Dissertations / Theses: 'Single nucleotide polymorphism (SNP)'

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Blanchard, Kimberly A. "Analysis of Single Nucleotide Polymorphism Panels for Bovine DNA Identification." DigitalCommons@USU, 2013. https://digitalcommons.usu.edu/etd/1712.

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Single nucleotide polymorphisms (SNPs) are single base-pair variations that exist between individuals. There are approximately a million or more SNPs located throughout the genome of each individual animal. Therefore, by taking advantage of these unique polymorphisms, SNPs can be used to resolve questions of unknown parentage in the livestock industry. Currently a panel of 88 SNPs, obtained from a panel of 121 SNPs originally created by USDA-MARC, is commercially available from Fluidigm®. The objective of this study was to determine whether the number of SNPs from the 88-SNP marker panel could be reduced to form a smaller, more cost-efficient parentage-testing SNP panel. A smaller panel would benefit farmers and researchers alike in reducing the time spent in running and analyzing the test, as well as reducing the overall cost for the procedure. Genotype data from over 3000 cattle samples containing offspring and potential parents were examined using two parentage calling software packages. Parentage assessment was analyzed using nine SNP panels of varying size. It was determined that a panel of 71 SNPs, chosen from the original 88 SNPs, was the minimum number required to maintain statistical accuracy and reliability.

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Pungliya, Manish S. "Single nucleotide polymorphism analysis in application to fine gene mapping." Digital WPI, 2001. https://digitalcommons.wpi.edu/etd-theses/642.

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Single nucleotide polymorphisms (SNPs) are single base variations among groups of individuals. In order to study their properties in fine gene mapping, I considered their occurrence as transitions and transversions. The aim of the study was to classify each polymorphism depending upon whether it was a transition or transversion and to calculate the proportions of transitions and transversions in the SNP data from the public databases. This ratio was found to be 2.35 for data from the Whitehead Institute for Genome Research database, 2.003 from the Genome Database, and 2.086 from the SNP Consortium database. These results indicate that the ratio of the numbers of transitions to transversions was very different than the expected ratio of 0.5. To study the effect of different transition to transversion ratios in fine gene mapping, a simulation study was performed to generate nucleotide sequence data. The study investigated the effect of different transition to transversion ratios on linkage disequilibrium parameter (LD), which is frequently used in association analysis to identify functional mutations. My results showed no considerable effect of different transition to transversion ratios on LD. I also studied the distribution of allele frequencies of biallelic SNPs from the Genome Database. My results showed that the most common SNPs are normally distributed with mean allele frequency of 0.7520 and standard deviation of 0.1272. These results can be useful in future studies for simulating SNP behavior. I also studied the simulated data provided by the Genetic Analysis Workshop 12 to identify functional SNPs in candidate genes by using the genotype-specific linkage disequilibrium method.

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Schwonbeck, Susanne. "Analyse von Single-Nucleotide-Polymorphisms an Glas-Oberflächen." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=974115568.

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Lin, Kuan-chin. "Candidate Gene Expression and SNP Analyses of Toxin-Induced Dilated Cardiomyopathy in the Turkey(Meleagris gallopavo)." Thesis, Virginia Tech, 2006. http://hdl.handle.net/10919/42012.

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Dilated cardiomyopathy (DCM), a heart disease, affects many vertebrates including humans and poultry. The disease can be either idiopathic (IDCM) or toxin-induced. Idiopathic DCM often occurs without a consensus cause. Though genetic and other studies of IDCM are extensive, the specific etiology of toxin-induced is still unknown. Here, our objective was to compare the level of mRNA expression of two candidate genes including troponin T (cTnT) and phospholamban (PLN) using quantitative reverse transcription polymerase chain reaction (RT-PCR) in toxin-induced DCM affected and unaffected turkeys. Cardiac TnT and PLN were chosen because their spontaneous expression has been reported to be associated with IDCM. We also scanned these genes for single nucleotide polymorphisms (SNPs) that could be useful in evaluating their functions in the incidence and severity of toxin-induced DCM in turkeys. There were no significant differences between affected and unaffected birds in the expression of both cTnT and PLN. A total of 12 SNPs were detected in cTnT and PLN DNA sequences. One of the seven haplotypes detected in cTnT was the most frequent. Linkage analysis showed that cTnT gene was unlinked on the current turkey genetic map. Resources developed here, including SNPs, haplotypes, cDNA sequences, and the PCR-RFLP genotype procedure will be used for future investigations involving cTnT and PLN and toxin-induced DCM. Master of Science

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Veldsman, Werner Pieter. "SNP based literature and data retrieval." Thesis, University of the Western Cape, 2016. http://hdl.handle.net/11394/5345.

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>Magister Scientiae - MSc Reference single nucleotide polymorphism (refSNP) identifiers are used to earmark SNPs in the human genome. These identifiers are often found in variant call format (VCF) files. RefSNPs can be useful to include as terms submitted to search engines when sourcing biomedical literature. In this thesis, the development of a bioinformatics software package is motivated, planned and implemented as a web application (http://sniphunter.sanbi.ac.za) with an application programming interface (API). The purpose is to allow scientists searching for relevant literature to query a database using refSNP identifiers and potential keywords assigned to scientific literature by the authors. Multiple queries can be simultaneously launched using either the web interface or the API. In addition, a VCF file parser was developed and packaged with the application to allow users to upload, extract and write information from VCF files to a file format that can be interpreted by the novel search engine created during this project. The parsing feature is seamlessly integrated with the web application's user interface, meaning there is no expectation on the user to learn a scripting language. This multi-faceted software system, called SNiPhunter, envisions saving researchers time during life sciences literature procurement, by suggesting articles based on the amount of times a reference SNP identifier has been mentioned in an article. This will allow the user to make a quantitative estimate as to the relevance of an article. A second novel feature is the inclusion of the email address of a correspondence author in the results returned to the user, which promotes communication between scientists. Moreover, links to external functional information are provided to allow researchers to examine annotations associated with their reference SNP identifier of interest. Standard information such as digital object identifiers and publishing dates, that are typically provided by other search engines, are also included in the results returned to the user. National Research Foundation (NRF) /The South African Research Chairs Initiative (SARChI)

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Howell, Walter Mathias. "SNP technology and Alzheimer's disease /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-473-9/.

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Kadioglu, Onat. "Determination Of Performance Parameters For Ahp Based Single Nucleotide Polymorphism (snp) Prioritization Approach On Alzheimers." Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613775/index.pdf.

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GWAS mainly aim to identify variations associated with certain phenotypes or diseases. Recently the combined p-value approach is described as the next step after GWAS to map the significant SNPs to genes and pathways to evaluate SNP-gene-disease associations. Major bottleneck of standard GWAS approaches is the prioritization of statistically significant results. The connection between statistical analysis and biological relevance should be established to understand the underlying molecular mechanisms of diseases. There are few tools offered for SNP prioritization but these are mainly based on user-defined subjective parameters, which are hard to standardize. Our group has recently developed a novel AHP based SNP prioritization algorithm. Beside statistical association AHP based SNP prioritization algorithm scores SNPs according to their biological relevance in terms of genomic location, functional consequence, evolutionary conservation, and gene-disease association. This allows researchers to evaluate the significantly associated SNPs quickly and objectively. Here, we have investigated the performance of the AHP based prioritization as the next step in the utilization of the algorithm in comparison to the other available tools for SNP prioritization. The user-defined parameters for AHP based prioritization have been investigated and our suggestion on how to use these parameters are presented. Additionally, the GWAS results from the analysis of two different sets of Alzheimer Disease Genotyping data with the newly proposed AHP based prioritization and the integrated software, METU-SNP, it was implemented, is reported and our new findings on the association of SNPs and genes with AD based on this analysis is discussed.

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Meyer, Jodokus [Verfasser], and Alexander [Akademischer Betreuer] Mellmann. "Single-Nucleotide-Polymorphism-(SNP)-Analyse im Kerngenom der HUSEC-Kollektion / Jodokus Meyer ; Betreuer: Alexander Mellmann." Münster : Universitäts- und Landesbibliothek Münster, 2014. http://d-nb.info/1138284351/34.

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Ramdayal, Kavisha. "Incidence and Regulatory Implications of Single Nucleotide Polymorphisms among Established Ovarian Cancer Genes." Thesis, Online access, 2009. http://etd.uwc.ac.za/usrfiles/modules/etd/docs/etd_gen8Srv25Nme4_5111_1277754725.pdf.

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Hrabik, Sarah A. "The Clinical Utility of a SNP Microarray in Patients with Epilepsy at a Tertiary Medical Center." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1368024881.

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Gowrisankar, Sivakumar. "Predicting Functional Impact of Coding and Non-Coding Single Nucleotide Polymorphisms." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1225422057.

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Mercer, Heather Milliken. "The Distribution of Single Nucleotide Polymorphisms in Pyoderma Gangrenosum: Biomarker Discovery." Kent State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=kent1383769612.

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Feuk, Lars. "SNP based strategies to study candidate genes for Alzheimer's disease /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-334-1.

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Silva, Fernanda Borges da. "Uso do Single Nucleotide Polymorphism Array (SNP-A) na investigação de alterações citogenéticas em pacientes com síndromes mielodisplásicas." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/17/17154/tde-29032017-164341/.

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As síndromes mielodisplásicas (SMD) constituem um grupo heterogêneo de doenças hematológicas de origem clonal, caracterizado por hematopoese ineficaz, citopenia e risco de evolução para leucemia mieloide aguda (LMA). As anormalidades citogenéticas adquiridas são marcadores prognósticos bem estabelecidos em SMD. No entanto, a técnica de citogenética metafásica apresenta limitações, incluindo baixa resolução e necessidade de divisão celular, sendo que defeitos cromossômicos podem não ser detectados. Tecnologias baseadas em microarranjo (array) de DNA, como o Single Nucleotide Polymorphism Array (SNP-A), são importantes para avaliação do genoma normal e neoplásico. O SNP-A foi desenvolvido para o estudo de todo o genoma, apresenta uma resolução superior a citogenética metafásica convencional, pode ser realizado em células na interfase, e detecta alterações cromossômicas não visualizadas pela citogenética metafásica. Além disso, o SNPA fornece dados de genotipagem para detecção de perda neutra de heterozigose, também denominada de dissomia uniparental somática. Regiões cromossômicas com deleção, perda neutra de heterozigose ou ganho são comuns em pacientes com neoplasias hematológicas e sugeriu genes candidatos a supressores de tumor e oncogenes. O objetivo do presente estudo foi a caracterização da coorte de pacientes com suspeita clínica de SMD e o uso integrado do método de citogenética convencional e SNP-A no serviço de hematologia da nossa instituição na investigação de alterações citogenéticas em pacientes com SMD e doenças relacionadas. Durante o período do estudo, foram recebidas um total de 114 amostras de pacientes com suspeita clínica de SMD. A análise clínica, morfológica e citogenética permitiu confirmar o diagnóstico de SMD ou doenças relacionadas em 43 pacientes (SMD [n=34], SMD/NMP [n=5], LMA com alterações mielodisplásicas [n=4]). Vinte e um pacientes foram classificados como citopenia idiopática de significado indeterminado (CISI) e 50 indivíduos apresentaram outros diagnósticos. SNP-A foi realizado em 17 pacientes com SMD e doenças relacionadas. Dentre os pacientes selecionados para o SNP-A, anormalidades cromossômicas foram observadas em 6/17 (35%) casos pelo cariótipo convencional e em 8/17 (47%) casos pela técnica de SNP-A. SNP-A não detectou quatro alterações cromossômicas previamente identificadas pela citogenética convencional: duas translocações balanceadas e duas alterações numéricas. SNP-A confirmou os demais achados identificados pela citogenética convencional e detectou um total de 32 novas lesões (1 ganho, 19 perdas e 12 UPDs) em 6 pacientes com SMD ou doenças relacionadas. SNP-A pode complementar a citogenética convencional na detecção de anormalidades cromossômicas em neoplasias mieloides. Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal hematopoietic diseases, characterized by inefficient hematopoiesis, peripheral blood cytopenias and a risk to progress to acute myeloid leukemia (AML). Acquired chromosomal abnormalities have prognostic value in MDS. However, metaphase cytogenetics has some limitations including low resolution and the requirement of cell division, and chromosomal abnormalities may not be detected. New technologies based on array, the Single Nucleotide Polymorphism Array (SNP-A), are able to evaluate the whole genome. The SNP-A has superior resolution compared to metaphase cytogenetics, may be used in interphase cells, and may detect chromosomal abnormalities not detected by metaphase cytogenetics. In addition, the SNP-A read-out includes genotyping calls and hybridization signal strength, corresponding to gene copy number, allowing detecting copy neutral loss of heterozigosity (CN-LOH), also known as uniparental dissomy (UPD). Deletions, copy neutral loss of heterozigosity or gain are frequent in patients with haematopoietic neoplasms and has already suggested the location of tumor suppressor genes and oncogenes. The aim of this study was to characterize the cohort of patients with clinical suspicion of MDS and to establish the integrative use of the conventional cytogenetic and the SNP-A in the investigation of chromosomal abnormalities in patients with MDS and related diseases followed at our institution. The clinical, morphological and cytogenetic evaluation allowed us to confirm the diagnosis of MDS or related disease in 43 patients (MDS [n=34], MDS/MPN [n=5], AML with myelodysplastic changes [n=4]). Twenty-one patients were diagnosed with idiopathic cytopenia with undetermined significance (ICUS) and 50 patients had other diagnosis. SNP-A were performed in 17 patients with MDS and related disease. Chromosomal abnormalities were observed in 6/17 (35%) cases by metaphase cytogenetics, and in 8/17 (47%) of the cases by SNP-A. SNP-A did not detected two balanced translocations and two numerical alterations previously observed by metaphase cytogenetics. SNP-A confirmed all the other findings observed by metaphase cytogenetics and SNP-A detected a total of 32 new lesions (1 gain, 19 losses and 12 UPDs) in 6 MDS and related diseases. SNP-A may complement metaphase cytogenetics to improve the detection of chromosomal abnormalities in myeloid neoplasms.

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Schwonbeck, Susanne. "Analyse von Single Nucleotide Polymorphisms an Glas-Oberflächen." Phd thesis, Universität Potsdam, 2004. http://opus.kobv.de/ubp/volltexte/2005/221/.

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Ziel der vorliegenden Arbeit war die Entwicklung einer SNP-Genotypisierungsmethode mit auf Mikroarrays immobilisierten PCR-Produkten. Für die Analyse wurde ein faseroptischer Affinitätssensor bzw. ein Durchfluss-Biochip-Scanner mit integrierter Fluoreszenzdetektion verwendet. An den immobilisierten Analyten (PCR-Produkten) wurde eine Fluoreszenzoligonukleotidsonde hybridisiert und anschließend die Dissoziation der Sonde im Fluss verfolgt. Die Diskriminierung von Wildtyp- und Mutanten-DNA erfolgte durch die kinetische Auswertung der Dissoziationskurven sowie durch die Analyse der Fluoreszenzintensität. Die Versuche am faseroptischen Affinitätssensor zeigten, dass DNA-DNA-Hybride sowohl von Oligonukleotiden als auch von PCR-Produkten ein typisches Dissoziationsverhalten aufweisen, wobei fehlgepaarte Hybride eine signifikant schnellere Dissoziation zeigen als perfekt passende Hybride. Dieser Geschwindigkeitsunterschied lässt sich durch den Vergleich der jeweiligen kinetischen Geschwindigkeitskonstanten kD quantitativ erfassen. Da die Kopplung des Analyten an der Chipoberfläche sowie die Hybridisierungs- und Dissoziationsparameter essentiell für die Methodenentwicklung war, wurden die Parameter für ein optimales Spotting und die Immobilisierung von PCR-Produkten ermittelt. Getestet wurden die affine Kopplung von biotinylierten PCR-Produkten an Streptavidin-, Avidin- und NeutrAvidin-Oberflächen sowie die kovalente Bindung von phosphorylierten Amplifikaten mit der EDC/Methylimidazol-Methode. Die besten Ergebnisse sowohl in Spotform und -homogenität als auch im Signal/Rausch-Verhältnis wurden an NeutrAvidin-Oberflächen erreicht. Für die Etablierung der Mikroarray-Genotypisierungsmethode durch kinetische Analyse nach einem Hybridisierungsexperiment wurden Sondenlänge, Puffersystem, Spotting-Konzentration des Analyten sowie Temperatur optimiert. Das Analysensystem erlaubte es, PCR-Produkte mit einer Konzentration von 250 ng/µl in einem HEPES-EDTA-NaCl-Puffer auf mit NeutrAvidin beschichtete Glasträger zu spotten. In den anschließenden Hybridisierungs- und Dissoziationsexperimenten bei 30 °C konnte die Diskriminierung von homocygoter Wildtyp- und homocygoter Mutanten- sowie heterocygoter DNA am Beispiel von Oligonukleotid-Hybriden erreicht werden. In einer Gruppe von 24 homocygoten Patienten wurde ein Polymorphismus im SULT1A1-Gen analysiert. Sowohl durch kinetische Auswertung als auch mit der Analyse der Fluoreszenzintensität wurde der Genotyp der Proben identifiziert. Die Ergebnisse wurden mit dem Referenzverfahren, der Restriktionschnittstellenanalyse (PCR-RFLP) validiert. Lediglich ein Genotyp wurde falsch bestimmt, die Genauigkeit lag bei 96%. In einer Gruppe von 44 Patienten wurde der Genotyp eines SNP in der Adiponectin-Promotor-Region untersucht. Nach Vergleich der Analysenergebnisse mit denen eines Referenzverfahrens konnten lediglich 14 der untersuchten Genotypen bestätigt werden. Ursache für die unzureichende Genauigkeit der Methode war vor allem das schlechte Signal/Rausch-Verhältnis. Zusammenfassend kann gesagt werden, dass das in dieser Arbeit entwickelte Analysesystem für die Genotypisierung von Einzelpunktmutationen geeignet ist, homocygote Patientenproben zuverlässig zu analysieren. Prinzipiell ist das auch bei heterocygoter DNA möglich. Da nach aktuellem Kenntnisstand eine SNP-Analysemethode an immobilisierten PCR-Produkten noch nicht veröffentlicht wurde, stellt das hier entwickelte Verfahren eine Alternative zu bisher bekannten Mikroarray-Verfahren dar. Als besonders vorteilhaft erweist sich der reverse Ansatz der Methode. Der hier vorgestellte Ansatz ist eine kostengünstigere und weniger hoch dimensionierte Lösung für Fragestellungen beispielsweise in der Ernährungswissenschaft, bei denen meist eine mittlere Anzahl Patienten auf nur einige wenige SNPs zu untersuchen ist. Wenn es gelingt, durch die Weiterentwicklung der Hardware bzw. weiterer Optimierung, eine Verbesserung des Signal/Rausch-Verhältnisses und damit die Diskriminierung von heterocygoter DNA zu erreichen, kann diese Methode zukünftig bei der Analyse von mittelgroßen Patientengruppen alternativ zu anderen Genotypisierungsmethoden verwendet werden. The aim of this thesis was the development of a SNP genotyping method involving PCR products immobilised on microarrays. For the analysis a fibre optic affinity biosensor and a flow-through biochip scanner were used. Fluorescent probes were hybridized with the immobilised PCR products. In order to start the dissociation process the surface was rinsed with buffer and the fluorescence intensity was measured. Two different cases were studied: First, the full-matched DNA hybrid (wildtyp single strand with complementary wildtype single strand), second the mis-matched hybrid (wildtype single strand and mutant single strand). After determinating the reaction rates (kD) as kinetic parameter the kD values of both cases were compared. The experiments showed a significant difference in the kD value of the full- and the mis-match hybrids. Therefore, mutant and wildtype DNA were discriminated by kinetic analysis of the dissociation process and analysis of the fluorescence intensity. To set up the complete analysis process the reaction parameters like coupling of the PCR products had to be optimised. Both affininty coupled (streptavidin, neutravidin, avidin - biotin) and covalent methods (EDC/methylimidazol) were carried out. Best results in spot homogeinity and spot appearance were obtained with coupling of biotinylated PCR products on neutravidin coated chip surfaces. Additionally, the length of the probe, the spotting concentration, the spotting buffer and the reaction temperature were optimised. In the optimised analysis PCR products (250 µg/µl) were spotted onto neutravidin coated surfaces. The hybridisation and dissociation processes were carried out at 30°C. A HEPES-EDTA-NaCl buffer was used for spotting, diluting of the fluorescent probe and rinsing the microarray surface. A fluorescent probe was used with 13 nucleotides in length. The mis- or full-matching base indicating the polymorphism was located in the center position of the probe. The analysis system was tested with the genomic DNA of a group of 24 homocygote individuals with a SNP in the SULT1A1 gene region. The hybridisation and dissociation processes were carried out and the reaction rates were determinated. Subsequently after the analysis in the flow-through biochip scanner the fluorescence intensity of the spots were measured. The results showed very good comparability with results of a PCR-RFLP analysis (one false genotype). Additionally, a group of 44 heterocygote DNA samples with one SNP in the adiponectin promotor region were also genotyped. Compared to a reference method only 14 genotypes were correctly determined. This was mostly due to a low signal-noise-ratio and needs to be further investigated. Besides the problem in analysing heterocygote DNA samples the developed analysis system is very useful for genotyping SNP in homocygote DNA samples. The successful analysis of heterocygote sample is principally possible and with further investigations/optimisation, a better analysis should be possible. The most important advantage of the developed method is the reverse approach of binding PCR products at the surface instead of oligonucleotides. This allows the parallel genotyping of several individuals. Other advantages include low costs and medium sized dimensions in terms of throughput.

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Rasmussen, Samantha. "Predicting feed efficiency in beef cattle; a comparison of direct measures, expected progeny differences, and single nucleotide polymorphism methodologies." OpenSIUC, 2020. https://opensiuc.lib.siu.edu/theses/2685.

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Single nucleotide polymorphism (SNP) methodology is being used as a means to determine genetic merit in beef cattle by interrogating animal genomes and associating the findings with performance traits. The ability to predict future trait performance is highly attractive to beef cattle producers as they can make important management and financial decisions earlier and with more certainty. To fully realize the potential of SNP testing technology the methodology must be vetted to assure producer confidence. The purpose of this project is to assess three sources of information for beef cattle trait assessment. These information sources are: SNP testing, Expected Progeny Differences (EPDs) and direct animal measures. To conduct this study, young beef bulls (n=181) consigned to the SIU Beef Evaluation Station were utilized in an 84-day period to obtain direct measures. The SIU Beef Evaluation Station uses the Calan-Broadbent confinement feeding system which allows researchers to monitor individual animal feed intake and weight gain. Feed efficiency traits are important to the cattle industry since feed is generally among the largest input cost to producers. The evaluation of bulls also assesses reproductive and carcass traits which are also important to the producer’s financial success.Individual animal performance information was sent to the bull’s respective breed association for determination of EPD’s. Blood samples were submitted to a commercial company for SNP testing (Igentiy Gold and Igenity Beef Profile, Neogen, Lincoln, NE). Data was analyzed using pairwise comparisons by source of information. Pearson correlations were used to determine the direction and the strength for sources of information to vary together. Data was determined to be correlated when the correlation coefficient was 0.3 < r < - 0.3. No correlation was observed between RFISIU :RFINEO (r = 0.042), RFINEO:F/GSIU (r = - 0.09), RFISIU:ADGNEO (r = 0.091), RFISIU:ADGSIU (r = - 0.039), RFINEO:ADGNEO (r = 0.236), BWNEO:BWSIU (r = 0.115), FRAMESIU:BWSIU (r = 0.111), FRAMESIU:BWEPD (r = 0.159), FRAMESIU:ADGSIU (r = 0.148), FRAMESIU:ADGNEO (r = -0.005), BWSIU:BWEPD (r = 0.256), and BWNEO:BWEPD (r = 0.226). Correlations were observed between RFISIU:F/GSIU (r = 0.455), ADGSIU :ADGNEO (r = 0.353), and FRAMESIU:BWNEO (r = 0.326).This study determined that beef bulls should continue to be performance tested due to discrepancies between sources of information for key animal performance traits. Assessment of SNPs used in the commercial test should continue.

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VILLAR, Kamila de Melo. "Associação de polimorfismos no gene IL22RA1 como os níveis séricos de IL-22 e com parâmetros clínicos de pacientes portadores de artrite reumatoide." Universidade Federal de Pernambuco, 2015. https://repositorio.ufpe.br/handle/123456789/17169.

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Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2016-06-28T18:09:11Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) dissertação Kamila_04.02.16 versao final completa.pdf: 2092777 bytes, checksum: 9e9782d9821d10b1a59b8f2a1a1ca8f7 (MD5) Made available in DSpace on 2016-06-28T18:09:11Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) dissertação Kamila_04.02.16 versao final completa.pdf: 2092777 bytes, checksum: 9e9782d9821d10b1a59b8f2a1a1ca8f7 (MD5) Previous issue date: 2015-10-10 CAPES O processo inflamatório associado à liberação de citocinas está diretamente envolvido na patogênese da artrite reumatóide (AR). Um estudo anterior do nosso grupo relatou que pacientes com AR apresentaram níveis elevados da citocina IL-22 em relação aos controles e este aumento foi associado a um pior quadro clinico. Polimorfismos em interleucinas ou nos receptores específicos podem modificá-los funcionalmente, e assim, contribuir para o desenvolvimento da AR. O objetivo deste estudo foi identificar polimorfismos no receptor da citocina IL-22 que possam estar associados ao risco de desenvolver AR. Cento e trinta e oito portadores de AR foram recrutados pelo Serviço de Reumatologia do HC - UFPE, cumprindo os critérios do Colégio Americano de Reumatologia foram genotipados para os polimorfismos no IL22RA1 (rs4292900 e rs10794665) através da metodologia TaqMan®; o grupo controle foi formado por cento e vinte e oito indivíduos sadios. Os SNPs foram identificados por meio de consulta ao site HapMap, com uma frequência do alelo menor (MAF) de pelo menos 0,1% em caucasianos. Todas as frequências genéticas foram verificadas quanto ao equilíbrio de Hardy-Weinberg e a comparação das proporções foi realizada através do qui-quadrado (X²) ou teste exato de Fisher. Resultados: O genótipo TT (rs4292900) foi significativamente associado a AR quando comparados aos controles (37.79% e 21.36%, respectivamente, p=0,0054, odds ratio=2.23). Os pacientes heterozigotos CT e homozigotos TT para o polimorfismo rs4292900 apresentaram níveis significativamente elevados da citocina IL-22 comparados ao homozigoto CC (p=0.0018 e p=0.0324, respectivamente). Quanto aos parâmetros clínicos o genótipo CT (rs4292900) apresentou valores maiores do índice de atividade da doença (CDAI) comparado aos homozigotos; o mesmo ocorreu com o rs1079466. Observamos que os indivíduos TT para o rs 4292900 apresentaram maiores valores do hemossedimentação (VSH) comparados aos heterozigotos (p=0.016). Conclusão: Nossos resultados sugerem uma associação entre o rs4292900 e uma maior susceptibilidade a artrite reumatóide. Os dois SNPs não foram associados a pior quadro clínico da doença, no entanto o genótipo TT do rs4292900 foi associado com o altos níveis do VSH. The inflammatory process associated with the release of cytokines is directly involved in the pathogenesis of rheumatoid arthritis (RA). A previous study from our group reported that RA patients had higher levels of IL-22 cytokine compared to controls and this increase was associated worse clinical condition. Interleukins or polymorphisms in the specific receptors can modify them functionally, therefore contributing to the development of the RA. The objective of this study was to identify polymorphisms in the IL-22 cytokine receptor that may be associated with risk of developing RA. One hundred and thirty-eight patients with RA were recruited at the Rheumatology Service HC - UFPE, meeting the American College of Rheumatology criteria they were genotyped for polymorphisms in IL22RA1 (rs4292900 and rs10794665) through the TaqMan method; the control group consisted of one hundred twenty-eight healthy individuals. SNPs were identified by query of the HapMap site with a minor allele frequency (MAF) of at least 0.1% in Caucasians. All genetic frequencies were checked for Hardy-Weinberg and the comparison of proportions was performed using the chi-square (X²) or Fisher's exact test. Results: The TT genotype (rs4292900) was significantly associated with RA compared to controls (37.79% and 21:36% respectively, p = 0.0054, odds ratio = 2.23). Patients heterozygous CT, and homozygous TT for the polymorphism rs4292900 had significantly elevated levels of the cytokine IL-22 compared to the homozygous CC (p = 0.0018 and p = 0.0324, respectively). As for the clinical parameters the CT genotype (rs4292900) showed higher values of disease activity index (CDAI) compared to homozygous; so has the rs1079466. We observe that the TT individuals for rs4292900 showed higher erythrocyte sedimentation rate (ESR) values compared to heterozygotes (p = 0.016). Conclusion: Our results suggest an association between rs4292900 and increased susceptibility to rheumatoid arthritis. The two SNPs were not associated worse clinical disease, however the rs4292900 TT genotype was associated with high levels of ESR.

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Naidu, Alecia Geraldine. "The development of a single nucleotide polymorphism database for forensic identification of specified physical traits." Thesis, University of the Western Cape, 2009. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_9261_1297760101.

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Many Single Nucleotide Polymorphisms (SNPs) found in coding or regulatory regions within the human genome lead to phenotypic differences that make prediction of physical appearance, based on genetic analysis, potentially useful in forensic investigations. Complex traits such as pigmentation can be predicted from the genome sequence, provided that genes with strong effects on the trait exist and are known. Phenotypic traits may also be associated with variations in gene expression due to the presence of SNPs in promoter regions. In this project, the identification of genes associated with these physical traits of potential forensic relevance have been collated from the literature using a text mining platform and hand curation. The SNPs associated with these genes have been acquired from public SNP repositories such as the International HapMap project, dbSNP and Ensembl. Characterization of different population groups based on the SNPs has been performed and the results and data stored in a MySQL database. This database contains SNP genotyping data with respect to physical phenotypic differences of forensic interest. The potential forensicrelevance of the SNP information contained in this database has been verified through in silico SNP analysis aimed at establishing possible relationships between SNP occurrence and phenotype. The software used for this analysis is MATCH&trade .

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Aswathanarayanan, Subramanian. "A STUDY OF THE EFFECT OF SINGLE NUCLEOTIDE POLYMORPHISMS IN HUMAN GENOME ON THE SECONDARY STRUCTURE OF PROTEINS." University of Cincinnati / OhioLINK, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1024675762.

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Dai, Yu. "Genetic association studies : exploiting SNP-haplotype selection and covariate independence /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9582.

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Synnergren, Jane. "Wheat variety identification using genetic variations." Thesis, University of Skövde, Department of Computer Science, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-821.

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There is a continuous development of different crop varieties in the crop trade. The cultivated crops tend to be more and more alike which require an effective method for crop identification. Crop type and crop type purity has become a quality measure in crop trade both nationally and internationally. A number of well known quality attributes of interest in the crop trade can be correlated to the specific crop type and therefore it is of great importance to reliably be able to identify different crop varieties. It is well known from the literature that there exist genomic variations at the nucleotide level between different crop varieties and these variations might potentially be useful for automated variety identification.This project deals with the crop variety identification area where the possibilities of distinguishing between different wheat varieties are investigated. Experience from performing wheat variety identification at protein level has shown unsatisfactory results and therefore DNA-based techniques are proposed instead. DNA-based techniques are dependent upon the availability of sequence data from the wheat genome and some work has concerned examining the availability of sequence data from wheat. But the focus of the work has been on defining a method for computational detection of single nucleotide variations in ESTs from wheat and to experimentally test that method. Results from these experiments show that the method defined in this project detects polymorphic variations that can be correlated to variety variations

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Barnett, Catherine Margaret Eleanor. "Association of Single Nucleotide Polymorphisms in Surfactant Protein A and D with Otitis Media." The University of Waikato, 2007. http://hdl.handle.net/10289/2338.

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Otitis Media is one of the most common childhood diseases. Recurrent acute otitis media RAOM is characterized by repeated episodes of inflammation of the middle ear in conjunction with middle ear fluid, and often with an inflamed or bulging eardrum. Defective clearance by the Eustachian tube results in mucus build-up and is characteristic of otitis media with effusion (OME). Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, respiratory syncytial virus, and rhinovirus are the most common contributors to otitis media pathogenesis. In New Zealand, OME has been implicated with conductive hearing loss in childhood and has been shown to significantly impact on speech and language development. New Zealand Māori and Polynesian children have displayed significantly higher hearing test failure rates than European-Caucasian children. The collectins, Surfactant Protein (SP)-A and -D are encoded by three genes (SP-A1, SP-A2, and SP-D) and are host defense proteins present in the middle ear and Eustachian tube. Single nucleotide polymorphisms (SNPs) in SP-A1 and SP-A2 have been associated with increased or decreased susceptibility to otitis media, meningococcal disease, and range of respiratory diseases. Using allele-specific primers and real-time PCR with SYBR Green I melting curve analysis, four groups of individuals were genotyped for eleven SP-A1, SP-A2, and SP-D SNPs: European-Caucasian individuals with RAOM/OME; New Zealand Māori/Polynesian individuals with RAOM/OME; individuals with meningococcal disease; and a control group. The computer program, Haploview, was employed to perform χ2 analyses and identify statistically significant associations of alleles/haplotypes with RAOM/OME or meningococcal disease. In the European-Caucasian population, two SP-A1 alleles, one SP-A2 allele, and four haplotypes (CGAGC, 1A3, 1A9, and 1A10) were found to be associated with increased risk of RAOM/OME (P lt; 0.05). Conversely, haplotypes 6A2 and 1A2 were found to be protective against susceptibility to RAOM/OME (P lt; 0.05). In New Zealand Māori and Polynesian individuals, two SP-A1 alleles, three SP-A2 alleles, one SP-D allele, and four haplotypes (6A8, 6A10, 1A3, and 1A10) were found to be associated with increased risk of RAOM/OME (P lt; 0.05). An additional four haplotypes (6A2, 1A0, 1A2, and TA) were determined to be protective against susceptibility to RAOM/OME (P lt; 0.05). However, protective SPA1/SPA2/SPD haplotype 6A2-1A0-TA was significantly under-represented in the New Zealand Māori and Polynesian population (P lt; 0.05). A single allele and haplotype were associated with increased risk of meningococcal disease (P lt; 0.05). The findings of this study confirm that specific genetic variants of SP-A and SP-D are associated with either increased or decreased risk of developing RAOM and/or OME. Furthermore, it was demonstrated that New Zealand Māori and Polynesian individuals appear to exhibit more haplotypes susceptible to RAOM/OME. This may provide a partial explanation for the higher RAOM/OME-related failure rates of hearing tests in New Zealand Māori and Polynesian children. However, there are numerous socio-economic and environmental factors that also contribute to otitis media pathogenesis which were not considered in this study. The effects of the SP-A1, SP-A2, and SP-D alleles and haplotypes on the bacterial/viral binding efficiencies of SP-A and SP-D need to be investigated by further research, using a large population, to confirm the association with susceptibility or resistance with RAOM/OME.

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Krampe, Matthew Stephen. "Development of Single Nucleotide Polymorphism (SNP) Markers for Rapid, Inexpensive, and Standardized Identification of Pallid (Scaphirhynchus albus) and Shovelnose (S. platorynchus) Sturgeon Larvae." OpenSIUC, 2011. https://opensiuc.lib.siu.edu/theses/675.

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The purpose of this project was to develop inexpensive, standardized, and high throughput Single Nucleotide Polymorphism (SNP) markers that discriminate between pallid (Scaphirhynchus albus) and shovelnose (S. platorynchus) sturgeon for use as a larval identification tool. A total of 67 polymorphic sites was identified in DNA sequences from three genes: Recombination Activating Gene-1, Beta Actin, and Beta-2-Microglobulin. Allele frequencies from the 10 most variable SNPs were characterized for both pallid and shovelnose sturgeon in three geographically separated populations throughout the range of the pallid sturgeon. To create a standardized method of genotyping SNPs for larval pallid and shovelnose sturgeon, 5' nuclease allelic discrimination (TaqMan) assays were designed for two unlinked SNPs that exhibited the greatest allele frequency differences between species. A power analysis compared these SNP loci and their diagnostic power for species discrimination compared to sixteen microsatellite loci currently used for species discrimination (Schrey et al. 2007) One SNP locus was the most powerful marker for species identification in the upper and middle Missouri River. This study provides practical genetic tools for species discrimination between pallid and shovelnose that will facilitate understanding addressing questions that were previously too costly, labor intensive or technically challenging to answer.

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Shiue, Jai-Jün [Verfasser]. "Modifier-Gene in BRCA1/2-Mutationsträgerinnen: SNP-Analyse (single nucleotide polymorphism) in AKAP10, AKAP13 und c-MYC / Jai-Jün Shiue." Köln : Deutsche Zentralbibliothek für Medizin, 2014. http://d-nb.info/1049200160/34.

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Fletcher, Jeremy Charles. "THE USE OF PYROSEQUENCING FOR THE ANALYSIS OF Y CHROMOSOME SINGLE NUCLEOTIDE POLYMORPHISMS." Master's thesis, University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4487.

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The potential value of the Y chromosome for forensic applications has been recognized for some time with the current work dedicated to Short Tandem Repeat analysis and Single Nucleotide Polymorphism (SNP) discovery. This study examined the ability of two different SNP analysis methods to determine if they could be utilized in forensic applications and ultimately be developed into an established system for Y chromosome SNP analysis. This study examined two principle SNP analysis systems: single base extension and Pyrosequencing. Pyrosequencing was determined to be superior to single base extension, due to the wealth of information provided with sequencing and the flexibility of designing primers for analysis. Using Pyrosequencing, 50 Y chromosome loci were examined and the minimum loci required for maximum diversity for the development of a Y chromosome SNP analysis system were chosen. Thirteen loci were selected based on their ability to discriminate 60 different individuals from three different racial groups into 15 different haplogroups. The Y chromosome SNP analysis system developed utilized nested PCR for the amplification of all 13 loci. Then they were sequenced as groups, ranging from one to three loci, in a single reaction. The Y chromosome SNP analysis system developed here has the potential for forensic application since it has shown to be successful in the analysis of blood, buccal swabs, semen, and saliva, works with as little as 5 pg of starting DNA material, and will amplify only male DNA in the presence of male/female mixtures in which the female portion of the sample overwhelmed the male portion 30,000 to 1. M.S. Department of Chemistry Arts and Sciences Chemistry

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Reys, Brian D. "Correlations in Genetic Risk Scores Produced by Direct-to-Consumer Genetic Testing Companies." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1367925697.

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Costello, Mary-Ellen Clare. "Single nucleotide polymorphism (SNP) - genotyping of Community Acquired Methicillin-Resistant Staphylococcus aureus, including the subtyping of PVL toxin producers using Real-Time PCR." Thesis, Queensland University of Technology, 2010. https://eprints.qut.edu.au/37662/1/Mary-Ellen_Costello_Thesis.pdf.

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Staphylococcus aureus is a common pathogen that causes a variety of infections including soft tissue infections, impetigo, septicemia toxic shock and scalded skin syndrome. Traditionally, Methicillin-Resistant Staphylococcus aureus (MRSA) was considered a Hospital-Acquired (HA) infection. It is now recognised that the frequency of infections with MRSA is increasing in the community, and that these infections are not originating from hospital environments. A 2007 report by the Centers for Disease Control and Prevention (CDC) stated that Staphylococcus aureus is the most important cause of serious and fatal infections in the USA. Community-Acquired MRSA (CA-MRSA) are genetically diverse and distinct, meaning they are able to be identified and tracked by way of genotyping. Genotyping of MRSA using Single nucleotide polymorphisms (SNPs) is a rapid and robust method for monitoring MRSA, specifically ST93 (Queensland Clone) dissemination in the community. It has been shown that a large proportion of CA-MRSA infections in Queensland and New South Wales are caused by ST93. The rationale for this project was that SNP analysis of MLST genes is a rapid and cost-effective method for genotyping and monitoring MRSA dissemination in the community. In this study, 16 different sequence types (ST) were identified with 41% of isolates identified as ST93 making it the predominate clone. Males and Females were infected equally with an average patient age of 45yrs. Phenotypically, all of the ST93 had an identical antimicrobial resistance pattern. They were resistant to the β-lactams – Penicillin, Flu(di)cloxacillin and Cephalothin but sensitive to all other antibiotics tested. Virulence factors play an important role in allowing S. aureus to cause disease by way of colonising, replication and damage to the host. One virulence factor of particular interest is the toxin Panton-Valentine leukocidin (PVL), which is composed of two separate proteins encoded by two adjacent genes. PVL positive CA-MRSA are shown to cause recurrent, chronic or severe skin and soft tissue infections. As a result, it is important that PVL positive CA-MRSA is genotyped and tracked. Especially now that CA-MRSA infections are more prevalent than HA-MRSA infections and are now deemed endemic in Australia. 98% of all isolates in this study tested positive for the PVL toxin gene. This study showed that PVL is present in many different community based ST, not just ST93, which were all PVL positive. With this toxin becoming entrenched in CA-MRSA, genotyping would provide more accurate data and a way of tracking the dissemination. PVL gene can be sub-typed using an allele-specific Real-Time PCR (RT-PCR) followed by High resolution meltanalysis. This allows the identification of PVL subtypes within the CA-MRSA population and allow the tracking of these clones in the community.

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Mocker, Kristin. "Zytogenetische und molekularbiologische Untersuchungen an intrakraniellen Meningeomen unter Anwendung der GTG-Bänderung, SKY-Technik, FISH-Analyse und genomweiter SNP-A Karyotypisierung." Doctoral thesis, Universitätsbibliothek Leipzig, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-118823.

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Meningeome sind Tumore der Hirnhäute und stellen zirka 24-30% aller intrakraniellen Tumore dar. Obwohl sie in den meisten Fällen als solitär, langsam wachsend und benigne (WHO Grad 1) beschrieben werden, ist ihr ausgeprägtes Rezidivverhalten die größte Herausforderung in der Therapie. Bisherige Arbeiten verwendeten zur genetischen Analyse von Meningeomen meist Untersuchungstechniken mit eingeschränkter (molekular-)zytogenetischer Aussagekraft. Mit der Kombination der Methoden Giemsa-Bandendarstellung (GTG-Bänderung), Spektrale Karyotypisierung (SKY-Technik), Fluoreszenz in situ Hybridisierungstechniken (FISH-Analyse) und molekulare Karyotypisierung unter Verwendung von 100K beziehungsweise 6.0 SNP-Arrays (SNP-A Karyotypisierung) sollte es möglich sein, in effizienterer Form bislang unentdeckte chromosomale Aberrationen zu identifizieren und weiterführende tumormechanistische Hinweise zu erhalten. In der vorliegenden Arbeit wurde zunächst ein multipel aufgetretenes Meningeom mit zwei Tumoren unterschiedlicher Malignität (1 WHO Grad 1; 1 WHO Grad 2) analysiert, anschließend erfolgte die Untersuchung einer Gruppe von 10 Meningeomen (5 WHO Grad 1; 5 WHO Grad 2). Bisher nicht beschriebene Aberrationen wie ein dizentrisches Chromosomen 4, die parazentrische Inversion im chromosomalen Bereich 1p36 und die balancierte reziproke Translokation t(4;10)(q12;q26) wurden detektiert. Die genomweite SNP-A Karyotypisierung ermöglichte neben der genaueren Betrachtung der zytogenetischen Ergebnisse die simultane Analyse von Blut und Tumor-DNA der Patienten und lieferte Hinweise auf konstitutionelle Aberrationen. Es zeigte sich eine signifikante Anreicherung von rekurrenten Regionen kopienneutraler Verluste der Heterozygotie als Hinweis auf das Vorliegen potenzieller segmentaler Uniparentaler Disomie (UPD) jeweils in Blut und Tumor der Patienten. Außerdem wurden nur im Tumor befindliche potentielle rekurrente segmentale UPD Regionen detektiert. Die weitere Analyse der konstitutionellen sowie somatischen segmentalen UPD hinsichtlich ihrer Rolle im Rahmen der Tumorgenese ist eine wichtige Aufgabe für die Zukunft.

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Rickert, Andreas Marcus. "Entwicklung und Analyse von SNP-Markern (single nucleotide polymorphisms) in Pathogenresistenz-vermittelnden Regionen des Kartoffelgenoms." [S.l. : s.n.], 2002. http://deposit.ddb.de/cgi-bin/dokserv?idn=966253787.

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Valente, Tiago da Silva. "Estudo de associação de polimorfismos de nucleotídeo único (SNP) com características de temperamento em bovinos da raça Nelore /." Jaboticabal, 2016. http://hdl.handle.net/11449/143451.

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Orientador: Fernando Sebastian Baldi Rey Coorientador: Fernando Sebastián Baldi Rey Coorientador: Lucia Galvão de Albuquerque Banca: Marcos Vinícius Gualberto Barbosa da Silva Banca: Joslaine Noely dos Santos Gonçalves Cyrillo Banca: Josineudson Augusto II de Vasconcelos Silva Banca: Nedenia Bonvino Stafuzza Resumo: A variabilidade individual no temperamento dos bovinos é um importante fator que afeta a rentabilidade das empresas pecuárias, em função dos efeitos negativos na produção, no bem-estar animal e na segurança do trabalhador. Assim, esta característica vem despertando interesse crescente de produtores e pesquisadores, com o objetivo de entender quais os fatores genéticos e ambientais que influenciam a expressão do temperamento e os efeitos sobre o desempenho dos bovinos. Desta forma, esta tese foi desenvolvida com o objetivo de estudar a associação genômica entre polimorfismos de nucleotídeo único (SNP) com diferentes indicadores do temperamento de bovinos da raça Nelore. Os objetivos específicos foram: 1) Estudar a associação genômica entre SNP e diferentes indicadores de temperamento; 2) Avaliar a existência de regiões do genoma associadas, simultaneamente, com distintos indicadores de temperamento; 3) Identificar genes e as respectivas funções biológicas que influenciam o temperamento e; 4) Estimar parâmetros genéticos para os diferentes testes de temperamento incluindo a informação genômica. O temperamento dos bovinos foi avaliado entre 2010 e 2015, durante o manejo de pesagem aos 18 meses de idade, utilizando os seguintes indicadores: 1) escore de movimentação (MOV); 2) escore de tensão (TENS); 3) escore de agitação no tronco de contenção (CS); 4) velocidade de fuga (VF) e; 5) escore de temperamento (ET). Os animais foram genotipados utilizando painel de alta densidade com ... (Resumo completo, clicar acesso eletrônico abaixo) Abstract: The individual variability on cattle temperament is an important factor affecting the profitability of beef cattle enterprises, due to its adverse effects in production, animal welfare and labor safety. Thus, this characteristic has increasing interest of producers and researchers, who aim to understand the genetic and environmental factors affecting the expression of temperament and its effect on cattle performance. Thus, the objective of this thesis was to study the genomic association between single nucleotide polymorphisms (SNP) and temperament indicators of Nellore cattle. The specific objectives were: 1) Study the genomic association between SNP and different indicators of temperament; 2) Assess the existence of genomic regions associated, simultaneously, with distinct temperament indicators; 3) Identify genes and their biological functions that influences temperament and; 4) Estimate genetic parameters for different temperament indicators using genomic information. The temperament was evaluated between 2010 and 2015, during the weighing handling at 18 months of age, using the following indicators: 1) movement score (MOV); 2) tension score (TENS); 3) crush score (CS); 4) flight speed (FS) and; 5) temperament score (TS). The animals were genotyped using a panel with 777,962 SNP (Illumina BovineHD Beadchip). All analyses to estimate variance components and genetic parameters, as well as the genome-wide association study (GWAS), were performed using a single-step procedure... (Complete abstract click electronic access below) Doutor

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Toledo, Natália Martins de. "Estudo da estrutura genética de ovinos localmente adaptados do Brasil por meio de marcadores de base única (SNP - Single Nucleotide Polymorphism)." reponame:Repositório Institucional da UnB, 2014. http://repositorio.unb.br/handle/10482/16809.

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Dissertação (mestrado)—Universidade de Brasília, Faculdade de Agronomia e Veterinária, 2014. Submitted by Larissa Stefane Vieira Rodrigues (larissarodrigues@bce.unb.br) on 2014-11-06T17:18:06Z No. of bitstreams: 1 2014_NatáliaMartinsDeToledo.pdf: 1632413 bytes, checksum: b047cf6ecb4820b6901844d7a9043076 (MD5) Approved for entry into archive by Raquel Viana(raquelviana@bce.unb.br) on 2014-11-10T15:57:02Z (GMT) No. of bitstreams: 1 2014_NatáliaMartinsDeToledo.pdf: 1632413 bytes, checksum: b047cf6ecb4820b6901844d7a9043076 (MD5) Made available in DSpace on 2014-11-10T15:57:03Z (GMT). No. of bitstreams: 1 2014_NatáliaMartinsDeToledo.pdf: 1632413 bytes, checksum: b047cf6ecb4820b6901844d7a9043076 (MD5) Brasil possui diversas raças ovinas no seu territótio que surgiram em consequência tanto de múltiplas introduções desde o período da colonização bem como de eventos genéticos e demográficos. De forma a aumentar a compreensão da formação desses grupos genéticos, o objetivo dessa dissertação foi analisar a distribuição da diversidade genética de 721 indivíduos de 30 raças por meio do ovine SNP50 BeadChip. Foram utilizados oito grupos genéticos brasileiros, cinco deslanados e três lanados. Além disso, mais 22 raças foram analisadas como possíveis fundadoras das raças brasileiras. A partir dos resultados das distâncias genéticas geradas pelo índice Fst foi possível identificar que existem duas fontes de variação principais para as raças brasileiras: uma de origem Africana e outra com origem na região Mediterrânea da Europa. As raças lanadas Crioula e Bergamácia apresentaram maior proximidade genética com raças coletadas nas Américas (Corriedale, Gulf Coast Native, Ille de France, Hampshire e Suffolk) e Caribe (St.Elizabeth) do que com raças européias mediterrâneas. A análise de componentes principais (PCA) confirmou a proximidade genética entre as populações de Santa Inês e Bergamácia, e de Morada Nova com Rabo Largo observadas anteriormente com marcadores microssatélites. Além disso, a raça Somalis apresentou uma maior homogeneidade genética e diferenciação entre as raças localmente adaptadas. O grupo genético Pantaneiro apresentou relativa diferenciação genética da raça Crioula bem como uma maior proximidade da raça Bergamácia Brasileira. Os resultados desse estudo serão usados para direcionar o enriquecimento do Banco de germoplasma existente, bem como fornecer subsídios para as associações de criadores sobre a diversidade genética existente dentro de cada raça. ________________________________________________________________________________ ABSTRACT Brazil has several sheep breeds in their territory that arose as a result of multiple introductions from the period of colonization as well as genetic and demographic events. In order to increase the understanding of the formation of these genetic groups, the goal of this dissertation was to analyze the distribution of genetic diversity of 721 individuals of 30 breeds through the ovine SNP50 BeadChip. . Five Brazilian hair sheep breeds and three wool sheep breeds were used. In addition another 22 breeds were analyzed as possible founders of Brazilian breeds. Based on the results of genetic distances generated by Fst, two sources of variation for Brazilian breeds were found: one African and an other Mediterranean. The Crioula Lanada and Bergamacia showed greater genetic proximity breeds collected in the Americas (Corriedale, Gulf Coast Native, Ille de France, Hampshire e Suffolk) and the Caribbean (St.Elizabeth) than Mediterranean European breeds. Principal Components Analysis (PCA) detected close genetic relationships among populations of Santa Ines and Bergamacia , and Morada Nova with Rabo Largo, previously observed with microsatellite markers. In addition, the Somalis showed greater integrity and genetic differentiation between the locally adapted breeds. The analyzes are indicative of differentiation between Pantaneiro and Crioula Lanada, but are not conclusive to the general understanding of the sheep group Pantaneiro. The results of this study will be used to direct enrichment of the Bank of germplasm and to give subsidies to breeders associations on the genetic diversity within each breed.

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Svensson, Emma M. "Detecting Sex and Selection in Ancient Cattle Remains Using Single Nucleotide Polymorphisms." Doctoral thesis, Uppsala universitet, Evolutionsbiologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-123261.

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All contemporary taurine cattle originated some 10,000 years ago when their wild ancestor, the aurochs, was domesticated in the Near East. Although the aurochs was widespread also in Europe, there is no evidence for a local domestication. The aurochs has been extinct since 1627 and therefore little is known about its biology. Following domestication, cattle were selected for traits of interest to humans. All modern cattle breeds were developed in the 19th century and the only sources of information about prehistoric breeding practices, and breeds, come from a few ancient Roman Empire and medieval European written accounts. The aim for this thesis was to investigate the effects early selection may have had on the cattle genome and to investigate genetic variation in European aurochs. Using second-generation sequencing and coalescent simulation analyses of aurochs Y chromosomal DNA, I estimated effective population size to between 20,000-80,000 aurochs bulls, indicating that a large population was present when domestic cattle entered Europe. A Y chromosomal SNP revealed that the two male lineages present in modern cattle were also present in European aurochs, and that the frequency of these lineages in domestic cattle fluctuated over time. This indicates that cattle were mobile and that bottlenecks, possibly due to selective breeding, occurred. I used nuclear SNPs to trace genetic variation in North European cattle through time and show that when genetics is combined with archaeology and osteology, even small but notable changes in the use of cattle can be detected. There has been a significant decrease in genetic variation over time, with the most dramatic changes associated with the formation of breeds during the 19th century.

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Grochola, Lukasz Filip. "Identification and functional analysis of single nucleotide polymorphisms that affect human cancer." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:aacc7084-81a8-4e97-b1ac-024d9bed106e.

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Aims: The p53 regulatory network is crucial in directing the suppression of cancer formation and mediating the response to commonly used cancer therapies. Functional genetic variants in the genes comprising this network could help identify individuals at greater risk for cancer and patients with poorer responses to therapies, but few such variants have been identified as yet. Methods: We first develop and apply three different screens that utilize known characteristics of functional single nucleotide polymorphisms (SNPs) in the p53 network to search for variants that associate with allelic differences in (i) recent natural selection, (ii) chemosensitivity profiles, and (iii) the gender- and age- dependent incidence of soft-tissue sarcoma. Secondly, we study and explore the functional mechanisms associated with the identified variants. Results: We identify SNPs in the PPP2R5E, CD44, YWHAQ and ESR1 genes that associate with allelic differences in the age of tumour diagnosis (up to 32.5 years, p=0.031), cancer risk (up to 8.1 odds ratio, p=0.004) and overall survival (up to 2.85 relative risk, p=0.011) in sarcomas, ovarian and pancreatic cancers, and exhibit allelic differences in the cellular responses to cytotoxic chemotherapeutic agents (up to 5.4-fold, p=5.6x10-47). Lastly, we identify candidate causal SNPs in those genes and describe the regulatory mechanisms by which they might affect human cancer. Conclusions: Together, our work suggests that the inherited genetics of the p53 pathway have a great potential to further define populations in their abilities to react to stress, suppress tumor formation and respond to therapies.

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October, Firzana. "Proteomic and SNP analysis of the Cadherin 10 type-II (CDH10) gene, in the South African autistic population." University of the Western Cape, 2013. http://hdl.handle.net/11394/4826.

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>Magister Scientiae - MSc Autism or autism spectrum disorder (ASD) is a very diverse neurological disorder that manifests specifically in children and infants between the ages of two to three years of age. An individual suffering is deemed as autistic and individuals suffering would be classed under the banner of ASD. It is observed that sufferers have impairment in their social and interactive skills. It has both genetic and environmental factors that contribute to its diversity and although the primary cause of autism is still unclear, scientist are investigating both factors. In this study we aimed to investigate the molecular genetics of autism in the South African (SA) population. This was done in two parts, a genetic association study and afunctional genomics (proteomic study). An association study of the 2 single nucleotide polymorphisms (SNPs) of the Cadherin 10 type II gene (CDH10) (rs4307059 and rs4327572) was investigated in the SA healthy and autistic population. The proteomic approach was used to determine the differential expression of genes of the healthy population and compared to the autistic population of African descent. In both parts of the project, objectives were achieved. The SNPs were successfully genotyped however no association was determined for autism in the SA population. The urine protein profiles with 1 dimensional (1D) and 2dimensional (2D) Sodium Dodecyl Sulfate-Poly Acrylamide Gel Electrophoresis (SDSPAGE)generated in this study has revealed the following proteins, Uromodulin, Vitelline membrane outer layer protein homologue, kinninogen-1, Alpha-1-Antitrypsin, Ig Kappa chain region C, and CD59 glycoprotein that require further investigation. The results indicated that six of the identified proteins were expressed in both groups but were found to be either quantitatively or statistically significant. However, a statistically significant difference was observed in the expression of one protein (Uromodulin) which was observed to be expressed in the healthy group but absent in the experimental group. However further investigation is required validation of these findings.

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O’Mara, Tracy Ann-Maria. "The association of single nucleotide polymorphisms with endometrial cancer risk and prognosis." Thesis, Queensland University of Technology, 2013. https://eprints.qut.edu.au/63648/1/Tracy_O%E2%80%99Mara_Thesis.pdf.

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Endometrial cancer is one of the most common female diseases in developed nations and is the most commonly diagnosed gynaecological cancer in Australia. The disease is commonly classified by histology: endometrioid or non-endometrioid endometrial cancer. While non-endometrioid endometrial cancers are accepted to be high-grade, aggressive cancers, endometrioid cancers (comprising 80% of all endometrial cancers diagnosed) generally carry a favourable patient prognosis. However, endometrioid endometrial cancer patients endure significant morbidity due to surgery and radiotherapy used for disease treatment, and patients with recurrent disease have a 5-year survival rate of less than 50%. Genetic analysis of women with endometrial cancer could uncover novel markers associated with disease risk and/or prognosis, which could then be used to identify women at high risk and for the use of specialised treatments. Proteases are widely accepted to play an important role in the development and progression of cancer. This PhD project hypothesised that SNPs from two protease gene families, the matrix metalloproteases (MMPs, including their tissue inhibitors, TIMPs) and the tissue kallikrein-related peptidases (KLKs) would be associated with endometrial cancer susceptibility and/or prognosis. In the first part of this study, optimisation of the genotyping techniques was performed. Results from previously published endometrial cancer genetic association studies were attempted to be validated in a large, multicentre replication set (maximum cases n = 2,888, controls n = 4,483, 3 studies). The rs11224561 progesterone receptor SNP (PGR, A/G) was observed to be associated with increased endometrial cancer risk (per A allele OR 1.31, 95% CI 1.12-1.53; p-trend = 0.001), a result which was initially reported among a Chinese sample set. Previously reported associations for the remaining 8 SNPs investigated for this section of the PhD study were not confirmed, thereby reinforcing the importance of validation of genetic association studies. To examine the effect of SNPs from the MMP and KLK families on endometrial cancer risk, we selected the most significantly associated MMP and KLK SNPs from genome-wide association study analysis (GWAS) to be genotyped in the GWAS replication set (cases n = 4,725, controls n = 9,803, 13 studies). The significance of the MMP24 rs932562 SNP was unchanged after incorporation of the stage 2 samples (Stage 1 per allele OR 1.18, p = 0.002; Combined Stage 1 and 2 OR 1.09, p = 0.002). The rs10426 SNP, located 3' to KLK10 was predicted by bioinformatic analysis to effect miRNA binding. This SNP was observed in the GWAS stage 1 result to exhibit a recessive effect on endometrial cancer risk, a result which was not validated in the stage 2 sample set (Stage 1 OR 1.44, p = 0.007; Combined Stage 1 and 2 OR 1.14, p = 0.08). Investigation of the regions imputed surrounding the MMP, TIMP and KLK genes did not reveal any significant targets for further analysis. Analysis of the case data from the endometrial cancer GWAS to identify genetic variation associated with cancer grade did not reveal SNPs from the MMP, TIMP or KLK genes to be statistically significant. However, the representation of SNPs from the MMP, TIMP and KLK families by the GWAS genotyping platform used in this PhD project was examined and observed to be very low, with the genetic variation of four genes (MMP23A, MMP23B, MMP28 and TIMP1) not captured at all by this technique. This suggests that comprehensive candidate gene association studies will be required to assess the role of SNPs from these genes with endometrial cancer risk and prognosis. Meta-analysis of gene expression microarray datasets curated as part of this PhD study identified a number of MMP, TIMP and KLK genes to display differential expression by endometrial cancer status (MMP2, MMP10, MMP11, MMP13, MMP19, MMP25 and KLK1) and histology (MMP2, MMP11, MMP12, MMP26, MMP28, TIMP2, TIMP3, KLK6, KLK7, KLK11 and KLK12). In light of these findings these genes should be prioritised for future targeted genetic association studies. Two SNPs located 43.5 Mb apart on chromosome 15 were observed from the GWAS analysis to be associated with increased endometrial cancer grade, results that were validated in silico in two independent datasets. One of these SNPs, rs8035725 is located in the 5' untranslated region of a MYC promoter binding protein DENND4A (Stage 1 OR 1.15, p = 9.85 x 10P -5 P, combined Stage 1 and in silico validation OR 1.13, p = 5.24 x 10P -6 P). This SNP has previously been reported to alter the expression of PTPLAD1, a gene involved in the synthesis of very long fatty acid chains and in the Rac1 signaling pathway. Meta-analysis of gene expression microarray data found PTPLAD1 to display increased expression in the aggressive non-endometrioid histology compared with endometrioid endometrial cancer, suggesting that the causal SNP underlying the observed genetic association may influence expression of this gene. Neither rs8035725 nor significant SNPs identified by imputation were predicted bioinformatically to affect transcription factor binding sites, indicating that further studies are required to assess their potential effect on other regulatory elements. The other grade- associated SNP, rs6606792, is located upstream of an inferred pseudogene, ELMO2P1 (Stage 1 OR 1.12, p = 5 x 10P -5 P; combined Stage 1 and in silico validation OR 1.09, p = 3.56 x 10P -5 P). Imputation of the ±1 Mb region surrounding this SNP revealed a cluster of significantly associated variants which are predicted to abolish various transcription factor binding sites, and would be expected to decrease gene expression. ELMO2P1 was not included on the microarray platforms collected for this PhD, and so its expression could not be investigated. However, the high sequence homology of ELMO2P1 with ELMO2, a gene important to cell motility, indicates that ELMO2 could be the parent gene for ELMO2P1 and as such, ELMO2P1 could function to regulate the expression of ELMO2. Increased expression of ELMO2 was seen to be associated with increasing endometrial cancer grade, as well as with aggressive endometrial cancer histological subtypes by microarray meta-analysis. Thus, it is hypothesised that SNPs in linkage disequilibrium with rs6606792 decrease the transcription of ELMO2P1, reducing the regulatory effect of ELMO2P1 on ELMO2 expression. Consequently, ELMO2 expression is increased, cell motility is enhanced leading to an aggressive endometrial cancer phenotype. In summary, these findings have identified several areas of research for further study. The results presented in this thesis provide evidence that a SNP in PGR is associated with risk of developing endometrial cancer. This PhD study also reports two independent loci on chromosome 15 to be associated with increased endometrial cancer grade, and furthermore, genes associated with these SNPs to be differentially expressed according in aggressive subtypes and/or by grade. The studies reported in this thesis support the need for comprehensive SNP association studies on prioritised MMP, TIMP and KLK genes in large sample sets. Until these studies are performed, the role of MMP, TIMP and KLK genetic variation remains unclear. Overall, this PhD study has contributed to the understanding of genetic variation involvement in endometrial cancer susceptibility and prognosis. Importantly, the genetic regions highlighted in this study could lead to the identification of novel gene targets to better understand the biology of endometrial cancer and also aid in the development of therapeutics directed at treating this disease.

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Neureuther, Katharina. "Association of single nucleotide polymorphisms in the LPA gene region with serum Lp(a) levels and myocardial infarction." kostenfrei, 2008. http://www.opus-bayern.de/uni-regensburg/volltexte/2008/1002/.

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Marconi, Thiago Gibbin. "Mapa funcional em cana-de-açúcar utilizando marcadores moleculares baseados em SSR e SNP." [s.n.], 2011. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316492.

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Orientadores: Anete Pereira de Souza, Antonio Augusto Franco Garcia Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia Made available in DSpace on 2018-08-19T06:27:16Z (GMT). No. of bitstreams: 1 Marconi_ThiagoGibbin_D.pdf: 16468359 bytes, checksum: 01e191ac164eff1d269733328f5be31e (MD5) Previous issue date: 2011 Resumo: A utilização dos marcadores moleculares em estudos de mapeamento genético e de QTLs (Quantitative Trait Loci) tem proporcionado um importante progresso no conhecimento da genética e da estrutura genômica da cana-de-açúcar. O projeto de sequenciamento de ESTs (Expressed Sequence Tags) do programa Genoma da FAPESP (SUCEST) identificou aproximadamente 43 mil clusters que representam os genes de cana-de-açúcar. Sabe-se que os ESTs apresentam grande potencial para serem utilizados no desenvolvimento de marcadores genético-moleculares. Tendo em vista os avanços possíveis no melhoramento genético da cana-de-açúcar com a construção de um mapa genético funcional a partir de ESTs de interesse, este trabalho teve como objetivos o mapeamento genético em uma população F1 de cana-de-açúcar utilizando marcadores moleculares do tipo EST-SSRs (Expressed Sequence Tags - Simple Sequence Repeats) e SNP (Single Nucleotide Polymorphism), desenvolvidos a partir de seqüências ESTs homólogas a genes de interesse. Os SNPs desenvolvidos e mapeados demonstraram novos tipos de segregações possíveis de serem incorporadas ao mapeamento genético em cana-de-açúcar, representando avanços para a análise genética de poliplóides e possibilitando a saturação do mapa genético com marcadores completamente informativos. Os marcadores moleculares EST-SSRs e SNPs desenvolvidos e integrados ao mapa genético da cana-de-açúcar aumentaram sua resolução e também as possibilidades de mapeamento dos QTLs com maior precisão Abstract: The use of molecular markers in genetic mapping studies and QTL (Quantitative Trait Loci) has provided an important advance in knowledge of genetics and genomic structure of sugarcane. The sequencing project of ESTs (Expressed Sequence Tags) form FAPESP's Genome Program (SUCEST) identified approximately 43 000 clusters representing the sugarcane genes. It is known that the ESTs have great potential for use in the development of genetic molecular markers. Given the possible advances in genetic breeding of sugarcane with the construction of a functional genetic map from ESTs of interest, the aim of this study was the construction of a genetic map in a F1 population of sugarcane using molecular markers EST-SSR (Expressed Sequence Tags - Simple Sequence Repeats) and SNP (Single Nucleotide Polymorphism) derived from ESTs sequences homologous to genes of interest. The developed and mapped SNPs demonstrated new types of segregation ratio that could be incorporated in the genetic mapping of sugarcane, representing advances for the genetic analysis of polyploid and allowing the saturation of the genetic map with fully informative markers. The EST-SSR markers and SNPs developed and integrated into the genetic map of sugarcane increased the resolution, coverage of the genome and also the possibilities of mapping QTLs with greater precision Doutorado Genetica Vegetal e Melhoramento Doutor em Genetica e Biologia Molecular

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Robertson, Gail Alexandra. "Computerised methods for selecting a small number of single nucleotide polymorphisms that enable bacterial strain discrimination." Queensland University of Technology, 2006. http://eprints.qut.edu.au/16284/.

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The possibility of identifying single nucleotide polymorphisms (SNPs) that would be useful for rapid bacterial typing was investigated. Neisseria meningitidis was the organism chosen for modelling the approach since informative SNPs could be found amongst the sequence data available for multi-locus sequence typing (MLST) at http://www.mlst.net. The hypothesis tested was that a small number of SNPs located within the seven gene fragments sequenced for MLST provide information equivalent to MLST. Preliminary investigations revealed that a small number of SNPs could be utilised to highly discriminate sequence types (STs) of clinical interest. Laboratory procedures demonstrated that SNP fingerprinting of N. meningitidis isolates is achievable. Further tests showed that laboratory identification of a defining SNP in the genome of isolates was to be a practical method of obtaining relevant typing information. Identification of the most discriminating SNPs amongst the ever-increasing amount of MLST sequence data summoned the need for computer-based assistance. Two methods of SNP selection devised by the author of this thesis were translated into computer-based algorithms by contributing team members. Software for two computer programs was produced. The algorithms facilitate the optimal selection of SNPs useful for (1) distinguishing specific STs and (2) differentiating non-specific STs. Current input information can be obtained from the MLST database and consequently the programs can be applied to any bacterial species for which MLST data have been entered. The two algorithms for the selection of SNPs were designed to serve contrasting purposes. The first of these was to determine the ST identity of isolates from an outbreak of disease. In this case, isolates would be tested for their membership to any of the STs known to be associated with disease. It was shown that one SNP per ST could distinguish each of four hyperinvasive STs of N. meningitidis from between 92.5% and 97.5% of all other STs. With two SNPs per ST, between 96.7% and 99.0% discrimination is achieved. The SNPs were selected from MLST loci with the assistance of the first algorithm which scores SNPs according to the number of base mismatches in a sequence alignment between an allele of an ST of interest and alleles belonging to all other STs at a specified locus. The second purpose was to determine whether or not isolates from different sources belong to the same ST, regardless of their actual ST identity. It was shown that with seven SNPs, four sample STs of N. meningitidis could, on average, be discriminated from 97.1% of all other STs. The SNPs were selected with the aid of the second algorithm which scores SNPs at MLST loci for the relative frequency of each nucleotide base in a sequence alignment as a measure of the extent of their polymorphism. A third algorithm for selecting SNPs has been discussed. By altering the method of scoring SNPs, it is possible to overcome the limitations inherent in the two algorithms that were utilised for finding SNPs. In addition, the third approach caters for finding SNPs that distinguish members of a complex from non-members.

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Sandenbergh, Lise. "Identification of SNPs associated with robustness and greater reproductive success in the South African merino sheep using SNP chip technology." Thesis, Stellenbosch : Stellenbosch University, 2015. http://hdl.handle.net/10019.1/97093.

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Thesis (PhD)--Stellenbosch University, 2015. ENGLISH ABSTRACT: Reproduction and robustness traits are integral in ensuring sustainable, efficient and profitable sheep farming. Increases in genetic gain of reproduction and robustness traits are however, hampered by low heritability coupled with the difficulty in quantification of these traits for traditional selective breeding strategies. The aim of the current study was therefore to identify genomic regions underlying variation in reproduction traits and elucidate quantitative trait loci (QTL) and/or genes associated with reproductive traits. The Elsenburg Merino flock has been divergently selected for the ability to raise multiple offspring and has resulted in a High and a Low line that differ markedly with regard to reproductive output and other robustness traits. The flock thus served as an ideal platform to identify genomic regions subject to selection for reproductive traits. To pinpoint genomic regions subject to selection, a whole-genome genotyping platform, the OvineSNP50 chip, was selected to determine the genotype of more than 50 000 SNPs spread evenly across the ovine genome. The utility of the OvineSNP50 chip was determined for the Elsenburg Merino flock as well as additional South African Merino samples and three other important South African sheep breeds, the Blackheaded Dorper, South African Mutton Merino (SAMM) and the Namaqua Afrikaner. Although genotyping analysis of the Elsenburg Merino flock indicated some signs of poor genotype quality, the overall utility of the genotype data were successfully demonstrated for the South African Merino and the other two commercial breeds, the Dorper and SAMM. Genotyping results of the Namaqua Afrikaner and possibly other indigenous African breeds may be influenced by SNP ascertainment bias due to the limited number of indigenous African breeds used during SNP discovery. Analysis of pedigree, phenotypic records and SNP genotype data of the Elsenburg Merino cohort used in the current study, confirmed that the lines are phenotypically as well as genetically distinct. Numerous putative genomic regions subject to selection were identified by either an FST outlier approach or a genomic scan for regions of homozygosity (ROH) in the High and Low lines. Although annotated genes with putative roles in reproduction were identified, the exact mechanism of involvement with variation in reproduction traits could not be determined for all regions and genes. Putative ROH overlapped with QTL for several reproduction, milk, production and parasite resistance traits, and sheds some light on the possible function of these regions. The overlap between QTL for production and parasite resistance with putative ROH may indicate that several, seemingly unrelated traits add to the net-reproduction and may have been indirectly selected in the Elsenburg Merino flock. A SNP genotyping panel based solely on reproduction traits may therefore be ineffective to capture the variation in all traits influencing reproduction and robustness traits. A holistic selection strategy taking several important traits, such as robustness, reproduction and production into account may as such be a more effective strategy to breed animals with the ability to produce and reproduce more efficiently and thereby ensure profitable and sustainable sheep farming in South Africa. AFRIKAANSE OPSOMMING: Reproduksie- en gehardheids-eienskappe is noodsaaklik om volhoubare, doeltreffende en winsgewende skaapboerdery te verseker. ‘n Toename in genetiese vordering in reproduksie- en gehardheids-eienskappe word egter bemoeilik deur lae oorerflikhede tesame met die probleme in kwantifisering van hierdie eienskappe vir tradisionele selektiewe diereteelt strategieë. Die doel van die huidige studie was dus om gebiede in die genoom onderliggend tot variasie in reproduksie-eienskappe te identifiseer en die rol van verwante kwantitatiewe eienskap loki (KEL) en/of gene met reproduktiewe eienskappe te bepaal. Die Elsenburg Merinokudde is uiteenlopend geselekteer vir die vermoë om meerlinge groot te maak en het gelei tot 'n Hoë en 'n Lae lyn wat merkbaar verskil ten opsigte van reproduksie-uitsette en ander gehardheids-eienskappe. Die kudde het dus gedien as 'n ideale platform om genomiese areas onderhewig aan seleksie vir reproduksie-eienskappe te identifiseer. Om vas te stel waar genomiese areas onderhewig aan seleksie gevind kan word, is ‘n heel-genoom genotiperingsplatform, die OvineSNP50 skyfie, gekies om die genotipes van meer as 50 000 enkel nukleotied polimorfismes (ENPs) eweredig versprei oor die skaap genoom, te bepaal. Die nut van die OvineSNP50 skyfie is bepaal vir die Elsenburg Merinokudde sowel as addisionele Suid-Afrikaanse Merinos en drie ander belangrike Suid-Afrikaanse skaaprasse, die Swartkop Dorper, Suid-Afrikaanse Vleismerino (SAVM) en die Namakwa Afrikaner. Hoewel genotipe resultate van die Elsenburg Merino kudde sommige tekens van swak genotipe gehalte getoon het, kon die algehele nut van die genotipering resultate vir die Suid-Afrikaanse Merino en die ander twee kommersiële rasse, die Dorper en SAVM, bevestig word. Genotipering resultate van die Namakwa Afrikaner en moontlik ook ander inheemse Afrika rasse kan deur ENP vasstellingspartydigheid beïnvloed word as gevolg van die beperkte aantal inheemse Afrika rasse gebruik tydens ENP ontdekking. Ontleding van stamboom inligting, fenotipe rekords en ENP genotipe data van die Elsenburg Merino-kohort gebruik in die huidige studie, het bevestig dat die lyne fenotipies asook geneties verskil. Talle vermeende genomiese areas onderhewig aan seleksie is geïdentifiseer deur 'n FST uitskieter benadering of deur ‘n genomiese skandering vir gebiede van homogositeit (GVH) in die Hoë en Lae lyne. Hoewel geannoteerde gene met potensiële rolle in reproduksie geïdentifiseer is, kan die presiese meganisme van betrokkenheid by variasie in reproduksie-eienskappe nie bevestig word vir al die gebiede en gene nie. Vermeende GVH oorvleuel met KEL vir 'n paar reproduksie-, melk-, produksie- en parasietweerstand-eienskappe, en werp daarom lig op die moontlike funksie van hierdie gebiede. Die oorvleueling tussen KEL vir produksie en parasietweerstand met vermeende GVH kan daarop dui dat 'n hele paar, skynbaar onverwante, eienskappe bydrae tot net-reproduksie, wat indirek geselekteer mag wees in die Elsenburg Merino-kudde. ‘n ENP genotiperingspaneel uitsluitlik gebaseer op reproduksie-eienskappe mag daarom onvoldoende wees om die variasie in alle eienskappe wat betrekking het op reproduksie- en gehardheids-eienskappe, in te sluit. ‘n Holistiese seleksie strategie wat verskeie belangrike eienskappe, soos gehardheid, reproduksie en produksie in ag neem, mag ‘n meer effektiewe strategie wees om diere te teel met die vermoë om in 'n meer doeltreffende manier te produseer en reproduseer en om daardeur winsgewende en volhoubare skaapboerdery in Suid-Afrika te verseker.

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Leonhardt, Mareike. "Eine Analyse ausgewählter genomischer Varianten im FIGF- und ACE2-Gen und deren Bedeutung in der molekularen Pathogenese intrakranieller Aneurysmen." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-24980.

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In der vorliegenden Arbeit untersuchten wir an einer europäischen Population ausgewählte Polymorphismen zweier Gene auf eine Assoziation zu IA. Beide Gene FIGF und ACE2 sind lokalisiert auf Chromosom Xp22 und stellen damit positionelle Kandidatengene dar, aber auch funktionell sind sie von Interesse, da sie v.a. in Prozesse des Gefäßwachstums (FIGF) und der Blutdruckregulierung (ACE2) involviert sind; Vorgänge also, die möglicherweise in die pathophysiologische Erklärung der IA Entstehung mit hineinspielen. In keinem der insgesamt neun analysierten Polymorphismen konnten wir jedoch eine signifikante Assoziation zu IA finden. Auch eine Analyse möglicher intra- und intergenetischer Haplotypen aller untersuchten Varianten erbrachte kein signifikantes Ergebnis.

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Blaauw, Sonja. "SNP screening and validation in Haliotis midae." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/19976.

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Thesis (MSc)--Stellenbosch University, 2012. ENGLISH ABSTRACT: Haliotis midae (commonly referred to as perlemoen) is the only one of five endemic species in South Africa that is commercially valued both locally and internationally. Unfortunately, natural perlemoen populations have become a dwindling resource due to commercial exploitation, poaching and the influx of natural threats, such as the West Coast rock lobster, Jasus lalandii. To preserve the natural diversity and sustainability of natural populations as well as commercial stocks, genetic management and improvement of perlemoen is critical. Genetic management requires the utilisation of molecular markers, which aid in the construction of linkage maps and the identification of quantitative trait loci (QTL) associated with economically significant traits. This will allow improvement of commercial stock management in terms of broodstock selection as well as provide valuable insight into natural population dynamics. Single Nucleotide Polymorphisms (SNPs) were selected as the marker of choice due to their successful employment as molecular markers and their wide distribution and abundance within the genomes of various marine species. This study focuses on the characterisation of novel SNPs from transcript sequences generated by Next Generation Sequencing technology. Approximately 40% of the transcripts facilitated the isolation of 105 putative markers, indicating a SNP frequency of ~1% within the H. midae genome. A subset of 24 markers, in addition to 24 previously developed markers, was characterised using the Illumina GoldenGate genotyping assay with the VeraCode technology, a medium to high-throughput genotyping technology. This is the first reported medium- to highthroughput characterisation of SNPs in H. midae. The selected markers were used to determine the efficiency and overall success rate of the GoldenGate platform. Marker characterisation was completed in both natural and commercial populations to determine the utility of these markers for genetic diversity and population structure inference. An 85% genotyping success rate was achieved with the platform. Statistical analysis indicated that the markers developed in this study are suitable for applications including population genetic structure inference, genetic diversity estimation and possibly other downstream applications such as linkage mapping. These markers are considered to be invaluable for future work regarding the genetic management and conservation of H. midae. AFRIKAANSE OPSOMMING: Haliotis midae (ook bekend as perlemoen) is die enigste van vyf inheemse spesies in Suid-Afrika wat noemenswaardige kommersiële waarde toon plaaslik sowel as internasionaal. Ongelukkig het kommersiële uitbuiting, wildstropery en natuurlike bedreiging (bv. die Weskus kreef Jasus lalandii), wilde perlemoen populasies noemenswaardig verminder. Dus, om natuurlike diversiteit en die voortbestaan van beide wilde en kommersiële populasies te beskerm, is genetiese bestuur en verbetering absoluut noodsaaklik. Genetiese bestuur vereis die gebruik van molekulêre merkers as ’n hulpmiddel in die opstellingvan koppelingskaarte, en die identifisering van die relevante kwantitatiewe eienskap loki (QTL) tipies geassosieer met ekonomies belangrike eienskappe. Die laasgenoemde beoog om kommersiële voorraad bestuur te verbeter, kragtens deur broeidier seleksie sowel as om insig te verskaf m.b.t. wilde bevolking dinamika. Enkel Nukleotied Polimorfismes (SNPs) is gekies as die toepaslike merker vanweë die omvattende toepaslikheid van hierdie merkers binne die genome van verskeie mariene spesies. Hierdie studie fokus op die karakterisering van nuwe SNPs vanuit transkript volgordes ontwikkel deur middel van Volgende Generasie Volgordebepaling (“Next Generation Sequencing”). ’n Beraamde 40% van transkripte het gelei tot die ontwikkeling van 105 potensiëlemerkers, aanduidend van ’n SNP frekwensie van ~1% binne die H. midae genoom. ’n Sub-versameling van 24 merkers, tesame met 24 bestaande merkers, is gekarakteriseer deur die Illumina GoldenGate genotiperings toets met die VeraCode tegnologie, ’n medium tot hoë deurvloei genotiperingstegnologie. Hierdie is die eerste berig van medium tot hoë deurvloei karakterisering van SNPs in H. midae. Die geselekteerde merkers is gebruik om die doeltreffendheid van die GoldenGate platform te bepaal. Merker karakterisering is uitgevoer in beide wilde en kommersiële bevolkings om die effektiewe bruikbaarheid van hierdie merkers m.b.t. genetiese diversiteit, en bevolking struktuur bepaling, te ondersoek. Die platform het ’n 85% genotiperingsukses syfer getoon. Statistiese analise dui daarop dat merkers ontwikkel tydens hierdie studie toepaslik is vir bevolking genetiese struktuur bepaling, genetiese diversiteitberaming en moontlik ook genetiese koppelingskartering. Hierdie merkers word bestempel as onmisbaar vir toekomstige navorsing in genetiese bestuur en bewaring van H. midae.

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Rosa, Carlos Renato Echeveste. "Identificação de marcadores SNP (Single Nucleotide Polymorphism) associados ao gene de resistência Rpp4 da soja (Glycine max L. Merr.) a ferrugem (Phakopsora pachyrhizi Sydow)." reponame:Repositório Institucional da UnB, 2015. http://dx.doi.org/10.26512/2015.11.T.19342.

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Tese (doutorado)—Universidade de Brasília, Faculdade de Agronomia e Medicina Veterinária, Programa de Pós-graduação em Agronomia, 2015. Submitted by Tania Milca Carvalho Malheiros (tania@bce.unb.br) on 2016-01-19T15:08:05Z No. of bitstreams: 1 2015_CarlosRenatoEchevestedaRosa.pdf: 2968825 bytes, checksum: b7a0b9b6185f76bd3c85da5dcdf8aebe (MD5) Approved for entry into archive by Marília Freitas(marilia@bce.unb.br) on 2016-01-26T12:05:20Z (GMT) No. of bitstreams: 1 2015_CarlosRenatoEchevestedaRosa.pdf: 2968825 bytes, checksum: b7a0b9b6185f76bd3c85da5dcdf8aebe (MD5) Made available in DSpace on 2016-01-26T12:05:20Z (GMT). No. of bitstreams: 1 2015_CarlosRenatoEchevestedaRosa.pdf: 2968825 bytes, checksum: b7a0b9b6185f76bd3c85da5dcdf8aebe (MD5) A ferrugem asiática da soja (Phakopsora pachyrhizi) caracteriza-se como a doença foliar mais destrutiva da soja. No entanto, devido à limitada disponibilidade de variedades resistentes adaptadas, os fungicidas ainda são a principal ferramenta de manejo disponível. Assim, a transferência de genes de resistência, assistida por marcadores moleculares, é uma estratégia promissora para o desenvolvimento de variedades resistentes em programas de melhoramento. Os objetivos deste trabalho foram estudar a virulência de isolados de ferrugem frente a diferentes genes de resistência e identificar marcadores moleculares SNP (Single Nucleotide Polymorphism) associados a genes de resistência. Para isso, foram caracterizados isolados de P. pachyrhizi frente a genótipos portadores de diferentes genes de resistências. Também foram identificados marcadores moleculares foi realizada através do estudo de populações segregantes, geradas a partir do cruzamento entre genótipos resistentes e suscetíveis. Os resultados deste trabalho sugerem a ocorrência de variação na virulência de isolados de ferrugem asiática aos diferentes genes de resistência conhecidos, e a existência de marcador molecular SNP associado ao gene de resistência Rpp4 no cromossomo 18 da soja. The Asian soybean rust (Phakopsora pachyrhizi) is characterized as the most destructive foliar disease of soybean. Due the limited availability of resistant varieties fungicides are still the main available management tool. Thus, the transfer of resistance genes, by marker assisted selection in breeding programs, is a promising strategy for the development of resistant varieties. Our objectives were to study the virulence of rust isolates against different resistance genes and identify SNP (Single Nucleotide Polymorphism) molecular markers associated with resistance genes. To this, isolates of P. pachyrhizi were characterized against genotypes carrying different resistance genes. A SNP molecular markers were also identified through the study of segregating populations. The populations were generated from crosses between resistant and susceptible genotypes. The results of this research suggest the occurrence of variation in the virulence of Asian rust, and the presence of a SNP molecular marker associated to Rpp4 resistance gene on chromosome 18 of soybean.

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Robertson, Gail Alexandra. "Computerised methods for selecting a small number of single nucleotide polymorphisms that enable bacterial strain discrimination." Thesis, Queensland University of Technology, 2006. https://eprints.qut.edu.au/16284/1/Gail_Robertson_Thesis.pdf.

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The possibility of identifying single nucleotide polymorphisms (SNPs) that would be useful for rapid bacterial typing was investigated. Neisseria meningitidis was the organism chosen for modelling the approach since informative SNPs could be found amongst the sequence data available for multi-locus sequence typing (MLST) at http://www.mlst.net. The hypothesis tested was that a small number of SNPs located within the seven gene fragments sequenced for MLST provide information equivalent to MLST. Preliminary investigations revealed that a small number of SNPs could be utilised to highly discriminate sequence types (STs) of clinical interest. Laboratory procedures demonstrated that SNP fingerprinting of N. meningitidis isolates is achievable. Further tests showed that laboratory identification of a defining SNP in the genome of isolates was to be a practical method of obtaining relevant typing information. Identification of the most discriminating SNPs amongst the ever-increasing amount of MLST sequence data summoned the need for computer-based assistance. Two methods of SNP selection devised by the author of this thesis were translated into computer-based algorithms by contributing team members. Software for two computer programs was produced. The algorithms facilitate the optimal selection of SNPs useful for (1) distinguishing specific STs and (2) differentiating non-specific STs. Current input information can be obtained from the MLST database and consequently the programs can be applied to any bacterial species for which MLST data have been entered. The two algorithms for the selection of SNPs were designed to serve contrasting purposes. The first of these was to determine the ST identity of isolates from an outbreak of disease. In this case, isolates would be tested for their membership to any of the STs known to be associated with disease. It was shown that one SNP per ST could distinguish each of four hyperinvasive STs of N. meningitidis from between 92.5% and 97.5% of all other STs. With two SNPs per ST, between 96.7% and 99.0% discrimination is achieved. The SNPs were selected from MLST loci with the assistance of the first algorithm which scores SNPs according to the number of base mismatches in a sequence alignment between an allele of an ST of interest and alleles belonging to all other STs at a specified locus. The second purpose was to determine whether or not isolates from different sources belong to the same ST, regardless of their actual ST identity. It was shown that with seven SNPs, four sample STs of N. meningitidis could, on average, be discriminated from 97.1% of all other STs. The SNPs were selected with the aid of the second algorithm which scores SNPs at MLST loci for the relative frequency of each nucleotide base in a sequence alignment as a measure of the extent of their polymorphism. A third algorithm for selecting SNPs has been discussed. By altering the method of scoring SNPs, it is possible to overcome the limitations inherent in the two algorithms that were utilised for finding SNPs. In addition, the third approach caters for finding SNPs that distinguish members of a complex from non-members.

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Wang, Xiao Wei. "IDH1/2 (isocitrate dehydrogenase 1/2) Mutations in Gliomas : Genotype-Phenotype Correlation, Prognostic impact, and Response to Irradiation." Phd thesis, Université Paris Sud - Paris XI, 2012. http://tel.archives-ouvertes.fr/tel-00996458.

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Since Parsons et al. (2008) found the frequent mutations of IDH1 (12%) in GBMs, various reports have studied the prevalence and characteristic of IDH1 and IDH2 mutations.The mutations in the isocitrate dehydrogenase 1 (IDH1) gene occur in nearly 40% of gliomas. The frequency of IDH1 mutations are inversely connected with grade II (~80%), III (~50%), and IV (~ 10%) gliomas. Importantly, the status of IDH1 mutations is associated with a better outcome and demonstrated a diagnostic value. We analyzed also these mutations in distribution, association with tumor-derived other genetic alterations and the diagnostic and prognostic value in a cohort of 1332 glioma patients.A synonymous single nucleotide polymorphism [SNP rs 11554137; C (cytosine) substituted by T (thymin)] has been studied in gliomas patients. The SNP rs 11554137 (in codon 105) are located in the same exon with the IDH1 R132 mutations (in codon 132). And gliomas patients with SNP rs 11554137: C>T had a poorer outcome than patients without SNP rs 11554137. This was observed a similarly adverse effect in survival in patients with AML. Mutations in codon 132 can cause a decrease of IDH1/2 activity and also gain a new enzyme function for the NADPH dependent reduction of alpha-ketoglutarate to 2-hydroxyglutarate. High 2HG and low NADPH levels might sensitize tumors to oxidative stress, potentiating response to radiotherapy, and may account for the prolonged survival of patients harboring the mutations. So we studied further the alterations of function in IDH1R132H mutant cells in vitro. Based on the decrease of defence and the increase of impairing factors in tumor cells, we found that the tumors harbouring IDH1 mutations may have an elevated radiosensitivity. In the present study, we described the impact of IDH1 mutations in gliomas and search for new perspectives for the treatment strategy.

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Ahlford, Annika. "Applications of Four-Colour Fluorescent Primer Extension Technology for SNP Analysis and Discovery." Doctoral thesis, Uppsala universitet, Molekylär medicin, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129221.

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Studies on genetic variation can reveal effects on traits and disease, both in humans and in model organisms. Good technology for the analysis of DNA sequence variations is critical. Currently the development towards assays for large-scale and parallel DNA sequencing and genotyping is progressing rapidly. Single base primer extension (SBE) is a robust reaction principle based on four-colour fluorescent terminating nucleotides to interrogate all four DNA nucleotides in a single reaction. In this thesis, SBE methods were applied to the analysis and discovery of single nucleotide polymorphism (SNP) in the model organism Drosophila melanogaster and in humans. The tag-array minisequencing system in a microarray format is convenient for intermediate sized genotyping projects. The system is scalable and flexible to adapt to specialized and novel applications. In Study I of the thesis a tool was established to automate quality control of clustered genotype data. By calculating “Silhouette scores”, the SNP genotype assignment can be evaluated by a single numeric measure. Silhouette scores were then applied in Study I to compare the performance of four DNA polymerases and in Study III to evaluate freeze-dried reagents in the tag-array minisequencing system. The characteristics of the tag-array minisequencing system makes it suitable for inexpensive genome-wide gene mapping in the fruit fly. In Study II a high-resolution SNP map, and 293 genotyping assays, were established across the X, 2nd and 3rd chromosomes to distinguish commonly used Drosophila strains. A database of the SNP markers and a program for automatic allele calling and identification of map positions of mutants was also developed. The utility of the system was demonstrated by rapid mapping of 14 genes that disrupt embryonic muscle patterning. In Study III the tag-array minisequencing system was adapted to a lab-on-a-chip format for diagnostic testing for mutations in the TP53 gene. Freeze-drying was evaluated for storing reagents, including thermo-sensitive enzymes, on the microchip to reduce the complexity of the integrated test. Correct genotyping results were obtained using freeze-dried reagents in each reaction step of the genotyping protocol, both in test tubes and in single polymer test chambers. The results showed the potential of the approach to be implemented in fully integrated systems. The four-colour chemistry of SBE has been developed further to allow massively parallel sequencing (MPS) of short DNA fragments as in the Genome Analyzer system (Solexa/Illumina). In Study IV MPS was used to compare Nimblegen arrays and the SureSelect solution-based system for targeted enrichment of 56 continuous human candidate-gene regions totalling 3.1 Mb in size. Both methods detected known SNPs and discovered novel SNPs in the target regions, demonstrating the feasibility for complexity reduction of sequencing libraries by hybridization methods.

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Engel, Anne [Verfasser], and Peter A. [Akademischer Betreuer] Fasching. "Methoden der Statistik zur Analyse von Single Nucleotide Polymorphism (SNP) anhand der Auswertung von Genotypdaten aus einer neoadjuvanten Chemotherapiestudie / Anne Engel. Gutachter: Peter A. Fasching." Erlangen : Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2015. http://d-nb.info/1079067647/34.

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Roshyara, Nab Raj, Holger Kirsten, Katrin Horn, Peter Ahnert, and Markus Scholz. "Impact of pre-imputation SNP-filtering on genotype imputation results." Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-151874.

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Background: Imputation of partially missing or unobserved genotypes is an indispensable tool for SNP data analyses. However, research and understanding of the impact of initial SNP-data quality control on imputation results is still limited. In this paper, we aim to evaluate the effect of different strategies of pre-imputation quality filtering on the performance of the widely used imputation algorithms MaCH and IMPUTE. Results: We considered three scenarios: imputation of partially missing genotypes with usage of an external reference panel, without usage of an external reference panel, as well as imputation of ompletely un-typed SNPs using an external reference panel. We first created various datasets applying different SNP quality filters and masking certain percentages of randomly selected high-quality SNPs. We imputed these SNPs and compared the results between the different filtering scenarios by using established and newly proposed measures of imputation quality. While the established measures assess certainty of imputation results, our newly proposed measures focus on the agreement with true genotypes. These measures showed that pre-imputation SNP-filtering might be detrimental regarding imputation quality. Moreover, the strongest drivers of imputation quality were in general the burden of missingness and the number of SNPs used for imputation. We also found that using a reference panel always improves imputation quality of partially missing genotypes. MaCH performed slightly better than IMPUTE2 in most of our scenarios. Again, these results were more pronounced when using our newly defined measures of imputation quality. Conclusion: Even a moderate filtering has a detrimental effect on the imputation quality. Therefore little or no SNP filtering prior to imputation appears to be the best strategy for imputing small to moderately sized datasets. Our results also showed that for these datasets, MaCH performs slightly better than IMPUTE2 in most scenarios at the cost of increased computing time.

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Smith, Scott Matthew. "Application of Genome Reduction, Next Generation Sequencing, and KASPar Genotyping in Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths and Quinoa." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/3548.

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The grain amaranths (Amaranthus sp.) and quinoa (Chenopodium quinoa Willd.) are important seed crops in South America. These crops have gained international attention in recent years for their nutritional quality and tolerance to abiotic stress. We report the identification and development of functional single nucleotide polymorphism (SNP) assays for both amaranth and quinoa. SNPs were identified using a genome reduction protocol and next generation sequencing. SNP assays are based on KASPar genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen consisting of 41 amaranth accessions showed that the minor allele frequency (MAF) of the amaranth markers ranged from 0.05 to 0.5 with an average MAF of 0.27. A diversity screen of 113 quinoa accessions showed that the MAF of the quinoa markers ranged from 0.02 to 0.5 with an average MAF of 0.28. Linkage mapping in amaranth produced a linkage map consisting of 16 linkage groups, presumably corresponding to each of the 16 amaranth haploid chromosomes. This map spans 1288 cM with an average marker density of 3.1 cM per marker. Linkage mapping in quinoa resulted in a linkage map consisting of 29 linkage groups with 20 large linkage groups, spanning 1,404 cM with a marker density of 3.1 cM per SNP marker. The SNPs identified here represent important genomic tools needed for genetic dissection of agronomically important characteristics and advanced genetic analysis of agronomic traits in amaranth and quinoa. We also describe in detail the scalable and cost effective SNP genotyping method used in this research. This method is based on KBioscience's competitive allele specific PCR amplification of target sequences and endpoint fluorescence genotyping (KASPar) using a FRET capable plate reader or Fluidigm's dynamic array high throughput platform.

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Dubois, Julie. "Syndromes myélodysplasiques de novo et secondaires à un traitement anti-cancéreux : recherche de marqueurs génétiques de susceptibilité individuelle." Thesis, Bordeaux 2, 2012. http://www.theses.fr/2012BOR21990/document.

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Les syndromes myélodysplasiques (SMD) sont des hémopathies myéloïdes clonales évoluant vers une leucémie aiguë (LA). Les SMD et LA secondaires, survenant après traitement par chimiothérapie et/ou radiothérapie, ont un pronostic très péjoratif. Cependant seule une partie des sujets exposés aux traitements cytotoxiques développent un SMD secondaire, ce qui suggère une composante génétique dans la susceptibilité individuelle au risque de développer un SMD secondaire. Les objectifs de ce travail ont été d’identifier des polymorphismes génétiques de type SNP (Single Nucleotide Polymorphism) significativement associés à des caractères cliniques et biologiques des SMD tel leur caractère secondaire. Une « puce » à façon a sélectionné 384 SNP de fréquence allélique supérieure à 10 % impliqués dans la réparation de l’ADN, le métabolisme, le transport et la détoxication des xénobiotiques. L’ADN constitutionnel de 65 patients atteints de SMD primaire et secondaire a été recueilli et génotypé pour ces 384 SNP. La seule association significative par test exact de Fisher (p = 0,009 après correction de Benjamini-Hochberg) a été observée pour le caractère secondaire des SMD et la présence de l’allèle variant de MGMT (MéthylGuanine MéthylTransférase) sur deux SNP en déséquilibre de liaison, rs2308321 (Ile143Val) et rs2308327 (Lys178Arg). Nous avons recherché le caractère prédictif de la présence de l’allèle variant de MGMT pour le risque de SMD/LA secondaire chez des patientes ayant reçu un traitement cytotoxique pour un cancer du sein, et ayant développé une LA secondaire. Enfin, nous avons construit des lignées cellulaires stables, isogéniques, exprimant soit la forme sauvage soit la forme variante de MGMT. Les études fonctionnelles par tests de cytotoxicité, co-cultures à long terme et étude des demi-vies des protéines, sous traitement alkylant, montrent respectivement des différences de sensibilité, de prolifération ou de dégradation entre les formes variante et sauvage de MGMT Myelodysplastic syndromes (MDS) are clonal hematopoietic disorders evolving toward acute myeloid leukaemia (AML). Therapy-related MDS and AML occur after chemo- and/or radiotherapy for previous cancer and have a very poor outcome. However, only a minimal proportion of patients exposed to anticancer drugs develop secondary MDS, suggesting a genetic component in individual susceptibility. The aim of our study was to identify gene polymorphisms significantly associated with MDS in patients. We have selected 384 SNPs (single nucleotide polymorphisms) with allele frequency >10% in genes involved in DNA repair and drug metabolism and transport. DNA extracts were obtained from blood and cheek samples from a population of 65 MDS patients, and the 384 SNPs were genotyped. We analysed the associations existing between each genotype and several pathological features, especially the treatment-related character of MDS. The Fisher exact test with Benjamini-Hochberg correction for multiple testing was applied for statistical analysis. The only significant association (p = 0.009 after correction) was observed for the treatment-related character of MDS and the presence of a variant allele in MGMT (methylguanine methyltransferase, a gene involved in DNA repair), characterised by two SNPs in complete linkage disequilibrium: rs2308321 (Ile143Val) and rs2308327 (Lys178Arg). An epidemiological study was performed to assess the predictive value of the variant allele in MGMT for the development of secondary acute leukaemia among patients treated for breast cancer. We have constructed isogenic stable cell lines expressing either the wild-type or the variant allele of MGMT. Functional studies (analysis of response to alkylating agents, allele quantification of mixed cultures of wild-type and variant cells and half-lives study of the proteins) show differences in sensitivity to DNA-damaging agents, proliferative capacity and MGMT rate of degradation between the wild-type and the variant MGMT

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Andersson, Eva. "TaqMan^® Sample-to-SNP Kit™ : evaluation of kit for low-cost and fast preparing of DNA-samples before genotype analysis." Thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-105963.

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Genotyping can be used to link genetic variation among individuals to certain diseases or conditions. Some known disorders and states that are dependent on single nucleotide polymorphism (SNPs) are lactose intolerance, venous thrombosis, hereditary hemochromatosis and the difference in sensibility among people to metabolise drugs. In this project a new kit, TaqManÒ Sample-to-SNP KitÔ for extraction of DNA and preparation of the extract for genotyping with real-time PCR and allelic discrimination, was evaluated. QIAamp® DNA Blood Biorobot® MDx Kit was used as the reference method. The purpose of the comparison was to find a method that makes DNA extraction from blood samples cheaper and faster, but with the same reliability as the reference procedure. The results of the evaluation showed a complete agreement of the genotype results between the methods tested, which means that the new method was as reliable as the reference method. The costs of reagents and material would be reduced with 52% if the new method is adopted, that alone would result in a cost reduction of 144 000SEK a year with a sample volume of 650 samples/month. The time for DNA extraction would also be reduced with the new procedure.

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Dissertations / Theses on the topic 'Single nucleotide polymorphism (SNP)'

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