Made available in DSpace on 2015-06-17T19:34:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-02-27. Added 1 bitstream(s) on 2015-06-18T12:48:59Z : No. of bitstreams: 1 000834512.pdf: 473043 bytes, checksum: 44d24e6dcb2fb5220f4b7b5945c123fe (MD5) / CNVs (copy number variation - variação no número de cópias) são segmentos de DNA de tamanho igual ou maior a 1 Kb e estão presentes em número variável de cópias em comparação com um genoma referência e podem estar associadas com a expressão gênica e variâncias fenotípicas. Assim, esse trabalho teve como objetivo identificar regiões com variações no número de cópias nos segmentos de DNA em um total de 366 indivíduos de 5 raças bovinas autóctones de corte espanholas, distribuídos em 25 famílias formadas por pai-mãe-progênie, denominados trios. Os animais pertencentes às raças Asturiana de los Valles (75 indivíduos, 25 trios), Avileña-Negra Ibérica (74 indivíduos, 24 trios completos, um trio com pai repetido), Morucha (Mo, 75 indivíduos, 25 trios), Pirenaica (74 indivíduos, 24 trios completos, um trio com pai repetido) e Retinta (68 indivíduos, 18 trios completos, 7 trios com pais repetidos) foram genotipados com o painel Illumina BovineHD Beadchip de 777K A identificação das CNVs foi realizada por meio do modelo das cadeias ocultas de Markov implementado no software PennCNV. As regiões de CNV (copy number variation region - CNVR) foram determinadas pela sobreposição de agrupamentos das CNVs identificados em diferentes animais. Genes candidatos localizados nas CNVR encontradas foram investigados por meio de análises nas plataformas NCBI e Ensembl. Foram detectadas 8061 CNVs, sendo 2852 cópias e 5592 deleções e 1293 regiões, sendo 876 deleções e 314 cópias, cobrindo 3,6% do genoma autossômico bovino. Foram encontrados dentro dessas regiões 1.263 genes, com alguns deles fazendo parte de processos biológicos como crescimento e sistema imune. Encontrou-se um grande número de CNVs sendo compartilhadas entre as raças Asturiana de los Valles e Morucha, o que sugere proximidade entre essas raças durante seu... / Copy number variation (CNV) are DNA segments that are present at variable copy number compared to a reference genome. Classes of CNVs include insertions, deletions, duplications and inversions. CNVs can be associated with gene expression and phenotypic variation, providing genetic variability among individuals and, thus, are an important tool to production and healthy traits selection. The goal of this study was to identify regions with copy number variation in a total of 366 individuals from 5 autochthonous Spanish breeds of beef cattle, distributed into 25 families for breed, composed of sire-dam-offspring, called trios. The animals belonged to Asturiana de los Valles (75 individuals, 25 trios), Avileña-Negra Ibérica (74 individuals, 24 complete trios, one sire-repeated trio), Morucha (Mo, 75 individuals, 25 trios), Pirenaica (74 individuals, 24 24 complete trios, one sire-repeated trio) e Retinta (68 individuals, 18 complete trios, 7 sire-repeated trios) and were genotyped with the Illumina BovineHD Beadchip. The PennCNV software performed the CNVs identification. The CNV regions (CNVR) were determined by the overlapping of the CNVs. Candidates genes placed within the found CNVRs were investigated by analysis into the NCBI and Ensembl data platform. It has been detected a total of 8,061 CNV, which 2852 are gain and 5592 are loss of a DNA segment. A great amount of sharing CNVs between Asturiana de los Valles and Morucha breeds had been observed, which suggests a proximity during their formation process. We found also 1,293 regions of CNVs, spanning 3.6% of the autosomal bovine genome and 1,263 genes were present within these regions, and were involved in biological processes such as growth and immune system

Made available in DSpace on 2014-11-10T11:09:51Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-02-27Bitstream added on 2014-11-10T11:57:53Z : No. of bitstreams: 1 000791427.pdf: 858212 bytes, checksum: 73468dc580b32c2569a024a91ace55d2 (MD5) / O objetivo do presente trabalho foi avaliar a acurácia de predição dos valores genéticos genômicos para características de diferentes herdabilidades, em populações simuladas de aves com diferentes níveis de endogamia. Os dados fenotípicos e genotípicos foram simulados com base na estrutura populacional de uma população experimental de aves poedeiras. Foram simulados os fenótipos e os genótipos de aves para características de taxa de postura total de ovos (PTO) e peso dos ovos as 32 semanas de idade (PO), com herdabilidades de 0,15 e 0,37 respectivamente. Foi simulada uma população histórica a fim de gerar desequilíbrio de ligação na população e esta deu origem as populações recentes em que foram simulados três cenários populacionais, visando maximizar (REC1), minimizar (REC2) e aleatorizar (REC3) os acasalamentos endogâmicos. Ao longo de 10 gerações recentes, os animais foram selecionados com base nos maiores valores genéticos preditos (VGP), utilizando o BLUP (best linear unbiased prediction) tradicional. O genoma das aves foi simulado ao longo dos 958 Mb do genoma Gallus gallus 4.0 com 3.747 QTL (loci de caracteres quantitativos) aleatoriamente distribuídos e 49.978 marcadores SNP uniformemente distribuídos. A fim de alterar as frequências alélicas e gerar variabilidade genética ao longo das gerações, foram simulados eventos de deriva genética, taxa de recombinação e mutação recorrente. Para avaliar os efeitos da endogamia nas populações recentes, foram calculados os desequilíbrios de ligação (DL), o tamanho efetivo da população (Ne) e as tendências genéticas em todos os cenários de populações recentes em ambas as características simuladas. Para predizer os valores genéticos genômicos preditos (VGGP), as populações recentes foram subdivididas em populações de treinamento e validação. Nas subpopulações de treinamento, os 960 animais ... / The objective of this study was to evaluate the prediction accuracy of genomic breeding values for traits of different heritability in simulated populations with different inbreeding. Phenotypic and genotypic data were simulated based on the population structure of an experimental population of White Leghorn hens at Embrapa Suínos e Aves. The phenotypes and genotypes were simulated for the rate of total egg production (PTO) and egg weight to 32 weeks of age (PO) with heritability of 0.15 and 0.37, respectively. The historical population was simulated to generate linkage disequilibrium in the population. Three scenarios in recent populations were simulated for each trait: REC1, REC2 and REC3 to maximize inbreeding, minimize inbreeding and random mating, respectively. The animals were selected based on the largest breeding values along 10 generations. The genome of the birds was simulated with eight macro-chromosomes and 19 micro-chromosomes with 3.747 QTL randomly distributed and 49.978 SNPs markers evenly spaced along the 958 cM. Recombination, random drift and recurrent mutation were simulated in order to generate genetic variability. The linkage disequilibrium (LD), effective population (Ne) and genetic trends were calculated for all scenarios. Each recent population was divided in training and validation sets In order to predict the genomic breeding values. The training set included the genotypes and phenotypes of 960 animals, which had higher breeding values’ accuracy. The validation set had 1120 animals of the last generation of the recent population. The average inbreeding ranged from 0.06 ± 0.30 to 0.22 ± 0.12 for PTO and 0.05 ± 0.03 to 0.20 ± 0.12 for PO. The REC1 populations had higher inbreeding along generations compared, both for PTO and PO, compared to REC2 and REC 3, and consequently higher level of LD. The highest accuracy for PTO and PO were ...

Made available in DSpace on 2014-11-10T11:09:51Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-02-19Bitstream added on 2014-11-10T11:57:52Z : No. of bitstreams: 1 000791334.pdf: 1246832 bytes, checksum: a218fc15109d0f914149e0a8bee3fbf4 (MD5) / Painéis de marcadores genéticos de alta densidade (HD) possuem forte desequilíbrio de ligação, que permite melhores predições de valores genômicos. Entretanto, genotipar animais com estes painéis apresenta custo elevado, tornando-se uma limitação para a genotipagem de todos os candidatos à seleção. Uma alternativa para a redução desses custos é utilizar imputação de genótipos. A imputação é um método em que marcadores de uma população genotipada com painéis de baixa densidade (LD) são inferidos utilizando informações provenientes de uma população referência genotipada com painéis HD. O objetivo deste trabalho foi comparar em diferentes cenários metodologias de imputação de marcadores moleculares de polimorfismos de nucleotídeos únicos (SNP) em bovinos de corte da raça Canchim. Foram utilizadas informações de 285 animais da raça Canchim, 114 do grupo genético “MA” e 1 touro da raça Charolês genotipados com painel Illumina BovineHD BeadChip (786.799 SNP), nascidos entre 1999 e 2005 e provenientes da base de dados genômicos da Embrapa Pecuária Sudeste, São Carlos, SP. A edição dos dados foi realizada no software R e em linguagem C++. Para a frequência mínima de alelos (MAF) foram aplicados 3 diferentes critérios: sem remover MAF (QC1); SNP com MAF menor que 0,0025 (QC2) e menor que 0,10 (QC3) foram excluídos. O painel HD original foi reduzido para painéis de baixa densidade (LD) 3K, 6K, 9K, 50K, 20K, 80K e 90K, selecionando os marcadores em comum entre o painel HD original e os painéis comerciais Illumina Bovine3K (3K), BovineLD (6K), GeneSeek Genomic Profiler (GGP) Beef LD (9K), BovineSNP50 (50K), GGP Indicus LD (20K) ,GGP Beef HD (80K) e GGP Indicus HD (90K). Os animais foram divididos em diferentes cenários, denominados de população referência e imputação, sendo o cenário 1 (C1): População referência formada por animais nascidos ... / High-density panels (HD) have strong level linkage disequilibrium among genetic markers (i.e. single nucleotide polymorphism - SNP), which allows better predictions of genomic breeding values. However, HD genotyping still expensive and became a limitation for the quantity of candidate animals used in genomic studies. As an alternative to decrease costs, imputation methods are powerful tools to infer missing marker genotypes from low-density (LD) panels to HD. Imputation uses information from a reference population of animals genotyped with a HD panel to impute variants that are not directly genotyped in LD panels. The objective of this study was to compare different scenarios and methodologies of imputation for the Canchim cattle. Data set was provided by Embrapa Pecuária Sudeste and comprised 285 Canchim animals, 114 MA genetic group animals, and 1 ancestor Charolais bull. Animals born between 1999 and 2005 were genotyped with the Illumina BovineHD panel (786,799 SNP). Data editing was performed in the R software and in C ++ language. Multiple scenarios combining different minor allele frequencies (MAF) thresholds for SNPs were tested: no MAF filter (QC1), and exclusion of SNPs with MAF lower than 0.0025 (QC2) and MAF lower than 0.10 (QC3). LD panels were created by masking SNPs originally present in the HD panel, and then assigning markers into the Illumina Bovine3K (3K), Illumina BovineLD (6K), Beef LD GeneSeek Genomic Profiler (9K), Indicus LD GeneSeek Genomic Profiler (20K), Illumina BovineSNP50 (50K), GeneSeek Genomic Profiler Beef HD (80K) and GeneSeek Genomic Profiler Indicus HD (90K) panels. Reference and target populations were defined as scenario 1 (C1), reference animals were born up until 2004 and target animals were born in 2005; scenario 2A (C2A), reference animals from Canchim breed and target animals from MA genetic group; scenario 2B (C2B), reference animals from MA genetic ...

Made available in DSpace on 2015-03-03T11:52:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-07-15Bitstream added on 2015-03-03T12:07:19Z : No. of bitstreams: 1 000810819.pdf: 308723 bytes, checksum: 524c7c0a9ecb8ecef63e198e5ccb23d3 (MD5) / A seleção genômica tem sido apontada como uma tecnologia que propiciará aumentos expressivos nas taxas de progresso genético em programas de melhoramento animal. Um dos fatores limitantes para a aplicação da seleção genômica é o custo associado à necessidade de genotipagem de um número grande de animais, com painéis de alta densidade, para a obtenção de boa habilidade de predição dos valores genéticos. Uma alternativa para reduzir custos seria genotipar parte dos animais com painéis menos densos e utilizar técnicas de imputação de genótipos. Em bovinos da raça Nelore, ainda não há consenso quanto à densidade dos painéis a serem utilizados e quanto à estratégia de genotipagem e imputação. Assim, objetivou-se com o presente projeto avaliar a habilidade de predição da seleção genômica utilizando painéis de marcadores moleculares de diferentes densidades, assim como o efeito da utilização de genótipos imputados na habilidade de predição da seleção genômica, em bovinos da raça Nelore. A característica considerada foi precocidade de terminação. Um total de 2035 animais geneticamente avaliados para essa característica e genotipados com o chip Ilumina ® HD Bovina (780k) foram utilizados nas análises, simulando uma situação em que os animais teriam sido genotipados com chips de densidade mais baixa. Análises de seleção genômica também foram executadas utilizando parte dos marcadores do painel de 780k , disponibilizando apenas os SNPs em comum com as seguintes painéis: Illumina® BovineLD (7K), Illumina® BovineSNP50 v2 (50K) e GeneSeek® Genomic Profiler 20K e 75K para Bos indicus. A imputação dos genótipos foi feita com o uso do programa FImpute e as predições genômicas foram conduzidas utilizando os métodos GBLUP e LASSO Bayesiano. Ambas análises, de imputação e de predição genômica, foram conduzidas de forma repetida, seguindo um esquema de validação cruzada, com a formação ... / Genomic selection has been considered as a technique that will allow significant increase in the genetic progress of animal breeding programs. A constrain for genomic selection application is the cost of genotyping several animals with high density chips in order to obtain a good prediction equation. An alternative to reduce costs is to genotype part of the animals with a lower density chip and to impute the unobserved genotypes. In Nelore cattle, there is no consensus about which chip and genotyping strategy should be adopted. Therefore, the aim of the present study was to evaluate the predictive ability of genomic selection in Nelore cattle using chips with different densities, and also to assess the effect of using imputed genotypes. The trait considered was finishing precocity. A total of 2,035 animals genetically evaluated for this trait and genotyped with the Illumina® Bovine HD chip (780K) were used in the analyses, mimicking a situation where the animals would have been genotyped with lower density chips. Genomic selection analyses were also run masking part of the 780K genotypes, making available just the SNPs in common with the following chips: Illumina® BovineLD (7K), Illumina® BovineSNP50 v2 (50K), GeneSeek® Genomic Profiler 20K and 75K for Bos indicus. Genomic prediction analyses were run with or without imputing the masked genotypes, using the software FImpute, and under the GBLUP and Bayesian LASSO methods. A 5- fold cross-validation scheme was adopted to perform the analyses, randomly assigning the groups. Results showed that the 50K and 75K chips presented the same predictive ability as the 780K chip. The results also indicated that if the 780K was considered as the target chip for applying genomic selection in the Nelore breed, its cost effectiveness could be improved with the strategy of genotyping part of the animals with a lower density chip (7K or 20K) and imputing their 780K missing genotypes. Further studies ...

abstract: Cancer is a heterogeneous disease with discrete oncogenic mechanisms. P53 mutation is the most common oncogenic mutation in many cancers including breast cancer. This dissertation focuses on fundamental genetic alterations enforced by p53 mutation as an indirect target. p53 mutation upregulates the mevalonate pathway genes altering cholesterol biosynthesis and prenylation. Prenylation, a lipid modification, is required for small GTPases signaling cascades. Project 1 demonstrates that prenylation inhibition can specifically target cells harboring p53 mutation resulting in reduced tumor proliferation and migration. Mutating p53 is associated with Ras and RhoA activation and statin prevents this activity by inhibiting prenylation. Ras-related pathway genes were selected from the transcriptomic analysis for evaluating correlation to statin sensitivity. A gene signature of seventeen genes and TP53 genotype (referred to as MPR signature) is generated to predict response to statins. MPR signature is validated through two datasets of drug screening in cell lines. As advancements in targeted gene modification are rising, the CRISPR-Cas9 technology has emerged as a new cancer therapeutic strategy. One of the important risk factors in gene therapy is the immune recognition of the exogenous therapeutic tool, resulting in obstruction of treatment and possibly serious health consequences. Project 2 describes a method development that can potentially improve the safety and efficacy of gene-targeting proteins. A cohort of 155 healthy individuals was screened for pre-existing B cell and T cell immune response to the S. pyogenes Cas9 protein. We detected antibodies against Cas9 in more than 10% of the healthy population and identified two immunodominant T cell epitopes of this protein. A de-immunized Cas9 that maintains the wild-type functionality was engineered by mutating the identified T cell epitopes. The gene signature and method described here have the potential to improve strategies for genome-driven tumor targeting. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2017

Orientador: Luiz Francisco Zafalon / Coorientador: Fernando Antônio de Ávila / Coorientador: Oswaldo Durival Rossi Junior / Banca: Maurício de Alvarenga Mudadu / Banca: Luciano Menezes Ferreira / Banca: Hélio José Montassier / Banca: Marita Vedovelli Cardozo / Resumo: Tendo em vista a importância e o crescente interesse na produção de leite de búfala e seus derivados e da ocorrência de Staphylococcus coagulase negativa (SCN) como patógenos da mastite tanto em bovinos como em bubalinos. O presente estudo objetivou avaliar genes de virulência, a resistência a antimicrobianos, bem como metodologias para correta identificação destes SCN em ambiente de ordenha e no leite de bubalinos. Foram colhidas 320 amostras de leite de quartos mamários de 80 búfalas escolhidas aleatoriamente, 20 amostras de narinas e 20 amostras da boca dos bezerros bubalinos, 16 amostras das mãos dos ordenhadores e 64 amostras de insufladores das teteiras, coletadas durante a ordenha. Vinte e sete cepas de Staphylococcus coagulase negativa foram positivas para o gene eno, 10 para o gene ebps, 10 para o gene fnbA. Em relação aos genes relacionados com a produção de enterotoxinas, apenas uma cepa foi positiva para o gene sea, uma para o gene see e para os genes relacionados a resistência antimicrobiana, uma cepa foi positiva para o gene mecA. A identificação das espécies isoladas foi realizada utilizando-se a metodologia de MALDI-TOF MS e confirmada por iniciadores espécie-especifico desenhados neste estudo, exceto para S. agnetis o qual foi erroneamente identificado como S. hyiucs por espectofotometria de massa. Neste trabalho a identificação destas duas espécies foi confirmada por sequenciamento genômico de um isolado representativo. Foram observadas quatro amostras resis... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Due to the importance and the growing interest in buffalo milk production and its derivate and the concurrency of coagulase negative staphylococci as major mastitis pathogens both in cattle and in buffalo. This study aimed to search for virulence genes, antimicrobial resistance, and to evaluate methodologies for the identification of these microorganisms in samples of buffalo milk and from milking environment. For this, a total of 320 milk samples were collected from mammary quarters of 80 randomly selected buffaloes, 20 samples from nostrils and 20 samples from buffalo calves 'mouths, 16 samples from milking hands and 64 samples from liners were collected at the time of milking. Twenty-seven strains of coagulase negative staphylococci were positive for the eno gene, ten for ebpS gene, ten for the fnbA. Regarding genes related to enterotoxins production. Only one strain was positive for the sea and see gene and one for the mecA gene. The identification of the isolates was correctly done by MALDI-TOF MS and subsequently confirmed by species specific primers, except for S. agnetes that was wrongly identified as S. hyiucs. This identification was confirmed by genomic sequencing of a representative isolate from each species. There were four strains resistant to clindamycin, nine to vancomycin, one to chloramphenicol, seven to rifanmpicina, four to cefepime, seven to oxacillin, 17 to penicillin, 13 to erythromycin, 15 to cotrimoxazole and three to tetracycline. Furthermore, resistance to two or more antibiotics were observed in 21 isolates. The present study results may contribute to incidence prevention and control of mastitis in buffalo, caused by coagulase negative Staphylococcus. The main SCN species isolated were S. chromogenes, S. agnetis and S. epidermidis., the detection of genes related to adhesion and the production of enterotoxins m... (Complete abstract click electronic access below) / Doutor

Submitted by Flávia Regina Florencio de Athayde null (flavinhaflorencio@hotmail.com) on 2017-01-27T14:01:09Z No. of bitstreams: 1 Athayde_F_R_F_diss.mestrado.pdf: 1648129 bytes, checksum: a278e99a1cfea6cf938f7ec4bb928519 (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-01-31T13:33:23Z (GMT) No. of bitstreams: 1 athayde_frf_me_araca.pdf: 1648129 bytes, checksum: a278e99a1cfea6cf938f7ec4bb928519 (MD5) / Made available in DSpace on 2017-01-31T13:33:23Z (GMT). No. of bitstreams: 1 athayde_frf_me_araca.pdf: 1648129 bytes, checksum: a278e99a1cfea6cf938f7ec4bb928519 (MD5) Previous issue date: 2016-12-09 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Os protozoários do gênero Leishmania, da família Trypanosomatidae, são responsáveis por causar as leishmanioses, zoonoses de distribuição mundial que atingem países de regiões tropicais e subtropicais, representando um importante problema de saúde pública. As espécies de Leishmania patogênicas à humanos são classificadas em dois subgêneros, Leishmania e Viannia, sendo responsáveis pelas três formas clínicas mais comuns da doença. O subgênero Leishmania tem representantes no Velho e no Novo Mundo, enquanto que as espécies do subgênero Viannia estão presentes somente nas regiões tropicais das Américas, sendo responsáveis pela manifestação tegumentar na forma cutânea e mucocutânea. O avanço nas tecnologias de sequenciamento e montagem dos genomas de espécies de Leishmania têm possibilitado melhor entendimento das leishmanioses, da relação parasita-hospedeiro e até mesmo a identificação diferencial das espécies, auxiliando no entendimento das diferenças nas manifestações clínicas. Com o intuito de ampliar as informações genômicas das espécies de Leishmania e do subgênero Viannia, trabalhamos com o sequenciamento de DNA genômico e ferramentas de bioinformática para a montagem do genoma e anotação de proteínas de duas espécies, Leishmania (Viannia) guyanensis e Leishmania (Viannia) shawi. / The protozoa of the Trypanosomatidae family Leishmania genus, are responsible for causing leishmaniosis, zoonosis of global distribution that affects countries in tropical and subtropical regions, representing an important public health problem. The Leishmania species pathogenic to humans are classified into two subgenera, Leishmania and Viannia, which are responsible for three of the most common clinical manifestations of this disease. The subgenus Leishmania has representatives in the Old and New World, while the Viannia species are present only in the tropical regions of the Americas. These are responsible for the tegumentary manifestation of the cutaneous and mucocutaneous forms. The advance in the technologies of sequencing and the assembly of the genomes of Leishmania species have allowe to better understand the leishmaniosis, the parasite-host relationship and even the differential identification of the species thus, helping to understand the differences in the clinical manifestations. In order to expand the genomic information of the Leishmania species and the subgenus Viannia, we worked with genomic DNA sequencing and bioinformatics tools for assembling the genome and annotating proteins of two species, Leishmania (Viannia) guyanensis and Leishmania (Viannia) shawi.

Orientador: Danísio Prado Munari / Coorientador: Rodrigo Pelicioni Savegnago / Coorientador: Marcos Vinícius Gualberto Barbosa da Silva / Banca: Marcos Eli Buzanskas / Banca: Ana Fabrícia Braga Magalhães / Banca: Adriana Santana do Carmo / Banca: Fernando Sebastián Baldi Rey / Resumo: A implementação de dados de sequenciamento de nova geração - "next-generation sequence" (NGS) em programas de melhoramento genético animal representa a mais recente ferramenta na utilização de dados genotípicos nos modelos de associação genômica, tendo em vista que todo polimorfismo é considerado nas associações entre registros fenotípicos e dados de sequenciamento. Como em toda nova tecnologia, a prospecção das variantes ainda representa um desafio no sentido computacional e de viabilidade dos custos para sua implementação em larga escala. Diante desses desafios, neste trabalho buscou-se meios de explorar os benefícios na utilização da NGS nas predições genômicas e superar as limitações inerentes a esse processo. Registros fenotípicos e genotípicos (Illumina Bovine HD BeadChip) de 2.279 animais da raça Gir (Bos taurus indicus) foram disponibilizados pela Embrapa Gado de Leite (MG) e utilizados para as análises de associação genômica. Além disso, dados de sequenciamento de 53 animais do 1000 "Bulls Project" deram origem à população de referência de imputação. Visando verificar a eficiência de imputação, foram testados diferentes cenários quanto a sua acurácia de imputação por meio da análise "leave-one-out", utilizando apenas os dados de sequenciamento, que apresentaram eficiências de até 84%, no cenário com todos os 51 animais disponíveis após o controle de qualidade. Também foram verificadas as influências das variantes em baixa frequência na acurácia de imputação em difere... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: - Implementing "next-generation sequence" (NGS) data in animal breeding programs represents the latest tool in the use of genotypic data in genomic association models, since all polymorphisms are considered in the associations between phenotypic records and sequencing data. As with any new technology, variant prospecting still represents a computational and cost-effective challenge for large-scale implementation. Front to these challenges, this work sought ways to explore the benefits of using NGS in genomic predictions and overcome the inherent limitations of this process. Phenotypic and genotypic (Illumina Bovine HD BeadChip) records of 2,279 Gir animals (Bos taurus indicus) were made available by Embrapa Gado de Leite (MG) and used for genomic association analysis. In addition, sequence data of 53 animals from the 1000 Bulls Project gave rise to the imputation reference population. In order to verify the imputation efficiency, different scenarios were tested for their imputation accuracy through the leave-one-out analysis, using only the sequencing data, which presented efficiencies of up to 84%, in the scenario with all the 51 animals available after quality control. Influences from the low-frequency variants on the accuracy of imputation in different regions of the genome were also verified. After identifying the best reference population structure of imputation and applying the quality controls in the NGS and genomic data, it was possible to impute the 2 237 genotyped a... (Complete abstract click electronic access below) / Doutor

Genome Wide Association Studies (GWAS) have uncovered many genetic regions which are associated with autoimmune disease risk. In this thesis, I present methods which I have developed to build upon these studies and enable the analysis of the causal variants of these diseases. Colocalization methods disentangle whether potential causal variants are shared or distinct in related diseases, and enable the discovery of novel associations below the single-trait significance threshold. However, existing approaches require independent datasets to accomplish this. I extended two methods to allow for the shared-control design; one of these extensions also enables fine mapping in the case of shared variants. My analysis of four autoimmune diseases identified 90 regions associated with at least one disease, 33 of which were associated with 2 or more disorders; 14 of these had evidence of distinct causal variants. Once associated variants have been identified, we may wish to test some aggregate property, such as enrichment within an annotation of interest. However, the null distribution of GWAS signals showing association with a trait and preserving expected correlation due to linkage disequilibrium is complicated. I present an algorithm which computes the expected output of a GWAS, given any arbitrary definition of "null", and hence can be used to simulate the null distribution required for such a test. Commonly, GWAS report only summary data, and determining which genetic variants are causal is more difficult; the strongest signal may merely be correlated with the true causal variant. I have developed a statistical method for fine mapping a region, requiring only GWAS p-values and publicly available reference datasets. I sample from the space of potential causal models, rejecting those leading to expected summary data excessively different from that observed. This removes the need for the assumption of a single causal variant. In contrast to other summary statistic methods which allow for multiple causal variants, it does not depend upon availability of effect size estimates, or the allelic direction of effect and it can infer whether the pattern of association is likely caused by a non-genotyped SNP without requiring imputation. I discuss the effect of choice of reference dataset, and the implications for other summary statistics techniques.

Obesity and type-2 diabetes are major global health crises. The synthetic retinoid compound 4-hydroxy(phenyl)retinamide (Fenretinide, FEN), has been shown to inhibit adiposity and reverse insulin resistance in pre-clinical studies. Fenretinide acts via several different mechanisms, including induction of retinoid signalling and increased hepatic lipid oxidation to exert its metabolic effects. However, the signalling mechanisms behind these effects have yet to be fully elucidated. A number of approaches were taken in this thesis to investigate the signalling mechanisms of Fenretinide. To characterise the relationship between Fenretinide and leptin signalling, Fenretinide treatment was administered in two different leptin-deficient mouse models. Fenretinide effects on hepatic signalling mechanisms were further characterised by performing global transcriptomics analysis in liver from mice receiving HFD ± Fenretinide. In this analysis, the important metabolic hormone fibroblast growth factor (FGF) 21 was identified as a novel retinoid-dependent target of Fenretinide signalling, which was further characterised in multiple mouse models. Retinoic-acid receptor-specific ChIP-sequencing was performed in order to identify other liver genes that are regulated by Fenretinide via retinoid-dependent signalling mechanisms. This work has shown that the beneficial effects of Fenretinide on adiposity occur via a mechanism independent of that through which Fenretinide mediates effects on glucose homeostasis. Fenretinide effects on insulin sensitivity and glucose homeostasis are most likely mediated via the inhibition of ceramide synthesis in the liver and other metabolically active tissues. This work also shows that Fenretinide can normalise the effects of chronic HFD-feeding by targeting the expression of a set of PPARα-target genes in the liver via a retinoid-dependent signalling mechanism. Overall, the work described in this thesis both uncovers more detail about the signalling mechanisms of Fenretinide and identifies novel target genes that may be exploited for the development of new therapeutics to treat obesity and type 2 diabetes.