Background: Canada continues to face an opioid epidemic with 5,368 opioid apparent related deaths occurring between January and September of 2021. Methadone Maintenance Treatment (MMT), a form of Medication Assisted Treatment used to treat Opioid Use Disorder (OUD), has been reported to decrease opioid cravings and opioid use, however, individual differences exist in the effective dose of methadone. Further, individuals living with an OUD have higher rates of substance use including cannabis. A genetic component has been suggested to exist for both cannabis use and MMT outcomes, however inconsistent findings have been reported. Methods: Knowledge synthesis and primary genetic association studies were conducted. A protocol was prepared for the planning of a systematic review for Genome-Wide Association Studies (GWASs) of cannabis use. The full systematic review was then conducted, providing an assessment of the literature and a description of studies quality. A GWAS and Polygenic Risk Score (PRS) was then conducted for cannabis use and MMT outcomes, separately, in Europeans only. The top Single Nucleotide Polymorphisms (SNPs) were then analyzed separately by sex and sex interactions were conducted. Results: The systematic review included 6 studies, identifying 96 genetic variants associated with cannabis use. The GWASs for both cannabis use and MMT outcomes did not identify any significant results. A significant PRS was found for regular cannabis use and methadone dose. No sex-specific results were identified. Discussion: This thesis summarised the evidence on the genetics of cannabis use as well as employed GWASs and PRSs to investigate cannabis use and MMT outcomes within a European population. We were able to highlight gaps within the genetic literature of cannabis and MMT outcomes as well as identify areas of interest for future research. / Dissertation / Doctor of Philosophy (PhD) / Cannabis use rates in Canada are increasing, with Opioid Use Disorder (OUD) patients having high rates of cannabis use despite inconsistent findings on the impacts. To combat the opioid crisis, Methadone Maintenance Treatment (MMT) is utilized to reduce opioid cravings and use. However, individuals on MMT are likely to use other substances, including cannabis. This thesis explores the genetic literature on cannabis use and conducts a Genome-Wide Association Study (GWAS) and a Polygenetic Risk Score (PRS). The GWAS investigates genetic variants throughout the whole genome associated with a trait, while the PRS creates a genetic weight risk score. GWAS and PRS methods were used to investigate cannabis use and MMT outcomes within Europeans with OUD. While no significant GWAS results were found, a statistically significant PRS was found for regular cannabis use and methadone dose, suggesting each respective score can estimate an individual’s risk of that trait.

Polygenic risk scores are scores used in precision medicine in order to assess an individual's risk of having a certain quantitative trait based on his or her genetics. Previous works have shown that machine learning, namely Gradient Boosted Regression Trees, can be successfully applied to calibrate the weights of the risk score to improve its predictive power in a target population. Neural networks are a very powerful class of machine learning algorithms that have demonstrated success in various elds of genetics, and in this work, we examined the predictive power of a polygenic risk score that uses neural networks to perform the weight calibration. Using a single neural network, we were able to obtain prediction R2 of 0.234 and 0.074 for height and BMI, respectively. We further experimented with changing the dimension of the input features, using ensembled models, and varying the number of splits used to train the models in order to obtain a nal prediction R2 of 0.242 for height and 0.0804 for BMI, achieving a relative improvement of 1.26% in prediction R2 for height. Furthermore, we performed extensive analysis of the behaviour of the neural network-calibrated weights. In our analysis, we highlighted several potential drawbacks of using neural networks, as well as machine learning algorithms in general when performing the weight calibration, and o er several suggestions for improving the consistency and performance of machine learning-calibrated weights for future research. / Thesis / Master of Science (MSc)

Background: South Asians are at an increased risk of developing dysglycemia during and after pregnancy. In pregnant women, dysglycemia often develops in the form of gestational diabetes mellitus (GDM), which may predispose their newborns to adverse health outcomes through abnormal cord blood insulin levels. However, reasons for the elevated risk of dysglycemia in South Asians have not been extensively studied. Genetic factors may contribute to the heritability of GDM and abnormal cord blood insulin levels in South Asians. Objectives: The objectives of this thesis were to test the association of: 1) A type 2 diabetes polygenic risk score with GDM in South Asian pregnant women from the South Asian Birth Cohort (START); 2) maternal and newborn insulin-based polygenic risk scores with cord blood insulin and glucose/insulin ratio in South Asian newborns from START Methods: Three polygenic risk scores were created to test their association with participant data (N=1012) from START. GDM was defined using cut-offs established by the Born in Bradford cohort of South Asian women. The type 2 diabetes polygenic risk score was created in 832 START mothers and included 35,274 independent variants. The maternal and newborn insulin-based polygenic risk scores were created in 604 START newborns and included 1128017 independent variants. Univariate and multiple logistic and linear regression models were used to test the associations between the polygenic risk scores and dysglycemia outcomes. Results: The type 2 diabetes polygenic risk score was associated with GDM in both univariate (OR: 2.00, 95% CI: 1.46-2.75, P<0.001), and multivariable models (OR: 1.81, 95% CI: 1.30-2.53, P<0.001). The maternal insulin-based polygenic risk score was not associated with cord blood insulin or cord glucose/insulin ratio. However, the newborn insulin-based polygenic risk score was associated with cord blood insulin in a multivariable model adjusted for maternal insulin-based polygenic risk score (β = 0.036, 95% CI: 0.002 – 0.069; P=0.038 among other factors. Conclusion: A type 2 diabetes polygenic risk score and a newborn insulin-based polygenic risk score may be associated with maternal and newborn dysglycemia. / Thesis / Master of Science (MSc) / Background: South Asians are approximately two times more at risk for developing gestational diabetes mellitus (GDM) compared to white Caucasians. Genetic factors may contribute to this elevated risk. Polygenic risk scores (PRSs), which combine the effects of multiple disease loci and variants associated with the disease into one variable could be useful in further understanding how GDM develops in South Asians. Methods: Data from the South Asian Birth Cohort (START) was used to test the association of three PRSs with the outcomes of interest. Results: The type 2 diabetes PRS was independently associated with GDM. The insulin-based maternal PRS was not associated with cord blood insulin but the insulin-based newborn PRS was independently associated with cord blood insulin. However, neither the insulin-based maternal nor newborn PRS was associated with cord blood glucose/insulin ratio. Conclusion: The PRSs suggests a possible genetic component, which contributes to abnormal glycemic status development in South Asian mothers and their newborns.

Sleep disturbances and insomnia are prevalent, with around 33% of adults indicating that they experience at least one main symptom of insomnia, and bidirectional relationships exist with common psychopathology, particularly major depressive disorder (MDD). However, genetic and environmental (e.g., traumatic event exposure) contributions to the etiology of these phenotypes are not yet well understood. A genetically informative sample of approximately 12,000 Han Chinese women aged 30-60 (50% with recurrent MDD) was used to address several gaps within the sleep literature. Sleep disturbances were assessed in all individuals using a general item addressing sleeplessness (GS). A sleep within depression sum score (SDS) was also created in MDD cases, combining information from the GS and two insomnia items within MDD. A total of 11 traumatic events were assessed and additional information on childhood sexual abuse (CSA) was also obtained. First, factor analyses were conducted to determine trauma factor structure. The best-fit solution included 3 factors: interpersonal, child interpersonal, and non-assaultive, and composite variables were constructed accordingly. A series of hierarchical regressions were run to examine differential effects of trauma type and timing on sleeplessness. All traumatic events predicted sleeplessness at similar magnitudes, although population models indicated that childhood interpersonal trauma may be particularly potent. An association between CSA and sleeplessness was also replicated. A series of genetic analyses demonstrated that the single nucleotide polymorphism-based heritability of sleep phenotypes did not differ significantly from zero. Further, association analyses did not identify any genome-wide significant loci. However, using a liberal false discovery rate threshold of 0.5, two genes of interest, KCNK9 and ALDH1A2, emerged for the SDS. Polygenic risk score (PRS) analyses demonstrated genetic overlap between the SDS in MDD cases and GS in MDD controls, with PRSs explaining 0.2-0.3% of the variance. A final combined model of both genetic and environmental risk indicated that both PRS and traumatic events were significant predictors of sleeplessness. While genetic results should be interpreted with caution given the lack of heritability, additional research into the genetic and environmental contributions to insomnia, utilizing more standardized phenotypes and properly ascertained samples, is clearly warranted.

Family-based and genome-wide association studies (GWAS) of alcohol dependence (AD) have reported numerous associated variants. The clinical validity of these variants for predicting AD compared to family history has not yet been reported. These studies aim to explore the aggregate impact of multiple genetic variants with small effect sizes on risk prediction in order to provide a clinical interpretation of genetic contributions to AD. Data simulations showed that given AD’s prevalence and heritability, a risk prediction model incorporating all genetic contributions would have an area under the receiver operating characteristic curve (AUC) approaching 0.80, which is often a target AUC for screening. Adding additional environmental factors could increase the AUC to 0.95. Using the Collaborative Study on the Genetics of Alcoholism (COGA) and the Study of Addiction: Genes and Environment (SAGE) GWAS samples, we used several different sources to capture genetic information associated with AD in discovery samples, and then tested genetic sum scores created based on this information for predictive accuracy in validation samples. Scores were assessed separately for single nucleotide polymorphisms (SNPs) associated in candidate gene studies and in GWAS analyses. Candidate gene sum scores did not exhibit significant predictive accuracy, but SNPs meeting less stringent p-value thresholds in GWAS analyses did, ranging from mean estimates of 0.549 for SNPs meeting p<0.01 to 0.565 for SNPs meeting p<0.50. Variants associated with subtypes of AD showed that there is similarly modest and significant predictive ability for an externalizing subtype. Scores created based on all individual SNP effects in aggregate across the entire genome accounted for 0.46%-0.57% of the variance in AD symptom count, and have AUCs of 0.527 to 0.549. Additional covariates and environmental factors that are correlated with AD increased the AUC to 0.865. Family history was a better classifier of case-control status than genetic sum scores, with an AUC of 0.686 in COGA and 0.614 in SAGE. This project suggests that SNPs from candidate gene studies and genome-wide association studies currently have limited clinical validity, but there is potential for enhanced predictive ability with better detection of genetic factors contributing to AD.

Schizophrenia is a severe psychiatric disorder associated with cognitive impairments. Polygenic risk for schizophrenia (SCZ-PGR) has been associated with poor performance in cognitive tasks, both in patients and in healthy individuals. It has also been suggested that schizophrenia is associated with accelerated aging. This study examines the association between SCZ-PGR and accelerated non-pathological cognitive aging by performing longitudinal analyses using linear mixed-effects models. We hypothesize that higher SCZ-PGR is associated with accelerated rate of cognitive decline in healthy elderly. The study sample consist of 1746 Caucasian individuals with genetic data. Their performance in general cognition, episodic memory, semantic memory and visuospatial memory was tested over 25 years. SCZ-PGR was significantly associated with poor cognitive function but was not associated with cognitive decline over time with any of the cognitive domains. Our results indicate that genetics of schizophrenia may not be associated with rate of cognitive aging. / Schizofreni är en svår psykiatrisk sjukdom som är associerad med kognitiv nedsättning. Polygenetisk risk för schizofreni (SCZ-PGR) har associerats med sämre resultat på kognitiva test, både hos schizofrenipatienter och friska individer. Det har även föreslagits att schizofreni är associerad med accelererat åldrande. Denna studie avser undersöka associationen mellan SCZPGR och accelererad icke-patologisk kognitivt åldrande genom att genomföra longitudinella analyser i lineära mixade-effekt-modeller. Vår hypotes är att högre SCZ-PGR är associerad med accelererad kognitivt åldrande hos friska. I denna studie ingår 1746 deltagare, där deltagarnas kognitiva förmåga testades under 25 år. Vi analyserade deras SCZ-PGR i relation till generell kognitiv förmåga, episodminne, semantiskt minne och visuo-spatialt minne, samt associationen mellan SCZ-PGR och förändringen av dessa variabler över tid. SCZ-PGR var signifikant associerad med sämre kognitiv förmåga, men inte med kognitiv försämring över tid. Dessa resultat indikerar att gener relaterade till schizofreni inte är associerade till kognitivt åldrande.

<p>Complex traits are influenced by genetic and environmental factors and their interactions. Most common human disorders such as cardiovascular, metabolic, autoimmune, and neurological diseases are complex. Understanding their genetic architecture and etiology is an important step to prevent, diagnose and treat these conditions. Genome Wide Association Studies (GWAS) have emerged as a powerful and widely used tool that can be used to explore and identify the genetic variants associated with complex traits. In this dissertation, we present some of the downstream applications of GWAS studies to analyze and understand the genetic risk and etiology of complex traits and provide important insights into the genetic architecture and background of several complex phenotypes. First, we examined whether prevalence of complex disorders around the world correlates to Polygenic Risk Scores (PRS). To do so, we determined the average PRS of 14 such complex disorders across 24 world populations using results of GWAS studies. We found variation in risk across populations and significant correlation was obtained between average disease risk and prevalence for seven of the studied disorders. Further exploring the power of PRS- based calculations, we performed a PRS - based phenome wide association study (PheWAS) for Tourette Syndrome (TS) and identified 57 phenotypic outcomes significantly associated with TS PRS. The strongest associations were found between TS PRS and mental health factors. Cross- disorder comparisons of phenotypic associations with genetic risk for other childhood-onset disorders (e.g.: attention deficit hyperactivity disorder [ADHD], autism spectrum disorder [ASD], and obsessive-compulsive disorder [OCD]) indicated an overlap in associations between TS and these disorders. Furthermore, we performed a sex specific PheWAS that highlighted differences in associations of complex disorders with TS PRS in males and females. Finally, we used large- scale GWAS results to identify causal associations between different biological markers (proteins, metabolites, and microbes) and subcortical brain structure volumes using Mendelian Randomization (MR) analysis. We identified eleven proteins and six metabolites to be significantly associated with subcortical brain volume structures. Enrichment analysis indicated that the associated proteins were enriched for proteolytic functions and regulation of apoptotic pathways. Overall, our work demonstrates the power of GWAS studies to help disentangle the genetic basis of complex diseases and also provides important insights into the etiology of the studied complex traits. </p>

No description available.

No description available.

京都大学 / 新制・論文博士 / 博士(医学) / 乙第13398号 / 論医博第2222号 / 新制||医||1051(附属図書館) / (主査)教授 妹尾 浩, 教授 中山 健夫, 教授 西浦 博 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM