The genetic architecture of placental abruption (PA) remains poorly understood. We examined variations in SNPs of circadian clock-related genes in placenta with PA risk. We also explored placental and maternal genomic contributions to PA risk. Placental genomic DNA samples were isolated from 280 PA cases and 244 controls. Genotyping was performed using the Illumina Cardio-MetaboChip. We examined 116 SNPs in 13 genes known to moderate circadian rhythms. Logistic regression models were fit to estimate odds ratios (ORs). The combined effect of multiple SNPs on PA risk was estimated using a weighted genetic risk score. We examined independent and joint associations of wGRS derived from placental and maternal genomes with PA. Seven SNPs in five genes (ARNTL2, CRY2, DEC1, PER3 and RORA), in the placental genome, were associated with PA risk. Each copy of the minor allele (G) of a SNP in the RORA gene (rs2899663) was associated with a 30% reduced odds of PA (95% CI 0.52-0.95). The odds of PA increased with increasing placental-wGRS (P_trend<0.001). The ORs were 1.00, 2.16, 3.24 and 4.48 across quartiles. Associations persisted after the maternal-wGRS was included in the model. There was evidence of an additive contribution of placental and maternal genetic contributions to PA risk. Participants with placental- and maternal-wGRS in the highest quartile, compared with those in the lowest quartile, had a 15.57-fold (95% CI 3.34- 72.60) increased odds of PA. Placental variants in circadian clock-related genes are associated with PA risk; and the association persists after control of genetic variants in the maternal genome

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Polimorfismos de um nucleotídeo (SNPs) podem alterar, além de códons de leitura da tradução de genes, posições genômicas importantes do processo de regulação gênica, como sítios de iniciação de transcrição, de splicing e, mais especificamente, sítios alvos de microRNAs (miRNAs). Em parti- cular, a identificação de SNPs alterando sítios alvos de miRNAs é um problema em aberto, embora venha ganhando um importante destaque nos últimos anos decorrente dos avanços descobertos sobre a capacidade dos miRNAs como elementos reguladores do genoma, associados inclusive a muitas doenças como o câncer e vários transtornos psiquiátricos. Os recursos computacionais atualmente disponíveis para esta finalidade (alguns bancos de dados e uma ferramenta) estão restritos à análise de SNPs na região 3UTR (UnTranslated Regions) de RNAs mensageiros, onde miRNAs geralmente se ligam para reprimir sua tradução. No entanto, essa é uma simplificação do problema, dado que já se conhece a regulação por miRNAs ativando ou reprimindo a transcrição gênica quando ligados à sua região promotora, aumentando a efetividade da regulação negativa da tradução quando ligados à região codificante do gene ou ainda miRNAs se ligando a RNAs não codificantes. Esses recursos se limitam também à identificação de SNPs na região seed dos sítios de miRNAs, e portanto só identificam criação ou ruptura de sítios. Porém, SNPs localizados fora dessa região não só podem colaborar na criação e ruptura de sítios como também interferir na estabilidade de ligação de miRNAs e, por- tanto, na efetividade da regulação. Além disso, considerando toda a extensão do sítio, não somente a seed , é possível ocorrer mais de um SNP e, sendo assim, a combinação desses SNPs pode ter uma influência ainda maior na ligação com o miRNA. Os recursos atuais também não informam quais alelos dos SNPs, muito menos quais combinações deles, estão causando qual efeito. Por fim, tais recursos estão restritos a Homo sapiens e Mus musculus. Assim, este trabalho apresenta a ferramenta computacional SIMTar (SNPs Interfering in MicroRNA Targets), desenvolvida para identificar SNPs que alteram sítios alvos de miRNAs e que preenche as lacunas mencionadas. Além disso, é descrita uma aplicação de SIMTar na análise de 114 SNPs associados à esquizofrenia, na qual todos foram preditos interferindo em sítios alvos de miRNAs. / Single nucleotide polymorphisms (SNPs) can be involved in alteration of not only open reading frame but also important genomic positions of gene regulation process such as transcription initiation sites, splicing sites and microRNA target sites. In particular, the identification of SNPs interfering on microRNA target sites is still an open problem, despite its increasing prominence in recent years due to the discoveries about the microRNA abilities as regulatory elements in the genome and association with severals diseases such as cancer and psychiatric disorders. The computational resources currently available for this purpose (four databases and one tool) are restricted to the analysis of SNPs in the 3UTR (UnTranslated Regions) of mRNAs, where the microRNAs typically bind in order to repress their translation. However, this is a simplification of the problem, since it is already known the gene transcription activation by microRNAs bound to its promoter region, increasing of the effectiveness of negative regulation of translation when microRNAs are bound to the coding region of the gene or binding of microRNA into non-coding RNAs. These resources are also limited to the identification of SNPs in the seed region of miRNAs, and therefore they can only identify sites creation or disruption. However, SNPs located outside this region can not only create and disrupt target sites but also interfere on the stability of miRNAs binding and therefore on the regulation effectiveness. Moreover, considering the target site length, more than one SNP can occur inside of a site and thus, the combination of these SNPs can have an even greater influence on the microRNA binding. Also, current resources do not display which alleles of SNPs or what combinations of them are causing which effect. Finally, these features are restricted to the Homo sapiens and Mus musculus species. This work presents the computational tool SIMTar (SNPs Interfering on MicroRNA Targets), developed to identify SNPs that alter miRNA target sites and fills the mentioned gaps. Finally, it is described an application of SIMTar on the analysis of 114 SNPs associated with schizophrenia, all of them being predicted interfering with miRNA target sites.

Cordova (Curated Online Reference Database Of Variation Annotations) is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with population study information and pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician-scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research.

<p>The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock.</p><p>In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones.</p><p>Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.</p>

<p>Autism is a pervasive developmental disorder (PDD) that&rsquo / s incidence is approximately 1 in 158. It is four times more prevalent in males than females and is believed to be caused by both genetic and environmental factors. Research indicates that several genes are involved in autism and it is believed that these genes act together to produce autism. Many genes implicated in this disorder are involved with brain structure formation and brain functioning. Studies have identified the reelin (RELN) gene as necessary for proper formation of brain, which indicates that RELN abnormalities could contribute to the aetiology of several neurogenetic diseases such as schizophrenia, bipolar and autism. The aims of the study were (i) to genotype two SNPs (exonic rs3622691 and intronic rs736707) in the RELN gene using Taqman&reg / SNP Genotyping assays to detect association with autism in three distinct South African (SA) ethnic groups (Black, Caucasian and Mixed), and (ii) to detect candidate genes that are over and under-expressed in the samples taken from a SA Caucasian autistic group and compare those with samples taken from a healthy Caucasian group using cDNA microarray. The Taqman&reg / study indicated significant association for the intronic SNP, rs736707, with a p-value of 0.0009 in the total SA group. More so, the Mixed group displayed the highest significance amongst the ethnic groups, with a p-value of 0.00014. The microarray study yielded 21 genes with 95% significance in the Caucasian sample group. Most genes were hypothetical proteins and formed part of the FAM90A family. The LOC83459 showed the highest level of expression in the autistic samples, while the BTNL8 gene was shown to be highly suppressed in the control samples.</p>

The aurochs Bos primigenius, extinct since 1627, was the wild progenitor of cattle. It is believed that all European cattle originate from one domestication event in the Near East 10 000 years ago. However, it is evident from the archaeological record that the aurochs survived into historic time and spent many years existing alongside domestic cattle. Thus, a question posed is whether aurochsen were locally domesticated or incorporated into early domestic cattle stock. In this thesis, genetic techniques are applied to ancient and modern DNA from bovids in order to study questions relating to the origin of early European cattle. DNA from ancient specimens is fragmented and in greatly reduced quantity. Therefore mitochondrial DNA, present in many copies in the living cell, has long been dominating the ancient DNA research field. Analyses of ancient DNA presented in this work are based on both mitochondrial DNA and nuclear DNA, through the study of Single Nuclear Polymorohism (SNPs). A method for typing ancient SNPs was developed and applied to ancient cattle bones. Mitochondrial DNA of cattle is structured into five geographically distributed lineages, the dominant lineage in Europe is also found in the Near East where additional lineages are found. This pattern has been attributed to the proposed domestication event in the Near East from where cattle carrying the single lineage were brought to Europe. However, the results presented here show that cattle domestication was more complicated than previously suggested. SNP data from extant cattle and bones from cattle and aurochs point towards a hybridisation event. European cattle appear indeed to have been domesticated in the Near East and brought in to the European continent from there. However, once in Europe, hybridisation with local aurochsen took place. It appears therefore that today’s cattle descend both from both Anatolian and European aurochsen.

Fibromyalgia (FM) is a highly disabling syndrome defined by a low pain threshold and a permanent state of pain. Widespread pain is accompanied by a constellation of symptoms such as fatigue, sleep disturbances and cognitive impairment, among others. The mechanisms explaining this chronic pain remain unclear. Nowadays, the most established/ plausible hypothesis underlying FM ethiopathogenesis is the existence of a dysfunction in pain processing, as supported by alterations in neuroimaging and neurotransmitters levels. The etiology of FM involves the interaction of environmental and genetic susceptibility factors. The genetic contribution to FM has been proven by the presence of a higher concordance of monozygotic than dizygotic twins as well as family aggregation. However, the individual genetic and environmental factors involved have not been identified. The aim of this thesis was to elucidate genetic susceptibility factors for fibromyalgia. We assessed this objective through three main approaches: the identification of FM clinically homogeneous subgroups with a two step cluster analyses, a genome-wide association study in order to evaluate the possible contribution of single nucleotide polymorphisms with Illumina 1 million duo array, and array comparative genomic hybridization experiments to identify regions varying in copy number that could be involved in FM susceptibility,using Agilent 2X400K platform. 48 variables were evaluated in 1,446 Spanish FM cases fulfilling 1990 ACR FM criteria. A partitioning analysis was performed to find groups of variables similar to each other. Variables clustered into three independent dimensions: “symptomatology”, “comorbidities” and “clinical scales”. Only the two first dimensions were considered for the construction of FM subgroups, classifying FM samples into three subgroups: low symptomatology and comorbidities (Cluster 1), high symptomatology and comorbidities (Cluster 2), and high symptomatology but low comorbidities (Cluster 3). These subgroups showed differences in measures of disease severity and were further implemented in genetic analysis. Genome-wide association study was performed in 300 FM cases and 203 controls. No SNP reached GWAS association threshold, but 21 of the most associated SNPs were chosen for replication in over 900 cases and 900 pain free-controls. Four of the strongest associated SNPs selected for replication showed a nominal association in the joint analysis. In particular, rs11127292 (MYT1L) was found to be associated to FM with low comorbidities. Array comparative genomic hybridization detected 5 differentially hybridized regions. They were followed up and one of these regions was validated though a multiplex PCR experiment. An intronic deletion in NRXN3 showed to be associated to female cases of FM and in particular those with low levels of comorbidities. Replication analysis showed a stronger association when considering only female cases and controls and low comorbidities. This enhance the importance of gender in FM etiopathogenesis and could be pointing to the existence of a different genetic background for FM in males and females highlights the importance of identifying FM homogeneous subgroups for the detection of FM genetic susceptibility factors. If the proposed FM candidate genes are further validated in replication studies, this would constitute a change in the FM ethiologycal concept, as several of these candidates are known neuropsychiatric disease associated genes (autism, addiction, mental disability). This would highlight a novel neurocognitive involvement in this disorder, currently considered musculoskeletal and affective. / La fibromialgia (FM) es una enfermedad de etiología desconocida que se caracteriza por dolor crónico generalizado, junto a una amplia constelación de síntomas acompañantes. La base etiopatogénica que explica este estado permanente de dolor es aún desconocida. Hasta la fecha la teoría más plausible es la existencia de una disfunción en la transmisión del dolor. Los estudios familiares han mostrado una considerable agregación familiar en FM,sugiriendo la importancia de los factores genéticos en el desarrollo de estos cuadros. Con la presente tesis se ha pretendido estudiar e identificar variantes del genoma (polimorfismos de base única (SNPs)- y variantes en el número de copia –CNVs) asociadas a FM, con el objetivo de profundizar en la etiología de la enfermedad. Para ello, se han llevado a cabo tres grandes aproximaciones: la identificación de subgrupos clínicos homogéneos de FM mediante un análisis de clusters, un estudio de genoma completo (GWAS) para el análisis directo de SNPs y experimentos de hibridación genómica comparada mediante arrays (aCGH) con el fin de identificar regiones variables en el número de copia asociadas a FM. El análisis de clusters ha permitido la identificación de tres subgrupos de FM en función de los niveles de sintomatología y de comorbilidad personal y familiar. Los resultados del GWAS indican una posible contribución del sistema nervioso central en el desarrollo de FM, ya que las enfermedades neurológicas aparecen como sobrerrepresentadas en el estudio de pathways realizado en los SNPs que presentaban mayor asociación, y un SNP en el gen MYT1L ha presentado asociación estadísticamente significativa con FM con niveles bajos de comorbilidad, poniendo de manifiesto la importancia de identificar subgrupos clínicamente homogéneos para la detección de factores de susceptibilidad genética para FM. Un CNV en el gen neurexina3 ha mostrado, asimismo, asociación en mujeres con FM, y en particular, en aquellas con bajos niveles de comorbilidad, siendo un nuevo argumento a favor de la implicación del SNC. La confirmación de las variantes detectadas en nuevas cohortes de fibromialgia supondría un giro conceptual de la enfermedad hacia una visión más neurocognitiva que osteomuscular.

The human genome contains slightly more than 20 000 genes that are expressed in a tissue specific manner. Transcription factors play a key role in gene regulation. By mapping the transcription factor binding sites genome-wide we can understand their role in different biological processes. In this thesis we have mapped transcription factors and histone marks along with nucleosome positions and RNA levels. In papers I and II, we used ChIP-seq to map five liver specific transcription factors that are crucial for liver development and function. We showed that the mapped transcription factors are involved in metabolism and other cellular processes. We showed that ChIP-seq can also be used to detect protein-protein interactions and functional SNPs. Finally, we showed that the epigenetic histone mark studied in paper I is associated with transcriptional activity at promoters. In paper III, we mapped nucleosome positions before and after treatment with transforming growth factor  β (TGFβ) and found that many nucleosomes changed positions when expression changed. After treatment with TGFβ, the transcription factor HNF4α was replaced by a nucleosome in some regions. In paper IV, we mapped USF1 transcription factor and three active chromatin marks in normal liver tissue and in liver tissue of patients diagnosed with alcoholic steatohepatitis. Using gene ontology, we as expected identified many metabolism related genes as active in normal samples whereas genes in cancer pathways were active in steatohepatitis tissue. Cancer is a common complication to the disease and early signs of this were found. We also found many novel and GWAS catalogue SNPs that are candidates to be functional. In conclusion, our results have provided information on location and structure of regulatory elements which will lead to better knowledge on liver function and disease.