Introduction The present study evaluated reported methodological characteristics of GWAS, investigating relationships between reported methodological characteristics and outcomes observed. Methods GWAS were identified from NHGRI’s catalogue of GWAS (2005 to 2009). Multivariate meta-regression models (random effects) were produced to identify the impact of reported study characteristics and the strength of relationships between the variables and outcomes. Results The summary odds ratios for replication components of GWAS in cancer was 1.34 (95% CI 1.25, 1.43) and neuropsychiatric disorders was 1.43 (95% CI 1.30, 1.57). Heterogeneity was accounted for by nature of the control group, relationship between case/control groups, whether cases/controls were drawn from the same population, if data was a primary collection or a build on pre-existing data, if quality assurance was reported, and if the study reported power/sample size. Conclusion Evidence supports the existence of variability in reporting, with index components demonstrating less variability than replication components in the GWAS.

Introduction The present study evaluated reported methodological characteristics of GWAS, investigating relationships between reported methodological characteristics and outcomes observed. Methods GWAS were identified from NHGRI’s catalogue of GWAS (2005 to 2009). Multivariate meta-regression models (random effects) were produced to identify the impact of reported study characteristics and the strength of relationships between the variables and outcomes. Results The summary odds ratios for replication components of GWAS in cancer was 1.34 (95% CI 1.25, 1.43) and neuropsychiatric disorders was 1.43 (95% CI 1.30, 1.57). Heterogeneity was accounted for by nature of the control group, relationship between case/control groups, whether cases/controls were drawn from the same population, if data was a primary collection or a build on pre-existing data, if quality assurance was reported, and if the study reported power/sample size. Conclusion Evidence supports the existence of variability in reporting, with index components demonstrating less variability than replication components in the GWAS.

Waves of bovine genomic data have been produced as a result of the bovine genome sequencing projects. In addition to the massive amounts of genomic sequence, significant annotation including single nucleotide polymorphisms, sequence tagged sites and haplotype blocks have been produced by the Bovine HapMap Project. Furthermore, many agriculturally significant traits in cattle such as milk yield and carcass weight are measured on a quantitative scale and have been genetically mapped as quantitative trait loci (QTL). QTL data can be used to generate another form of bovine annotation linking phenotype to genotype. However, it is impossible for humans to be able to analyze genomic scale data without computer based tools. Bioinformatic tools have been shown to greatly increase productivity and improve efficiency when dealing with large data sets. My dissertation presents an integrated, extensible database that houses SNPs, STSs, haplotypes, and QTL. The database is presented to researchers through a restructured, object oriented Bovine QTL Viewer that displays multiple levels of bovine annotation synergistically. Evaluation of use of the viewer was performed using a survey based approach and measured quantitatively. In addition, the QTL data from the database was used to analyze the frequency of gene ontology (GO) annotations within QTL regions. QTL regions were divided into 8 trait based groups. GO terms were counted within each category of QTL and in non- QTL regions of the genome. Top level GO term frequencies were generated from the counts and these frequencies were compared between QTL and non-QTL portions of the genome. Furthermore, specific sets of GO terms believed to be related to QTL categories were also used to determine if QTL regions were enriched for genes annotated with such GO terms. As a result, we determined that gene density varied significantly across QTL regions and that many QTL categories showed GO term frequency differences that could be related to the trait’s biology. Furthermore, our selected GO term sets were shown to be significantly enriched in some QTL categories.

Introduction The present study evaluated reported methodological characteristics of GWAS, investigating relationships between reported methodological characteristics and outcomes observed. Methods GWAS were identified from NHGRI’s catalogue of GWAS (2005 to 2009). Multivariate meta-regression models (random effects) were produced to identify the impact of reported study characteristics and the strength of relationships between the variables and outcomes. Results The summary odds ratios for replication components of GWAS in cancer was 1.34 (95% CI 1.25, 1.43) and neuropsychiatric disorders was 1.43 (95% CI 1.30, 1.57). Heterogeneity was accounted for by nature of the control group, relationship between case/control groups, whether cases/controls were drawn from the same population, if data was a primary collection or a build on pre-existing data, if quality assurance was reported, and if the study reported power/sample size. Conclusion Evidence supports the existence of variability in reporting, with index components demonstrating less variability than replication components in the GWAS.

Introduction The present study evaluated reported methodological characteristics of GWAS, investigating relationships between reported methodological characteristics and outcomes observed. Methods GWAS were identified from NHGRI’s catalogue of GWAS (2005 to 2009). Multivariate meta-regression models (random effects) were produced to identify the impact of reported study characteristics and the strength of relationships between the variables and outcomes. Results The summary odds ratios for replication components of GWAS in cancer was 1.34 (95% CI 1.25, 1.43) and neuropsychiatric disorders was 1.43 (95% CI 1.30, 1.57). Heterogeneity was accounted for by nature of the control group, relationship between case/control groups, whether cases/controls were drawn from the same population, if data was a primary collection or a build on pre-existing data, if quality assurance was reported, and if the study reported power/sample size. Conclusion Evidence supports the existence of variability in reporting, with index components demonstrating less variability than replication components in the GWAS.

Acute myeloid leukemia (AML) is a highly fatal blood cancer that is characterized by disruption of healthy differentiation of stem cells into functional blood cells in the bone marrow. Most patients with AML consequently die from infections due to the lack of immune cells. For decades, the standard method of remission induction for AML has been chemotherapy using an antineoplastic drug known as AraC. However, even after successful remission induction, aggressive, refractory relapse occurs in the majority of patients within 3 years with dismal survival rates. Here, we sought to develop a genome-wide screening approach to determine the causative genes in AML relapse. In the developed procedure, protein-coding genes of the human genome are screened using a leading-edge technology known as CRISPR (clustered regularly interspaced short palindromic repeats) activation screening. This involves usage of a pooled guide RNA library that upregulates a unique gene for each individual AML cell. By treating these cells with AraC in a mouse xenograft model, the bone marrow will gradually be enriched with cells that carry a guide RNA for a relapse-conducive gene. By harvesting and sequencing all enriched guide RNAs at relapse, the causative genes in AML relapse can be determined. All parameters of the in vivo CRISPR-activation screen have been optimized, and the workflow from preparation to the end of screening has been detailed. Follow-up studies that will validate the results of the screen have also been described. The long-term goal of this developed screen is to elucidate the mechanisms of AML relapse and find ways to clinically target these pathways in conjunction with standard the AraC-based chemotherapy. / Thesis / Master of Science (MSc)

Marek’s disease virus (MDV), the causative agent of Marek’s disease in chicken, is an important oncogenic avian pathogen which leads to world-wide economic losses in the poultry industry. It targets the chicken's immune system by initially causing a lytic infection in B-lymphocytes in lymphoid organs (spleen, bursa of Fabricius and thymus), followed by a latent infection of T-lymphocytes, which may lead to tumour formation. Despite the presence of well-established vaccination programs against MDV, it is still a major concern for the poultry industry due to the emergence of more virulent strains. As MDV is also considered an excellent model for herpesvirusinduced oncogenicity and immunosuppression, a better understanding of its pathogenesis, including the functional roles of individual MDV proteins, is of both biomedical as well as economical importance. All open reading frames (ORFs) of the CVI988 vaccine strain and the RB1B virulent strain were PCR-amplified from BAC DNA and cloned into the pDONR 207 entry vector by recombinatorial cloning (Gateway® system). Subsequently, all ORFs were subcloned into the yeast-two-hybrid (Y2H) vectors pGBKT7–DEST (bait) and pGADT7-DEST (prey), as well as other expression vectors. The Y2H bait and prey vector clone collections were transformed into the yeast strains AH109 and Y187, respectively. More than 140 ORFs, or ORF fragments, were analysed against each other in a comprehensive Y2H assay. Of > 20.000 interactions tested, 435 positive interactions between 115 ORFs were observed. Several of these interactions have previously been reported in other species of herpesvirus indicating that they may be conserved within the family. A subset of the positive interactions were confirmed using co-immunoprecipitation and LUMIER pull-down assays as a second independent assay. In the second part of the project all MDV proteins were tested for their ability to inhibit the chicken interferon-alpha (chIFN-α)-induced immune response. In functional luciferase reporter assay with a chicken Mx1 promoter containing an interferon stimulated responsive element (ISRE), four MDV-encoded chIFN-α inhibitors were identified, including UL12, UL26, UL50, and Meq, the main MDV oncoprotein. Both isoforms Meq and L-Meq derived from the oncogenic and the non-oncogenic vaccine strain, respectively, similarly inhibited the interferon response in a dose-dependent way, and Meq deletion mutants revealed that the Cterminal, proline-rich transactivating domain is not required for this inhibitory effect. In transient transfection experiments, Meq induced a dose-dependent proteasomal degradation of the chicken interferon regulatory factor 7 (chIRF7), which is required for chIFN-α- induced activation of ISRE. Over-expression of chIRF7 lead to a dosedependent degradation of Meq and its accumulation in the cytoplasm, suggesting that proteasomal degradation of both Meq and chIRF-7 is linked. Consistent with these findings, MDV deletion mutant lacking both copies of the Meq gene was more sensitive to chIFN-α treatment compared to wild-type virus.

To dissect the genetic architecture of blood pressure and assess effects on target organ damage, we analyzed 128,272 SNPs from targeted and genome-wide arrays in 201,529 individuals of European ancestry, and genotypes from an additional 140,886 individuals were used for validation. We identified 66 blood pressure-associated loci, of which 17 were new; 15 harbored multiple distinct association signals. The 66 index SNPs were enriched for cis-regulatory elements, particularly in vascular endothelial cells, consistent with a primary role in blood pressure control through modulation of vascular tone across multiple tissues. The 66 index SNPs combined in a risk score showed comparable effects in 64,421 individuals of non-European descent. The 66-SNP blood pressure risk score was significantly associated with target organ damage in multiple tissues but with minor effects in the kidney. Our findings expand current knowledge of blood pressure-related pathways and highlight tissues beyond the classical renal system in blood pressure regulation.

Primary rhegmatogenous retinal detachment (RRD) is one of the most common ophthalmic emergencies. RRD is caused by a full thickness break in the retina which initiates separation of the neurosensory retina from the underlying retinal pigment epithelium. The subsequent accumulation of fluid within this potential space extends the area of detachment and causes visual loss. Previous assessments of RRD incidence have demonstrated large differences in case definition and methodology, with incidence estimates varying 3-fold geographically and in different time periods. To date there have been no systematic or prospective incidence estimates of primary RRD in the U.K. In this thesis I present the findings of a 2-year epidemiology study that prospectively aimed to recruit all incident cases of primary RRD diagnosed in Scotland. Case recruitment from consenting participants comprised a detailed questionnaire and a blood sample. In this thesis, I present the findings of the Scottish retinal detachment study that examined the incidence, demographic features, temporal incidence trends, as well as clinical and socio-economic associations of primary RRD in Scotland. From the clinical and genetic resource I assembled, I calculated the first population based estimate of the sibling recurrence risk ratio for RRD and designed and assisted in the analysis of the first case-control genome wide association study of this condition. Results from this study have estimated the annual incidence of primary RRD in Scotland to be 12.05 per 100,000 population. Based on this estimate, there are approximately 7,300 new cases annually in the United Kingdom. RRD incidence increases with age, is more common in men and right eyes, and is strongly associated with socio-economic affluence. In addition, using hospital episode data, the overall age-standardised incidence of RRD in Scotland was shown to be steadily increasing since 1987 with an average annual increase of 1.9%. Analysis of the clinical findings highlighted that the majority of RRD cases are caused by more than one retinal break; an important consideration for appropriate surgical management. Ocular trauma, previous cataract surgery, family history, and retinal degeneration are important predisposing features. In addition, over a 2 year period approximately 7% of individuals will suffer a RRD in the fellow eye representing an important risk of bilateral visual loss. Furthermore, I demonstrate that the risk of having an affected sibling with RRD is increased 2-fold given that one sibling has had the condition, substantiating a genetic component to the pathogenesis of this condition. In the final aspect of this thesis I will present the design and analysis of a two stage case-control genome-wide association study examining the role of common genetic variants and selected candidate genes in predisposing to RRD development.

Autism Spectrum Conditions (henceforth, autism) refers to a group of neurodevelopmental conditions characterized by difficulties in social interaction and communication, difficulties in adjusting to unexpected change, alongside unusually narrow interests and repetitive behaviour, and sensory hyper-sensitivity. Twin and family-based studies have consistently identified high heritabilities for autism and autistic traits, with recent studies converging at 60 – 90% heritability. Common genetic variants are thought to additively contribute to as much as 50% of the total risk for autism. In this thesis, I investigate the contribution of common genetics variants (including SNPs, and InDels) to autism and related traits. In Chapter 1, I discuss the recent advances in the field of autism genetics, focussing on the contribution of common genetic variants to the risk for autism. Chapters 2 – 7 report the results of various studies investigating the genetic correlates of autism and related traits. In Chapter 2, I surveyed the evidence for 552 candidate genes associated with autism, and conducted a meta-analysis for 58 common variants in 27 genes, investigated in at least 3 independent cohorts. Meta-analysis did not identify any SNPs that were replicably associated with autism in the Psychiatric Genetics Consortium genome-wide association study (PGC-GWAS) dataset after Bonferroni correction, suggesting that candidate gene association studies are not statistically well-powered. In Chapters 3 – 7, I conducted genome-wide association studies (GWAS) for 6 traits associated with autism: self-reported empathy (N = 46,861, Chapter 3), cognitive empathy (N = 89,553, Chapter 4), theory of mind in adolescents (N = 4,577, Chapter 5), friendship satisfaction (Neffective = 158,116) and family relationship satisfaction (Neffective = 164,112, both Chapter 6), and systemizing (N = 51,564, Chapter 7). GWAS identified significant loci for self-reported empathy, systemizing, friendship and family relationship satisfaction, and cognitive empathy. Genetic correlation analyses replicably identified a significant negative genetic correlation between autism and family relationship satisfaction and friendship satisfaction, and a significant positive genetic correlation between autism and systemizing. In addition, there was a negative genetic correlation between autism and self-reported empathy. Chapter 8 draws all of these studies together, concluding that there may be at least two independent sources of genetic risk for autism: one stemming from social traits and another from non-social traits. I discuss some future directions about how this can be leveraged using polygenic scores from multiple phenotypes to potentially stratify individuals within the autism spectrum, and both the strengths and limitations of the reported studies.