Philosophiae Doctor - PhD / Solute carrier transporters belonging to the major facilitator family of membrane transporter are increasingly being recognized as a possible mechanism to explain inter-individual variation in drug efficacy and response. Genetic factors are estimated to be responsible for approximately 15-30% of inter-individual variation in drug disposition and response. The aims of this study were to determine the minor allele frequencies of 78 previously identified single nucleotide polymorphisms in the pharmacogenomically relevant SLC22A1-3 and SLCO1B1 genes in the Admixed population of South Africa. Thereafter, to determine whether allele and genotype frequencies for these SNP were different from that reported for other African, Caucasian, and Asian populations. The inferred haplotypes from the genetic information possessed the potential to subsequently be used in future to design and interpret results of pharmacogenomic association studies involving these genes and their substrate drugs. Furthermore, to determine whether the Cape Admixed population harbour novel SNPs in the proximal promoter regions of SLC22A1- 3 and SLCO1B1-3 genes, that encodes hOCT1-3 and hOATP1 and hOATP3, respectively. SNaPshot™ multiplex single base mini-sequencing systems were developed and optimized for each of SLC22A1, SLC22A2, SLC22A3, and SLCO1B1 genes covering the previously identified 78 SNPs. These systems were then used to genotype the alleles of 130 healthy Cape Admixed subjects residing in Cape Town, South Africa. In addition, the proximal promoter regions of the SLC22A1-3 and SLCO1B1-3 genes of 96 of the participants were screened for novel SNPs by direct sequencing. The Cape Admixed subjects investigated displayed a lack of variation and were monomorphic for 78% of the SNPs screened. None of the SLC22A3 SNPs investigated was observed in this study. Sequencing of the proximal promoter regions of the SLC22 and SLCO genes did not reveal any novel SNPs in the 96 Cape Admixed subjects that were screened. This study highlights the fact that African populations do not have the same allele frequencies for SNPs in harmacogenomically relevant genes. Furthermore, the Cape Admixed and other African populations do not share all reduced-function variants of the SLC22A1-3 and SLCO1B1-3 genes with Caucasian and Asian populations. In addition, previously identified novel regulatory variants in SLC22A2 did not exhibit a significant effect on the ability of the promoter to drive transcription. However, it must be noted that these results were observed at 95% confidence interval, and that a 99% confidence interval the significance may increase theoretically. Additionally, it should be noted that more intensive studies are required to determine the potential effect these novel variants may well cause. This study lays the foundation for the design and interpretation of future pharmacogenomic association studies between the variant alleles of the SLC22A and SLCO genes in the Cape Admixed population, as well as optimizations for future expression, and more importantly, drug transport assays with respect to drug disposition and efficacy. / National Research Foundation (NRF) and the Medical Research Council (MRC)

>Magister Scientiae - MSc / In this study the 10 Y-specific loci of the University of the Western Cape (DYS710, DYS518 385a/b, DYS644, DYS612, DYS626, DYS504, DYS447, DYS447, and DYS481) were analysed in 492 individuals from South African population groups. Four different populations namely; Zulu, Coloured, Afrikaner and Asian Indian were sampled. A total of 488 haplotypes were observed, 412 of which were unique. Haplotype diversity was 0.9981. Gene Diversity values ranged from 0.8075 for DYS447 to 0.9209 for DYS710. The discriminatory capacity was 0.9106 which is high. The study showed that the University of the Western Cape 10 locus is a powerful discrimination tool for routine forensic applications and could be used in genealogical investigations as compared to other commercial kits when used on the South African populations (Zulu, Coloured, Afrikaner and Asian Indian) considering its high discriminatory capacity. This data will be used for the establishment of a Y-STR DNA databases for South African population which would aid law enforcement authorities in the investigation and resolution of crimes AMOVA computed using haplotype frequencies showed that when male haplotypes from the four different populations were compared, 0.22 % of the total genetic variation was due to the variability among populations and 99.78 % of the total variation is found within populations. However AMOVA computed using distance matrix showed that 5.97 % of the total variation was due to variability among populations and 94.07 % of the total variation is found within populations. Genetic substructure was found among the four studied South African population groups. All the six population pairwise comparisons using AMOVA were significant .Therefore Y-STRs are very useful in comparing closely related populations. It should be noted that their utility for evolutionary purposes, they need to be combined more stable Y-DNA markers such as single nucleotide polymorphisms (SNPs). Factorial Correspondence Analysis (FCA) showed that the Coloured population has large genetic contribution from Afrikaner population and lesser contribution from the Zulu and Asian Indian population groups. / National Research Foundation (NFR)

>Magister Scientiae - MSc / Genetic variability in genes encoding drug metabolizing enzymes, transporters and targets are known to be the main factors of inter-individual differences in therapeutic outcome. Genetic factors are estimated to be responsible for about 15-30% of inter-individual variation in drug disposition and response. Single-nucleotide polymorphisms (SNPs) are the most prevalent class of genetic variation that could explain the variability in drug efficacy and undesired side effects for patients. The aims of this study were to develop and evaluate the performance of robust and high throughput techniques for genotyping ten polymorphisms related to anticancer drugs and ten polymorphisms related to cholesterol lowering drugs. SNaPshot minisequencing and high resolution melt analysis (HRM) genotyping panels were developed, optimized, and their performances were evaluated and compared. SNaPshot minisequencing systems were developed and successfully optimized for the genotyping of ten SNPs associated with anticancer drug therapy, and ten SNPs associated with cholesterol lowering drugs. These systems were used to genotype the selected SNPs in 130 healthy Cape Admixed participants residing in Cape Town, South Africa. Population genetics data obtained for the studied SNPs were analysed using several statistical analysis software tools. Important population genetic parameters were calculated. Among others, allelic and genotypic frequencies were determined and compared with other populations in the world. High resolution melt analysis (HRM) genotyping panels were developed, optimized and their performance were evaluated and compared to the SNaPshot assays. HRM was explored as an alternative inexpensive and rapid methodology to genotype five SNPs related to anticancer therapy and five SNPs related to cholesterol lowering therapy (statins). Unlike the SNaPshot assays, rigorous optimization was required for the detection heterozygous genotypes via HRM. Both assays were validated using direct sequencing and compared to each other. The HRM system is a closed tube, cheap and (theoretically) rapid method for identifying genetic variations. HRM was however found to be more time consuming, needed further optimization, primer redesigning and more evaluation. The developed genotyping systems could be further validated using clinical samples from patients. This could help in optimizing drug therapy for cancer and cholesterol treatment.

Les poux humains (Pediculus humanus) sont des ectoparasites hématophages, ayant vécu avec leur hôte pendant des milliers d’années. Durant cette thèse, nous avons d’abord élaboré une large bibliographie nous permettant de rédiger une revue, puis d’apporter des réponses à certains nombres de questions restées en suspens à travers le traitement de certaines thématiques qui nous semblaient importantes. En effet, nous avons (i) démontré que les poux de tête et les poux de corps en Afrique peuvent être infectés par B. quintana quand les patients vivent dans des conditions économiques pauvres et sont aussi exposés aux poux de corps; identifié pour la première fois le clade mitochondrial des poux de tête du Mali, Kenya, Congo et Madagascar, et confirmé celui du Sénégal, Algérie, Ethiopie, Rwanda et Burundi, (ii) démontré que les poux de tête et les poux de corps chez les SDF doublement infestés appartiennent à la même population de poux de corps, et dans les conditions d’infestation massive, les poux de corps peuvent migrer et coloniser les cheveux et vice-versa, (iii) prouvé la nécessité de réaliser des enquêtes épidémiologiques nationales sur la pédiculose dans les régions du Mali, (iv) démontré par le modèle in vitro que la doxycycline a un effet direct sur la bactérie endosymbionte du pou Candidatus Riesia pediculicola via le mycetome. Ce dernier travail nous a permis de mettre en exergue l’efficacité synergique des antibiotiques + ivermectine permettant de lutter plus efficacement l’infestation des poux et éviter l’apparition de résistance. Ce travail a fait l’objet de dépôt d’un brevet. / Human lice (Pediculus humanus) are bloodsucking ectoparasites, having lived with their host for thousands of years. During this thesis, we first developed an extensive bibliography allowing us to write a review and provide answers to certain number of questions remained pending through treating some thematic that seemed us significant. Indeed, we have (i) demonstrated that head and body lice in Africa can be infected with B. quintana when patients live in poor economic conditions and are also exposed to body lice; identified for the first time the mitochondrial clade of lice Mali, Kenya, Congo and Madagascar, and confirmed that of Senegal, Algeria, Ethiopia, Rwanda and Burundi, (ii) demonstrated that head and body lice in SDF doubly infected belong to the same population of body lice, and under conditions of massive infestation, body lice can migrate and colonize the hair and vice versa, (iii) proved the need to make national epidemiological surveys on pediculosis in areas of Mali, (iv) demonstrated by in vitro model that doxycycline has a direct effect on endosymbiont bacteria of louse Candidatus Riesia pediculicola via mycetoma. This last work allowed us to highlight the synergistic efficacy of ivermectin + antibiotics to fight more effectively the infestation of lice and avoid the appearance of resistance. This work was subject of a patent.

Orientador: Edi Lúcia Sartorato / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T05:36:29Z (GMT). No. of bitstreams: 1 Martins_FabioTadeuArrojo_M.pdf: 6195877 bytes, checksum: 88704a1b2448dcb2851e78b62c37e6b9 (MD5) Previous issue date: 2013 / Resumo: 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, o presente trabalho propôs padronizar um layout para diagnóstico através de genotipagens utilizando uma tecnologia 'high-throughput' baseada em PCR (Polymerase Chain Reaction) em tempo real denominada TaqMan® OpenArrayTM Genotyping. Com esta, foi desenvolvido um layout das placas de genotipagem de OpenArrayTM, sendo possível analisar 32 alterações de 96 indivíduos simultâneamente por placa. Ao todo, foram analisados 376 indivíduos, sendo 94 deles controles ouvintes, totalizando 4 placas em duplicata. Todas as 31 alterações analisadas estavam presentes nos genes nucleares GJB2, GJB6, CRYL1, TMC1, SLC26A4, miR-96, OTOF e nos genes mitocondriais 12S rRNA e MT-TR1. As reações foram validadas posteriormente por técnicas previamente estabelecidas (sequenciamento direto, PCR Multiplex e RFLP-PCR) nos testes utilizados para o diagnótisco molecular da perda auditiva do Laboratório de Genética Humana do Centro de Biologia Molecular e Engenharia Genética (CBMEG) da Universidade Estadual de Campinas (UNICAMP). Ao total, foram realizadas 11.656 reações de genotipagem. Apenas 353 reações falharam, representando, aproximadamente, 3,03% das reações. Dentre as reações que falharam, estavam as amostras de nove indivíduos que não obedeciam aos requisitos mínimos de concentração, pureza e integridade do DNA para a realização dos experimentos. Com isso, calculou-se o rendimento médio das placas de genotipagem utilizando as placas de OpenArrayTM, que apresentou acurácia de, aproximadamente, 96,97%. Tais resultados comprovam a ótima acurácia, o baixo custo e a fácil reprodutibilidade da técnica, tornando este layout customizado para a plataforma TaqMan® OpenArrayTM Genotyping uma ferramenta ótima e confiável a ser empregada nos teste de diagnóstico molecular da perda auditiva no nosso país / Abstract: Hearing loss is the most common sensory deficit in humans, affecting approximately 10% of the entire world population. The restriction of communication by the oral expression results in changes in cognitive and psychological development of the affected individual. In developed countries, one in every 500 individuals has severe/profound bilateral sensorineural hearing loss. In cases of individuals with up to 5 years, the percentage is higher, reaching 0.27% of 1000 individuals, that number becomes even greater in cases where young people, reaching 0.35%. Among all the causes of hearing loss, more than 60% of congenital hearing loss is genetics. So far already aware of 150 loci and 103 genes involved in hearing loss, and most of them have at least 20 changes (point mutations, deletions, insertions, etc.) which may cause the loss. The gene that has the higher number of changes is the GJB2, encoding connexin 26, a protein related to ion exchange intercellular maintaining homeostasis potassium auditory system, essential for hearing. Only this gene has over 302 changes confirmed so far, being the main gene related to cases of hearing loss with genetic origin. Due to the great clinical and genetic heterogeneity of hearing loss and the importance of correct molecular diagnosis of individuals with hereditary hearing loss, this work proposes standardize a layout to the diagnosis by a genotyping technology using a high-throughput technique based on real-time PCR called TaqMan® OpenArrayTM Genotyping. With this, we customized a layout to the OpenArrayTM genotyping plates, being possible to analyze 32 changes of 96 individuals per plate simultaneously. Were analyzed 376 individuals, being 94 of them controls listeners, totaling 4 plates in duplicate. All 31 changes analyzed were present in the nuclear genes GJB2, GJB6, CRYL1, TMC1, SLC26A4, miR-96, OTOF and in the mitochondrial genes 12S rRNA and MT-TR1. Reactions were subsequently validated by previously established techniques (direct sequencing, multiplex PCR and RFLP-PCR), tests used for the molecular diagnostic of the hearing loss at Human Genetics Laboratory of the Center for Molecular Biology and Genetic Engineering (CBMEG), located at State University Campinas (UNICAMP). In total, 11.656 reactions of genotyping were performed using this platform. Only 353 reactions failed, representing approximately 3.03% of the reactions. Among the reactions that failed, were samples of nine individuals who did not meet the minimum concentration, purity and integrity of the DNA for the experiments. With this, was calculated the average income of the OpenArrayTM genotyping plates, which showed an accuracy of approximately 96.97%. These results and the comparative analysis of the costs among OpenArrayTM platform and the others molecular techniques demonstrated the great accuracy, low cost and easy reproducibility of the technique, making this layout customized for the platform TaqMan® OpenArrayTM Genotyping a good and reliable tool to be used in the molecular diagnostic of hearing loss in our country / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Orientador: José Andrés Yunes / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T10:43:45Z (GMT). No. of bitstreams: 1 Caminha_IsabelPereira_D.pdf: 4630571 bytes, checksum: d16d4c6474c6966dc1040d1c4185c4a5 (MD5) Previous issue date: 2015 / Resumo: A mutação germinativa p.R337H do gene TP53 está associada à alta incidência de tumores do córtex da adrenal (TCA) em regiões Sul e Sudeste do Brasil, onde as evidências indicam a ocorrência de efeito fundador. A alta frequência de relatos desta mutação no Sul do Brasil nos encorajou a desenvolver um método adequado para a detecção de mutações em larga escala, com o objetivo de determinar a incidência da p.R337H em uma população de São Paulo, o Estado mais populoso do Brasil. Um novo método foi desenvolvido a fim de detectar a mutação p.R337H em amostras armazenadas em papel filtro, utilizando PCR em tempo real. Amostras de DNA genômico de 34.344 recém-nascidos de uma região específica do Estado de São Paulo foram selecionadas para detectar a frequência desta mutação germinativa. PCR Alelo-específico e Nested-PCR foram utilizados para verificar a presença do haplótipo fundador brasileiro em recém-nascidos portadores da mutação. Entre as 34.344 amostras triadas, 75 foram identificadas como portadores da mutação p.R337H. Esta frequência (0,21%) é semelhante à encontrada na região Sul do Brasil. O haplótipo fundador brasileiro foi identificado em todos os pacientes em que a amostra foi adequada para esta análise. A distribuição da mutação mostrou-se heterogênea, sendo mais abundante em cidades da fronteira com o sul do Estado de Minas Gerais. Nossos dados indicam que a frequência encontrada na população analisada está próxima à encontrada em outras regiões do Brasil. Além disso, a presença do haplótipo fundador em todas as portadoras corrobora a hipótese de efeito fundador. Desenvolveu-se tecnologia adequada para triagem em larga escala, utilizando amostras coletadas em papel filtro. A identificação de portadores ao nascimento pode aumentar as chances de diagnóstico precoce, melhorando o prognóstico destes pacientes e alertando os membros da família sobre um aumento da susceptibilidade para outros tipos de câncer. Entretanto, estudos posteriores são necessários, por exemplo, para avaliar a ocorrência de câncer de adulto em portadores da mutação, bem como o impacto psicológico de um programa de triagem na população saudável e na grande maioria dos portadores, os quais não desenvolverão a doença / Abstract: The germline p.R337H mutation of TP53 gene is associated with high incidence of adrenocortical tumors (ACT) in South and Southeastern regions of Brazil, where evidence indicates the occurrence of founder effect. The high frequency of this mutation in Southern Brazil encouraged us to develop a suitable method for mutation detection on a large scale, aiming to determine the frequency of p.R337H in a population of the most populous state in Brazil, São Paulo. A novel method was developed in order to detect p.R337H mutation in samples collected on Guthrie card, using real time PCR. Genomic DNA samples from 34.344 newborns from a specific region of São Paulo State were screened for this germline mutation. Alelle-Specific-PCR and Nested-PCR Assays were used to verify the presence of the Brazilian founder p.R337H haplotype in newborn mutation carriers. Among the 34.344 screened samples, we found 75 carriers of the TP53 p.R337H mutation. This frequency (0,21%) is close to that found in Brazil Southern region. We identified the haplotype A3 in all patients in whom the sample was suitable for analysis. The distribution of the mutation was shown to be heterogeneous, being more abundant in cities bordering the south of Minas Gerais. Our data indicate that the frequency found in a population of the State of São Paulo is close to that found in other regions of Brazil. Furthermore, the presence of the founder haplotype in all carriers, support the hypothesis of founder effect. We developed an appropriate technology for large-scale screening, using samples collected on filter paper. The identification of patients at birth may increase the chances of early diagnosis, improving the prognosis of these patients and alerting family members about an increased susceptibility to other cancers. However, further studies are required, for example, to assess the occurrence of cancer in adult patients with the mutation as well as the psychological impact of a screening program in the healthy population and in most carriers, who do not develop the disease / Doutorado / Genetica Animal e Evolução / Doutora em Genética e Biologia Molecular

La selección genómica está cambiando profundamente el mercado del vacuno de leche. En la actualidad, es posible obtener una alta precisión en las valoraciones genéticas de animales muy jóvenes sin la necesidad del fenotipo propio o el de sus hijas. Por tanto, la respuesta genética de un programa genómico bien diseñado supera netamente a la selección tradicional. Esta mejora está modificando uno de los principios tradicionales del mercado de vacuno de leche como era la preferencia de uso de toros con altas fiabilidades frente a otros animales con valores genéticos a priori superiores. Esta tesis contiene seis capítulos en los cuales se estudian de las bases para la implementación del programa de selección genómica en el vacuno de leche español. Para ello se realizaron estudios de simulación y valoraciones genómicas con datos reales de la primera población nacional de referencia. El objetivo principal de esta tesis es contribuir a la implementación de la selección genómica en el vacuno de leche español. Los objetivos específicos son: (1) Estudiar alternativas de genotipado en poblaciones reducidas de vacuno lechero. (2) Desarrollar y validar metodología para la evaluación de grandes cantidades de genotipos. (3) Estudiar el efecto de los procesos de imputación de genotipos en la capacidad predictiva de los genotipos resultantes. Las principales cuestiones relacionadas con la selección genómica en vacuno lechero fueron discutidas en el capítulo 1 incluyendo: aspectos estadísticos y genéticos en los que se basa la selección genómica, diseño de poblaciones de referencia, revisión del estado del arte en cuanto a la metodología desarrollada para evaluación genómica, diseño y métodos de los algoritmos de imputación, e implementación de la selección genómica en vacuno de leche a nivel de programa de selección, centro de inseminación y de granja comercial. En el capítulo 2 se realizó un estudio de simulación comparando estrategias de genotipado selectivo en poblaciones de hembras frente al uso de selección tradicional o selección genómica con una población de referencia de machos. La población de referencia española estaba formada en principio por algo más de 1,600 toros con prueba de progenie. Este tamaño no es, en principio, suficiente para obtener predicciones genómicas de alta fiabilidad. Por tanto, debían evaluarse diferentes alternativas para incrementar la habilidad predictiva de las evaluaciones. Las estrategias que consisten en usar como población de referencia los animales en los extremos de la distribución fenotípica permitían mejorar la precisión de la evaluación. Los resultados usando 1,000 genotipos fueron 0.50 para el carácter de baja heredabilidad y 0.63 para el de heredabilidad media cuando la variable dependiente fue el fenotipo ajustado. Cuando se usaron valores genéticos como variable dependiente las correlaciones fueron 0.48 y 0.63 respectivamente. Para los mismos caracteres, una población de 996 machos obtuvo correlaciones de 0.48 y 0.55 en las predicciones posteriores. El estudio concluye que la estrategia de genotipado que proporciona la mayor correlación es la que incluye las hembras de ambas colas de la distribución de fenotipos. Por otro lado se pone de manifiesto que la mera inclusión de las hembras élite que son las habitualmente genotipadas en las poblaciones reales produce resultados no satisfactorios en la predicción de valores genómicos. En el capítulo 3, el Random Boosting (R-Boost) es comparado con otros métodos de evaluación genómica como Bayes-A, LASSO Bayesiano y G-BLUP. La población de referencia española y caracteres incluidos en las evaluaciones genéticas tradicionales de vacuno lechero fueron usados para comparar estos métodos en términos de precisión y sesgo. Las predicciones genómicas fueron más precisas que el índice de pedigrí tradicional a la hora de predecir los resultados de futuros test de progenie como era de esperar. Las ganancias en precisión debidas al empleo de la selección genómica dependen del carácter evaluado y variaron entre 0.04 (Profundidad de ubre) y 0.42 (Porcentaje de grasa) unidades de correlación de Pearson. Los resultados promediados entre caracteres mostraron que el LASSO Bayesiano obtuvo mayores correlaciones superando al R-Boost, Bayes-A y G-BLUP en 0.01, 0.03 y 0.03 unidades respectivamente. Las predicciones obtenidas con el LASSO Bayesiano también mostraron menos desviaciones en la media, 0.02, 0.03 y 0.10 menos que Bayes-A, R-Boost y G-BLUP, respectivamente. Las predicciones usando R-Boost obtuvieron coeficientes de regresión más próximos a la unidad que el resto de métodos y los errores medios cuadráticos fueron un 2%, 10% y 12% inferiores a los obtenidos a partir del B-LASSO, Bayes-A y G-BLUP, respectivamente. El estudio concluye que R- Boost es una metodología aplicable a selección genómica y competitiva en términos de capacidad predictiva. En el capítulo 4, el algoritmo de machine learning R-Boost evaluado en el capítulo 3 es descrito e implementado para selección genómica adaptado a la evaluación de grandes bases de datos de una forma eficiente. Tras la incorporación en el consorcio Eurogenomics, el programa genómico español pasó a disponer de más de 22,000 toros probados como población de referencia, por tanto era necesario implementar un método capaz de evaluar éste gran conjunto de datos en un tiempo razonable. El nuevo algoritmo denominado R-Boost realiza de forma secuencial un muestreo aleatorio de SNPs en cada iteración sobre los cuales se aplica un predictor débil. El algoritmo fue evaluado sobre datos reales de vacuno de leche empleados en el capítulo 3 estudiando más en profundidad el comportamiento de los parámetros de sintonización. Esta propuesta de modificación del Boosting puede obtener predicciones sin perdida de precisión o incrementos de sesgo empleando tan solo un 1% del tiempo de computación original. En el capítulo 5 se evalúa el efecto de usar genotipos de baja densidad imputados con el software Beagle en cuanto a su posterior habilidad predictiva cuando son incorporados a la población de referencia. Para ello se emplearon dos métodos de evaluación R-Boost y un BLUP con matriz genómica. Animales de los que se conocían los SNPs incluidos en los chips GoldenGate Bovine 3K y BovineLD BeadChip, fueron imputados hasta conocer los SNPs incluidos en el BovineSNP50v2 BeadChip. Posteriormente, un segundo proceso de imputación obtuvo los SNPs incluidos en el BovineHD BeadChip. Tras imputatar desde dos genotipados a baja densidad, se obtuvo similar capacidad predictiva a la obtenida empleando los originales en densidad 50K. Sin embargo, sólo se obtuvo una pequeña mejora (0.002 unidades de Pearson) al imputar a HD. El mayor incremento se obtuvo para el carácter días abiertos donde las correlaciones en el grupo de validación aumentaron en 0.06 unidades de Pearson las correlaciones en el grupo de validación cuando se emplearon los genotipos imputados a HD. En función de la densidad de genotipado, el algoritmo R-Boost mostró mayores diferencias que el G-BLUP. Ambos métodos obtuvieron resultados similares salvo en el caso de porcentaje de grasa, donde las predicciones obtenidas con el R-Boost fueron superiores a las del G-BLUP en 0.20 unidades de correlación de Pearson. El estudio concluye que la capacidad predictiva para algunos caracteres puede mejorar imputando la población de referencia a HD así como empleando métodos de evaluación capaces de adaptarse a las distintas arquitecturas genéticas posibles. Finalmente en el capitulo 6 se desarrolla una discusión general de los estudios presentados en los capítulos anteriores y se enlazan con la implementación de la selección genómica en el vacuno lechero español, que se ha desarrollado en paralelo a esta tesis doctoral. La primera población de referencia con unos 1.600 toros fue evaluada en el capítulo 4 y fue usada para comparar los distintos métodos y escenarios propuestos en los capítulos 3, 4 y 5. La primera evaluación genómica obtenida para los caracteres incluidos en el capítulo 4 de esta tesis estuvo disponible para los centros de inseminación incluidos en el programa en septiembre de 2011. La población de Eurogenomics se incorporó en Noviembre de dicho año, completándose la primera evaluación para los caracteres incluidos en el índice de selección ICO en Febrero de 2012 empleando el R-Boost descrito en el capítulo 3. En mayo de 2012 las evaluaciones del carácter proteína fueron validadas por Interbull y finalmente el 30 de Noviembre del 2012 las primeras evaluaciones genómicas oficiales fueron publicadas on-line por la federación de ganaderos CONAFE (http://www.conafe.com/noticias/20121130a.htm). / Jiménez Montero, JA. (2013). Selección genómica en poblaciones reducidas de vacuno de leche [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/27649 / TESIS

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22852号 / 農博第2435号 / 新制||農||1082(附属図書館) / 学位論文||R2||N5312(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 寺内 良平, 准教授 三瀬 和之, 教授 那須田 周平 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Pour l’amélioration de la lutte contre la tuberculose à Madagascar, nous avons décidé de mener des études sur l’analyse de la diversité et la distribution des génotypes de BK y circulant au cours du temps et dans l’espace afin de connaitre le mode de transmission de la TB et les sources potentielles de la TB malgache. Plus spécifiquement il s’agit premièrement, d’étudier la diversité génétique et la distribution des génotypes des BK dans le pays pour évaluer le niveau de transmission de la maladie et d’essayer de retracer les sources potentielles d’importation de la TB malgache ; deuxièmement, étudier la diversité de la souche endémique de Madagascar, le SIT109, afin de voir le niveau de transmission d’une souche à l’intérieur de l’île ainsi que son niveau d’évolution ; et troisièmement, identifier les zones de transmission de la TB par combinaison d’analyse spatiale et de génotypage en commençant par une étude pilote dans la capitale.Pour réaliser cela, 1014 souches représentatives de Madagascar isolés de 2005 à 2007 ont été typés par le spoligotypage. Les génotypes définis ont servi pour l’estimation de la transmission de la TB et l’identification des sources potentielles de la TB ; ensuite, 156 BK endémiques de Madagascar portant l’identité SIT109 ont été typés par la méthode des MIRU-VNTR (« Mycobacterial Interspersed Repetitive Units – Variable Number of Tandem Repeat ») afin d’étudier leur diversité, leur niveau d’évolution et le niveau de distribution de la TB au niveau d’une seule souche et enfin, 523 patients ont été recrutés à Antananarivo en 2013 afin de typer par le spoligotypage leur BK, d’identifier à partir de leur génotype ceux qui sont potentiellement associés à des cas de transmission récente et d’analyser leur clusterisation spatiale par la méthode de Kulldorff.Les résultats nous ont montré une grande diversité génétique des BK circulant dans le pays avec une prédomination de deux lignées de BK qui sont les souches « East african Indian » et « Tuscan » ; une distribution particulière des BK dans la capitale par rapport aux autres provinces ; des similitudes particulières des BK circulant avec des pays comme les USA, la France, l’Italie, le Danemark, l’Arabie Saoudite ou encore le Pays Bas ; une grande diversité des souches SIT109 ainsi que leur distribution dans tout le pays ; ainsi que quatre clusters spatiaux de cas de TB associé à la transmission récente dans la capitale.Cette étude nous a permis de déterminer que la transmission de la TB à Madagascar est toujours très active et se fait à très grande échelle, une petite part de la TB à Madagascar a pu être importée par les populations d’origines mais la majorité des cas actuels provient d’importation assez récente de BK de plusieurs régions du monde. Douze Fokontany de la capitale correspondent à des zones à risque de transmission de la TB et méritent une attention particulière aux responsables de la lutte contre la TB à Madagascar et enfin la méthode combinant génotypage et analyse spatiale permet la détection de ces zones à risque et pourrait servir pour le « Programme National de Lutte contre la Tuberculose » d’outil d’aide à la décision pour les stratégies de lutte contre la TB dans tout Madagascar. / For improving the fight against tuberculosis in Madagascar, we decided to conduct studies on the analysis of the diversity and spatio-temporally distribution of BK genotypes circulating in Madagascar for analyzing the TB transmission mode and the potential origins of Malagasy TB. More specifically, It is to study the genetic diversity and distribution of genotypes of M. tuberculosis strains in the country to assess the transmission level of the disease and to identify the potential sources of Malagasy TB; secondly, to study the diversity of the endemic strain of Madagascar, SIT109, in order to assess the transmission level of the strain inside the island and its level of evolution; and third, to identify TB transmission areas by combining spatial analysis and genotyping, starting with a pilot study in the capital.To achieve this, 1014 BK representative of Madagascar isolated in 2005 to 2007 were typed by the spoligotyping. Defined genotypes were used to estimate the TB transmission level and the identification of potential sources of malagasy TB; after, 156 endemic BK from Madagascar bearing the identity SIT109 were typed by the MIRU-VNTR (Mycobacterial Interspersed Repetitive Units – Variable Interspersed Repeatitive Units) method to study their diversity, their evolution level and the level of TB transmission at a single strain; and finally, 523 patients were recruited in Antananarivo in 2013 in order to type by spoligotyping their BK, to identify from their genotype those that are potentially associated with recent transmission cases and to analyze their spatial clustering by the Kulldorff method.The results showed a high genetic diversity of BK circulating in the country with a predominance of two strains, “East African Indian and “Tuscan”; a particular distribution of BK genotypes in the capital compared to the other provinces and particular similarities of the BK circulating with countries such as the USA, France, Italy, Denmark, Saudi Arabia or the Netherlands; a high variety of SIT109 strains and their distribution throughout the country; as well as four TB cases associated with recent transmission spatial clusters in the capital.This study allowed us to determine that the TB transmission in Madagascar is still very active and it is done on a very large scale, a small part of TB in Madagascar could be imported by the origin populations but the majority of cases is due to relatively recent importations of BK from several regions of the world. Twelve Fokontany in the capital corresponds to TB high risk transmission areas and need special attention to those responsible for the control of TB in Madagascar and finally the method combining genotyping and spatial analysis allows the detection of these high risk areas and could be used for the “Programme National de Lutte contre la TB” as a decision tool for orientation of the TB fight strategies throughout Madagascar

Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. This thesis contemplates the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates.