Cervical stenotic myelopathy (CSM) is an important musculoskeletal and neurologic disease of the horse. Clinical disease occurs due to malformations of the vertebrae in the neck causing stenosis of the cervical vertebral canal and subsequent spinal cord compression. The disease is multifactorial in nature, therefore a clearer understanding of the etiology and pathogenesis of CSM will allow for improved management and therapeutic practices. This thesis examines issues of equine CSM diagnosis, skeletal tissue pathology, and inherited genetic determinants utilizing advances in biomedical imaging technologies and equine genomics. Magnetic resonance imaging (MRI) data provided a more complete assessment of the cervical column through image acquisition in multiple planes. First, MRI was compared to standing cervical radiographs for detection of stenosis. Using canal area or the cord canal area ratio, MRI more accurately predicted sites of compression in CSM cases. Secondly, articular process skeletal pathology localized on MRI was found to be more frequent and severe in CSM horses compared to controls. In addition, lesions were generalized throughout the cervical column and not limited to the spinal cord compression sites. A subset of lesions identified on MRI was evaluated using micro-CT and histopathology. Osteochondrosis, osseous cyst-like structures, fibrous tissue replacement of bone, and osteosclerosis were observed. These lesions support likely developmental aberrations of vertebral bone and cartilage maturation with secondary biomechanical influences. Bone cyst-like structures are a novel finding in this disease. Finally, the long-standing question of the contribution of genetic determinants to CSM was investigated using a genome wide association study (GWAS). Multiple significant loci were identified supporting the influence of a complex genetic trait in clinical disease. A simple Mendelian trait controlled by one gene is unlikely given the detection of variants across multiple chromosomes. Major contributions from this research include documentation of articular process bone and cartilage pathology in horses with CSM, support for abnormal cervical vertebrae development being an important contributing factor in the etiology and/or pathogenesis of equine CSM, and evidence that multiple genetic loci contribute to the CSM disease phenotype.

No description available.

The release of the Illumina BovineSNP50 BeadChip in late 2007 has drawn attention from cattle breeders around the world to develop breeding programs that leverage association of these single nucleotide polymorphism (SNP) with economically important quantitative trait loci (QTL). In that context this project has come to study applications of the SNP panel in beef cattle. Analysis of linkage disequilibrium (LD) existing in Angus, Charolais, and crossbred animals revealed the pattern of LD within each breed group, as well as the persistence of LD phase between pairs of the breed groups. This is important for genomic selection where SNP are trained in one population and used to predict breeding value for animals in another population. Detection of chromosome regions potentially carrying QTL or causative mutations affecting the phenotypic variation in economically important traits was presented at individual SNP and haplotype levels. There were 269 SNP associated (P<0.001) with birth weight (BWT), weaning weight (WWT), average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), residual feed intake (RFI). They explained 1.64% - 8.06% of the phenotypic variation in these traits. There were 520 SNP associated (P<0.001) with carcass quality traits, namely hot carcass weight, back fat thickness, ribeye area, marbling scores, lean yield grade by Beef Improvement Federation, steak tenderness, and six rib dissection traits. These SNP explained 1.90 - 5.89% of the phenotypic variance of the traits. Many of the significant SNP were located on chromosome 6. Six haplotypes were found associated (P<0.05) with ADG, DMI, and RFI. In order for genomic selection to happen in beef cattle, higher density SNP panels should be made available at low genotyping cost. However, the cost of genotyping animals for high density SNP chip is still high, thus genotype imputation has come to practice. The last chapter of this thesis compared two approaches presently used in genotype imputation, investigated factors affecting imputation accuracy, as well as the impact of imputation accuracy on genomic estimated breeding value (GEBV). It proved that the highest possible accuracy of GEBV is attainable with sufficiently large groups of reference animals. / Ontario Ministry of Agriculture, Food and Rural Affairs. Ontario Cattlemen’s Association. Ontario Farm Innovation Program. Agriculture and Agri-Food Canada’s Growing Forward Program. Agriculture Adaptation Council. Ontario Research and Development Program. MITACS Accelerate. Beef Improvement Opportunities.

Hybrid male sterility (HMS) is typically the first mechanism fortifying reproductive isolation resulting from genomic incompatibilities. Three interspecies feline breeds derived from domestic cat crosses to wild cat species (Asian leopard cat and African serval) manifest HMS through several generations of backcrossing before eventually regaining fertility. This work utilized 199 hybrid individuals with varying fertilities in a genome wide association study (GWAS) comprising 63,000 genome wide SNPs. Leveraging these results with whole-testis transcriptome sequencing and quantitative real-time PCR data facilitated the comparison of transcripts in sterile and fertile hybrids. This dissertation describes four loci with highly significant and fifty with moderately significant association to sterility within each individual hybrid domestic breed and combinations of breeds. These associations help identify epistatic targets for hybrid incompatibility contributing to sterility. Comparative QTL mapping between pairs of species provides a framework to describe the accumulation of clade-specific reproductive isolating loci. Detailed exploration of gene misregulation between domestic and hybrid individuals, as well as between littermate hybrids of varying fertilities outlines a pattern of expression consistent with a meiotic sex-chromosome inactivation failure in early generations and apoptotic failure in later hybrid generations. Combining comparative genomic association and transcriptomic characterization among hybrid felids of varying divergence, new insight is gained into the mechanisms of mammalian reproductive isolation.

Après 25 ans de recherche intensive, aucun vaccin ou traitement définitif contre le SIDA n'existe, et les mécanismes moléculaires de pathogenèse de l'infection VIH-1 ne sont pas clairement élucidés. Les avancées technologiques permettent de comparer des sujets malades avec des sujets contrôles sur tout le génome. Il est ainsi possible d’identifier sans a priori des gènes potentiellement impliqués dans le développement de la maladie avec pour conséquence le développement rationnel de nouvelles stratégies diagnostiques ou thérapeutiques. Durant ma thèse, j’ai réalisé deux études d’association ‘génome entier’ dans le SIDA, en comparant les 275 non-progresseurs à long terme ou les 85 progresseurs rapides de la cohorte GRIV avec une cohorte de contrôles séronégatifs. J’ai réalisé une troisième analyse en exploitant les données issues de trois études ‘génome entier’ internationales dont la nôtre (France, Pays-Bas, USA), ciblant plus particulièrement les SNPs de fréquence faible (fréquence de l’allèle mineur, MAF<5%). Ces approches ‘génome entier’ ont réaffirmé le rôle central du HLA dans la progression vers le SIDA, mais aussi dévoilé de nouveaux gènes candidats très pertinents donnant une nouvelle lumière sur les mécanismes moléculaires de la maladie. / After 25 years of intensive research, no vaccine or cure exists against AIDS, and the molecular mechanisms of pathogenesis of HIV-1 infection are not clearly understood. Technological progress has made possible to compare cases versus controls over the whole genome. It is thus possible to identify genes potentially involved in disease development with no a priori, and consequently develop rationally new diagnostic or therapeutic strategies. During my PhD, I have completed two genome-wide association studies (GWAS) in AIDS, comparing 275 long term non-progressors or the 85 rapid progressors from the GRIV cohort with a cohort of seronegative controls. I have also completed a third analysis exploiting data from three international GWAS including ours (France, Netherlands, USA), targeting particularly low frequency SNPs (minor allele frequency, MAF <5%). These GWAS approaches have reaffirmed the central role of HLA for progression towards AIDS, but also revealed new relevant candidate genes, shedding a new light on the molecular mechanisms of disease progression.

Genetic associations have been discovered for many human complex traits, and yet for most associated loci the causal variants and molecular mechanisms remain unknown. Studies mapping quantitative trait loci (QTLs) for molecular phenotypes, such as gene expression, RNA splicing, and chromatin accessibility, provide rich data that can link variant effects in specific cell types with complex traits. These genetic effects can also now be modeled in vitro by differentiating human induced pluripotent stem cells (iPSCs) into specific cell types, including inaccessible cell types such as those of the brain. In this thesis, I explore a range of approaches for using QTLs to identify causal variants and to link these with molecular functions and complex traits. In Chapter 2, I describe QTL mapping in 123 sensory neuronal cell lines differentiated from human iPSCs. I observed that gene expression was highly variable across iPSC-derived neuronal cultures in specific gene categories, and that a portion of this variability was explained by commonly used iPSC culture conditions, which influenced differentiation efficiency. A number of QTLs overlapped with common disease associations; however, using simulations I showed that identifying causal regulatory variants with a recall-by- genotype approach in iPSC-derived neurons is likely to require large sample sizes, even for variants with moderately large effect sizes. In Chapter 3, I developed a computational model that uses publicly available gene expression QTL data, along with molecular annotations, to generate cell type-specific probability of regulatory function (PRF) scores for each variant. I found that predictive power was improved when the model was modified to use the quantitative value of annotations. PRF scores outperformed other genome-wide scores, including CADD and GWAVA, in identifying likely causal eQTL variants. In Chapter 4, I used PRF scores to identify relevant cell types and to fine map potential causal variants using summary association statistics in six complex traits. By examining individual loci in detail, I showed how the enrichments contributing to a high PRF score are transparent, which can help to distinguish plausible causal variant predictions from model misspecification.

L'Indonésie a été l'objet de la dispersion Austronésienne qui a débuté il y a environ 5000 ans depuis Taiwan, se propager à travers les Philippines et l'Indonésie, puis toucher l'Océanie à l'est, et à Madagascar à l'ouest. Malgré de nombreuses recherches en génétique sur la dispersion Austronésienne vers l'est, il y a très peu de données sur la dispersion vers l'ouest, laissant sans réponse de nombreuses questions, liées notamment au peuplement de Madagascar. Reposant sur l'analyse des données culturelles et biologiques, les populations d'Indonésie semblent avoir joué un rôle majeur dans la colonisation de Madagascar, le premier millénaire de notre ère. Cependant, le peu de populations Indonésiennes étudiées à ce jour n'a pas permis jusqu'à présent d'identifier la population indonésienne source. Dans ce présent travail, j'ai réalisé des études en génétique des populations de 12 populations Indonésiennes, qui à priori devraient éclairer l'histoire des migrations austronésiennes dans l'Océan Indien. Parmi elles sont inclus le Ma'anyan du sud-est de Bornéo qui sont les plus proches linguistiquement des Malgaches. En utilisant différents marqueurs génétiques, ma recherche a amélioré nos connaissances de la diversité génétique Indonésienne, et du lien génétique entre l'Indonésie et Madagascar. Résultats L'analyse des marqueurs uniparentaux (chr-Y et ADNmt) suggère que les Malgaches proviennent de plusieurs régions d'Indonésie, avec un lien privilégié avec le sud-est de Bornéo, le sud de Sulawesi et les îles de la Sonde. Etonnamment, les Ma'anyan partagent un nombre limité de lignées paternelles et maternelles avec les Malgaches, malgré leur proximité linguistique. Par ailleurs, en combinant l'analyse de fréquences des SNPs et l'analyse haplotypique à partir des données autosomales, il a été confirmé que la diversité génétique des Ma'anyan ne correspond pas à l'ancestralité asiatique des Malgaches. Cependant, en centrant l'analyse sur les populations du sud-est de Bornéo, l'origine de l'ancestralité asiatique des Malgaches est ancrée dans la population Banjar, un mélange de population Ma'anyan et Malaise, résultat des activités commerciales de l'empire Malais dans le sud-est de Bornéo, qui se sont poursuivies à travers l'océan Indien. Par ailleurs nos résultats ont aussi permis d'accroitre notre compréhension de la diversité génétique de l'Indonésie en identifiant (1) une nouvelle composante génétique austronésienne présente chez les Ma'anyan, et retrouvée à faible fréquence à travers l'Asie du Sud-Est, suggérant une plus grande complexité du modèle d'expansion austronésien dans la région et (2) le rôle joué par les nomades de la mer dans la structuration de la diversité génétique et les échanges entre populations dans l'Indonésie, soulignant l'histoire génétique complexe de populations suivant un mode de vie nomade. / Indonesia hosts a wide range of linguistic, ethnic and genetic diversity, comprising ~600 ethnic groups and 700 living languages. Indonesia has facilitated the last substantial wave of human migration was the Austronesian dispersal ~5,000 years ago, which is thought to have originated in Taiwan. Its influence spread through Philippines and Indonesia, ultimately impacting a wide geographical area, from Remote Oceania in the east and to Madagascar in the west. Despite considerable genetic research on the eastward Austronesian expansion, there is little equivalent research on the western edge, leaving major issues unresolved regarding the settlement of Madagascar. Based on cultural and biological studies, it has been suggested that Indonesian peoples played a major role in the colonization of Madagascar from around the mid-first millennium CE (Current Era). However, poor geographical coverage of Indonesian populations has prevented the Indonesian source populations from being identified. Here, I performed human population genetic studies on 12 new Indonesian populations, which were a priori expected to shed light on the westward migration of Austronesians across the Indian Ocean. This includes the Ma'anyan ethnic group from Southeast Borneo, who are the closest linguistic siblings to modern Malagasy. Using different genetic markers (Y-chromosome SNPs, mitochondrial DNA and genome-wide SNPs), my research has improved the description of Indonesian genetic diversity, and investigated the genetic links between Indonesia and Madagascar. Results Uniparental markers (Y-chromosome and mtDNA) analyses suggest that Malagasy derive from multiple regional sources in Indonesia, with a focus on southeastern Borneo, southern Sulawesi and the Lesser Sunda islands. Interestingly, the Ma'anyan share limited paternal and maternal lineages with the Malagasy, despite their linguistic connection. Furthermore, combining SNP frequency and haplotype-based analyses from autosomal genome-wide data, it was confirmed that the genetic diversity of the Ma'anyan does not match the Asian ancestry of the Malagasy. However, by focusing on Southeast Borneo populations, strong support was found for an origin of the Asian ancestry of Malagasy among the people of Banjar, an admixed population of Ma'anyan and Malay, likely resulting from trading activities by the Malay Empire in Southeast Borneo, and later continuing across the Indian Ocean arena. These results increase our understanding of genetic diversity across Indonesia by 1) identifying the unique and undiscovered Austronesian genetic component carried by the Ma'anyan, which occurs at low levels across Island Southeast Asia and suggests a more complex model for the Austronesian expansion in this region, and 2) describing the role played by sea-nomads in structuring genetic diversity and exchanges in central Indonesia, thus revealing the complex genetic history of populations living this rare nomadic lifestyle.

La peau est un excellent modèle d’étude du vieillissement général. En plus de facteurs environnementaux, les facteurs génétiques jouent un rôle majeur dans le vieillissement cutané. Dans le cadre de ma thèse, j’ai eu accès à une cohorte exceptionnelle de 502 femmes caucasiennes très bien caractérisées sur le plan cutané, pour effectuer deux études d’association « génome-entier ». La première étude a montré le rôle joué par le système immunitaire, et en particulier le gène HLA‑C, dans la sévérité des lentigines du visage. La seconde a mis en évidence une association entre le gène H2AFY2 et la sévérité de l’affaissement de la paupière supérieure. La recherche de voies de signalisation biologiques associées à différents indicateurs du vieillissement cutané a souligné le rôle de la mélanogénèse et des mécanismes de réparation de l’ADN.Ces résultats ouvrent de nouvelles perspectives dans la compréhension des mécanismes inhérents au vieillissement cutané et général. / The skin is an excellent model to study general ageing. In addition to environmental factors, genetic factors play a key role in skin ageing mechanisms. During my PhD, I have had access to a unique cohort of 502 Caucasian women very-well characterized regarding their facial features to perform two genome-wide association studies. The first one pointed to the role of the immune system, and especially the HLA‑C gene, in the severity of facial lentigines. The second one identified an association between the H2AFY2 gene and the severity of superior eyelid drooping. I also looked for associations between biological pathways and several skin ageing indicators which underlined the role of the melanogenesis and several mechanisms of DNA repair.Overall, these results lead to new insights in the understanding of the molecular mechanisms underlying skin and global ageing.

Les démences regroupent un ensemble de pathologies cérébrales affectant progressivement les fonctions cognitives et survenant plus fréquemment chez les personnes âgées. L’augmentation du nombre de cas liée au vieillissement de la population et la lourdeur de la prise en charge font des démences un problème de santé publique important.La maladie d’Alzheimer (MA) est la plus fréquente des démences. Elle apparaît généralement après 65 ans et possède une forte composante génétique. En dehors de certaines formes familiales précoces liées à des mutations dans les gènes du précurseur de la protéineamyloïde, et des présénilines 1 et 2, la grande majorité des cas résulte de l’interaction de facteurs environnementaux avec divers gènes de susceptibilité.L’approche gène candidat a permis l’identification de nombreux gènes associés au risquede MA. Cependant, en raison de problèmes techniques et méthodologiques, seul le gène de l’apoprotéine E (APOE) a pu être identifié de manière robuste par cette approche. Les études d’association pangénomiques permettent d’identifier sans a priori des variations génétiques fréquentes associées à une maladie sur l’ensemble du génome. À partir de 2009, plusieurs consortia ayant pour objectif de réaliser ce type d’étude dans le champs de la MA ont identifiéquatre nouveaux gènes d’intérêt pour la MA, CLU, PICALM, CR1 et BIN1. Cependant,ces gènes n’expliquent qu’une petite partie de la variabilité génétique de la maladie et denombreux autres variants restent à découvrir.Durant cette thèse, nous avons d’abord chercher à répliquer les résultats des principauxgènes identifiés par approche gène candidat en utilisant les données du consortium EuropeanAlzheimer’s Disease Initiative (EADI). Nous avons pu montrer qu’une grande partie deces gènes présentait un faible niveau d’association avec la MA. En utilisant l’approche pangénomique,nous avons ensuite pu identifier 19 gènes associés au risque de MA en dehorsd’APOE, dont 11 n’ayant pas été identifiés par les précédentes études, via la mise en placed’une collaboration informelle entre consortia puis au sein du International Genomics ofAlzheimer’s Disease Project (IGAP).Nous nous sommes également interessés à plusieurs phénotypes intermédiaires associésà la MA, et en particulier aux taux plasmatiques des peptides amyloïde b (Ab), en partantde l’hypothèse qu’ils pourraient permettre la recherche de variants impliqués dans des mécanismesphysiopathologiques pré-symptomatiques. Ce travail a permis l’identification d’uneassociation potentielle entre le gène CTXN3 et les taux plasmatiques d’Ab1−42.En conclusion, l’utilisation des études d’association pangénomiques a permis d’identifierde nombreux nouveaux gènes associés au risque de MA. Ces gènes ouvrent des voies derecherche intéressantes pour mieux comprendre la physiopathologie de la MA et permettrele développement de traitements efficaces qui font actuellement défaut. / Dementia is a syndrom caused by several brain diseases progressively deteriorating cognitivefunctions and occurs more frequently in the elderly. The increased number of patients withdementia due to the ageing of the general population and the high cost of care add up tomake dementia a concerning public health issue.Alzheimer’s disease (AD) is the most common form of dementia. It is often diagnosedafter 65 years old and has a strong genetic component. Familial forms exist and are mainlycaused by mutations in the amyloid-b protein precursor, presenilin 1 and presenilin 2 genes.However, the vast majority of cases result from the complex interaction of environmental factors with susceptibility genes.Using a candidate gene approach, numerous genes associated with AD risk were identified,but due to technical and methodological problems, only the apoliprotein E (APOE) genewas replicated. Genome-wide association studies (GWAS) aim to identify frequent geneticvariants associated with disease risk in a hypothesis-free manner. Starting 2009, severalconsortia aiming to perform this type of analyses in the field of AD robustly identified fournew genes associated with AD risk, CLU, PICALM, CR1 and BIN1. However, these genes puttogether only explain a small proportion of the total genetic variance of AD and the searchfor new susceptibility genes remains an important goal for AD research.In this work, we first tried to replicate the results of the top genes reported using thecandidate gene approach, using GWAS data from the European Alzheimer’s Disease Initiative(EADI). Most of these genes showed weak levels of association. Using GWAS, we were ableto identify 19 new genes associated with AD risk besides APOE, including 11 that had notbeen reported by previous studies, first through an informal collaboration between consortia,then under the name of International Genomics of Alzheimer’s Disease Project (IGAP).Assuming that use of endophenotypes related to AD would be relevant for the discoveryof genetic variants involved in the early pathophysiology of AD, we then performed aGWAS of plasma amyloid-b (Ab) concentrations. This study showed suggestive asssociationsbetween the CTXN3 gene on chromosome 5 and Ab1−42 plasma levels.To sum up, using GWAS enabled us to identify new genes associated with AD risk. Thesegenes point to interesting new research hypotheses and hopefully, to a better understandingof AD pathophysiology and development of effective drugs.

Brain disorders present a significant burden on affected individuals, their families and society at large. Existing diagnostic tests suffer from a lack of genetic biomarkers, particularly for substance use disorders, such as alcohol dependence (AD). Numerous studies have demonstrated that AD has a genetic heritability of 40-60%. The existing genetics literature of AD has primarily focused on linkage analyses in small family cohorts and more recently on genome-wide association analyses (GWAS) in large case-control cohorts, fueled by rapid advances in next generation sequencing (NGS). Numerous AD-associated genomic variations are present at a common frequency in the general population, making these variants of public health significance. However, known AD-associated variants explain only a fraction of the expected heritability. In this dissertation, we demonstrate that systems biology applications that integrate evolutionary genomics, rare variants and structural variation can dissect the genetic architecture of AD and elucidate its heritability. We identified several complex human diseases, including AD and other brain disorders, as potential targets of natural selection forces in diverse world populations. Further evidence of natural selection forces affecting AD was revealed when we identified an association between eye color, a trait under strong selection, and AD. These findings provide strong support for conducting GWAS on brain disorder phenotypes. However, with the ever-increasing abundance of rare genomic variants and large cohorts of multi-ethnic samples, population stratification becomes a serious confounding factor for GWAS. To address this problem, we designed a novel approach to identify ancestry informative single nucleotide polymorphisms (SNPs) for population stratification adjustment in association analyses. Furthermore, to leverage untyped variants from genotyping arrays – particularly rare variants – for GWAS and meta-analysis through rapid imputation, we designed a tool that converts genotype definitions across various array platforms. To further elucidate the genetic heritability of brain disorders, we designed approaches aimed at identifying Copy Number Variations (CNVs) and viral insertions into the human genome. We conducted the first CNV-based whole genome meta-analysis for AD. We also designed an integrated approach to estimate the sensitivity of NGS-based methods of viral insertion detection. For the first time in the literature, we identified herpesvirus in NGS data from an Alzheimer’s disease brain sample. The work in this dissertation represents a three-faceted advance in our understanding of brain disease etiology: 1) evolutionary genomic insights, 2) novel resources and tools to leverage rare variants, and 3) the discovery of disease-associated structural genomic aberrations. Our findings have broad implications on the genetics of complex human disease and hold promise for delivering clinically useful knowledge and resources.