR)-TB. However, as next-generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low- and middle-income high TB-burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance. Methods: We developed the Python-based MycTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs—Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data. Results: The MTBGT tool correctly transformed the single nucleotide polymorphism (SNP) data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin-susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda. Conclusion: Overall, the MTBGT tool allows low- and middle-income countries to make sense of the increasingly generated WGS in light of the readily available RDT.
Erasmus Mundus Joint Doctorate Fellowship grant 2016- 1346.
Vangchhia, Belinda Lallawmkimi. "Genetic structure and antimicrobial resistance of foodborne Escherichia coli in Australia." Phd thesis, 2017. http://hdl.handle.net/1885/144610.
Повний текст джерелаAuger, Jérémie. "Impact des antibiotiques céfprozil et céfoxitine sur le microbiote Eggerthella lenta, lié au métabolisme du cardiotonique digoxine." Thèse, 2018. http://hdl.handle.net/1866/23628.
Повний текст джерелаDigoxin is a widely used cardiotonic drug in the management of heart failure and atrial fibrillation. It has been known since the early 1980's that the main metabolite of digoxin, dihydrodigoxin, is synthesized by the gut microbiome during first pass metabolism and is exclusively produced by the bacteria Eggerthella lenta. In a clinical study done in the U.S.A., there were 14% of high metabolizers, for whom over 40% of the oral digoxin dose is transformed to the inactive metabolite and rapidly eliminated. Digoxin toxicity is the leading cause of hospitalization from medication's secondary effects. The toxicity events are often associated with the addition of an antibiotic (mostly from the macrolides class) to the patient's drugs regiments. The theory explored in this project could help explain the toxicity events in metabolizers. These patients have a higher daily digoxin maintenance dose to counteract the effects of the microbiome and are then prescribed antibiotics for an infection unrelated to their heart condition. The antibiotic alters E. lenta negatively, which cannot metabolize digoxin anymore and therefore augments the bioavailability of the cardiotonic. If the plasmatic concentration reaches dangerous levels (over 2ng/ml of plasma), the patients face adverse effects that include death. In the present project, we evaluated the susceptibility of E. lenta to two second generation cephalosporins, in vivo and in vitro. With the 18 healthy volunteers that were exposed to 2x500mg of cefprozil daily for 7 days, we observed a diminution of the abundance of the bacteria of interest by 58,3% from the initial levels. This change did not however produce statistically significant tests results. For the complete fecal microbiome that were cultivated in vitro, with or without cefprozil, the difference between the two conditions resulted in a statistically significant p-value of 0.0457, confirming the sensitivity of E. lenta to this cephalosporin. These results validate an important premise for the demonstration of the importance of the gut microbiome in the pharmacokinetics of digoxin and the clinical management of the drug to avoid toxicity events in clinical practice.