O Lupus Eritematoso Sistêmico (LES) é uma doença crônica auto-imune caracterizada pela alta produção de auto-anticorpos contra antígenos nucleares e pela formação de imunocomplexos que desencadeiam resposta citotóxica. As causas do LES são desconhecidas, porém se têm alguns indícios bem descritos que alterações genéticas, imunológicas e/ou ambientais podem desencadear processos autoimunes que levam ao LES. Esses fatores são, por exemplo, vírus e o mimetismo molecular causado por proteínas virais, ou genéticos que interfiram em rotas de processamento de imunocomplexos, produção de interferon (IFN) e transdução de sinal em linfócitos. Os receptores Toll-Like (TLR) são receptores de padrões moleculares de patógenos e estão envolvidos na produção de IFN, além de ser um elo importante entre a imunidade inata e a adquirida. Os TLR7/8/9 reconhecem ácidos nucléicos e são expressos em células dendríticas e células B, importantes na patogênese do LES. O objetivo do nosso trabalho foi avaliar a infuência dos polimorfismos genéticos potencialmente funcionais rs179008 no TLR7, rs3764880 no TLR8, rs5743836 e rs352140 no TLR9 em uma amostra de 370 pacientes com LES e em uma amostra de 415 indivíduos saudáveis provenientes do sul do Brasil. O polimorfismo rs5743836 foi genotipado através da técnica de PCR alelo específico BIPASA enquanto que os demais foram genotipados por PCR-RFLP. As freqüências genotípicas e haplotípicas foram comparadas usando o teste de Qui-Quadrado e as freqüências alélicas usando o teste Exato de Fisher. As comparações foram realizadas subdividindo os indivíduos de acordo com a origem étnica e sexo. As freqüências genotípicas e alélicas diferiram para rs179008 (P=0,020 e P=0,003; OR para presença do alelo T: 1,74 CI 95% 1,12-2,70) e rs5743836 (P=0,045 e P=0,017; OR para presença do alelo C: 1,59 CI 95% 0,99-2,57) nas comparações entre mulheres eurodescendentes controles e pacientes. Houve uma tendência na presença do alelo C em pacientes com Anti-Ro/SS-A comparados com pacientes sem Anti-Ro/SS-A (P corrigido = 0,06). As análises com haplótipos ou genótipos combinados não apresentaram diferenças estatisticamente significativas. Nossos dados sugerem que os alelos T do rs179008 e o alelo C do rs5743836 estão envolvidos na suscetibilidade/patogênese do LES em mulheres Eurodescedentes do sul do Brasil. / Systemic Lupus Erythematosus (SLE) is an autoimmune chronic disease characterized by high autoantibody production against nuclear antigens and by immunocomplexes formation that lead to citotoxicity. Causes of SLE are unknown, however there are some factors suggested to trigger autoimmune processes and result in SLE phenotype. These can be environmental, such as virus and molecular mimicry caused by their proteins, or genetic factors mainly related to immunocomplexes processing, interferon (IFN) production and the signal transduction pathway in lymphocytes. Toll-Like receptors (TLR) are pattern-recognition receptors and they are involved in IFN production, besides to be a link between the innate and acquired immune system. TLR7/8/9 recognize nucleic acids and are expressed mainly in dendritic and B cells. Our study aims to evaluate the prevalence of TLR7 rs179008, TLR8 rs3764880, TLR9 rs5743836 and rs352140, potencially functional polymorphisms, in 370 SLE patients and 415 healthy blood-donnors from southern Brazil. Rs5743836 polymorphism was genotyped trough allele-specific PCR BIPASA and the rest were genotyped through PCR-RFLP. Genotypic and allelic frequencies were compared using chi-square and exact fisher test, respectively. OR was calculated and clinical characteristics were evaluated. All comparisons were carried out grouping individuals according ethnicity and gender. Genotypic and allelic frequencies were significantly different for rs179008 (P=0.020 and P=0.003, OR for T allele carriers: 1.74, CI 95% 1.12-2.70) and rs5743836 (P=0.045 and P=0.017, OR for C allele carriers: 1.59, CI 95% 0.99-2.57) comparing European-derived SLE and control women. A trend in Anti-Ro/SS-A presence was observed for rs5743836 C allele carriers (corrected P=0.06). There were no statistical differences when haplotypes and combined genotypes were analyzed. Our data suggest both TLR7 rs179008 T allele and TLR9 rs5743836 C allele involved in SLE susceptibility/pathogenesis in women European-derived.

Orientador: Carmen Silvia Bertuzzo / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-11T07:49:42Z (GMT). No. of bitstreams: 1 Furgeri_DanielaTenorio_M.pdf: 2346117 bytes, checksum: 8c455774e8fcf28345f6135b0e9534a3 (MD5) Previous issue date: 2008 / Resumo: A Fibrose Cística (FC) é uma doença genética de padrão de herança autossômica recessiva com incidência de 1/2.500 indivíduos e uma freqüência de portadores de 1/25 nos indivíduos caucasóides. A doença é progressiva e apresenta como manifestação clínica a obstrução respiratória crônica, infertilidade masculina e deficiência de ganho de peso pelo dano ao pâncreas exócrino. A maioria dos pacientes tem níveis elevados de eletrólitos no suor. O gene responsável pela doença foi localizado no cromossomo 7, possui 27 éxons e é denominado CFTR (¿Cystic Fibrosis Transmembrane Conductance Regulator Gene¿). Existem mais de 1.000 mutações descritas em todo o gene, a mais freqüente, a ?F508, é caracterizada como uma deleção de três pares de bases, o que determina a perda de uma fenilalanina na posição 508 da proteína CFTR, a qual forma um canal para o transporte do íon cloro. O defeito básico está associado com a diminuição da condução de íons cloro através da membrana apical de células epiteliais. O objetivo desse trabalho foi verificar em uma amostra de núcleos familiares de pacientes com fibrose cística, os haplótipos existentes, a possibilidade de utilização de polimorfismos para diagnóstico pré-natal e pré-implantação e correlacionar a mutação ?F508 com os haplótipos encontrados. A análise de polimorfismos GATT foi realizada através da técnica da reação em cadeia da polimerase (PCR) e a análise dos polimorfismos MP6-D9, TUB09 e TUB18 foi realizada através da PCR e digestão enzimática específica. Em nossa casuística, nove haplótipos diferentes foram encontrados em 39 cromossomos. Vinte e cinco estão ligados à mutação ?F508 e 14 ligados a outras mutações (não-?F508). O haplótipo 6, +; G; C (GATT, MP6D9, TUB09 e TUB18) foi o mais freqüente (48%) em cromossomos com o gene CFTR alterado e está fortemente ligado à mutação ?F508 (64%). Em 43% das famílias analisadas pelo menos um polimorfismo informativo foi encontrado para o diagnóstico pré-natal ou pré-implantação. Em conclusão, estes polimorfismos constituem um excelente grupo de marcadores genéticos, úteis para observar a transmissão dos alelos mutados em famílias de pacientes com fibrose cística, onde não é possível estabelecer o genótipo completo. De acordo com os resultados obtidos, estes polimorfismos poderão ser amplamente utilizados para o diagnóstico pré-natal e pré-implantação, cumprindo com o objetivo do trabalho / Abstract: Cystic Fibrosis (FC) is a genetic autossomic recessive disease with an incidence of 1/2.500 life births and a carrier frequency of 1/25 in the caucasian population. The disease is progressive and present as a clinical manifestation the respiratory chronic blockage, male infertility and deficiency to gain weight caused for the damage to the exocrine pancreas. The majority of the patients has raised electrolyte levels in the sweat. The gene responsible is located in chromosome 7, and it has 27 éxons, and is called CFTR ("Cystic Fibrosis Transmembrane Conductance Regulator Gene"). Over 1.200 mutations have been described all over the gene and the mutation ?F508 is the most frequent, and is characterized as a deletion of three bases pairs, which determines the loss of a phenylalanine in position 508 of protein CFTR. The basic defect is associated with the reduction of the conduction of ions Cl- through the apical membrane of epithelial cells. The CFTR forms a channel for the transport of this ion. The aim of this work was to determine to verify in a cystic sample of nuclei familiates of patients with cystic fibrosis, the existing haplotypes, the possibility of use polymorphisms for prenatal and preimplantacion diagnosis and to correlate the mutation ?F508 with the joined haplotypes. The analysis of polymorphism GATT was performed by polymerase chain reaction (PCR) and the analysis of polymorphisms MP6-D9, TUB09 and TUB18 polymorphism was performed by PCR and enzymatic digestion. In our casuistic, nine differents haplotypes had been found in 39 chromosomes. Twenty-five with ?F508 mutation and 14 with other mutations (not-?F508), haplotype 6, +; G; C (GATT, MP6-D9, TUB09 and TUB18) was most frequent (48%) in chromosomes with mutated CFTR gene and is strong linked to the ?F508 mutation (64%). In 43% families analyzed at least an informative polymorphism were found for the prenatal diagnosis or preimplantacion. In conclusion, these polymorphisms constitute an excellent group of genetic useful markers to observe the transmission of the mutateds alleles in families of patients with cystic fibrosis, where it is not possible to establish the complete genotype. In accordance with the gotten results, these polymorphisms could be used for the prenatal and preimplantacion diagnosis, fulfilling with the objective of the work / Mestrado / Mestre em Farmacologia

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No. of bitstreams: 2 Dissertação - Vanderlei Alves Cardoso - 2016.pdf: 2005513 bytes, checksum: f02b1c68047a6e30b76b4cd7e996de8d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-07-15 / There are several factors that may affect the milk yield in cattle, among which the environmental characteristics and the genetic profile are the most important. The use of tools for genetic evaluation of animals, in particular the identification of SNPs, which are able to interfere with the production capacity, is being widely studied and used in animal production. In this sense, the objective of this study was to investigate the distribution of polymorphic variants of the promoter region and éxon8 in gene of growth hormone receptor (GHR) in Holstein cows in milk. They used data from lactations and milk composition in the first and second lactation of 106 cows in the municipality of Cristalina, Goiás. The blood samples were collected and the genomic material was purified (DNA). The genotypes were analyzed by PCR-FRLP technique using the AluI enzyme in the promoter region and Sspl to the exon8 of the GHR gene, respectively. For the data analysis of lactation and milk composition was performed analyses of varyance and Tukey test. Allelic frequencies of 47.64% were observed for AluI (-) and 52.36% for AluI (+) for the polymorphism of the promoter region, 49.53% for Ssp (-) and 50.47% for Ssp (+ ) for the polymorphism of exon8 of the gene. As to the genotypic frequencies, the promoter region had 12.26%, 70.76% and 16.98% for AluI genotypes (- / -), AluI (+/-) and AluI (+ / +) respectively. While the region of exon8 presented frequencies of 7.55%, 83.96% and 8.49% for genotypes Ssp (- / -), SspI (+/-), and SspI (+ / +) respectively. No statistically significant differences were found (P> 0.05) for the production and composition of milk on the effects of polymorphisms of the promoter region (AluI) and exon 8 (SspI) of the GHR gene. The composition EST and ESD were higher for SspI genotypes (- / -), but with significance level P = 0.06 and P = 0.05 respectively for EST and ESD. The interaction between the two polymorphisms and their effects on milk production and composition, no statistically significant differences were observed (P> 0.05). / Existem vários fatores que podem interferir na produção de leite em bovinos, entre os quais, as características ambientais e o perfil genético são os mais importantes. O uso de ferramentas para avaliação genética dos animais em especial a identificação de SNPs, os quais são capazes de interferir na capacidade produtiva, está sendo amplamente estudado e utilizado na produção animal. Neste sentido, o objetivo do presente trabalho foi verificar a distribuição das variantes polimórficas da região promotora e do éxon 8 no gene do Receptor do Hormônio do Crescimento (GHR) em vacas da raça Holandesa em lactação. Foram utilizados dados das lactações e composição do leite na primeira e segunda lactação de 106 vacas do município de Cristalina, Goiás. As amostras de sangue periférico foram coletadas e o material genômico foi purificado (DNA). Os genótipos foram analisados pela técnica de PCR-FRLP com o uso da enzima AluI na região promotora e SspI para o éxon 8 do gene do GHR, respectivamente. Para a análise dos dados das lactações e composição do leite foi realizada análise de variância e teste de tukey. Foram observadas frequências alélicas de 47,64% para AluI(-) e 52,36% para AluI(+), para o polimorfismo da região promotora, 49,53% para SspI(-) e 50,47% para SspI(+) para o polimorfismo do éxon 8 do gene. Quanto as frequências genotípicas, a região promotora apresentou 12,26%, 70,76% e 16,98% para os genótipos AluI(-/-), AluI(+/-) e AluI(+/+) respectivamente. Enquanto a região do éxon 8 apresentou frequências de 7,55%, 83,96% e 8,49% para os genótipos SspI(-/-),SspI(+/-) e SspI(+/+) respectivamente. Não foram encontradas diferenças estatisticamente significativas (P>0,05) para produção e composição do leite sobre o efeitos dos polimorfismos da região promotora (AluI) e éxon 8 (SspI) do gene do GHR. A composição em EST e ESD se mostraram maiores para os genótipos SspI(-/-) porem com níveis de significância P=0,06 e P=0,05 respectivamente para EST e ESD. Quanto a interação entre os dois polimorfismos e seus efeitos sobre a produção e composição do leite, não foram observadas diferenças estatisticamente significativa (P>0,05).

Phasing genotypes from sequence data is an important step betweendata gathering and downstream analysis in population genetics,disease studies, and multiple other fields. This determination ofthe sequences of markers corresponding to the individualchromosomes can be done on data where the markers are in lowdensity across the chromosome, such as from single nucleotidepolymorphism (SNP) microarrays, or on data with a higher localdensity of markers like in next generation sequencing (NGS). Thesorted markers may then be used for many different analyses anddata processing such as linkage analysis, or inference of missinggenotypes in the process of imputation cnF2freq is a haplotype phasing program that uses an uncommonapproach allowing it to divide big groups of related individualsinto smaller ones. It sets an initial haplotype phase and theniteratively changes it using estimations from Hidden MarkovModels. If a marker is judged to have been placed in the wronghaplotype, a switch needs to be made so that it belongs to thecorrect phase. The objective of this project was to go fromallowing only one individual within a group to be switched in aniteration to allowing multiple switches that are dependent on eachother. The result of this project is a theoretical solution for allowingmultiple dependent switches in cnF2freq, and an implementedsolution using the max-SAT solver toulbar2.

L’avènement du génotypage à haut débit permet aujourd’hui de mieux exploiter le phénomène d’association, appelé déséquilibre de liaison (LD), qui existe entre les allèles de différents loci sur le génome. Dans ce contexte, l’utilité de certains modèles utilisés en cartographie de locus à effets quantitatifs (QTL) est remise en question. Les objectifs de ce travail étaient de discriminer entre des modèles utilisés en routine en cartographie et d’apporter des éclaircissements sur la meilleure façon d’exploiter le LD, par l’utilisation d’haplotypes, afin d’optimiser les modèles basés sur ce concept. On montre que les modèles uni-marqueur de liaison, développés en génétique il y a vingtaine d’années, comportent peu d’intérêts aujourd’hui avec le génotypage à haut débit. Dans ce contexte, on montre que les modèles uni-marqueur d’association comportent plus d’avantages que les modèles uni-marqueur de liaison, surtout pour des QTL ayant un effet petit ou modéré sur le phénotype, à condition de bien maîtriser la structure génétique entre individus. Les puissances et les robustesses statistiques de ces modèles ont été étudiées, à la fois sur le plan théorique et par simulations, afin de valider les résultats obtenus pour la comparaison de l’association avec la liaison. Toutefois, les modèles uni-marqueur ne sont pas aussi efficaces que les modèles utilisant des haplotypes dans la prise en compte du LD pour une cartographie fine de QTL. Des propriétés mathématiques reliées à la cartographie de QTL par l’exploitation du LD multiallélique capté par les modèles haplotypiques ont été explicitées et étudiées à l’aide d’une distance matricielle définie entre deux positions sur le génome. Cette distance a été exprimée algébriquement comme une fonction des coefficients du LD multiallélique. Les propriétés mathématiques liées à cette fonction montrent qu’il est difficile de bien exploiter le LD multiallélique, pour un génotypage à haut débit, si l’on ne tient pas compte uniquement de la similarité totale entre des haplotypes. Des études sur données réelles et simulées ont illustré ces propriétés et montrent une corrélation supérieure à 0.9 entre une statistique basée sur la distance matricielle et des résultats de cartographie. Cette forte corrélation a donné lieu à la proposition d’une méthode, basée sur la distance matricielle, qui aide à discriminer entre les modèles utilisés en cartographie.

Orientadores: Felipe Rodrigues da Silva, Francisco Pereira Lobo / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T12:42:35Z (GMT). No. of bitstreams: 1 Castro_GiovanniMarquesde_M.pdf: 8706589 bytes, checksum: bd5b5d6428a549bafa82854367f811b9 (MD5) Previous issue date: 2015 / Resumo: A planta Fevillea cordifolia L. possui um grande potencial para produção de biodiesel. Buscando entender o metabolismo foi realizado um experimento exploratório de RNA-seq com sementes inteiras. No entanto, as análises da qualidade na biblioteca indicaram grande quantidade de sequências virais. Após a reconstrução do transcriptoma usando o programa TRINITY, também foi reconstruído o genoma completo do vírus. O vírus reconstruído possui identidade de 96% com o Papaya ringspot virus (PRSV) em um alinhamento global de nucleotídeos dos genomas completos. Avaliando a abundância dos contigs, o PRSV encontrado representa quase 60% das 24,6 milhões de leituras da biblioteca. Para identificar qual a origem do vírus encontrado, este foi comparado com 29 PRSVs existentes no Genbank através de análise filogenética usando do Algerian watermelon mosaic virus (AWMV) para enraizar a árvore. O vírus encontrado agrupa-se com os dois PRSVs do Brasil, dentro do grupo das Américas estando mais próximo do PRSV-W-C (DQ374152). A existência de recombinações entre os PRSVs foi analisada, porém não foi detectada recombinação recente. Devido à profundidade de sequenciamento maior que 10.000x, foi possível analisar as variações existentes do genoma viral reconstruído. Uma análise das variações dos códons virais foi realizada, mostrando uma tendência para ocorrência de indels para a região do genoma no fim do cístron NIb e início do cístron CP. Essas variações ocorrem devido à existência de haplótipos virais na amostra sequenciada. Para se estimar a diversidade de haplótipos virais da amostra, foi realizada uma reconstrução local da região de 500 nt com mais alta entropia. Foram reconstruídos 58 haplótipos, dos quais dois eram predominantes com frequências de 64,84% e 24,34%. Os haplótipos reconstruídos podem ser usados para o desenvolvimento de resistência mediada por RNAi, evitando que uma variante conhecida e preexistente na população possa quebrar a resistência / Abstract: The plant Fevillea cordifolia L. has a great potential for producing biodiesel. In order to understand its metabolic pathways an exploratory RNA-seq experiment was conducted with its whole-seeds. However the quality analysis of the library revealed a substantial amount of virus sequences. After the reconstruction of the transcriptome using the software TRINITY, the complete viral genome was obtained as well. The reconstructed viral genome had an identity of 96% with Papaya ringspot virus (PRSV) in a global nucleotide alignment using whole genomes. When estimating the abundance of the reconstructed sequences, this PRSV had almost 60% of the 24,6 million reads mapping to it. Aiming to elucidate the origin of this virus, its sequence was compared to 29 PRSVs from Genbank using phylogenetic analysis and the Algerian Watermelon Mosaic Virus (AWMV) as an outgroup. This PRSV clustered with the Brazilian isolates, being closer to PRSV-W-C (DQ374152). A recombination analysis was performed within the PRSVs but no recent recombination was detected. Due to the depth of the coverage sequencing being higher than 10.000x, it was possible to analyze the variations existing in the reconstructed genome. An analysis of the codons variations was performed, revealing a tendency for the occurrence of indels in a region at the end of NIb cistron and at the start of the CP cistron. These variations occur due to the existence of viral haplotypes sequenced in this sample. A local reconstruction of the 500nt region with the highest entropy was performed to estimate the diversity of viral haplotypes in this sample. 58 haplotypes were reconstructed, of which 2 were dominant with frequencies of 64,84% and 24,34%. The reconstructed haplotypes may be used for the development of RNAi-mediated resistance, avoiding the breaking of the resistance by variants that are known to exist in the population / Mestrado / Bioinformatica / Mestre em Genética e Biologia Molecular

The human forkhead box O1A (FOXO1A) gene on chromosome 13q14.1 is a key transcription factor in insulin signaling in liver and adipose tissue and plays a central role in the regulation of key pancreatic β-cell genes including IPF1. We hypothesized that sequence variants of FOXO1A contribute to the observed defects in hepatic and peripheral insulin action and altered β-cell compensation that characterize type 2 diabetes (T2DM). To test this hypothesis, we screened the three exons, 3′ untranslated region, and 5′ flanking region for sequence variants in Caucasian and African-American individuals with early onset (<45 years) T2DM. We identified only six variants; none altered the coding sequence, and except for one variant in the 3′ untranslated region, they were rare or absent in Caucasians. To increase coverage of the gene, we selected seven additional variants in the large first intron and 5′ flanking region, thus providing 13 variants that spanned 116.4 kb. Based on frequency and linkage disequilibrium patterns in a subset of individuals, we selected eight SNPs to type in a Caucasian population comprising 192 unrelated nondiabetic control individuals and 192 individuals with T2DM, and 10 SNPs to type in 182 controls and 352 diabetic individuals of African-American ancestry. No variant was associated with T2DM (African-Americans, p > 0.08; Caucasians, p > 0.09). Of the 8 Caucasian SNPs, six comprised a single haplotype block spanning over 100 kb and including most of the large first intron. In contrast, no block was observed among SNPs typed in African-Americans. No haplotype was associated with T2DM. FOXO1A variation is rare and is unlikely to contribute to T2DM in either Caucasian or African-American populations.

En sélection génomique, des marqueurs de l’ADN sont utilisés pour l’évaluation des grandes races laitières. La plupart des méthodes d’évaluation génomique actuelles utilisent des SNP, bien que l’utilisation d’haplotypes de SNP apporte un plus grand polymorphisme. Il n’y avait pas d’évaluation génomique en place en 2014 pour les races régionales (Abondance, Tarentaise, Vosgienne), plaçant ces races en position de faiblesse.Notre objectif principal a été de mesurer l’intérêt de l’utilisation d’haplotypes en évaluation génomique, y compris à partir d’une population d’apprentissage multiraciale. Nous avons montré que les haplotypes conduisent à de meilleurs résultats que les SNP et que la fréquence des allèles et l’étendu du déséquilibre de liaison sont importants pour une construction optimale des haplotypes. Nous avons développé deux critères incorporant ces informations qui améliorent la précision des évaluations tout en réduisant le nombre de marqueurs utilisés.Depuis 2015, un de ces critères a été inclus dans les évaluations génomiques officielles en France. Notre approche a donné dans les races régionales une précision similaire à celle obtenue après testage sur descendance. Une évaluation génomique de routine est en place pour 3 races régionales en France depuis Juin 2016. L’utilisation d’une puce Haute Densité n’a pas amélioré sa précision, alors qu’une population d’apprentissage multiraciale a été bénéfique uniquement pour certaines races. Le génotypage des nouvelle femelles a augmenté la précision de la sélection mais l’inclusion de mutations candidates détectées dans les grandes races laitières n’a conduit qu’à une légère amélioration chez les races régionales. / In genomic selection, DNA marker information is exploited for evaluation purposes in large dairy cattle breeds. Most of the current genomic evaluation methods rely today on SNP information, although haplotypes are expected to perform better due to their higher polymorphism. In 2014, genomic evaluation had not yet been implemented in regional breeds (Abondance, Tarentaise, Vosgienne), resulting in economic weaknesses for these breeds.Our aim was to assess the use of haplotypes in genomic evaluation with focus on their performance in combination with multi-breed reference populations. We found that haplotypes outperformed individual SNP markers for genomic evaluation. We also showed that information on haplotype allele frequency and on linkage pattern are relevant to select haplotypes for evaluation purposes. Our haplotype selection criteria also allowed a significant reduction of the number of markers used for genomic prediction.One of these criteria was incorporated into the French routine genomic evaluation in 2015. The performance of such an evaluation was then assessed in four regional breeds, leading to similar or higher accuracies than current progeny testing. Consequently, routine genomic evaluation was implemented in these breeds in 2016. The use of high density genotypes did not improve the performance of genomic evaluation in these breeds, while multi-breed training populations were beneficial only in some of them. Additional genotyped females led to notable increases in selection accuracies. Inclusion of candidate mutations identified in large breeds led to only minor improvements in regional breeds.

Mitochondria are essential cellular organelles and the location of the electron transport chain, the site of the majority of energy production in the cell. Mitochondria contain their own circular genome approximately 16,000 base pairs in length. The mitochondrial genome (mtDNA) encodes 11 protein-coding genes essential for the electron transport chain, 22 tRNA genes, and two rRNA genes. Mitochondrial malfunction occurs in many diseases, and changes in the mitochondrial genome lead to numerous disorders. Multiple mitochondrial haplotypes and sequence features are associated with Alzheimer's disease. In this dissertation we utilized TreeScanning, an evolutionary-based haplotype approach to identify haplotypes and sequence variation associated with specific phenotypes: Alzheimer's disease case-control status, mitochondrial copy number, and 16 neuroimaging phenotypes related to Alzheimer's disease neurodegeneration. In the first two studies we utilized 1007 complete mitochondrial genomes from participants in the Cache County Study on Memory Health and Aging. First, individuals with mitochondrial haplotypes H6A1A and H6A1B showed a reduced risk of AD. Our study is the largest to date and the only study with complete mtDNA genome sequence data. Next, each cell contains multiple mitochondria, and each mitochondrion contains multiple copies of its own circular genome. The ratio of mitochondrial genomes to nuclear genomes is referred to as mitochondrial copy number. Decreases in mitochondrial copy number are known to occur in many tissues as people age, and in certain diseases. Three variants belonging to mitochondrial haplogroups U5A1 and T2 were significantly associated with higher mitochondrial copy number in our dataset. Each of these three variants was associated with higher mitochondrial copy number and we suggest several hypotheses for how these variants influence mitochondrial copy number by interacting with known regulators of mitochondrial copy number. Our results are the first to report sequence variation in the mitochondrial genome that lead to changes in mitochondrial copy number. The identification of these variants that increase mtDNA copy number has important implications in understanding the pathological processes that underlie these phenotypes. Lastly, we used an endophenotype-based approach to further characterize mitochondrial genetic variation and its relationship to risk markers for Alzheimer's disease. We analyzed longitudinal data from non-demented, mild cognitive impairment, and late onset Alzheimer's disease participants in the Alzheimer's Disease Neuroimaging Initiative with genetic, brain imaging, and behavioral data. Four clades were associated with three different endophenotypes: whole brain volume, percent change in temporal pole thickness, and left hippocampal atrophy over two years. This was the first study of its kind to identify mitochondrial variation associated with brain imaging endophenotypes of Alzheimer's disease. Together, these projects provide evidence of mtDNA involvement in the risk and physiological changes of Alzheimer's disease.

Yes / Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects’ DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European–American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts. / The Technology Commercialization Innovation Program (Contracts #121668, #132043) of the Utah Governors Office of Commercial Development, the Scholarship Activities