Introdução: A cardiomiopatia hipertrófica (CH) é uma doença cardíaca estrutural primária, caracterizada por hipertrofia do ventrículo esquerdo, sem dilatação, geralmente assimétrica e predominantemente septal. Na população geral a prevalência estimada da CH é de 0,2% (1:500), correspondendo a 0,5% de todas as cardiopatias. Atualmente estão descritas mais de 1400 mutações associadas à CH em 20 genes relacionados com os miofilamentos do sarcômero, o disco-Z e o transporte de cálcio, sendo que os três mais associados são os genes MYH7, MYBPC3 e TNNT2, responsáveis por 50% do casos com diagnóstico molecular positivo no Brasil. Dessa forma, o advento de novas tecnologias de sequenciamento de DNA de alta performance promete revolucionar o diagnóstico molecular, tornando mais rápida e barata a identificação de alterações genéticas, impactando positivamente na custo-efetividade do manejo diagnóstico e terapêutico de pacientes e famílias com o diagnóstico de CH. Materiais e Métodos: Noventa e uma amostras de uma casuística de pacientes não relacionados, portadores de CH com diagnóstico molecular prévio para os 3 genes mais associados (19 positivas e 72 negativas) foram utilizadas juntamente com uma amostra referência do HapMap (NA12878) na validação de um pipeline proposto para a identificação de alterações genéticas em um painel com 74 genes associados à cardiomiopatias hereditárias, utilizando a plataforma Ion Torrent PGM. A etapa de chamada de variantes foi testada em dois limiares diferentes de cobertura de sequenciamento (30x e 10x) e três limiares de frequência de alelo variante (35%, 25% e 20%). A amostra NA12878 foi utilizada na aferição de valores de reprodutibilidade intra e inter-ensaio. As amostras da casuística de CH com diagnóstico molecular prévio negativo foram utilizadas na análise de ganho diagnóstico. Eram consideradas alterações potencialmente patogênicas aquelas que apresentassem associação prévia com CH ou classificação deletéria em dois de três algoritmos de predição de impacto funcional (PROVEAN, SIFT, PolyPhen2) e MAF<0,01, se disponível. Resultados: A plataforma de sequenciamento utilizada apresentou desempenho aceitável, gerando em média 165,9 ±13,1 Mb, com um valor médio de 146,9 ± 11,54 Mb acima de PhredQ>=20, por amostra. O valor médio de cobertura de sequenciamento por amostra foi de 250 ± 23,94x, com 95,2% das regiões alvo cobertas pelo menos 10x. A sensibilidade máxima observada para SNVs foi de 96,7% enquanto que para InDels foi 28,5%. Os valores de reprodutibilidade inter e intra-ensaio de 89,5% e 87,3%, respectivamente. Das 72 amostras negativas, 35 puderam ser reclassificadas como positivas, sendo que os dois genes com mais ocorrências de alterações genéticas foram FLNC e TRIM63, ambos já relacionados com CH. Vinte e duas amostras foram reclassificadas como inconclusivas e 15 permaneceram negativas. O ganho diagnóstico foi de 21,5%. Conclusões: A plataforma Ion Torrent PGM apresenta potencial no sequenciamento de genes relacionados à cardiomiopatias hereditárias e o pipeline validado mostrou valores analíticos praticáveis em uma rotina diagnóstica. A utilização do painel genético ampliado se mostrou viável na detecção de alterações genéticas, propiciando uma boa margem de ganho diagnóstico em comparação com o sequenciamento apenas dos três genes mais associados à CH / Introduction: Hypertrophic cardiomyopathy (HCM) is a primary cardiac disease, mainly characterized by unexplained left ventricle hypertrophy, in the absence of dilatation, usually asymmetric and predominantly septal. The estimated prevalence is 1:500 individuals in the general population, corresponding for 0.5% of all cardiac diseases. Up to now, more than 1400 mutations are associated with HCM in 20 genes related with sarcomeric myofibrils, Z-disc and calcium homeostasis, wherein the 3 most associated genes are MYH7, MYBPC3 and TNNT2, accounting for 50% of cases with positive molecular diagnostics in Brazil. Thus, the advent of new high throughput DNA sequencing technologies promise to revolutionize the use of molecular diagnostics, turning the identification of genetic mutations in a fast and cheap practice, increasing the cost-effectiveness of diagnostic and treatment of patients and families with HCM. Materials and Methods: Ninety one samples from an HCM casuistic of unrelated individuals with previous molecular diagnostics for the three most HCM-associated genes (19 positives and 72 negatives) were processed along with a reference HapMap sample (NA12878) in the validation process of a pipeline proposed for the detection of genetic alterations in a genetic panel composed of 74 genes associated with inherited cardiomyopathies, using Ion Torrent PGM platform. The variant call step was tested for two cutoffs of sequencing coverage (30x and 10x) and three cutoffs of variant allele frequency (35%, 25% and 20%). The sample NA12878 was used in the assessment of intra and inter-assay reproducibility. Negative samples from the HCM casuistic were used in the assessment of diagnostic yield. Variants were considered potentially pathogenic if previously described as associated with HCM or if presenting a deleterious score in at least two of three impact prediction algorithms tested (PROVEAN, SIFT and PolyPhen-2) and MAF < 0.01, if available. Results: The chosen next-generation sequencing platform presented an acceptable performance, with a mean throughput of 165,9 ±13,1 Mb, with a mean value of 146,9 ± 11,54 Mb above PhredQ >= 20. Mean sequencing coverage was 250 ± 23,94x, wherein 95.2% of target bases were covered at least 10x. Maximum achieved sensitivity for SNVs was 96.7% while for InDels was 28.5%. Both values of inter and intra-assay reproducibility were 89.5% and 87.3%, respectively. Of all 72 negative samples, 35 were reclassified as positive with the two most frequently mutated genes being FLNC and TRIM63, both already associated with HCM. Twenty two samples were reclassified as inconclusive and 15 remained negatives. Diagnostic yield was 21.5%. Conclusions: Ion Torrent PGM platform presented a feasible potential for the sequencing of inherited cardiomyopathies-associated genes and the designed pipeline presented reliable analytical values for diagnostic use. The expanded panel proved to be a good strategy for the detection of genetic alteration providing a good value of diagnostic yield in comparison with the sequencing of the three most HCM-associated genes alone

Made available in DSpace on 2016-08-17T18:39:33Z (GMT). No. of bitstreams: 1 3168.pdf: 2139042 bytes, checksum: 58468f87414d6567ebe9a007d0fc5966 (MD5) Previous issue date: 2010-07-30 / Financiadora de Estudos e Projetos / Because the close relationship between men and dogs, possibly some ectoparasites of dogs can be observed parasitizing man. The tick Rhipicecephalus sanguineus is an ectoparasite that has the ability to carry and transmit pathogens to humans. This arthropod, that is blood-feeding, is the main biological vector of the bacteria Ehrlichia canis. Currently, the diagnosis of this disease ehrlichiasis is based on blood, biochemical and serological tests, although they are unreliable for diagnosing the disease, since their clinical and clinicopathological features are largely nonspecific. Tetracyclines are commonly used in the treatment of ehrlichiosis, but studies show that some dogs remain positive for E. canis after treatment or after the loss of spontaneous infection. The chronic ehrlichiosis, having high prognosis fails, can result in high mortality. Therefore, more sensitive and reliable tests may help in the selection of dog carrying the disease. The PCR (polymerase chain reaction) has been used successfully in the diagnosis of E. canis. However, this molecular technology requires expensive equipment and specialized personnel to handle, which limits its use in laboratories routines. A more sensitive, specific, and simple to detect the microorganism method is desirable. In this work we develop the technique for detection of the bacterium Ehrlichia canis using the LAMP (Loop- Mediated Isothermal Amplification), which proved being very effective. Specific sequences of the E. canis dsb gene (disulfide bond) were used as target for the tested techniques. Dsb gene was highly specific in order to detect E. canis, since it is divergent of phylogenetically similar bacteria. Performed molecular tests showed a disease incidence greater than that indicated by authors using traditional diagnostic techniques. In the public kennel, 80% of the samples were infected, while in private clinics and veterinary hospital 40% had the disease. The developed diagnostic technique using LAMP is more sensitive than PCR, highly specific and does not require the prior DNA extraction to amplification. In addition, the product of amplification can be seen with the naked eye. We conclude that the diagnosis by the LAMP method enables the specific and high sensitivity identification of infected animals with minimal laboratory settings. These factors make possible the use of this diagnostic methodology for veterinary clinics, laboratories and educational institutions. / Devido à estreita relação entre o homem e o cão, eventualmente alguns ectoparasitas de cães podem ser observados parasitando o homem. O carrapato Rhipicecephalus sanguineus é um ectoparasita que possui a capacidade de carregar e transmitir patógenos aos seres humanos. Esse artrópode, por exercer hematofagia, é o principal vetor biológico e reservatório da bactéria Ehrlichia canis. Atualmente, o diagnóstico da erliquiose é baseado em testes hematológicos, bioquímicos e sorológicos, embora sejam pouco confiáveis para diagnostica-lá, uma vez que suas características clínicas e clinicopatológicas são amplamente inespecíficas. As tetraciclinas são comumente utilizadas no tratamento da Erliquiose, mas estudos mostram que alguns cães permanecem soropositivos para E. canis após o tratamento ou após a perda da infecção espontânea. A Erliquiose crônica por ter falhas de prognóstico, pode resultar em alta mortalidade. Portanto, testes mais sensíveis e confiáveis poderão auxiliar na seleção de cães portadores. A PCR (reação em cadeia da polimerase) tem sido usada com sucesso no diagnóstico da bactéria E. canis. Entretanto, esta tecnologia molecular necessita de equipamentos caros e pessoal especializado para sua execução, o que limita o seu uso na rotina dos laboratórios. Assim uma metodologia mais sensível, específica, e simples de detectar o microorganismo é desejável. Neste trabalho desenvolvemos a detecção da bactéria Ehrlichia canis pena da técnica de LAMP (Loop-Mediated Isothermal Amplification), que se mostrou muito eficaz. Utilizamos sequências específicas do gene dsb (disulfide bond) de E. canis como alvo para as técnicas testadas. O gene dsb mostrou-se altamente específico para a detecção de E. canis, já que é divergente até mesmo das bactérias filogeneticamente próximas. Os testes moleculares realizados mostram uma incidência maior da doença do que aquela preconizada por autores que utilizam técnicas diagnósticas tradicionais. No canil municipal, 80% das amostras estavam infectadas; das clínicas particulares e do hospital veterinário 40% apresentaram a doença pela técnica de PCR. A técnica de diagnóstico por LAMP que foi desenvolvida é mais sensível do que o PCR, altamente específica e não é necessária a extração do DNA para a sua amplificação. Além disso, o produto da amplificação pode ser visualizado a olho nu. Concluímos que o diagnóstico pela metodologia LAMP possibilita a identificação específica e com alta sensibilidade de animais infectados, com mínima estrutura laboratorial. Tais fatores viabilizam a utilização dessa metodologia diagnóstica para clínicas veterinárias, laboratórios e instituições de ensino.

Made available in DSpace on 2014-08-20T13:32:48Z (GMT). No. of bitstreams: 1 tese_priscila_marques_moura_de_leon.pdf: 3035474 bytes, checksum: 1dfa2e910533e830f4c6c01d06ca37e6 (MD5) Previous issue date: 2011-11-07 / In equine, the intersections between reproduction and genomics are numerous, however, little known about the genetic factors that acting on fertility. The conclusion of equine genome sequencing project, brings the oportunity to evaluate candidate genes and molecular biomarkers for specific reproductive characteristics. Based on this information, this PhD thesis aimed to develop genomic studies applied to equine reproduction. The first paper analyzed the expression of apoptotic-related genes (Bax, Bcl-2, survivin and p53) in equine cumulus-oocyte complex by qRT-PCR, comparing gene expression between morphologically distinct oocytes and cumulus cells during in vitro maturation. Results showed that survivin mRNA levels were higher (P<0.05) and p53 mRNA levels was lower (P<0.01) in oocytes compared to cumulus cells in morphologically healthy. On the other hand, expression of the Bax was significantly higher in morphologically healthy cumulus cells (P<0.02). The second paper analyzed a single nucleotide polymorphism (SNP) in the p53 gene, looking for associations with reproductive parameters in Thoroughbred mares. This is the first study demonstrating the Arginine/Proline SNP in equine exon 4 p53 gene. The heterozygous Arginine/Proline was found in 73.3% of Thoroughbreds compared to the homozygous Arg/Arg and Pro/Pro that was detected in 17.1% and 9.6% of mares, respectively. The Arginine/Proline genotype was significantly associated with abortion (P=0.02), while Proline/Proline mares had a lower probability of abortion (P<0.05). These results indicate that p53 may play a role in equine reproduction. The second paper analyzed a single nucleotide polymorphism (SNP) in the p53 gene, looking for associations with reproductive parameters in Thoroughbred mares. This is the first study demonstrating the Arginine/Proline SNP in equine exon 4 p53 gene. The heterozygous Arginine/Proline was found in 73.3% of Thoroughbreds compared to the homozygous Arg/Arg and Pro/Pro that was detected in 17.1% and 9.6% of mares, respectively. The Arginine/Proline genotype was significantly associated with abortion (P=0.02), while Proline/Proline mares had a lower probability of abortion (P<0.05). These results indicate that p53 may play a role in equine reproduction. The third article has determined the presence of circulating cell-free fetal DNA (ccffDNA) in pregnant mare s plasma, looking to develop a molecular test for the prenatal diagnosis of fetal sex determination using SRY gene amplification by PCR, reamplification by PCR (2nd-PCR) and real-time quantitative PCR (qPCR). This is the first report of ccffDNA in equine species. The molecular sexing test resulted in sensitivity of 72% and accuracy of 85% on the PCR. Using the 2nd-PCR and qPCR we obtained an increasing in the sexing sensitivity results (90.9%) and an accuracy of 95%. This study demonstrates for the first time the fetal sex determination in mares using ccffDNA. This PhD thesis resulted in the publication of three papers in international journals of reproduction and a patent application request. The results presented here collaborate to understand the equine reproductive biology, and indicate potential genetic markers to fertility parameters. / Em equinos, as intersecções entre a reprodução e a genômica são numerosas, no entanto, pouco se sabe sobre os fatores genéticos que atuam na fertilidade. Com o genoma equino completo, existe a possibilidade de análises moleculares e estudo de genes candidatos a biomarcadores para características reprodutivas específicas. Com base nestas informações, a presente tese teve como objetivo desenvolver estudos de genômica aplicada à reprodução equina. O primeiro artigo analisou a expressão de genes relacionados a apoptose (Bax, Bcl-2, survivin e p53) no complexo cumulus oócito equino através de qRT-PCR, comparando a expressão gênica entre oócitos e células do cumulus com diferentes características morfológicas durante a maturação in vitro. Como resultados, foi observada maior expressão do survivin (P<0.05) e menor expressão de p53 (P<0.01) em oócitos comparado a células do cumulus do grupo considerado morfologicamente saudável. Enquanto que a expressão de Bax foi maior (P<0.02) em células do cumulus do grupo saudável comparado ao grupo com características morfológicas não desejáveis. O segundo artigo analisou um polimorfismo de nucleotídeo único (SNP) no gene p53, relacionando-o a parâmetros reprodutivos de éguas Puro Sangue Inglês. Foi relatado pela primeira vez um SNP Arginina/Prolina na região do exon 4 do gene p53 equino. A prevalência foi de 73,3% para o genótipo heterozigoto, 17,1% do genótipo Arginina/Arginina e 9,6% do Prolina/Prolina. O genótipo Arginina/Prolina foi associado (P=0.02) a ocorrência de aborto, enquanto que o genótipo Prolina/Prolina foi associado (P<0.05) a menor probabilidade de aborto, indicando um papel da p53 na reprodução equina. O terceiro artigo determinou a presença de DNA fetal livre e circulante (ccffDNA) no plasma de éguas prenhas, desenvolvendo um teste molecular de diagnóstico pré-natal na determinação do sexo fetal através da amplificação do gene SRY pelas técnicas de PCR, de re-amplificação por PCR (2º-PCR) e de PCR quantitativo em tempo real (qPCR). Este é o primeiro relato do DNA fetal livre e circulante em equinos. O teste de sexagem molecular resultou em 72% de sensibilidade e 85% de acurácia na técnica de PCR. Com o 2º-PCR e qPCR a sensibilidade foi de 90,9% e 95% de acurácia. Este estudo demonstra pela primeira vez a determinação do sexo fetal em éguas utilizando o ccffDNA. Os resultados apresentados colaboram para o entendimento da biologia reprodutiva da espécie equina, e indicam marcadores genéticos em potencial para parâmetros de fertilidade. Esta tese resultou na publicação de três artigos em periódicos internacionais da área de Reprodução e um pedido de Patente de Invenção.

Nucleic acids are fundamental molecules of living organisms functioning essentially as the molecular information carriers of life. From how an organism is built to how it responds to external conditions, all of it, can be found in the form of nucleic acid sequences inside every single cell of every life form on earth. Therefore, accessing these sequences provides key information regarding the molecular identity and functional state of any living organism, this is very useful for areas like biomedicine, where accessing and understanding these molecular signatures is the key to develop strategies to understand, treat and diagnose diseases. Decades of research and technological advancements have led to the development of a number of molecular tools and engineering technologies that allow accessing the information contained in the nucleic acids. This thesis provides a general overview of the tools and technologies available for nucleic acid analysis, and proposes an illustrative concept on how molecular tools and emergent technologies can be combined in a modular fashion to design methods for addressing different biomedical questions. The studies included in this thesis, are focused on the particular use of the molecular tools named: padlock and selector probes, rolling circle amplification, and fluorescence detection of single molecules in combination with microfluidics and portable microscopy. By using this combination, it became possible to design and demonstrate novel approaches for integrated nucleic acid analysis, inexpensive digital quantification, mobile-phone based diagnostics and the description of viral infections. These studies represent a step forward towards the adoption of the selected group of tools and technologies, for the design and building of methods that can be used as powerful alternatives to conventional tools used in molecular diagnostics and virology. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 1: Manuscript.</p>

La tuberculose MDR/XDR (multi et ultrarésistante aux antituberculeux) causée par Mycobacterium tuberculosis constitue un problème de santé publique mondial. L’étude et l’identification des mutations responsables de la résistance sont des facteurs clés pour le contrôle et la surveillance de la tuberculose MDR/XDR. L’expansion de lignée L2/Beijing, une famille de souches originaire du Sud-Est de la Chine (Guangxi) potentiellement plus virulente, complique la maitrise de cette maladie. Dans ce contexte, nous avons développé le TB-EFI et le TB IS-NTF/RINT, deux méthodes moléculaires rapides, multiplexées et haut débit (développées sur le système Luminex xMap), prêtes à utilisation. Nous avons initié le développement d’une méthode moléculaire par la sélection de marqueurs moléculaires pertinents en vue de la discrimination des souches Beijing par la technique MLPA-Beijing. Le TB-EFI est un test qui permet d’identifier les mutations fréquentes (polymorphismes de nucléotides simples) dans les gènes associés à la résistance des souches de Mycobacterium tuberculosis aux antituberculeux de deuxième ligne dont la Fluoroquinolone, les Injectables, et à l’antituberculeux de première ligne, l’Ethambutol. Le TB-EFI pourrait être un test utilisable dans les études rétrospectives en vue du suivi de la résistance d’une population. Le test IS-NTF/RINT est un test spécifique aux souches Beijing qui type la séquence d’insertion IS6110 au sein du locus NTF (Ancien/moderne) et détecte les mutations responsables de la résistance de ces souches à la Rifampicine et l’Isoniazide (les deux antibiotiques principaux de première ligne). Ce test est d’une importance capitale pour l’identification et le contrôle des souches épidémiques, mais aussi pour une vision sur l’évolution du phénomène de résistance dans le temps et l’espace. Il est peu discriminant pour la différenciation des souches Beijing. En vue d’une discrimination complète et précise des souches Beijing, nous avons proposé un lot de SNP qui serviront pour la technique MLPA-Beijing. Par ailleurs, ces méthodes ainsi que le spoligotypage sur microbille, nous ont permis d’effectuer des études d’épidémiologie moléculaire de la tuberculose au Kazakhstan, en Nouvelle Guinée Papouasie, en Italie, au Mozambique, au Pérou. Les techniques développées dans cette thèse pourraient contribuer de manière significative au contrôle de la tuberculose XDR dans les zones « hot-spot », et à la surveillance mondiale de l’évolution des souches Beijing spécialement des souches MDR épidémiques. / MDR / XDR (multidrug and extensively resistant to tuberculosis) TB caused by Mycobacterium tuberculosis is still a global public health problem. The study and identification of mutations responsible for resistance are important factors for the control and surveillance of MDR / XDR TB. The expansion of the L2 / Beijing lineage, a family of strains originating from South-East of China (Guangxi) and potentially more virulent, complicates the control of this disease. In this context, we have developed TB-EFI and TB IS-NTF / RINT, two high-speed, multiplexed and high-throughput molecular methods ready to use (developed on the Luminex xMap system). We initiated the development of a molecular method by the selection of relevant molecular markers for the discrimination of Beijing strains by the MLPA technique. TB-EFI is a test that identifies frequent mutations (single nucleotide polymorphisms) in the genes associated with the resistance of Mycobacterium tuberculosis strains to second-line anti-TB drugs including Fluoroquinolone, Injectable, and first-line antituberculosis drug, Ethambutol. TB-EFI may be used in retrospective studies to monitor resistance in a population. The IS-NTF / RINT test is a test specific to Beijing strains that types the IS6110 insertion sequence within the NTF locus (Ancient / Modern) and detects the mutations responsible for the resistance of these strains to Rifampicin and Isoniazid (the two leading primary antibiotics). This test is of paramount importance for the identification and control of epidemic strains, but also for a vision on the evolution of the phenomenon of resistance in time and space. It is not very discriminating among Beijing strains. In view of complete and precise discrimination of the Beijing strains, we have proposed a set of SNPs that will be used for a technique that will be called MLPA-Beijing. In addition, these methods as well as spoligotyping on microbeads allowed us to carry out molecular epidemiological studies of tuberculosis in Kazakhstan, Papua New Guinea, Italy, Mozambique and Peru. The techniques developed in this thesis could contribute significantly to the control of XDR tuberculosis in hot-spot areas, and to the global monitoring of the evolution of Beijing strains especially epidemic MDR strains.