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Genotipagem de linhagens de Yersinia spp. por high-resolution melting analysis; Genotyping of Yersinia strains by high-resolution melting analysis

Souza, Roberto Antonio de
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 23/05/2013 PT
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O gênero Yersinia pertence à família Enterobacteriaceae e compreende 17 espécies. Y. pestis, Y. pseudotuberculosis e Y. enterocolitica são reconhecidamente patógenos de humanos e animais. Y. pestis cause a peste. Y. pseudotuberculosis e Y. enterocolitica são agentes causadores, sobretudo, de gastroenterites transmitidas por água e alimentos. As demais 14 espécies são, usualmente, consideradas não-patogênicas, com exceção de Y. ruckeri sorogrupo O:1 que causa infecções em peixes. Nas últimas décadas, a tipagem molecular tornou-se uma importante ferramenta nos estudos filogenéticos de numerosos micro-organismos e o desenvolvimento de sistemas de tipagem rápidos e baratos pode facilitar os estudos epidemiológicos de infecções bacterianas. No presente estudo objetivou-se desenvolver um método de genotipagem de Yersinia spp. baseado em high-resolution melting analysis (HRMA) para diferenciar os single-nucleotide polymorphisms (SNPs) presentes nas sequências dos genes 16S rRNA, glnA, gyrB, hsp60 e recA e aplicá-lo na tipagem de 40 linhagens de Y. pseudotuberculosis e 50 linhagens de Y. enterocolitica, bem como separar por HRMA as espécies Y. pseudotuberculosis e Y. enterocolitica. Os SNPs foram determinados nas sequências dos loci acima citados a partir de um conjunto de 119 linhagens de Yersinia spp. depositadas no GenBank/EMBL/DDBJ. Foram encontrados nas sequências dos genes analisados de Y. pseudotuberculosis...

Frequência do polimorfismo rs12979860, no gene da IL28B, em pacientes portadores de hepatite C crônica e em controles sadios: nova metodologia de baixo custo e menor tempo para genotipagem; Frequency of rs12979860 polymorphism in theIL28B gene in patients with chronic hepatitis C and healthy controls: new methodology for low cost and shorter time for genotyping

Ferreira, Camila da Silva
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 08/05/2013 PT
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INTRODUÇÃO: Aproximadamente 170 milhões de pessoas são portadores de hepatite C crônica, sendo esta atualmente a principal causa de transplantes hepáticos no mundo. Os pacientes com hepatite crônica C são atualmente tratados com interferon e ribavirina (IFN/RBV). Estudos de associação do genoma associaram à resposta ao tratamento com IFN/RBV a um polimorfismo de nucleotídeo único (SNP) nas proximidades do gene da Interleucina 28B, que codifica a interferona-?. OBJETIVOS: Padronizar nova metodologia de baixo custo e menor tempo de execução para a genotipagem do polimorfismo rs12979860. Investigar a frequência do polimorfismo rs12979860, em uma coorte de pacientes com hepatite crônica C e sua associação com a resposta ao tratamento no Hospital das Clínicas da Universidade de São Paulo. MÉTODOS: A genotipagem foi realizada, por novo método diagnóstico, PCR multiplex CTPP (confronto de dois pares de iniciadores) e validado através de sequenciamento direto e PCR em tempo real. Um estudo retrospectivo foi realizado em 248 portadores de hepatite C crônica, tratados com interferon e ribavirina; 138 portadores de hepatite C crônica, virgens de tratamento e 240 doadores de sangue. Foi analisado o DNA, dados clínicos e demográficos...

Validação de Marcadores Inserção/Deleção para Genotipagem Fetal não Invasiva; Insertion/Deletion Markers Validation for non Invasice Fetal Genotyping

Ng, Ayling Martins
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 15/05/2015 PT
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A presença de DNA fetal livre de células no plasma materno possibilitou o surgimento de novas tecnologias para o diagnóstico pré natal não invasivo. Existem técnicas de genotipagem fetal já estabelecidas em investigações de sequências exclusivas fetais, mas a sua aplicação para a identificação humana em testes de paternidade ainda é pouco conhecida. A metodologia de genotipagem fetal não invasiva foi padronizada com o uso de três lócus InDels e iniciadores inserção-específicos. Entretanto, para que se alcance o poder satisfatório, é necessário investigar elevado número de lócus informativos. Para suprir a ausência de informações suficientes sobre lócus deste tipo, são descritas, no presente trabalho, as condições laboratoriais para PCR e as frequências alélicas de um conjunto de lócus InDels, ainda inéditos, em uma amostra representativa da população urbana brasileira, visando aumentar a robustez e a confiabilidade da genotipagem fetal não invasiva na investigação de paternidade. Foram selecionados 20 lócus, um em cada cromossomo. Em um dos lócus polimórficos foi encontrado um alelo novo, não registrado no banco de dados do NCBI. O poder de discriminação e o poder de exclusão dos 16 lócus polimórficos combinados (0...

Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Boligon, A. A.; Long, N.; Albuquerque, Lucia Galvão de; Weigel, K. A.; Gianola, D.; Rosa, G. J. M.
Fonte: Amer Soc Animal Science Publicador: Amer Soc Animal Science
Tipo: Artigo de Revista Científica Formato: 4716-4722
ENG
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Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values...

Cerebrospinal fluid can be used for HIV genotyping when it fails in blood

Rotta,Indianara; Raboni,Sonia Mara; Ribeiro,Cléa Elisa Lopes; Riedel,Maristela; Winhescki,Maria da Graça; Smith,Davey M.; Ellis,Ronald J.; Almeida,Sérgio Monteiro de
Fonte: Academia Brasileira de Neurologia - ABNEURO Publicador: Academia Brasileira de Neurologia - ABNEURO
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/07/2014 EN
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Blood plasma specimens are the clinical standard for HIV-1 pol gene genotyping from viral populations; however, it is not always successful, often from low viral loads or the presence of polymerase chain reaction (PCR) inhibitors. Objective To describe the successful of HIV-1 genotyping in two samples of cerebrospinal fluid (CSF), after genotype procedures failed from blood. Method Two HIV-infected patients enrolled in a neurocognitive research study were evaluated when standard HIV-1 genotyping failed from blood plasma samples. Genotyping was performed using the commercial system TRUGENE® HIV-1 Genotyping Kit and the OpenGene® DNA Sequencing System (Siemens Healthcare Diagnostics, Tarrytown, NY, USA). Results CSF genotyping was performed via the same commercial platform and was successful in both cases. Conclusion This report demonstrates that CSF could be used as an alternate clinical specimen for HIV-1 genotyping when it fails from blood.

Human immunodeficiency virus type 1 (HIV-1) genotyping in Rio de Janeiro, Brazil: assessing subtype and drug-resistance associated mutations in HIV-1 infected individuals failing highly active antiretroviral therapy

Couto-Fernandez,JC; Silva-de-Jesus,C; Veloso,VG; Rachid,M; Gracie,RSG; Chequer-Fernandez,SL; Oliveira,SM; Arakaki-Sanchez,D; Chequer,PJN; Morgado,MG
Fonte: Instituto Oswaldo Cruz, Ministério da Saúde Publicador: Instituto Oswaldo Cruz, Ministério da Saúde
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/02/2005 EN
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In order to assess the human immunodeficiency virus type 1 (HIV-1) drug resistance mutation profiles and evaluate the distribution of the genetic subtypes in the state of Rio de Janeiro, Brazil, blood samples from 547 HIV-1 infected patients failing antiretroviral (ARV) therapy, were collected during the years 2002 and 2003 to perform the viral resistance genotyping at the Renageno Laboratory from Rio de Janeiro (Oswaldo Cruz Foundation). Viral resistance genotyping was performed using ViroSeqTM Genotyping System (Celera Diagnostic-Abbott, US). The HIV-1 subtyping based on polymerase (pol) gene sequences (protease and reverse transcriptase-RT regions) was as follows: subtype B (91.2%), subtype F (4.9%), and B/F viral recombinant forms (3.3%). The subtype C was identified in two patients (0.4%) and the recombinant CRF_02/AG virus was found infecting one patient (0.2%). The HIV-1 genotyping profile associated to the reverse transcriptase inhibitors has shown a high frequency of the M184V mutation followed by the timidine-associated mutations. The K103N mutation was the most prevalent to the non-nucleoside RT inhibitor and the resistance associated to protease inhibitor showed the minor mutations L63P, L10F/R, and A71V as the more prevalent. A large proportion of subtype B was observed in HIV-1 treated patients from Rio de Janeiro. In addition...

Fetal rhd genotyping from maternal plasma in a population with a highly diverse ethnic background

Machado,Isabela Nelly; Castilho,Lilian; Pellegrino Jr.,Jordão; Barini,Ricardo
Fonte: Associação Médica Brasileira Publicador: Associação Médica Brasileira
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/08/2006 EN
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OBJECTIVE: To establish the performance of conventional PCR as a noninvasive method for fetal genotyping, by free fetal DNA analysis of distinct RHD regions from maternal plasma, in a population of a diverse ethnic origin. METHODS: We conducted a validity of the diagnostic test by analyzing 81 plasma samples from RhD-negative Brazilian pregnant women, from 4 to 41 gestational weeks. We tested for exon 10 and intron 4 gene regions by allele specific-PCR. Fetal RHD genotyping by PCR on maternal plasma was compared to serologic RhD typing in the neonatal period. RESULTS: Samples were obtained as follows: 15 in the 1st, 37 in the 2nd and 29 in the 3rd trimester. General accuracy was 97.3%, sensitivity of 98.3% and specificity of 93.8%. CONCLUSIONS: Conventional PCR is an accurate method for fetal RHD genotyping on maternal plasma, even in a population of mixed ethnic origin.

Treatment switch guided by HIV-1 genotyping in Brazil

Tupinambás,Unaí; Ribeiro,Flávia Andrade; Aleixo,Agdemir; Greco,Dirceu
Fonte: Brazilian Society of Infectious Diseases Publicador: Brazilian Society of Infectious Diseases
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/04/2006 EN
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We assessed the performance of HIV-1 genotyping tests in rescue therapy. Patients were divided into two groups: group 1 (genotyped), included those switching to new antiretroviral drugs based on HIV-1 genotyping data, and group 2 (standard of care -SOC), comprised those in rescue therapy who had not used this test. This was an open and non-randomized study, with 74 patients, followed up for a mean period of 12 months, from February 2002 to May 2003. The groups differed in the duration of antiretroviral use, experience with diverse drug classes (non-nucleoside reverse transcriptase inhibitors and protease inhibitors) and viral load <2.6 log10 copies/mL at any time during treatment. In 23 patients (group 1), the switch in antiretroviral (ARV) regimen was based on genotyping data; this test was not used for 51 patients (group 2). Two CD4 + lymphocyte counts and viral load counts were made for each patient during the study. Data from the pharmacy where patients received antiretroviral agents, medical charts, and direct interviews with patients to assess compliance to treatment, were analyzed. In the genotyped group, the average drop in viral load was 2.8 log10, compared with a 1.5 log10 difference in group 2; the difference was significant in the first assessment performed six months after switching (p=0.001). Considering the patients with viral load < 2.6 log10 (400 copies/mL) after switching...

Dombrock genotyping in Brazilian blood donors reveals different regional frequencies of the HY allele

Piassi,Fabiana Chagas Camargos; Santos,Silvana Maria Eloi; Castilho,Lilian Maria de; Baleotti Junior,Wilson; Suzuki,Rodrigo Buzinaro; Cunha,Debora Moura da
Fonte: Associação Brasileira de Hematologia e Hemoterapia e Terapia Celular Publicador: Associação Brasileira de Hematologia e Hemoterapia e Terapia Celular
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/12/2013 EN
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Background: Dombrock blood group system genotyping has revealed various rearrangements of the Dombrock gene and identified new variant alleles in Brazil (i.e., DO*A-SH, DO*A-WL and DO*B-WL). Because of the high heterogeneity of the Brazilian population, interregional differences are expected during the investigation of Dombrock genotypes. Objective: The present study aims to determine the frequencies of Dombrock genotypes in blood donors from Minas Gerais and compare the frequencies of the HY and JO alleles to those of another population in Brazil. Methods: The frequencies of the DO alleles in Minas Gerais, a southeastern state of Brazil, were determined from the genotyping of 270 blood donors. Genotyping involved polymerase chain reaction and restriction fragment length polymorphism analysis to identify the 323G>T, 350C>T, 793A>G, and 898C>G mutations, which are related to the HY, JO, DO*A/DO*B, and DO*A-WL/DO*B-WL alleles, respectively. Moreover, the frequencies of rare HY and JO alleles were statistically compared using the chi-square test with data from another Brazilian region. Results: The HY allele frequency in Minas Gerais (2.4%) was almost twice that of the JO allele (1.5%). The frequency of the HY allele was significantly higher (p-value = 0.001) than that in another Brazilian population and includes a rare homozygous donor with the Hy- phenotype. In addition...

SNPs genotyping technologies and their applications in farm animals breeding programs: review

Koopaee,Hamed Kharrati; Koshkoiyeh,Ali Esmailizadeh
Fonte: Instituto de Tecnologia do Paraná - Tecpar Publicador: Instituto de Tecnologia do Paraná - Tecpar
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/02/2014 EN
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Single nucleotide polymorphisms (SNPs) are DNA sequence variations that occur when a single nucleotide: adenine (A), thymine (T), cytosine (C) or guanine (G) in the genome sequence is altered. Traditional and high throughput methods are two main strategies for SNPs genotyping. The SNPs genotyping technologies provide powerful resources for animal breeding programs.Genomic selection using SNPs is a new tool for choosing the best breeding animals. In addition, the high density maps using SNPs can provide useful genetic tools to study quantitative traits genetic variations. There are many sources of SNPs and exhaustive numbers of methods of SNP detection to be considered. For many traits in farm animals, the rate of genetic improvement can be nearly doubled when SNPs information is used compared to the current methods of genetic evaluation. The goal of this review is to characterize the SNPs genotyping methods and their applications in farm animals breeding.

P56-M High-Throughput Genotyping of International HapMap Project Populations with Applied Biosystems TaqMan Drug Metabolism Genotyping Assays: An Automated Laboratory and Analysis Pipeline

Haque, K. A.; Wronka, L. M.; Dagnall, C. L.; Stefan, C. M.; Beerman, M. B.; Hicks, B. D.; Welch, R. A.
Fonte: The Association of Biomolecular Resource Facilities Publicador: The Association of Biomolecular Resource Facilities
Tipo: Artigo de Revista Científica
Publicado em /02/2007 EN
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Although high-density whole-genome SNP scans are available for association studies, the tagging SNP approach used to design many of these panels from International HapMap Project data may miss a substantial number of coding functional variations of drug metabolism enzymes (DME). In fact, more than 40 DME genes are not covered by the HapMap Project, probably due to the difficulties in assay design for these highly homologous gene families. Additionally, many of these technologies do not provide detection in a high number of known DME genes, leading to further gaps in whole-genome scans. Of the polymorphic putative functional DME variants not typed in Hap-Map, a large proportion is untagged by any combination of HapMap SNPs. Therefore, to correlate phenotypes to putative functional DME variations in pharmacogenomic studies, direct genotyping of these functional SNPs will be necessary. Applied Biosystems has developed a panel of N = 2394 TaqMan Drug Metabolism Genotyping Assays to interrogate putative functional variations in N = 220 DME genes. At the National Cancer Institute’s Core Genotyping Facility, an automated, high-throughput pipeline has been created to genotype these assays on the International HapMap Project population. DNA sample preparation and handling...

Feasibility of High-Throughput Genome-Wide Genotyping using DNA from Stored Buccal Cell Samples

Loomis, Stephanie J.; Olson, Lana M.; Mirel, Daniel; Crenshaw, Andrew; Rahhal, Brandon; Tetreault, Stephanie; Kraft, Peter; Haines, Jonathan L.; Pasquale, Louis; Wiggs, Janey Lee; Parkin, Melissa; Tworoger, Shelley Slate; Kang, Jae Hee Hee
Fonte: Libertas Academica Publicador: Libertas Academica
Tipo: Artigo de Revista Científica
EN_US
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It is unclear if buccal cell samples contain sufficient human DNA with adequately sized fragments for high throughput genetic bioassays. Yet buccal cell sample collection is an attractive alternative to gathering blood samples for genetic epidemiologists engaged in large-scale genetic biomarker studies. We assessed the genotyping efficiency (GE) and genotyping concordance (GC) of buccal cell DNA samples compared to corresponding blood DNA samples, from 32 Nurses’ Health Study (NHS) participants using the Illumina Infinium 660W-Quad platform. We also assessed how GE and GC accuracy varied as a function of DNA concentration using serial dilutions of buccal DNA samples. Finally we determined the nature and genomic distribution of discordant genotypes in buccal DNA samples. The mean GE of undiluted buccal cell DNA samples was high (99.32%), as was the GC between the paired buccal and blood samples (99.29%). GC between the dilutions versus the undiluted buccal DNA was also very high (greater than 97%), though both GE and GC notably declined at DNA concentrations less than 5 ng/μl. Most (greater than 95%) genotype determinations in buccal cell samples were of the “missing call” variety (as opposed to the “alternative genotype call” variety) across the spectrum of buccal DNA concentrations studied. Finally...

Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

Lank, Simon M; Golbach, Brittney A; Creager, Hannah M; Wiseman, Roger W; Keskin, Derin Benerci; Reinherz, Ellis Leonard; Brusic, Vladimir; O’Connor, David H
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
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Background: High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. Results: We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third...

Avaliação de critérios de compatibilidade entre pares de primers para otimização de sistemas multiplex de genotipagem; Evaluation of compatibility criteria among primers pairs for optimizing multiplex genotyping systems

BARBOSA, Ana Clara de Oliveira Ferraz
Fonte: Universidade Federal de Goiás; BR; UFG; Mestrado em Biologia; Ciências Biolóicas Publicador: Universidade Federal de Goiás; BR; UFG; Mestrado em Biologia; Ciências Biolóicas
Tipo: Dissertação Formato: application/pdf
POR
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The progress of Molecular Biology and Genetics provided the appearance of several molecular markers that detect the genetic polymorphism directly at DNA. Among these markers are the microsatellites (SSR), which are distinguished by their high degree of polymorphism. The use of these markers for individual genotyping has evolved into multiplex systems, which allow many SSR fragments to be detected and analyzed simultaneously. Currently there are several articles in literature discussing the criteria to be used in the primer design for use in PCR, as well as various softwares are available for this end. However, there are few studies and tools for the analysis of compatibility between pairs of primers for use in multiplex systems, where multiple fragments are simultaneously amplified using PCR. This paper evaluated different criteria for compatibility between pairs of primers. A set of 74 combinations of pairs of primers, involving the amplification of 94 SSR loci were evaluated in duplex systems. The same combinations were evaluated according to different criteria, including the degree of complementarity between primers, the magnitude of differences of denaturation temperatures (Tm) and the tendency to annealing between pairs of primers based on the Gibbs free energy resulting from the association between them. The comparison between the different criteria allowed the identification of a set of criteria with positive predictive value equal to 94%. These criteria were implemented for use in a software called Multiplexer...

Effectiveness of selective genotyping for detection of quantitative trait loci: an analysis of grain and malt quality traits in three barley populations

Ayoub, M.; Mather, D.
Fonte: Natl Research Council Canada Publicador: Natl Research Council Canada
Tipo: Artigo de Revista Científica
Publicado em //2002 EN
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Marker genotype data and grain and malt quality phenotype data from three barley (Hordeum vulgare L.) mapping populations were used to investigate the feasibility of selective genotyping for detection of quantitative trait loci (QTLs). With selective genotyping, only individuals with high and low phenotypic values for the trait of interest are genotyped. Here, genotyping of 10 to 70% of each population (i.e., 5 to 35% in each tail of the phenotypic distribution) was considered. Genomic positions detected by selective genotyping were compared to QTL position estimates from interval mapping analysis using marker genotype data from the entire population. Selective genotyping reliably detected almost all of the mapped QTLs, often with only 10% of the population genotyped. Selective genotyping also detected spurious QTLs in regions of the genome where no significant QTL had been mapped. Even with additional genotyping to verify putative QTLs, the total genotyping effort for detection of QTLs for a single trait by selective genotyping was usually less than 30% of that required for conventional interval mapping. Simultaneous investigation of two or more traits by selective genotyping would require additional genotyping effort, but could still be worthwhile.; M. Ayoub and D.E. Mather; © 2002 NRC Canada

Application of an allele-specific PCR to clinical HIV genotyping samples detects additional K103N mutations in both therapy naive and experienced patients

Carr, J.; Green, T.; Shaw, D.; Daly, L.; Hart, W.; Ratcliff, R.; Higgins, G.; Burrell, C.; Li, P.; Qiao, M.
Fonte: Wiley-liss Publicador: Wiley-liss
Tipo: Artigo de Revista Científica
Publicado em //2009 EN
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Low-level drug resistance is not detected by routine consensus sequence genotype analysis (CSA) but low levels of specific mutations, such as the non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistant mutation K103N, can be quantitated by allele-specific PCR (ASP). This study has applied an ASP to quantitate low-level K103N in patients presenting for clinical HIV genotyping and assess the correlation with antiretroviral treatment history and outcomes. HIV RNA was extracted from patient plasma and subjected to PCR amplification of the reverse transcriptase (RT) region followed by genotyping by CSA and real-time ASP for K103N. When applied to samples from patients presenting for genotyping, the ASP detects K103N, not K103 nor K103R, but cross-reacts with K103S. ASP identified all samples that were K103N by CSA (10.5%) and an additional 14% by ASP only, representing patients who were therapy naïve and with NNRTI treatment history. ASP detected therapy-acquired K103N at low levels up to 6 years after cessation of NNRTI therapy. In three patients with new HIV diagnosis and K103N detected by ASP only, K103N virus declined rapidly from the circulation but persisted in PBMC DNA at >12 months post-diagnosis. Efavirenz (EFV) combination therapy in three patients with low-level K103N suppressed successfully viral load...

Automated MALDI-TOF Mass Spectrometry based SNP Genotyping

Pusch, Wolfgang; Fröhlich, Thomas; Kräuter, Karl-Otto; Wenzel, Thomas; Stalgies, Yves; Kostrzewa, Markus
Fonte: Universität Tübingen Publicador: Universität Tübingen
Tipo: Sonstiges; info:eu-repo/semantics/other
DE_DE
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With the advancement of the human genome project the determination of the general structure of the human genome approaches its completion. A 'working draft' covering 90% of the genomic sequence has already been published. Pharmacogenomic research now has to elucidate the molecular polymorphisms underlying individual phenotypic differences. This knowledge will significantly increase the understanding of individual predispositions to certain diseases, as well as the efficacy and potential adverse effects of certain drugs. The most common genetic variations are single nucleotide polymorphisms (SNPs). A SNP is the occurence of a different nucleotide in different individuals at a given chromosomal position. It is estimated that SNPs account for approximately 90% of the individual genotypic variations. SNP genotyping can be addressed by several different methods and technologies. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) measures directly a physical property of the analyte - its molecular mass. Accordingly, MALDI-TOF MS SNP genotyping is not susceptible to background problems resulting from hybridization based detection reactions. Here we present our MALDI-TOF MS SNP genotyping system that allows fully automated data acquisition and SNP genotyping (Bruker Daltonik...

The Development, Validation and Implementation of a Broad-Based ADME Genotyping Assay into Research and Clinical Trials

Brown, Andrew M.K.
Fonte: Université de Montréal Publicador: Université de Montréal
Tipo: Thèse ou Mémoire numérique / Electronic Thesis or Dissertation
EN
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Afin d’adresser la variabilité interindividuelle observée dans la réponse pharmacocinétique à de nombreux médicaments, nous avons créé un panel de génotypage personnalisée en utilisant des méthodes de conception et d’élaboration d’essais uniques. Celles-ci ont pour but premier de capturer les variations génétiques présentent dans les gènes clés impliqués dans les processus d'absorption, de distribution, de métabolisme et d’excrétion (ADME) de nombreux agents thérapeutiques. Bien que ces gènes et voies de signalement sont impliqués dans plusieurs mécanismes pharmacocinétiques qui sont bien connues, il y a eu jusqu’à présent peu d'efforts envers l’évaluation simultanée d’un grand nombre de ces gènes moyennant un seul outil expérimental. La recherche pharmacogénomique peut être réalisée en utilisant deux approches: 1) les marqueurs fonctionnels peuvent être utilisés pour présélectionner ou stratifier les populations de patients en se basant sur des états métaboliques connus; 2) les marqueurs Tag peuvent être utilisés pour découvrir de nouvelles corrélations génotype-phénotype. Présentement, il existe un besoin pour un outil de recherche qui englobe un grand nombre de gènes ADME et variantes et dont le contenu est applicable à ces deux modèles d'étude. Dans le cadre de cette thèse...

Otimização de rastreamento simultâneo das principais mutações envolvidas na surdez neurossensorial não-sindrômica utilizando a plataforma TaqMan 'MARCA REGISTRADA' OpenArray 'TRADE MARK' Genotyping; Optimization simultaeous screening of the main mutations involved in non-syndromic deafness using TaqMan 'TRADEMARK' OpenArray 'TRADE MARK' Genotyping

Fábio Tadeu Arrojo Martins
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 27/07/2013 PT
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36.92%
A perda auditiva é a deficiência sensorial mais frequente em humanos, atingindo aproximadamente 10% de toda a população mundial. A restrição da comunicação pela expressão oral resulta em alterações no desenvolvimento cognitivo e psicológico do indivíduo afetado. Em países desenvolvidos, um a cada 500 indivíduos apresenta perda auditiva neurossensorial bilateral profunda/severa. Já nos casos de indivíduos com até 5 anos, a porcentagem é maior, atingindo 0,27% de 1000 indivíduos, número que se torna maior ainda nos casos em jovens, chegando a 0,35%. Dentre as causas da perda auditiva, mais de 60% dos casos de perda auditiva congênita são genéticos. Até o momento já se tem conhecimento de 150 loci e 103 genes envolvidos com a perda auditiva, sendo que a maioria deles apresenta, no mínimo, 20 alterações (mutações de ponto, deleções, inserções, etc.) que podem causar a perda. O gene que apresenta maior número de alterações é o GJB2, codificador da conexina 26, uma proteína relacionada a trocas iônicas intercelulares, mantendo a homeostase de potássio do sistema auditivo, essencial para a audição. Apenas este gene apresenta mais de 302 alterações confirmadas até o presente momento, sendo o principal gene relacionado aos casos de perda auditiva de origem genética. Tendo em vista a grande heterogeneidade clínica e genética da perda auditiva e a importância do diagnóstico molecular correto dos indivíduos que apresentam perda auditiva hereditária...

High Resolution Melt Analysis (HRMA); a Viable Alternative to Agarose Gel Electrophoresis for Mouse Genotyping

Thomsen, Nicole; Ali, Radiya G.; Ahmed, Jehangir N.; Arkell, Ruth M.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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36.88%
Most mouse genetics laboratories maintain mouse strains that require genotyping in order to identify the genetically modified animals. The plethora of mutagenesis strategies and publicly available mouse alleles means that any one laboratory may maintain alleles with random or targeted insertions of orthologous or unrelated sequences as well as random or targeted deletions and point mutants. Many experiments require that different strains be cross bred conferring the need to genotype progeny at more than one locus. In contrast to the range of new technologies for mouse mutagenesis, genotyping methods have remained relatively static with alleles typically discriminated by agarose gel electrophoresis of PCR products. This requires a large amount of researcher time. Additionally it is susceptible to contamination of future genotyping experiments because it requires that tubes containing PCR products be opened for analysis. Progress has been made with the genotyping of mouse point mutants because a range of new high-throughput techniques have been developed for the detection of Single Nucleotide Polymorphisms. Some of these techniques are suitable for genotyping point mutants but do not detect insertion or deletion alleles. Ideally, mouse genetics laboratories would use a single...