Equine protozoal myeloencephalitis (EPM) is a progressive neurological disease of horses caused by Sarcocystis neurona. Two projects were conducted to identify factors involved in the development of EPM. The first study explored a possible genetic susceptibility to EPM by attempting a genome-wide association study (GWAS) on formalin-fixed, paraffin-embedded (FFPE) tissue from 24 definitively-positive EPM horses. DNA extracted from tissues older than 14 months was inadequate for SNP analysis on the Illumina Equine SNP50 BeadChip probably due to degradation and formalin cross-linking. Results were inconclusive as analysis was not possible with the small sample set. The second study evaluated an artificial infection method in creating a reliable equine EPM model. Five horses were injected intravenously at 4 time points with autologous blood incubated with 1,000,000S. neurona merozoites. Challenged horses progressively developed mild to moderate clinical signs and had detectable S. neurona serum antibodies on day 42 post challenge. Horses appeared to have produced a Th1 immune response and cleared the infection by the conclusion of the study on day 89. No histopathological evidence of S. neurona infection was found within central nervous system tissue. This artificial infection method was not effective in replicating the severe clinical EPM seen in natural infections.

Thesis (Ph. D.)--University of Texas Health Science Center at Houston, School of Public Health, 2007. / Source: Dissertation Abstracts International, Volume: 68-10, Section: B, page: 6419. Advisers: Christopher I. Amos; Ralph F. Frankowski. Includes bibliographical references.

Despite the success of vaccines in routine use worldwide, there are substantial challenges hampering our ability to develop vaccines against extant diseases including malaria and tuberculosis. Novel approaches are urgently required to help us understand immunological correlates of protection against disease and facilitate our understanding of the impact of human genetic variation on the success of diverse vaccines. To identify host genetic factors responsible for variation in antibody responses against vaccine antigens delivered routinely to infants worldwide I performed a genome-wide association study (GWAS) involving 2,499 infants recruited from three diverse sites across Africa. I identified strong genetic associations between variants in the class II major histocompatibility complex (MHC) locus and responses against five antigens: pertussis toxin (PT), filamentous haemagglutinin (FHA) and pertactin; diphtheria toxin (DT); and hepatitis B surface antigen. To characterise these associations at the gene and allelic level I developed a large, high-resolution (6-digit 'G') population-specific human leukocyte antigen (HLA) imputation reference panel including 697 individuals from the vaccine GWAS typed at 11 genes, highlighting the diversity of HLA across the African continent. Using this panel I imputed HLA into the remaining GWAS dataset to fine-map the associations to specific HLA alleles, amino acid and single nucleotide polymorphism sites; some of which were found to be African specific. I then used these HLA association findings observed with PT response to correlate, through genetics, this trait with susceptibility to whooping cough in an independently recruited and analysed set of cohorts from the UK. I further used these genetic correlations to demonstrate the relevance of levels of PT-specific circulating follicular helper T-cells and TRBV29-1 T-cell receptor gene expression levels in the development of this protective immune response against PT. By using HLA-peptide binding studies I also demonstrate the diversity of mechanisms that are involved in HLA-disease association, showing that the breadth and affinity of DT-peptide binding are increased with HLA-DRB1 alleles associated with increased DT antibody responses. Taken together, these data represent the first comprehensive genetic association study of multiple vaccine responses undertaken in African infants. These results highlight the importance of human genetics in modulating protective responses against vaccine antigens and demonstrate how such associations can be harnessed to understand biological mechanisms of protective efficacy in greater detail that may in turn facilitate future vaccine development.

Comme pour toute pathologie, la survenue d’un cancer du sein est conditionnée par l’association de facteurs génétiques héréditaires et de facteurs environnementaux acquis. Les facteurs génétiques connus comprennent à la fois des mutations pathogènes rares induisant un risque élevé de développer un cancer du sein et des variants génétiques fréquents (single nucleotides polymorphisms - SNP) responsables d’une faible augmentation du risque. L’ensemble des résultats de ce manuscrit plaide en faveur d’un impact majeur des facteurs génétiques constitutionnels à la fois en ce qui concerne le risque de développer un cancer du sein mais aussi en tant que déterminants du type de cancer du sein, voire du pronostic. La survenue d’un cancer du sein exprimant les récepteurs aux estrogènes et HER2-négatif est associée à 4 SNP introniques du gène FGFR2. Le pronostic des cancers du sein n’est pas associé aux variants impliquant un risque de développer un cancer. Quatre SNP indépendants sont associés à une évolution péjorative des cancers du sein triple-négatifs.La séquence d’événements qui mène du génome du patient à celui de la tumeur reste complexe, mal connue et probablement spécifique à chaque cancer comme l’illustrent les deux cas liés à des mutations germinales BRCA1/2 étudiés en deuxième partie de manuscrit. Le dernier travail permet de faire un lien vers la pratique clinique et rapporte une prévalence des mutations germinales BRCA1/2 d’environ 3% dans une cohorte prospective de patientes présentant un cancer du sein métastatique, non sélectionnées en fonction de leur âge, type de cancer ou antécédents familiaux. / As in any disease, the development of breast cancer depends on genetic hereditary factors and environmental acquired factors. Genetic factors of breast cancer involve rare pathogenic mutations with high risk of developing a breast cancer and frequent genetic variants (single nucleotides polymorphisms - SNP) responsible for a low increase in the risk of cancer. The works presented in this manuscript show that germline genetic factors strongly determine the risk of developing a breast cancer, but also the subtype of breast cancer and may impact the prognosis. Estrogen-positive, HER2-negative breast cancer development is associated with 4 intronic SNP in FGFR2 gene. Breast cancer prognosis is not associated with variants conferring a risk of developing a breast cancer. Four independent SNP are associated with bad outcomes in triple-negative breast cancers.The way that leads from patient genome to tumor genome is complex, mainly unknown and probably different for each case, as illustrated in the two case reports involving BRCA1/2 germline mutations described in the second part of the manuscript. Last work is a clinical research trial and shows a prevalence of BRCA1/2 mutations of around 3%, in a prospective cohort with metastatic breast cancer patients unselected on their age, cancer type or family history.

Les variétés modernes de canne à sucre sont d'origine bispécifique et possèdent une structure génétique complexe, aneuploïde et hautement polyploïde rendant difficile les études de résistance génétique. La feuille jaune de la canne a sucre est une maladie dont l'agent causal est le sugarcane yellow leaf virus (scylv). Ce virus a une large diversité. Seuls trois génotypes viraux, différenciables par rtpcr, ont été trouves en Guadeloupe. Les objectifs de l'étude sont d'évaluer: l/la possibilité de marquer la résistance de la plante au scylv grâce a une étude d'association pan-génomique 2/l'impact de la diversité de l'agent pathogène sur la résistance de la canne a sucre au scylv. Les études d'association ont été menées avec plus de 4000 marqueurs aflp et d'art sur quatre types de données phénotypiques (intensité et densité virale dans les feuilles et les tiges). Les phénotypes ont été mesures sur 189 variétés de cannes à sucre dans deux essais successifs dans un dispositif en trois blocs randomises. De ces variétés, 40 ont été sélectionnées et ont permis d'obtenir 10 croisements biparentaux. Les descendances obtenues ont été suivies sur deux essais. L'incidence et la diversité du scylv ont été évaluées pour les 40 variétés et les descendances. L'héritabilité au sens strict de la résistance aux scylv a été déterminée. Six marqueurs de résistance au scylv ont été identifies ainsi que deux gènes ayant potentiellement un rôle dans la résistance au virus. L'étude montre également que la résistance de la plante est variable en fonction du génotype du scylv et que cette résistance est en partie transmise aux descendances. Créer des variétés résistantes au scylv est donc possible. / Modern varieties of sugarcane have a bispecific origin and a complex genetic structure, aneuploid and highly polyploid, maklng genetic resistance study uneasy to perform. Yellow leaf of sugarcane is a viral disease whose causal agent is the sugarcane yellow leaf virus (scylv). This virus has a wide range of diversity. Only three viral genotypes, distinguishable by rt-pcr, were found in guadeloupe. The objectives of this srudy are to assess: l/the possibility to find markers associated with plant resistance to scylv through a genome wide association study 2 1 the impact of the pathogen diversity on the resistance of sugarcane to scylv. Association studies have been conducted with more than 4000 aflp and dart markers on four types of phenotypic data (virus intensity and density in leaves and canes). Phenotypes were measured on 189 varieties of sugarcane in two successive trials in a three randomized complete block design. From these varieties, 40 were selected and allowed to obtain 10 biparental crosses. The offspring were followed during two trials. The incidence and the diversity of scylv were evaluated in the 40 varieties and the offspring. The narrow sense heritability of the resistance to the scylvs was determined. Six markers of the resistance to the scylv and two genes, with potential contribution in virus resistance, have been identified. The study also shows that the resistance of the plant is variable depending on the scylv genotype and that this resistance is partly transmitted to the offspring. Breeding for scylv resistance is practicable.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22344号 / 医博第4585号 / 新制||医||1042(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 藤渕 航, 教授 渡邊 直樹, 教授 玉木 敬二 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第22791号 / 人博第962号 / 新制||人||228(附属図書館) / 2020||人博||962(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 瀬戸口 浩彰, 教授 市岡 孝朗, 教授 宮下 英明 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

Fusarium head blight (FHB) is a devastating wheat (Triticum aestivum L.) disease worldwide. Presently, there is insufficient FHB resistance in the Canadian wheat germplasm. Genome-wide association study (GWAS) and genomic selection (GS) can be utilized to identify sources of resistance that could benefit wheat breeding. To define the genetic architecture of FHB resistance, association panels from a spring and a winter collection were evaluated using the Wheat Illumina Infinium 90K array. A total of 206 accessions from the spring panel and 73 from the winter panel were evaluated in field trials for 3-4 years at two locations, namely Morden (Manitoba) and Ottawa (Ontario). These accessions were phenotyped for FHB incidence (INC), severity (SEV), visual rating index (VRI), and deoxynivalenol (DON) content. Significant (p < 0.05) differences among genotypes for all traits were found. Genetic characterization using the wheat 90K array identified a set of 20,501 single nucleotide polymorphisms (SNPs). The probe sequences (~100 bp) of these SNPs were mapped to the Chinese Spring reference genome v2.0 to identify 13,760 SNPs in the spring panel, and 10,421 SNPs in the winter panel covering all 21 wheat chromosomes. GWAS was performed to identify novel FHB resistance loci for INC, SEV, VRI and DON content for the spring and the combined panels separately using these 13,760 SNPs and for the winter panel using 10,421 SNPs. A total of 107, 157, 174 unique quantitative trait loci (QTNs) were identified for the four traits using two single-locus and seven multi-locus GWAS models for the spring, winter, and combined panels, respectively. These QTNs represent a valuable genetic resource for the improvement of FHB resistance in commercially grown wheat cultivars. In addition, these GWAS-defined QTNs were further used for GS to determine the breeding value (BV) of individuals as outlined below. In order to understand the role of the model and that of the marker type and density in trait prediction modelling, a GS study was conducted. GS is considered as an important tool for increasing genetic gain for economically important traits such as FHB resistance. GS uses genome-wide molecular markers to develop statistical models that predict genomic estimated breeding values (GEBVs) of an individual. Our results support genomic prediction (GP) as an alternative to phenotypic selection to predict the BVs of individuals for this trait. GS accounts for minor effect QTNs, which is beneficial when breeding for quantitative traits. Moderate to high GP accuracies can be achieved for FHB resistance-related traits when implemented in a breeding program. The correlation between the estimate of the missing phenotypic value and the observed phenotype is known as predictive ability (r). Overall, the predictive ability increased significantly using a QTN-based GP approach for FHB traits in wheat and its wild relatives. DON content had the highest predictive ability among all FHB traits, and that was in the winter panel, highlighting the importance of objectively measured traits in breeding for disease resistant genotypes. Interestingly, the winter panel contained several wild relative species that may harbor genes of interest to prevent the accumulation of mycotoxins in the grain. This study showed the usability of genomic prediction by improving the predictive ability of the FHB traits, which can be applied in early generation selection to accelerate the improvement of FHB resistance in wheat. The results show that GS can be successfully implemented in wheat breeding programs over multiple breeding cycles and can be effective for economically important traits. It is anticipated that GS will play a substantial role in the future of wheat breeding.

A comprehensive understanding about how genetic variants and mutations contribute to phenotypic variations and alterations entails experimental technologies and analytical methodologies that are able to detect genetic variants/mutations from various biological samples in a timely and accurate manner. High-throughput sequencing technology represents the latest achievement in a series of efforts to facilitate genetic variants discovery and genotyping and promises to transform the way we tackle healthcare and biomedical problems. The tremendous amount of data generated by this new technology, however, needs to be processed and analyzed in an accurate and efficient way in order to fully harness its potential. Structural variation (SV) encompasses a wide range of genetic variations with different sizes and generated by diverse mechanisms. Due to the technical difficulties of reliably detecting SVs, their characterization lags behind that of SNPs and indels. In this dissertation I presented two novel computational methods: one for detecting transposable element (TE) transpositions and the other for detecting SVs in general using a local assembly approach. Both methods are able to pinpoint breakpoint junctions at single-nucleotide resolution and estimate variant allele frequencies in the sample. I also applied those methods to study the impact of TE transpositions on the genomic stability, the inheritance patterns of TE insertions in the population and the molecular mechanisms and potential functional consequences of somatic SVs in cancer genomes.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19402号 / 医博第4053号 / 新制||医||1012(附属図書館) / 32427 / 京都大学大学院医学研究科医学専攻 / (主査)教授 佐藤 俊哉, 教授 小川 誠司, 教授 横出 正之 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM