Polygenic risk scores (PRS) are relatively novel tools for risk prediction, serving as a quantitative singular value which depicts a patient’s genetic disposition for a certain disease. Given that many current clinical risk predictors do not address heritability within their calculations, PRS are likely to improve prediction, especially in the case of complex diseases which are influenced by a combination of genetic, environmental and lifestyle factors. Altogether, PRS studies have been pursued for their abilities in trait detection, therapeutic intervention and disease protection, with much potential in personalized/precision medicine where each interpretation is unique and based on a patient’s genotype. However, despite the numerous advances over years, PRS have yet to reach the level where they can be implemented into standard clinical practices as originally intended. The goal is to develop PRS which are applicable to global populations, which has yet to be achieved due to the inconsistency and general skepticism regarding the method. Furthermore, PRS have yet to reach the upper threshold for risk prediction, as indicated by the heritability that remains unaccounted for with PRS calculations. Thus, this thesis addresses how PRS can inform and guide clinical decision-making for complex decisions with strong, genetic dispositions. It also presents novel approach to PRS aimed at mitigating some of its current limitations. / Thesis / Doctor of Philosophy (PhD) / Many common diseases, like coronary artery disease (CAD) and diabetes, are influenced not only by lifestyle and environmental factors, but also by genetics. Therefore, incorporating genetic information into disease risk prediction for patients in clinical settings would be logical, especially since genetic data can be obtained early in life. One tool for quantifying risk based on genetics is the polygenic risk score (PRS). PRS assigns a numerical value based on an individual’s genetic profile, calculated by summing up risk variants in their DNA. The risk level corresponds to the variant’s association with the trait, as determined by genome-wide association studies (GWAS). PRS have become increasingly popular for guiding disease treatment and personalized medicine. However, there’s still work to be done to make PRS suitable for clinical use. Many methods have attempted to enhance the predictive ability of PRS, but there’s still room for improvement. This thesis introduces various applications for PRS, along with a novel prediction method that potentially addresses some limitations and explores the applications of PRS in common diseases.

This thesis examines various methods for generating multi-trait polygenic risk scores (PRS). The primary objective is to see which multi-trait method performs best and are there any simpler methods that can perform as well. The thesis evaluates each method by comparing the weighted-average multi-trait PRS with true phenotype values (target traits), using the correlation coefficient (ρ) for continuous traits and the area under the receiver operating characteristic curve (AUC) for binary traits. It also investigates how different simulation parameters influence performance. Two additional novel multi-trait PRS methods are introduced in this work: mt-lm and mt-CVb. mt-lm is essentially a multiple linear regression for a continuous focal trait and logistic regression for a binary focal trait, while mt-CVb combines cross-validation and bagging techniques in a hybrid approach to improve model performance. The existing multi-trait method wMT-SBLUP consistently achieves the best performance, outperforming all other methods in most scenarios. While the two novel methods are not the top performers, they demonstrate better results compared to other methods (excluding wMT-SBLUP) for both continuous and binary focal traits across various parameter settings. Moreover, mt-lm offers the additional advantage of being faster than wMT-SBLUP. / Thesis / Master of Science (MSc)

Genome-wide approaches including polygenic risk scores (PRSs) are now widely used in medical research; however, few studies have been conducted in low- and middle-income countries (LMICs), especially in South America. This study was designed to test the transferability of psychiatric PRSs to individuals with different ancestral and cultural backgrounds and to provide genome-wide association study (GWAS) results for psychiatric outcomes in this sample. The PrOMIS cohort (N = 3308) was recruited from prenatal care clinics at the Instituto Nacional Materno Perinatal (INMP) in Lima, Peru. Three major psychiatric outcomes (depression, PTSD, and suicidal ideation and/or self-harm) were scored by interviewers using valid Spanish questionnaires. Illumina Multi-Ethnic Global chip was used for genotyping. Standard procedures for PRSs and GWAS were used along with extra steps to rule out confounding due to ancestry. Depression PRSs significantly predicted depression, PTSD, and suicidal ideation/self-harm and explained up to 0.6% of phenotypic variation (minimum p = 3.9 × 10−6). The associations were robust to sensitivity analyses using more homogeneous subgroups of participants and alternative choices of principal components. Successful polygenic prediction of three psychiatric phenotypes in this Peruvian cohort suggests that genetic influences on depression, PTSD, and suicidal ideation/self-harm are at least partially shared across global populations. These PRS and GWAS results from this large Peruvian cohort advance genetic research (and the potential for improved treatments) for diverse global populations. / National Institutes of Health / Revisión por pares

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Yes / Importance: Myopia is a leading cause of untreatable visual impairment and is increasing in prevalence worldwide. Interventions for slowing childhood myopia progression have shown success in randomized clinical trials; hence, there is a need to identify which children would benefit most from treatment intervention. Objectives: To examine whether genetic information alone can identify children at risk of myopia development and whether including a child’s genetic predisposition to educational attainment is associated with improved genetic prediction of the risk of myopia. Design, Setting, and Participants: Meta-analysis of 3 genome-wide association studies (GWAS) including a total of 711 984 individuals. These were a published GWAS for educational attainment and 2 GWAS for refractive error in the UK Biobank, which is a multisite cohort study that recruited participants between January 2006 and October 2010. A polygenic risk score was applied in a population-based validation sample examined between September 1998 and September 2000 (Avon Longitudinal Study of Parents and Children [ALSPAC] mothers). Data analysis was performed from February 2018 to May 2019. Main Outcomes and Measures: The primary outcome was the area under the receiver operating characteristic curve (AUROC) in analyses for predicting myopia, using noncycloplegic autorefraction measurements for myopia severity levels of less than or equal to −0.75 diopter (D) (any), less than or equal to -3.00 D (moderate), or less than or equal to −5.00 D (high). The predictor variable was a polygenic risk score (PRS) derived from genome-wide association study data for refractive error (n = 95 619), age of onset of spectacle wear (n = 287 448), and educational attainment (n = 328 917). Results: A total of 383 067 adults aged 40 to 69 years from the UK Biobank were included in the new GWAS analyses. The PRS was evaluated in 1516 adults aged 24 to 51 years from the ALSPAC mothers cohort. The PRS had an AUROC of 0.67 (95% CI, 0.65-0.70) for myopia, 0.75 (95% CI, 0.70-0.79) for moderate myopia, and 0.73 (95% CI, 0.66-0.80) for high myopia. Inclusion in the PRS of information associated with genetic predisposition to educational attainment marginally improved the AUROC for myopia (AUROC, 0.674 vs 0.668; P = .02), but not those for moderate and high myopia. Individuals with a PRS in the top 10% were at 6.1-fold higher risk (95% CI, 3.4–10.9) of high myopia. Conclusions and Relevance: A personalized medicine approach may be feasible for detecting very young children at risk of myopia. However, accuracy must improve further to merit uptake in clinical practice; currently, cycloplegic autorefraction remains a better indicator of myopia risk (AUROC, 0.87). / PhD studentship grant from the College of Optometrists (Drs Guggenheim and Williams; supporting Mr Mojarrad) entitled Genetic prediction of individuals at-risk for myopia development) and National Institute for Health Research (NIHR) Senior Research Fellowship award SRF-2015-08-005 (Dr Williams). The UK Medical Research Council and Wellcome grant 102215/2/13/2 and the University of Bristol provide core support for the Avon Longitudinal Study of Parents and Children (ALSPAC). A comprehensive list of grants funding is available on the ALSPAC website (http://www.bristol.ac.uk/alspac/external/documents/grant-acknowledgements.pdf). This research was conducted using the UK Biobank Resource (application 17351). The UK Biobank was established by the Wellcome Trust, the UK Medical Research Council, the Department for Health (London, England), the Scottish government (Edinburgh, Scotland), and the Northwest Regional Development Agency (Warrington, England). It also received funding from the Welsh Assembly Government (Cardiff, Wales), the British Heart Foundation, and Diabetes UK.

Yes / Background: Myopia has been shown to have a complex mode of inheritance, being influenced by both genetic and environmental factors. Here, an introduction into myopia genetics is given, with the shortcomings of current genetic prediction for myopia discussed, including the proportionally limited research on genetic prediction in people of non-European ancestry. A previously developed genetic risk score derived from European participants was evaluated in participants of non-European ancestry. Methods: Participants from UK Biobank who self-reported their ethnicity as “Asian”, “Chinese”, or “Black” and who had refractive error and genetic data available were included in the analysis. Ancestral homogeneity was confirmed using principal component analysis, resulting in samples of 3500 Asian, 444 Chinese, and 3132 Black participants. A published refractive error GWAS meta-analysis of 711,984 participants of European ancestry was used to create a weighted genetic risk score model which was then applied to participants from each ethnic group. Accuracy of genetic prediction of refractive error was estimated as the proportion of variance explained (PVE). Receiver operating characteristic (ROC) curves were developed to estimate myopia prediction performance at three thresholds: any myopia (equal to or more than 0.75D), moderate myopia (between -3.00D and -4.99D) and high myopia (equal to or more than -5.00D). Odds ratios for myopia were calculated for the participants in the top 10th or 5th percentile of genetic risk score distribution, comparing them to the remainder of the population. Results: The PVE value for refractive error was 6.4%, 6.2%, and 1.5% for those with Asian, Chinese and Black ethnicity, respectively (compared to 11.2% in Europeans). Odds ratios for any myopia and moderate myopia development for those within the top 10th and 5th percentile of genetic risk were significant in all ethnic groups P<0.05). However, the genetic risk score was not able to reliably identify those at risk of high myopia, other than for participants of Chinese ethnicity (P<0.05). Conclusion: Prediction of refractive error in Asian, Chinese and Black participants was ~57%, 55% and 13% as accurate in comparison to prediction in European participants. Further research in diverse ethnic populations is needed to improve prediction accuracy. / This research has been conducted using the UK Biobank Resource (applications #17351). UK Biobank was established by the Wellcome Trust; the UK Medical Research Council; the Department for Health (London, UK); Scottish Government (Edinburgh, UK); and the Northwest Regional Development Agency (Warrington, UK). It also received funding from the Welsh Assembly Government (Cardiff, UK); the British Heart Foundation; and Diabetes UK. Collection of eye and vision data was supported by The Department for Health through an award made by the NIHR to the Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust, and UCL Institute of Ophthalmology, London, United Kingdom (grant no. BRC2_009). Additional support was provided by The Special Trustees of Moorfields Eye Hospital, London, United Kingdom (grant no. ST 12 09). Many parts of this project were performed during the time that author Neema Ghorbani Mojarrad was supported by the College of Optometrists with a Postgraduate Scholarship.

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Deficits in a number of cognitive domains have been associated with core symptoms of schizophrenia, including working memory, attention, motor skills, reaction time, episodic memory and executive function. Bipolar Disorder is also associated with cognitive impairment; however the level of impairment appears to be less severe than that seen in schizophrenia. A translocation (t(1;11)) containing the Disrupted-in-Schizophrenia 1 (DISC1) gene has been found to be highly associated with schizophrenia, bipolar disorder and major depressive disorder. As such, this gene has been the focus of much research and to date DISC1 has been found to be associated with brain development, brain structure and the glutamate system - all key factors in current models of schizophrenia and affective disorders. The aim of this PhD is to identify cognitive domains that are differentially impaired or unimpaired in a large Scottish family, some of whom carry this rare DISC1 variant, a balanced translocation (t (1;11) (q 42; q14.3)), that segregates with schizophrenia and affective disorders, as well as psychiatric patients with schizophrenia and bipolar disorder and healthy control subjects. All participants have undergone standardised cognitive assessments to measure premorbid I.Q. (NART), current I.Q. (WASI) verbal memory, working memory, verbal fluency, processing speed, motor skills, executive function (BACS) and selected CANTAB tasks to assess simple and five-choice reaction time. Polygenic risk profile scores and self-report questionnaire data have also been investigated. Results indicate an impact of the DISC1 t(1;11) translocation on general intelligence and attention and processing speed. Significant differences were also identified between DISC1 t(1;11) carriers and non-carriers on self-report questionnaire data. Mean scores for polygenic risk for bipolar disorder were significantly different between DISC1 t(1;11) carriers and non-carriers and polygenic risk for schizophrenia was significantly associated with symptom severity, as measured by the Positive and Negative Symptom Scale (PANSS). Within the patient groups, a measure of processing speed (the token motor task) was found to be significantly different between those with schizophrenia and bipolar disorder and there was also a trend for attention and processing speed. As expected, I.Q. was significantly different between patients and control participants. Clinical ratings were significantly associated with neuropsychological and self-report measures. Polygenic risk for major depressive disorder was found to be significantly associated with impaired general intelligence (current IQ) and slowed reaction time in patients who were not currently depressed, suggesting there may be genetic risk markers in this population which impact on cognition. This is a novel finding and further suggests the possibility of a biological component related to the genetics of depression. In conclusion, and in line with the literature, psychosis has a negative impact on cognition with reduced performance across several neuropsychological tasks between patient groups, with schizophrenia patients performing worse than patients with bipolar disorder and both patient groups performing worse than healthy control participants. Cognition is markedly more impaired in DISC1 t(1;11) translocation carriers and especially in those with psychosis. The DISC1 t(1;11) translocation and psychosis may therefore confer a “double hit” on cognition - in addition to psychosis itself - which is known to impair cognitive function, significantly increasing the level of cognitive impairment and increasing the risk for psychosis in general.

Alcohol use (AU) and alcohol use disorder (AUD) are leading causes of morbidity, premature death, and economic burden. They are also associated with high levels of disability and many other negative outcomes. Twin and family studies have consistently shown that AU and AUD are complex traits influenced by both genetic and environmental factors. Although much has been learned about the genetic and environmental etiology of AU and AUD, significant gaps remain. These include the need for a more comprehensive understanding of the roles of risk and protective factors, and the nature of developmental trajectories underpinning the progression from AU to AUD. The aims of this dissertation are: (1) to examine the roles of resilience and personality disorders in the etiology of AU and AUD; (2) to investigate the nature of longitudinal changes in genetic and environmental risk factors responsible for individual differences in AU; and (3) to determine the moderating roles of key environmental risk factors on the impact of aggregate molecular, or polygenic, risk for AU during adolescence. Using both biometrical behavioral genetic and molecular genetic methodologies, five key findings were observed: (1) Resilience is strongly associated with a reduction in risk for AUD, and this relationship appears to be the result of overlapping genetic and shared environmental influences; (2) Borderline and antisocial personality disorders are the strongest and most stable personality pathology predictors of the phenotypic and genotypic liability to AU and AUD across time; (3) Genetic influences on the development of AUD from early adulthood to mid-adulthood are dynamic, whereby two sets of genetic risk factors contribute to AUD risk; (4) The specific genetic influences on AU follow an unfolding pattern of growth over time, whereas unique environmental risk factors are consistent with an accumulation of environmental impacts and risks across time; and (5) High peer group deviance and low parental monitoring are associated with increased AU, while early parental monitoring moderates the polygenic risk for AU at age 20. The implications of these results with regard to prevention and intervention efforts are discussed.

Indiana University-Purdue University Indianapolis (IUPUI) / Determining an individual’s genetic susceptibility in complex diseases like Alzheimer’s disease (AD) is challenging as multiple variants each contribute a small portion of the overall risk. Polygenic Risk Scores (PRS) are a mathematical construct or composite that aggregates the small effects of multiple variants into a single score. Potential applications of PRS include risk stratification, biomarker discovery and increased prognostic accuracy. A systematic review demonstrated that methodological refinement of PRS is an active research area, mostly focused on large case-control genome-wide association studies (GWAS). In AD, where there is considerable phenotypic and genetic heterogeneity, we hypothesized that PRS based on endophenotypes, and pathway-relevant genetic information would be particularly informative. In the first study, data from the NIA Alzheimer’s Disease Neuroimaging Initiative (ADNI) was used to develop endophenotype-based PRS based on amyloid (A), tau (T), neurodegeneration (N) and cerebrovascular (V) biomarkers, as well as an overall/combined endophenotype-PRS. Results indicated that combined phenotype-PRS predicted neurodegeneration biomarkers and overall AD risk. By contrast, amyloid and tau-PRSs were strongly linked to the corresponding biomarkers. Finally, extrinsic significance of the PRS approach was demonstrated by application of AD biological pathway-informed PRS to prediction of cognitive changes among older women with breast cancer (BC). Results from PRS analysis of the multicenter Thinking and Living with Cancer (TLC) study indicated that older BC patients with high AD genetic susceptibility within the immune-response and endocytosis pathways have worse cognition following chemotherapy±hormonal therapy rather than hormonal-only therapy. In conclusion, PRSs based on biomarker- or pathway- specific genetic information may provide mechanistic insights beyond disease susceptibility, supporting development of precision medicine with potential application to AD and other age-associated cognitive disorders.