Since apoE allele status is the predominant Alzheimers disease (AD) genetic risk factor, functional single nucleotide polymorphisms (SNPs) in brain apoE receptors represent excellent candidates for association with AD. Therefore, three low density lipoprotein receptor (LDLR) SNPs were evaluated by TaqMan allelic discrimination assays for association with AD and I found that certain haplotypes alter the odds of AD. A SNP within LDLR exon 12, rs688, was identified in silico as neutralizing a putative exon splicing enhancer (ESE). Since LDLR is a major apoE receptor in the brain, I hypothesized that rs688 modulates LDLR splicing in neural tissues and associates with AD. To evaluate this hypothesis, I analyzed splicing patterns in human hippocampus samples and established that this SNP was associated with significantly decreased LDLR exon 12 splicing efficiency when the minor allele T is present in vivo. Lastly, I evaluated whether rs688 associates with AD by genotyping DNA from the Religious Orders Study (ROS) series. The rs688T/T genotype was associated with increased AD odds in males, but not in females, in a dataset consisting of 1,457 men and 2,055 women drawn from three case-control series. The rs688T/T genotype was associated with increased AD odds in males (recessive model, odds ratio (OR) of 1.49, 95% confidence interval (CI) of 1.13- 1.97, uncorrected p=0.005), but not in females. In summary, these studies identify a functional apoE receptor SNP that is associated with AD in a sex-dependent fashion.

<p>Trichome formation in Arabidopsis lyrata is a naturally occurring trait with phenotypic polymorphisms within wild populations. In Swedish accessions of A. lyrata, three genetic polymorphisms situated in the coding region of GL1, an important transcription factor in trichome production, have been identified, and these are candidates for being the cause of a glabrous phenotype. In this study a complementation test has been performed to clarify which mutation/mutations that are detrimental for trichome formation. A set of constructs has been transformed into A. thaliana, a close relative to A. lyrata, and subsequent generations of plants were examined for phenotype, genotype and gene expression. A SNP (Single Nucleotide Polymorphism) in the R3 MYB domain of GL1, resulting in a change of an alanine to aspartic acid, was identified as the critical polymorphism. The other two mutations, two indels, were harmless to protein function. The inserted constructs were under control of the native GL1 promoter. Plants that, because of the SNP, lacked trichome production, became totally glabrous.</p>

The aim of this thesis is to explore the role of common genetic variation, identified through genome-wide association (GWA) studies, in human traits and diseases, using height as a model polygenic trait, type 2 diabetes as a model common polygenic disease, and maturity onset diabetes of the young (MODY) as a model monogenic disease. The wave of the initial GWA studies, such as the Wellcome Trust Case-Control Consortium (WTCCC) study of seven common diseases, substantially increased the number of common variants associated with a range of different multifactorial traits and diseases. The initial excitement, however, seems to have been followed by some disappointment that the identified variants explain a relatively small proportion of the genetic variance of the studied trait, and that only few large effect or causal variants have been identified. Inevitably, this has led to criticism of the GWA studies, mainly that the findings are of limited clinical, or indeed scientific, benefit. Using height as a model, Chapter 2 explores the utility of GWA studies in terms of identifying regions that contain relevant genes, and in answering some general questions about the genetic architecture of highly polygenic traits. Chapter 3 takes this further into a large collaborative study and the largest sample size in a GWA study to date, mainly focusing on demonstrating the biological relevance of the identified variants, even when a large number of associated regions throughout the genome is implicated by these associations. Furthermore, it shows examples of different features of the genetic architecture, such as allelic heterogeneity and pleiotropy. Chapter 4 looks at the predictive value and, therefore, clinical utility, of variants found to associate with type 2 diabetes, a common multifactorial disease that is increasing in prevalence despite known environmental risk factors. This is a disease where knowledge of the genetic risk has potentially substantial clinical relevance. Finally, Chapter 5 approaches the monogenic-polygenic disease bridge in the direction opposite to that approached in the past: most studies have investigated genes mutated in monogenic diseases as candidates for harboring common variants predisposing to related polygenic diseases. This chapter looks at the common type 2 diabetes variants as modifiers of disease onset in patients with a monogenic but clinically heterogeneous disease, maturity onset diabetes of the young (MODY).

Y chromosome is due to its special characteristics the ideal tool of archaeogenetic studies. Its diversity is influenced by several factors and I analysed two of them (geographical location and subsistence). I generated SNPs and STRs data from several loci of samples from Slovakia (156 samples, 5 regions) and sub-Saharan Africa, where I analysed samples of sedentary farmers (481 samples, 18 regions) and nomadic pastorals (405 samples, 16 regions). Slovakia is situated at the meeting point of two migration ways. First of them was spread from the east to the west and is associated with enlargement of haplogroup R1a in Europe. The second came from the Iberian Peninsula eastward and is associated with enlargement of haplogroup R1b. Results of MDS graphs replicate the geographical map of Europe. Slovakia is situated in the middle of Russian, Balkanian and Iberian samples. Correlation between genetics and geographic distances is indicated by hierarchical AMOVA analysis and Mantel tests. Populations in sub-Saharan Africa differ from each other by the subsistence pattern. Different life style influence the diversity of the Y chromosome. Nomadic pastoralists and sedentary farmers share different haplogroups, for example, while haplogroup R1b was detected only in nomadic pastoral groups, sedentary farmers...

Submitted by PPG Biologia Celular e Molecular (bcm@pucrs.br) on 2018-02-26T11:20:29Z No. of bitstreams: 1 FERNANDA_ROSA_SAWITSKI_TES.pdf: 5519043 bytes, checksum: d8234f6f341fd9d5f2c4a39db88b714c (MD5) / Approved for entry into archive by Caroline Xavier (caroline.xavier@pucrs.br) on 2018-02-26T20:03:16Z (GMT) No. of bitstreams: 1 FERNANDA_ROSA_SAWITSKI_TES.pdf: 5519043 bytes, checksum: d8234f6f341fd9d5f2c4a39db88b714c (MD5) / Made available in DSpace on 2018-02-26T20:08:29Z (GMT). No. of bitstreams: 1 FERNANDA_ROSA_SAWITSKI_TES.pdf: 5519043 bytes, checksum: d8234f6f341fd9d5f2c4a39db88b714c (MD5) Previous issue date: 2017-11-07 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / Genes related to externally visible characteristics (EVC) present a great importance for the prediction of skin and eye colors in humans. In this study, we tested the ability of a set of SNPs in pigment-related genes to predict skin and eye colors in an admixed south Brazilian population. First, we used the Cinderella - Tiana - Snow White model to analyze the allelic distribution of eight biallelic SNPs in pigment-related. Cinderella and Tiana patterns have respectively low and high melanin content in skin and eyes; Cinderella has white skin and blue eyes (low melanin content; LMC) and Tiana has dark skin and eyes (high melanin content; HMC). Comparative investigation between frequencies of genetic variants in Cinderella-Like versus Tiana-Like subjects may indicate which polymorphic variant is associated with melanin synthesis in skin and eyes. Coordinately, studies with Snow White-Like subjects may be informative to reveal any tissue-specific expression, since these individuals have both white skin (LMC) and dark eyes (HMC). Based on allele frequencies of different human popullations, allele ?L? was used for the alleles associated with low melanin content populations (Cinderela-like subjects), and allele ?H? was used for the alleles associated with high melanin content populations (Tiana-like subjects). Allelic distribution of eight SNPs showed that 100% of Cinderella- like subjects (N= 73) had less than eight H alleles, and 82% of Tiana-Like subjects (N= 61) had eight or more H alleles. The AUC (Area Under the Receiver Operating Characteristic Curve) value was 0.99, and the calculation of PGL (Pathway Genetic Load) and GP (Genetic Probability) showed that the SNP set presented 93% and 91% concordance between DNA genotype and phenotypes, respectively. Factorial discriminant analyses (FDA) performed in the Snow White group (light skin and dark eyes; N= 116) showed an association between SNPs rs16891982 (SLC45A2), rs8045560 (MC1R), rs1426654 (SLC24A5), rs2733832 (TYRP1), and rs1042602 (TYR) and the Cinderella cluster for skin phenotype, and an association between SNPS rs4778138 (OCA2), rs12913832 (HERC2), and rs916977 (HERC2) and the Tiana cluster for eye phenotype. Lastly, we studied 436 South Brazilian subjects with different skin and eye colors to construct a multinomial logistic regression model able to predict phenotype. The model was tested in 40 random subjects to measure the efficiency of the prediction. The data presented 93% concordance between the predicted and the observed phenotype, showing the successful phenotype prediction of the model in South Brazilian individuals. This is important since Brazil has an ethnically mixed population in which genomic structure may favor epistatic and pleiotropic effects not observed in populations that are more homogeneous. The analyses presented here are an important contribution to forensic DNA phenotyping scenario. / Os genes relacionados a caracter?sticas externamente vis?veis (EVC) apresentam grande import?ncia para a previs?o de cores de pele e olho em humanos. Neste estudo, testamos a capacidade de um conjunto de SNPs em genes relacionados ? s?ntese de pigmento melanina para prever cores de pele e olho em uma popula??o sul-brasileira. Inicialmente, utilizamos o modelo Cinderela - Tiana - Neve Branca para analisar a distribui??o al?lica de oito SNPs bial?licos associados ? produ??o da melanina. Os padr?es Cinderela e Tiana possuem respectivamente baixo e alto conte?do de melanina na pele e nos olhos; Cinderela tem pele branca e olhos azuis (baixo conte?do de melanina, LMC) e Tiana tem pele e olhos escuros (alto conte?do de melanina, HMC). A investiga??o comparativa entre frequ?ncias de variantes gen?ticas em indiv?duos com Cinderela-Like versus Tiana-Like pode indicar qual variante polim?rfica est? associada ? s?ntese de melanina na pele e nos olhos. De forma coordenada, os estudos com indiv?duos Branca de Neve-Like podem ser informativos para revelar a express?o tecido-espec?fica, uma vez que esses indiv?duos t?m pele branca (LMC) e olhos escuros (HMC). Com base em frequ?ncias de alelos de diferentes popula??es humanas, o nome alelo "L" foi utilizado para os alelos associados a popula??es de baixo conte?do de melanina (indiv?duos Cinderela-Like) e o nome alelo "H" foi utilizado para os alelos associados a popula??es de alto conte?do de melanina (Indiv?duos Tiana-Like). A distribui??o al?lica de oito SNPs mostrou que 100% de indiv?duos com Cinderela-Like (N= 73) tinham menos de oito alelos H e 82% de indiv?duos Tiana-Like (N= 61) tinham oito ou mais alelos H. O valor AUC (Area Under the Receiver Operating Characteristic Curve) foi de 0,99 e o c?lculo de PGL (Pathway Genetic Load) e GP (Probabilidade Gen?tica) mostrou que o conjunto de SNP apresentou concord?ncia de 93% e 91% entre gen?tipo e fen?tipo, respectivamente. As an?lises discriminantes fatoriais (FDA) realizadas no grupo Branca de Neve-Like (pele clara e olhos escuros; N= 116) mostraram associa??o positiva entre SNPs rs16891982 (SLC45A2), rs8045560 (MC1R), rs1426654 (SLC24A5), rs2733832 (TYRP1) e rs1042602 (TYR) e o cluster de Cinderela para o fen?tipo da pele, e associa??o positiva entre SNPS rs4778138 (OCA2), rs12913832 (HERC2) e rs916977 (HERC2) e o cluster Tiana para o fen?tipo dos olhos. Por fim, estudamos 436 sujeitos sul-brasileiros com diferentes cores de pele e de olhos para construir um modelo de regress?o log?stica multinomial capaz de prever o fen?tipo. O modelo foi testado em 40 indiv?duos aleat?rios para medir a efici?ncia da predi??o. Os dados apresentaram concord?ncia de 93% entre o fen?tipo previsto e observado, mostrando a previs?o fenot?pica bem-sucedida do modelo em indiv?duos sul-brasileiros. Isso ? importante, uma vez que o Brasil tem uma popula??o etnicamente mista, na qual a estrutura gen?mica pode favorecer os efeitos epistaticos e pleiotr?picos n?o observados em popula??es mais homog?neas. As an?lises aqui apresentadas s?o uma importante contribui??o para a ?rea da fenotipagem por DNA.

Single nucleotide polymorphisms (SNPs) are single base variations among groups of individuals. In order to study their properties in fine gene mapping, I considered their occurrence as transitions and transversions. The aim of the study was to classify each polymorphism depending upon whether it was a transition or transversion and to calculate the proportions of transitions and transversions in the SNP data from the public databases. This ratio was found to be 2.35 for data from the Whitehead Institute for Genome Research database, 2.003 from the Genome Database, and 2.086 from the SNP Consortium database. These results indicate that the ratio of the numbers of transitions to transversions was very different than the expected ratio of 0.5. To study the effect of different transition to transversion ratios in fine gene mapping, a simulation study was performed to generate nucleotide sequence data. The study investigated the effect of different transition to transversion ratios on linkage disequilibrium parameter (LD), which is frequently used in association analysis to identify functional mutations. My results showed no considerable effect of different transition to transversion ratios on LD. I also studied the distribution of allele frequencies of biallelic SNPs from the Genome Database. My results showed that the most common SNPs are normally distributed with mean allele frequency of 0.7520 and standard deviation of 0.1272. These results can be useful in future studies for simulating SNP behavior. I also studied the simulated data provided by the Genetic Analysis Workshop 12 to identify functional SNPs in candidate genes by using the genotype-specific linkage disequilibrium method.

Glycosylation is among the most common post-translational protein modifications. Glycans are complex carbohydrates attached to the surface of many proteins, but are rarely extensively studied in a high-throughput manner. However, there is an increasing evidence of their involvement in various physiological processes and diseases. Glycosylation of Immunglobulin G was shown to be important in adaptive immunity, where it can act as a "safety switch" for different types of the immune response. Although the main enzymes of the glycosylation pathway are known, little is understood about how this template-independent process is regulated to result in a faithful synthesis of a specific glycoform. This question was previously addressed using genome-wide association studies (GWAS) and 9 loci were identified as being significantly associated with IgG N-glycosylation. Only 4 of these loci were the known glycosylation enzymes. An additional five loci were discovered by applying a newly developed multivariate GWAS method on the same dataset. Here, by performing a GWAS on 77 IgG N-glycan traits measured by ultra-performance liquid chromatography in more than 8000 samples from four European cohorts the number of genome-wide significant (p? ≤ 2.4 x 10−9) loci increased to 27, 15 of which are novel, with 6 additional loci being suggestively associated (p? ≤ 2.4 x 10−8). To assess which of the genes from the associated loci are more likely to be regulating IgG glycosylation, different gene prioritising strategies were employed. For 7 loci evidence of a non-synonymous amino acid change was found, two of which were predicted to be deleterious. Evidence of regulation through changes in gene expression levels in B-cells, the cell lineage responsible for production of IgG, was found for 4 genes, with an additional 11 genes exhibiting the same evidence with expression in peripheral blood or other immune cells. For the remaining loci the most likely candidate gene was proposed based on co-expression with genes from the enriched gene-sets or based on a physical proximity to the variant with the strongest association. To narrow down the most important loci for a functional follow-up, the omics nature of this data was used to compare glycome-wide SNP effects and suggest how newly discovered loci form a functional network that regulates the established members of the glycosylation pathway. The potential role of IgG glycosylation in various complex traits and diseases was explored by assessing the pleiotropy of the associated SNPs. The inflation of SNPs related to autoimmune, digestive and neurological diseases was observed in glycosylation SNPs. To assess whether IgG N-glycosylation is likely to share the same causal variant as the identified pleiotropic traits and diseases, regional association patterns were compared using summary data based Mendelian Randomisation analyses. This work demonstrates that an increased sample size empowered the identification of novel loci, enabling further insights into the molecular mechanisms underlying protein glycosylation and its relationship with complex human diseases. It also shows that such analyses of omic traits can assist in creating a functional network of the identified loci, prioritising the most important genes and allowing a more focused approach to future experimental functional follow-up.

Marine bivalves are a group of species composed of clams, mussels and oysters. Bivalves are keystone species in coastal ecosystems and represent an increasingly important segment of the global aquaculture industry. Domestication of shellfish species is in the early stages, with few organized breeding programmes and a heavy reliance on wild seed. Consequently, the development and use of genomic markers may significantly assist shellfish aquaculture breeding and production. However, molecular genetic markers typically exhibit unusual patterns of segregation in bivalve species, which result in deviations from Mendelian expectations, and could potentially limit their use in parental assignment, mapping of quantitative trait loci and genomic prediction. Previous studies have suggested that segregation distortions originate at the larval stage, as a result of the linkage of markers to deleterious mutations. This high genetic load has been associated with the high fecundity of bivalve species. However, no direct evidence of a high incidence of de novo mutations has been provided. The aim of this thesis is to gain further insight into segregation distortions in bivalve species by studying the phenomenon at a genome-wide scale, using modern high-throughput sequencing technology. The studies presented in this thesis derive from experiments involving genotyping of parents and offspring from pair-crosses of three different bivalve species (the Pacific oyster Crassostrea gigas, the Blue mussel Mytilus edulis, and the GreenshellTM mussel Perna canaliculus) using high throughput sequencing and SNP arrays. The parent and offspring genotype data were used to characterize patterns of segregation distortion at a genome-wide level, followed by exploratory analyses to test hypotheses related to possible causes of this distortion. Three main findings resulted from the genome-wide analysis of segregation patterns. First, by using Restriction site Associated DNA sequencing (RAD-Seq) we observe that technical artefacts are more widespread than previously considered, contributing to apparent distortions via unreliable genotype calls. By analysing read depth data from RAD-Seq, we suggest that apparent homozygous genotype calls may actually be hemizygous, suggesting a very high frequency of null alleles which contribute to distorted segregation patterns. Bioinformatic pipelines to improve RAD-Seq locus assembly and marker genotyping for bivalve species are presented. Second, by using a high-density SNP array and RAD-Seq in pair crosses of Pacific oyster and aligning to the reference genome assembly, we find that segregation distortions cover extensive regions of the genome, and that certain genomic regions are consistently distorted in different families. Finally, following previous suggestions that the reproductive strategies of bivalve species may favour a high mutation rate, we provide preliminary evidence of a high incidence of de novo mutations that appear spontaneously (i) during male and female gamete formation and (ii) post-zygotically, during larval development. This putative high de novo mutation rate is likely to also contribute to deviations from Mendelian inheritance patterns in these species. New genomic technologies have allowed us to gain substantial insight into the intriguing yet poorly understood phenomena related to inheritance in bivalve species. The results have both fundamental and practical implications for genetic analysis interpretation and selective breeding for aquaculture in this large and highly diverse group of species.

Die Aufmerksamkeitsdefizit-/Hyperaktivitätsstörung ist eine der häufigsten psychiatrischen Erkrankung des Kindesalters, die eine hohe Heritabilität aufweist und häufig bis ins Erwachsenenalter persistiert und lebenslang zu sozialen, gesundheitlichen und ökonomischen Problemen führt. Die ADHS tritt bei vielen Patienten in Kombina-tion mit anderen psychiatrischen und nicht-psychiatrischen Erkrankungen auf. In den letzten Jahren rückte zunehmend die häufig zur ADHS komorbid auftretende Adipositas in den Fokus der Forschung. Auf der Suche nach copy number variations in Zusammenhang mit ADHS, wurde eine Duplikation auf Chromosom 7p15 – dem Genlocus des NPY – entdeckt. NPY, ist ein endogenes orexigenes Peptid, welches physiologischerweise die Nahrungsaufnahme stimuliert und neben zahlreichen Effekten, wie Blutdruck- und Knochenregulation, auch in Zusammenhang mit neuropsychiatrischen Erkrankungen gebracht werden konnte. Diese Duplikation auf einem Genort, dessen Produkt für die Regulation von Energiehaushalt und Körpergewicht zuständig ist, bildete die Grundlage, eine Assoziationsuntersuchung zu NPY-Genvarianten und dem Körpergewicht bei Kindern durchzuführen. Untersucht wurden bei 269 an ADHS erkrankten Kindern und 142 gesunden Kontrollkindern die Assoziation zwischen NPY-Genvarianten (rs16147, rs16139, rs5574, rs16124) und ADHS, sowie die Assoziation zwischen NPY-Genvarianten und BMI-Perzentilen bei ADHS. Es ergab sich keine signifikante Assoziation bezüglich der aufgestellten Hypothesen. / The attention-deficit/hyperactivity disorder (ADHD) is one of the most frequent psychiatric disorders in children. It is highly heritable, often persists until adulthood and causes social, economic and health problems. While psychiatric comorbidities of ADHD have been extensively explored, in the last decade mounting evidence pointed to a possible association between ADHD and obesity. In search of copy number variations related to ADHD and this new comorbidity, a duplication on chromosome 7p15 – the gene of Neuropeptide Y (NPY) - has been identified. NPY is an orexigenic peptide, which stimulates food intake and it has also been implicated in other psychiatric diseases. Therefor we performed an association study in a case contol study design including 269 children with ADHD and 142 healthy controls. The objectiv of our investigation was to study the association between four single nucleotid polymorphisms of the NPY- gene (rs16147, rs16139, rs5574, rs16124) and ADHD, and the association between the NPY-polymorphisms and the bmi-percentiles in children with ADHD. Results: No association between the polymorphisms and ADHD in children was found. No association between bmi-percentiles and the polymorphisms was found in children with ADHD.

Mon sujet de thèse repose sur une observation initiale réalisée sur le panel de 60 lignées cellulaires tumorales humaines du National Cancer Institute (NCI) et concerne des polymorphismes de gènes impliqués dans la réponse aux agents anticancéreux, les gènes ERCC2 et ERCC5 ( à l'origine des protéines XPD et XPG) qui interviennent dans la réparation de l'ADN par le mécanisme du Nucléotide Excicion Repair (NER). Nous avons identifié une association entres ces polymorphismes et la cytotoxicité in vitro d'agents anticancéreux, en particulier celle des taxanes. A partir de ce travail initial, nos recherches se sont établies dans deux directions : (1) une approche clinique visant à chercher un lien significatif entre ces deux polymorphismes et la sensibilité aux taxanes chez des patients traités par chimiothérapie; (2) une approche biochimique visant à comprendre les mécanismes moléculaires expliquant l'association entre ces deux polymorphismes et la sensibilité cellulaire aux taxanes. Ce travail a permis de montrer que le niveau d'expression de ERCC2 modifié par le polymorphisme du codon 751, ainsi que la variation protéique entrainée par le polymorphisme du codon 1104 de ERCC5, étaient impliqués dans la régulation du cycle cellulaire par modification de l'activité CDK1. La réponse au paclitaxel se trouve ainsi modifiée du fait de ce mécanisme. A défaut d'être définitifs, nos résultats de l'étude clinique sont encourageants et montrent une tendance à une probabilité de réponse plus élevée chez les patientes de génotype ERCC2 homozygote variant et chez les patientes de génotype ERCC5 homozygote sauvage ou hétéroygote lorsque la chimiothérapie contient un taxane, le docetaxel.