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Tesi sul tema "Whole genome amplification"

Autore: Grafiati

Pubblicato: 4 giugno 2021

Ultima modifica: 9 marzo 2023

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1

Glentis, S. "Whole genome amplification for PGD and PND : molecular and a-CGH diagnosis." Thesis, University College London (University of London), 2009. http://discovery.ucl.ac.uk/18554/.

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Whole genome amplification amplifies the entire genome in a few hours from samples of minimal DNA quantities, even from single cells. This may have many applications, especially in prenatal diagnosis, PGD and PGS. The hypothesis for chapter 3 was: Can multiple displacement amplification (MDA) be used as a universal step prior to molecular analysis for PGD? WGA using MDA (Qiagen) was used on single cells in order to overcome the problem of limited DNA in PGD. MDA allows the diagnosis through haplotyping or a combination of direct and indirect mutation analysis. Different cell types, including b

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2

Jiang, Sheng. "Application of nested PCR, whole genome amplification and comparative genomic hybridisation for single cell genetic analysis." Thesis, University of Glasgow, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366140.

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3

Anscombe, C. J. "Multiple displacement amplification and whole genome sequencing for the diagnosis of infectious diseases." Thesis, Queen Mary, University of London, 2016. http://qmro.qmul.ac.uk/xmlui/handle/123456789/18409.

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Next-generation sequencing technologies are revolutionising our ability to characterise and investigate infectious diseases. Utilising the power of high throughput sequencing, this study reports, the development of a sensitive, non-PCR based, unbiased amplification method, which allows the rapid and accurate sequencing of multiple microbial pathogens directly from clinical samples. The method employs Φ29 DNA polymerase, a highly efficient enzyme able to produce strand displacement during the polymerisation process with high fidelity. Problems with DNA secondary structure were overcome and the

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4

Borgström, Erik. "Technologies for Single Cell Genome Analysis." Doctoral thesis, KTH, Genteknologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-181059.

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During the last decade high throughput DNA sequencing of single cells has evolved from an idea to one of the most high profile fields of research. Much of this development has been possible due to the dramatic reduction in costs for massively parallel sequencing. The four papers included in this thesis describe or evaluate technological advancements for high throughput DNA sequencing of single cells and single molecules. As the sequencing technologies improve, more samples are analyzed in parallel. In paper 1, an automated procedure for preparation of samples prior to massively parallel sequen

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5

Dillon, Candace. "Assessment of pre-PCR whole genome amplification of single pollen grains using flowering dogwood (Cornus florida)." VCU Scholars Compass, 2009. http://scholarscompass.vcu.edu/etd/1865.

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Studies of gene flow in natural plant populations often focus on either historical or abiotic dispersal methods (e.g. wind, water, gravity), but there is little information available on contemporary, animal-mediated pollen dispersal patterns. Emerging molecular laboratory techniques allow unprecedented insights into spatial patterns of pollen-mediated gene flow. However, to date, technical challenges have limited their widespread application. The genome of a pollen grain can be amplified via whole genome amplification (WGA) prior to traditional amplification via polymerase chain reaction (P

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6

Freedman, Benjamin Gordon. "Degenerate oligonucleotide primed amplification of genomic DNA for combinatorial screening libraries and strain enrichment." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/71346.

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Combinatorial approaches in metabolic engineering can make use of randomized mutations and/or overexpression of randomized DNA fragments. When DNA fragments are obtained from a common genome or metagenome and packaged into the same expression vector, this is referred to as a DNA library. Generating quality DNA libraries that incorporate broad genetic diversity is challenging, despite the availability of published protocols. In response, a novel, efficient, and reproducible technique for creating DNA libraries was created in this research based on whole genome amplification using degenerate oli

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7

Lu, Sijia. "Label-Free Optical Imaging of Chromophores and Genome Analysis at the Single Cell Level." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10563.

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Since the emergence of biology as a quantitative science in the past century, a lot of biological discoveries have been driven by milestone technical advances such as X-ray crystallography, fluorescence microscopy and high-throughput sequencing. Fluorescence microscopy is widely used to explore the nanoscale cellular world because of its superb sensitivity and spatial resolution. However, many species (e.g. lipids, small proteins) are non-fluorescent and are difficult to label without disturbing their native functions. In the first part of the dissertation, we explore using three different con

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8

Du, Breil de Pontbriand Alexandra. "Cartographie des génomes par HAPPY mapping. Développement d'une amplification "whole genome" et validation sur cartes comparatives homme/chimpanzé/gorille." Rennes 1, 2003. http://www.theses.fr/2003REN10104.

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La comparaison des génomes de grands singes et de l'homme devrait apporter de nouvelles informations concernant l'évolution de l'homme, ces différents genomes restant très proches. Le caryotype humain possède une paire de chromosomes en moins, le chromosome 2 humain étant issu de la fusion télomérique de deux chromosomes ancestraux de singes. Afin de pouvoir mettre en evidence les réarrangements qui ont amené à l'apparition de l'espèce humaine, nous avons décidé d'entreprendre une étude comparative entre l'homme, le chimpanzé et le gorille. Pour y parvenir, nous avons utilisé le HAPPY mapping

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9

Sandberg, Julia. "Massively parallel analysis of cells and nucleic acids." Doctoral thesis, KTH, Genteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-45671.

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Recent proceedings in biotechnology have enabled completely new avenues in life science research to be explored. By allowing increased parallelization an ever-increasing complexity of cell samples or experiments can be investigated in shorter time and at a lower cost. This facilitates for example large-scale efforts to study cell heterogeneity at the single cell level, by analyzing cells in parallel that also can include global genomic analyses. The work presented in this thesis focuses on massively parallel analysis of cells or nucleic acid samples, demonstrating technology developments in th

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10

Gabrieli, A. "STUDIO DI TECNOLOGIE DI AMPLIFICAZIONE E GENOTIPIZZAZIONE DEL GENOMA SU CAMPIONI DI DNA PROVENIENTI DA SANGUE E DA CELLULE DELLA BOCCA PER APPLICAZIONI IN AMBITO EPIDEMIOLOGICO." Doctoral thesis, Università degli Studi di Milano, 2010. http://hdl.handle.net/2434/150115.

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In epidemiological studies the amount of biological material available is a limiting factor. Many studies use DNA as biological sample obtained by venipuncture, but this collection method is invasive especially if donors are children and the elderly. The use of mouth cells can be an alternative source, although you get DNA of poor quality and quantity. To increase the amount of DNA extracted from buccal cells, you can use the "Whole Genome Amplification”. The aim of my PhD project was to develop a method to extract DNA from buccal cells and to study amplification technologies and subsequent ge

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11

Forst, Jannine. "Detecting and sequencing Mycobacterium tuberculosis aDNA from archaeological remains." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/detecting-and-sequencing-mycobacterium-tuberculosis-adna-from-archaeological-remains(a806f3a9-8d22-4395-a1ff-a3ffbcb1c8cc).html.

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Tuberculosis has been an important disease throughout human history, shaping countless past populations. The archaeological study of the causative agents of tuberculosis, members of the Mycobacterium tuberculosis Complex (MTBC), is hindered by the non-diagnostic nature of tuberculosis-associated skeletal changes. As such, ancient DNA (aDNA) or palaeogenetic analyses have become an important tool for identifying tuberculosis in past populations. However, due to the age and variable preservation of aDNA, there are often issues with sporadic results and false negatives. The overall aim of the wor

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12

Jere, Khuzwayo Chidiwa. "Whole genome characterisation and engineering of chimaeric rotavirus-like particles using African rotavirus field strains / Khuzwayo Chidiwa Jere." Thesis, North-West University, 2012. http://hdl.handle.net/10394/8502.

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Despite the global licensure of two live-attenuated rotavirus vaccines, Rotarix® and RotaTeq®, rotavirus remains the major cause of severe dehydrating diarrhoea in young mammals and the need for further development of additional rotavirus vaccines, especially vaccines effective against regional strains in developing country settings, is increasing. The design and formulation of new effective multivalent rotavirus vaccines is complicated by the wide rotavirus strain diversity. Novel rotavirus strains emerge periodically due to the propensity of rotaviruses to evolve using mechanisms such as poi

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13

Adèle-dit-Renseville, Nathalie. "Développement d'une technique d'analyse d'échantillons limites en quantité d'ADN adaptée aux applications médicales et médico-légales." Nantes, 2010. http://www.theses.fr/2010NANT2113.

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14

Jiao, Xiang. "Somatic Mutations in Breast Cancer Genomes : Discovery and Validation of Breast Cancer Genes." Doctoral thesis, Uppsala universitet, Institutionen för immunologi, genetik och patologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-182319.

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Breast cancer is the most common cancer in women worldwide. However, the genetic alterations that lead to breast cancer are not fully understood. This thesis aims to identify novel genes of potential mechanistic, diagnostic or therapeutic interest in breast cancers by mutational analysis and whole-genome sequencing. In paper I, sequencing of 36 previously identified candidate genes in 96 breast tumors with patient-matched normal DNA determined the somatic mutation prevalence of these candidate genes and identified additional mutations in Notch, NF-κB, PI3K, and Hedgehog pathways as well as in

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15

Rönn, Ann-Charlotte. "Analysis of Nucleotide Variations in Non-human Primates." Doctoral thesis, Uppsala University, Molecular Medicine, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7904.

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<p>Many of our closest relatives, the primates, are endangered and could be extinct in a near future. To increase the knowledge of non-human primate genomes, and at the same time acquire information on our own genomic evolution, studies using high-throughput technologies are applied, which raises the demand for large amounts of high quality DNA.</p><p>In study I and II, we evaluated the multiple displacement amplification (MDA) technique, a whole genome amplification method, on a wide range of DNA sources, such as blood, hair and semen, by comparing MDA products to genomic DNA as templates for

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16

Halilovic, Amina. "SÄKERSTÄLLNING AV SÄLLSYNTA DNA-KONTROLLER MED HELGENOMAMPLIFIERING I KLINISKT SYFTE." Thesis, Malmö högskola, Fakulteten för hälsa och samhälle (HS), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:mau:diva-24387.

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Vid klinisk enbaspolymorfi (SNP) analys inkluderas DNA-kontroller med kända genotyper i varje analysomgång för att säkerställa riktigheten vad gäller analysresultatet. DNA-kontrollerna har en central roll för resultatens trovärdighet vid genotypningen. Vissa kontrollprover som används är av sällsynt genotyp och kan vara mycket svåra att få tag på. Detta arbete har utförts för att undersöka om det går att erhålla DNA-material från sällsynta genotyper med hjälp av helgenomamplifiering och på så sätt säkerställa en tillgång till dessa. I arbetet testades helgenomamplifiering med hjälp av två olik

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17

Muharam, Firman Alamsyah. "Overcoming problems with limiting DNA samples in forensics and clinical diagnostics using multiple displacement amplification." Thesis, Queensland University of Technology, 2006. https://eprints.qut.edu.au/16207/1/Firman_Muharam_Thesis.pdf.

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The availability of DNA samples that are of adequate quality and quantity is essential for any genetic analysis. The fields of forensic biology and clinical diagnostic pathology testing often suffer from limited samples that yield insufficient DNA material to allow extensive analysis. This study examined the utility of a recently introduced whole genome amplification method termed Multiple Displacement Amplification (MDA) for amplifying a variety of limited sample types that are commonly encountered in the fields of forensic biology and clinical diagnostics. The MDA reaction, which employs the

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18

Muharam, Firman Alamsyah. "Overcoming problems with limiting DNA samples in forensics and clinical diagnostics using multiple displacement amplification." Queensland University of Technology, 2006. http://eprints.qut.edu.au/16207/.

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Abstract (sommario):

The availability of DNA samples that are of adequate quality and quantity is essential for any genetic analysis. The fields of forensic biology and clinical diagnostic pathology testing often suffer from limited samples that yield insufficient DNA material to allow extensive analysis. This study examined the utility of a recently introduced whole genome amplification method termed Multiple Displacement Amplification (MDA) for amplifying a variety of limited sample types that are commonly encountered in the fields of forensic biology and clinical diagnostics. The MDA reaction, which employs the

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19

Björnerfeldt, Susanne. "Consequences of the Domestication of Man’s Best Friend, The Dog." Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7799.

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The dog was the first animal to be domesticated and the process started at least 15 000 years ago. Today it is the most morphologically diverse mammal, with a huge variation in size and shape. Dogs have always been useful to humans in several ways, from being a food source, hunting companion, guard, social companion and lately also a model for scientific research. This thesis describes some of the changes that have occurred in the dog’s genome, both during the domestication process and later through breed creation. To give a more comprehensive view, three genetic systems were studied: maternal

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20

Darp, Revati A. "Insights into the Role of Oncogenic BRAF in Tetraploidy and Melanoma Initiation." eScholarship@UMMS, 2021. https://escholarship.umassmed.edu/gsbs_diss/1129.

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Melanoma, the most lethal form of skin cancer, arises from altered cells in the melanocyte lineage, but the mechanisms by which these cells progress to melanoma are unknown. To understand the early cellular events that contribute to melanoma formation, we examined melanocytes in melanoma-prone zebrafish strains expressing BRAFV600E, the most common oncogenic form of the BRAF kinase that is mutated in nearly 50% of human melanomas. We found that, unlike wild-type melanocytes, melanocytes in transgenic BRAFV600Eanimals were binucleate and tetraploid. Furthermore, melanocytes in p53-deficient tra

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21

Ambers, Angie D. "Investigation of Strategies for Improving STR Typing of Degraded and Low Copy DNA from Human Skeletal Remains and Bloodstains." Thesis, University of North Texas, 2014. https://digital.library.unt.edu/ark:/67531/metadc799472/.

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Forensic STR analysis is limited by the quality and quantity of DNA. Significant damage or alteration to the molecular structure of DNA by depurination, crosslinking, base modification, and strand breakage can impact typing success. Two methods that could potentially improve STR typing of challenged samples were explored: an in vitro DNA repair assay (PreCR™ Repair Mix) and whole genome amplification. Results with the repair assay showed trends of improved performance of STR profiling of bleach-damaged DNA. However, the repair assay did not improve DNA profiles from environmentally-damaged b

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Turnbough, Meredith A. "Applications of Molecular Genetics to Human Identity." Thesis, University of North Texas, 2008. https://digital.library.unt.edu/ark:/67531/metadc9730/.

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The primary objectives of this project were: 1. to develop improved methods for extraction of DNA from human skeletal remains, 2. to improve STR profiling success of low-copy DNA samples by employing whole genome amplification to amplify the total pool of DNA prior to STR analysis, and 3. to improve STR profiling success of damaged DNA templates by using DNA repair enzymes to reduce the number/severity of lesions that interfere with STR profiling. The data from this study support the following conclusions. Inhibitory compounds must be removed prior to enzymatic amplification; either during bon

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23

Raikar, Sanjeev Vencu. "Protoplast fusion of Lolium perenne and Lotus corniculatus for gene introgression." Phd thesis, Lincoln University. Bio-Protection and Ecology Division, 2007. http://theses.lincoln.ac.nz/public/adt-NZLIU20080214.105406/.

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Protoplast fusion of Lolium perenne and Lotus corniculatus for gene introgression by Sanjeev V. Raikar Lolium perenne is one of the most important forage crops globally and in New Zealand. Lotus corniculatus is a dicotyledonous forage that contains valuable traits such as high levels of condensed tannins, increased digestibility, and high nitrogen fixing abilities. However, conventional breeding between these two forage crops is impossible due to their markedly different taxonomic origin. Protoplast fusion (somatic hybridisation) provides an opportunity for gene introgression between these two

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24

Fredriksson, Mona. "Using Minisequencing Technology for Analysing Genetic Variation in DNA and RNA." Doctoral thesis, Uppsala University, Department of Medical Sciences, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4789.

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<p>In this thesis, the four-color fluorescence tag-microarray minisequencing system pioneered by our group was further developed and applied for analysing genetic variation in human DNA and RNA. A SNP marker panel representing different chromosomal regions was established and used for identification of informative SNP markers for monitoring chimerism after stem cell transplantation (SCT). The success of SCT was monitored by measuring the allelic ratios of informative SNPs in follow-up samples from nine patients with leukaemia. The results agreed with data obtained using microsatellite markers.

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25

Lovmar, Lovisa. "Methods for Analysis of Disease Associated Genomic Sequence Variation." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4525.

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26

Konstantinidis, Michalis. "Preimplantation genetic diagnosis : new methods for the detection of genetic abnormalities in human preimplantation embryos." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:28611f65-7729-4293-9c3f-4fc3f0cc39d7.

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Preimplantation genetic diagnosis (PGD) refers to the testing of embryos produced through in vitro fertilization (IVF) in order to identify those unaffected by a specific genetic disorder or chromosomal abnormality. In this study, different methodologies were examined and developed for performance of PGD. Investigation of various whole genome amplification (WGA) methods identified multiple displacement amplification as a reliable method for genotyping single cells. Furthermore, this technology was shown to be compatible with subsequent analysis using single nucleotide polymorphism (SNP) microa

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Raikar, S. V. "Protoplast fusion of Lolium perenne and Lotus corniculatus for gene introgression." Diss., Lincoln University, 2007. http://hdl.handle.net/10182/301.

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Lolium perenne is one of the most important forage crops globally and in New Zealand. Lotus corniculatus is a dicotyledonous forage that contains valuable traits such as high levels of condensed tannins, increased digestibility, and high nitrogen fixing abilities. However, conventional breeding between these two forage crops is impossible due to their markedly different taxonomic origin. Protoplast fusion (somatic hybridisation) provides an opportunity for gene introgression between these two species. This thesis describes the somatic hybridisation, the regeneration and the molecular analysis

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28

Alawi, Mariah. "Optimizing a Selective Whole Genome Amplification (SWGA) Strategy for Clinical Malaria Infections." Thesis, 2019. http://hdl.handle.net/10754/656568.

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Plasmodium is a genus well known for causing malaria, a life-threatening infection for many people where malaria is endemic. The blood-borne disease is transmitted by the female Anopheles mosquito. Till date, eight parasite species have been reported to cause malaria in humans that include P. falciparum, P. vivax, P. malariae, P. ovale curtisi, P. ovale wallikeri, P. cynomolgi, P. knowlesi and more recently P. simium. Amongst them, the most genetically understood species is P. falciparum, causing most of the deaths in children from malaria. Understanding genome variation at the population lev

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29

Schoenborn, Veit. "Whole Genome Amplification von Plasma-DNA und Entwicklung eines Ausschlusskriteriums zur Verbesserung der Genotypisierungsqualität." Doctoral thesis, 2008. https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-37136.

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Plasma- und Serumproben waren in früheren epidemiologischen Studien häufig das einzige biologische Material, das gesammelt und untersucht wurde. Diese Studien besitzen gerade durch ihren sehr langen Untersuchungszeitraum einen riesigen Informationsgehalt und wären ein unbezahlbarer Schatz für genetische Analysen. Oft ist aufgrund damals mangelnder Akquirierung jedoch keine genomische DNA verfügbar. Um die in Plasmaproben in geringer Menge vorkommende DNA verwenden zu können, extrahierten wir die DNA mit Hilfe von magnetischen Partikeln und setzten sie in eine Whole Genome Amplification (WGA) m

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Lee, Tai-Chun, and 李黛君. "Comparison with Linker adaptor and MDA Two Methodsof Whole Genome Amplification for Single Cell GenomeAmplification Efficiency." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/08385668836849829311.

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碩士<br>國立臺灣大學<br>分子醫學研究所<br>95<br>Preimplantation genetic diagnosis (PGD) of single gene disorders relies on PCR-based tests performed on single cells (polar bodies or blastomeres). Single cell PCR protocols are subject to serious difficulties, including contamination, amplification failure, and preferential amplification or the complete absence of one allele (allele dropout, ADO) in heterozygous loci, but it remains the only tool for detecting specific mutation in PGD. The DNA content of single cell was limited. Different whole genome amplification (WGA) techniques have been developed to incre

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Fang, Mei-Ya, and 方美雅. "Establishment of a new strategy for preimplantation genetic diagnosis using whole genome amplification and blastocyst biopsy." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/19165916479697061799.

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碩士<br>國立臺灣大學<br>分子醫學研究所<br>99<br>Preimplantation genetic diagnosis (PGD) is an alternative for prenatal diagnosis. For families with genetic diseases, PGD offers a chance to have an unaffected child, without facing termination of pregnancy. There are three stages of biopsy: polar bodies, one or two blastomeres from the cleavage-stage embryos, and trophectoderm cells from the blastocyst-stage embryos. Validation of polymerase chain reaction (PCR)-based assays are challenging because only limited genetic material can be obtained for PGD. The whole genome amplification (WGA) can amplify the limit

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32

Meehan, Conor J., G. A. Goig, T. A. Kohl, L. Verboven, A. Dippenaar, M. Ezewudo, M. R. Farhat, et al. "Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues." 2019. http://hdl.handle.net/10454/17276.

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No<br>Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validatio

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Schoenborn, Veit [Verfasser]. "Whole genome amplification von Plasma-DNA und Entwicklung eines Ausschlusskriteriums zur Verbesserung der Genotypisierungsqualität / vorgelegt von Veit Schoenborn." 2009. http://d-nb.info/995554153/34.

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Svensson, Ulrika. "Whole genome amplification of bacterial DNA: Identification of SHV-, LEN- and OPK-genes with SP6 and T7 sequence tagged PCR amplicons." Thesis, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-204697.

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Seifertová, Eva. "Genetické mapování u rodu Xenopus." Doctoral thesis, 2014. http://www.nusl.cz/ntk/nusl-342246.

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The diploid amphibian Xenopus tropicalis represents a significant model organism for studies of early development, genes function and evolution. Such techniques as gynogenesis, injection of morpholino antisense oligonucleotide into fertilized eggs or transgenesis were established. In the recent ten years, many efforts have been made to complete the sequence information. X. tropicalis genome has been sequenced but the completion of its assembly only on the basis of sequence data has been impossible. Therefore, our first work was focused on one of approaches for a genome completing- genetic mapp

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