Risk-taking behavior (RTB) is defined as behavior involving the probability of reward with concurrent probability of some negative outcome. Peer influence is among the most robust predictors of RTB, such that greater peer influence, particularly deviant or delinquent peer influence, is associated with increased RTB. Evidence suggests that those with genetic predispositions for RTB may also be more susceptible to peer influence as a function of genotype. Given that genetic polymorphisms within the dopaminergic system have evidenced associations with various forms of RTB and delinquent peer affiliation, it is possible that these genes may interact with peer influence to predict increased RTB, a process called gene × environment interaction (G×E). We expected that those genetically at risk would take more risks in the presence of a peer than alone. To test this effect, five polymorphisms within the dopaminergic system were genotyped in a sample of 85 undergraduate students. Participants completed a behavioral risk task alone and in the presence of a peer providing "risky" feedback. No significant G×Es were identified for any of the dependent variables. However, participants took significantly more risks in the presence of a risky peer than when taking risks alone. These results suggest that G×E may not be a relevant process for peer-influenced RTB during late adolescence. It is possible that G×E is a relevant process during early adolescence, while gene-environment correlation (rGE) is the dominant process during late adolescence. Future research would benefit from testing whether these genes are relevant to G×E in early adolescence, as well as to rGE during late adolescence.

Anxiety is the most commonly reported mental health problem among adolescents. Still, many adolescents in need of treatment are not detected and the clinical characteristics and etiological pathways of adolescent anxiety are under-researched topics. This thesis examined the clinical utility of the Swedish versions of the Spence Children’s Anxiety Scale (SCAS) and the clinical characteristics of multiple anxiety disorders among psychiatrically referred adolescents, and the influence of parenting and oxytocin gene (OXT) variants on anxiety among adolescents in the general population.  Studies employed cross-sectional and longitudinal designs and were based on questionnaire, interview, and genotype data. Support for the reliability and validity of both SCAS and SCAS-P was obtained. The overall ability to predict anxiety among referred adolescents ranged from fair to excellent for both scales.  Among adolescents psychiatrically referred for any reason, the prevalence of any anxiety disorder was 46%. Homotypic comorbidity was observed in 43%, and heterotypic comorbidity in 91%. Early adolescent anxiety influenced homotypic anxiety in late adolescence independent of parental rejection and control. The mediating role of parenting was small with indirect effect sizes no larger than one-tenth the size of direct effects, irrespective of the informant on parenting behavior. Significant interaction effects with positive and negative parenting were observed for OXT variants rs4813625 and rs2770378 in relation to social anxiety. The nature of the interactions was in line with the differential susceptibility framework for rs4813625, whereas for rs2770378, results indicated a diathesis–stress type of interaction. The findings suggest that psychiatrically referred adolescents with anxiety disorders are best characterized as a highly complex patient group and call attention to the necessity of structured assessment. For this purpose, this thesis provides evidence for the clinical utility of the SCAS; routine utilization of this questionnaire can improve detection of adolescents in need of anxiety treatment. Findings of this theses further suggest that the influence of positive and negative parenting behaviors on anxiety may be of greater importance among some adolescents than others, depending on individual differences in sensitivity to parenting. The etiology of anxiety among adolescents may therefore involve differential susceptibility effects of the interplay between genes and parenting behaviors.

Gene-environment (GE) interactions involving the IGF pathway may affect childhood obesity. Detecting such interactions using longitudinal family studies requires accounting for individual and familial correlations. Simulations were performed to study three methods to test for GE interactions in longitudinal family data using repeated outcomes (linear mixed model) or individual outcome averages as summary statistics (twin model, partition based score I test). Interactions between the IGF pathway genes (IGF-1, IGFALS) and environmental factors (physical activity, daycare attendance and sleep duration) were tested using the Quebec Newborn Twin Study data. The twin model yielded the best performance. Results from the QNTS analysis showed suggestive association for an IGF-1 variant at position 102791894 of chromosome 12 interacting with physical activity. However, this association was not statistically significant after multiple testing correction. More robust methods and studies are needed to better understand the IGF pathway’s role in childhood obesity.

Objective: To investigate the association of previously reported single nucleotide polymorphisms (SNPs) in relation to orofacial clefts and assess their interaction with environmental factors. Methods: Genome-wide SNP genotypes were obtained for case-parent triads from the EUROCRAN and ITALCLEFT studies. Candidate SNPs were selected from a previous genome-wide association study (Shi et al., 2012) along with surrounding SNPS for a total of 2142 genotyped and imputed SNPs. A total of 411 case-parent triads and 25 case-parent dyads were analyzed using log-linear models to test for maternal and parent-of-origin effects along with their interaction with maternal smoking and maternal folic acid consumption. Results: A significant association (q = 0.025) was detected for a region in the ATXN3 gene. This significance refers to the interaction between maternal periconceptional smoking and maternal genetic effects. Nominally significant associations in genes relating to the brain were also detected. Conclusion: SNPs in the ATXN3 region warrant further investigation.

Genome-wide association studies(GWAS) are used to find associations betweengenetic markers and diseases. One part of GWAS is to study interactions be-tween markers which can play an important role in the risk for the disease. Thesearch for interactions can be computationally intensive. The aim of this thesiswas to improve the performance of software used for gene-environment interac-tion by using parallel programming techniques on graphical processors. A studyof the new programs performance, speedup and efficiency was made using mul-tiple simulated datasets. The program shows significantly better performancecompared with the older program.

Synthetic xenoestrogens have differential estrogenic properties. Research has shown that exposures to xenoestrogens could promote breast cancer by disrupting normal function of the human epidermal growth factor receptor 2 (Her2) gene. Although animal models demonstrated a connection between xenoestrogen exposure and Her2 activity, no study using human cells has systematically examined their carcinogenic potential influencing the Her2 gene expression. Furthermore, breast cancer cells are phenotypically disparate (ER+, Her2+), with some phenotypes (Her2+), leading to more aggressive disease. This study aimed to dosimetrically assess the carcinogenic potential of commonly used xenoestrogens influencing Her2 gene expression, and delineate cellular phenotypes at greater risk of more aggressive disease. The study assessed whether the composition, concentrations, and exposure duration of BPA, EE, NPH, and DDT significantly altered Her2 copy numbers in estrogen and Her2 receptor positive or negative breast cancer lines. Each line was randomly assigned to cases (exposed) and control (unexposed) groups using a randomized block design. Fluorescent in-situ hybridization measured Her2 gene copies. Mann Whitney, Kruskal Wallis, and Incidence Rate Ratios revealed Her2 copy gains in all 4 xenoestrogens and receptor types with persistent exposures. A 44% increase in Her2 was observed in the normal ER and Her2 line, marking a shift in its Her2 status, and a 30-times greater risk was noted in the Her2+ lines. These findings promote positive social change by revealing all 4 xenoestrogens as risk factors for breast cancer. This information can be used by breast cancer advocacy groups, health educators, and steering committees to educate women and formulating policies.

The missing heritability in genome-wide association studies (GWAS) is an intriguing open scientific problem which has attracted great recent interest. The interaction effects among risk factors, both genetic and environmental, are hypothesized to be one of the main missing heritability sources. Moreover, detection of multilocus interaction effect may also have great implications for revealing disease/biological mechanisms, for accurate risk prediction, personalized clinical management, and targeted drug design. However, current analysis of GWAS largely ignores interaction effects, partly due to the lack of tools that meet the statistical and computational challenges posed by taking into account interaction effects. Here, we propose a novel statistically-based framework (Significant Conditional Association) for systematically exploring, assessing significance, and detecting interaction effect. Further, our SCA work has also revealed new theoretical results and insights on interaction detection, as well as theoretical performance bounds. Using in silico data, we show that the new approach has detection power significantly better than that of peer methods, while controlling the running time within a permissible range. More importantly, we applied our methods on several real data sets, confirming well-validated interactions with more convincing evidence (generating smaller p-values and requiring fewer samples) than those obtained through conventional methods, eliminating inconsistent results in the original reports, and observing novel discoveries that are otherwise undetectable. The proposed methods provide a useful tool to mine new knowledge from existing GWAS and generate new hypotheses for further research. Microarray gene expression studies provide new opportunities for the molecular characterization of heterogeneous diseases. Multiclass gene selection is an imperative task for identifying phenotype-associated mechanistic genes and achieving accurate diagnostic classification. Most existing multiclass gene selection methods heavily rely on the direct extension of two-class gene selection methods. However, simple extensions of binary discriminant analysis to multiclass gene selection are suboptimal and not well-matched to the unique characteristics of the multi-category classification problem. We report a simpler and yet more accurate strategy than previous works for multicategory classification of heterogeneous diseases. Our method selects the union of one-versus-everyone phenotypic up-regulated genes (OVEPUGs) and matches this gene selection with a one-versus-rest support vector machine. Our approach provides even-handed gene resources for discriminating both neighboring and well-separated classes, and intends to assure the statistical reproducibility and biological plausibility of the selected genes. We evaluated the fold changes of OVEPUGs and found that only a small number of high-ranked genes were required to achieve superior accuracy for multicategory classification. We tested the proposed OVEPUG method on six real microarray gene expression data sets (five public benchmarks and one in-house data set) and two simulation data sets, observing significantly improved performance with lower error rates, fewer marker genes, and higher performance sustainability, as compared to several widely-adopted gene selection and classification methods. / Ph. D.

Decades of work has led researchers to believe that risk for complex behavioral phenotypes, such as alcohol use disorders, is likely influenced by multiple genes of small effect acting in conjunction with each other and the environment. Currently, the field of psychiatric genetics is developing methodologies for the identification of genetic risk variants that predispose individuals to the development of complex behavioral disorders. Several challenges related to the complex and polygenic nature of these phenotypes, must be considered. This dissertation study attempts to address these important challenges in the context of alcohol use disorders and related phenotypes. A rich twin and family study literature has indicated that 40-70% of the variance in alcohol use disorders (AUDs) is influenced by genetics. Recent attempts to identify specific x genetic risk variants associated with AUDs have been met with limited success. Meanwhile, evidence of the moderating effects of the environment on AUDs has been mounting, providing a strong rationale for examining gene-environment interaction. In the following chapters several studies will be described that integrate established twin methodologies into gene identification projects in an effort to reduce heterogeneity (both phenotypic and genotypic), elucidate environmental constructs that moderate genetic influences, and to enhance statistical power to detect the subtle genetic influences on alcohol related phenotypes.

O advento das tecnologias de sequenciamento de DNA e sua revolução na ciência tem gerado uma quantidade imensa e sem precedentes de informações moleculares. Assim, estudos atuais em diversas áreas objetivam principalmente analisar a associação entre centenas a milhões de variantes genéticas e fenótipos de interesse. Dentre essas variações moleculares, destaque tem sido dado aos SNPs (polimorfismos de nucleotídeo único) e CNVs (variações no número de cópias), os quais têm sido implicados na variabilidade e manifestação de diversos fenótipos, incluindo os relacionados à atividade fisica e desempenho esportivo. No Brasil, algumas iniciativas têm trazido luz à contribuição genética nessas características, como o Projeto Atletas do Futuro e o Projeto Corações de Baependi. Considerando a alta miscigenação que caracteriza a população brasileira, a qual traz grandes desafios, e levando em conta que este último estudo é pioneiro em considerar a estrutura familiar com uma riqueza de informações moleculares e fenotípicas única, nosso objetivo neste trabalho é, fazendo uso desses dados, investigar o papel de variantes genéticas, em particular SNPs e CNVs, na manifestação de comportamentos sedentários e no engajar em atividade física leve, moderada e intensa, verificando a possível existência de heterogeneidades relativamente ao sexo dos indivíduos. As informações referentes a SNPs e CNVs são provenientes do Affymetrix Genome-Wide Human SNP Array 6.0 que, após processamento e limpeza, consiste de um número final de cerca de 843.039 SNPs e 8.974 CNVs. Dados fenotípicos de atividade física e sedentarismo para 760 indivíduos foram derivados do questionário IPAQ-SF e ajustados por uma medida de gasto energético de equivalentes metabólicos de tarefa (METs). A análise descritiva dessas variáveis mostrou uma prevalência de atividade física de 55,3%, sendo maior para homens que para mulheres. Além disso, utilizando os modelos lineares mistos poligênicos e a abordagem de componentes de variância, estimamos a herdabilidade (h2) desses fenótipos obtendo valores de 0,21, 0,11, 0,22 e 0,28 para atividade física total, leve, moderada-vigorosa e sedentarismo, respectivamente. Foi identificado heterogeneidade em relação ao sexo, em geral com h2 de homens sendo maiores que a de mulheres. O mapeamento gênico (GWAS) de SNPs e CNVs identificou potenciais picos de associação sob a correção de Bonferroni e sob um critério mais flexível, especialmente nos cromossomos 3, 5 e 6. Essas variantes carecem ainda de informação quanto às suas funções biológicas, as quais podem ser melhor compreendidas através de procedimentos de anotação usando bases de dados como o SCAN. / The onset of DNA sequencing technologies and its revolution in Science generates an unprecedent and large amount of molecular information. Thus, the current studies in multiple areas aim to evaluate the association between hundreds to thousands of genetic variants and phenotypes of interest. Among these variants, the ones that have received most of the focus are Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs), which have been implicated in the variability and manifestation of multiple phenotypes, including the ones related to physical activity and sports performance. In Brazil, some initiatives have brought light to the genetic contribution in these features, such as the project Atletas do Futuro and the project Corações de Baependi. The later is a pioneer study that considers the pedigree structure of a highly admixed population with a unique and rich amount of molecular and phenotypic information. Thus, our role is to investigate the role of genetic variants, in particular SNPs and CNVs, in the manifestation of sedentary behaviour and practice of light, moderate and vigorous physical activity, checking for the existence of heterogeneity related to sex. SNP and CNV information was acquired through the Affymetrics TM 6.0 SNP Array, processed and cleaned, leading to a final number of 843,039 SNPs. and 8,794 CNVs. Sedentarism and physical activity data of 760 individuals were gathered through the IPAQ-SF and adjusted by a measure of metabolic energy cost named metabolic equivalent tasks (METs). The descriptive analysis showed a total physical activity prevalence of 55.3% and mens one was higher than womens. In addition, using linear mixed polygenic model and the variance components approach, we estimated the heritability of these phenotypes obtaining the values 0.21, 0.11, 0.22 e 0.28 for total, weak, moderate-vigorous physical activities and sedentary behaviour, respectively. There was sex-related heterogeneity in the h2, with men having higher estimates than women for most of the evaluated phenotypes. In addition, GWAS of SNPs and CNVs showed several potential candidate markers, especially after using a more flexible significance criteria. These markers were present mainly in chromosomes 3, 5 and 6, and their possible biological functions remain to be clarified through annotation procedures, using databases such as SCAN.

This thesis investigated (1) social status and shaming experiences in relation to aggressive behaviour and depression, and (2) gene-environment interactions between two genetic polymorphisms related to the serotonergic system – MAOA-VNTR and 5HTTLPR – and experiences of maltreatment in relation to delinquent behaviour and depression among adolescents. The four included studies are based on questionnaire data from the Survey of Adolescent Life in Vestmanland 2006 (SALVe-2006). A total of 5396 students in 9th (15-16 years old) grade of elementary school and 2nd (17-18 years old) grade of high school comprised the target population. The students in 2nd grade of high school also provided a saliva sample for gene extraction. There were strong associations between shaming experiences and both aggressive behaviour and depression. In addition, individuals who reported many shaming experiences and had either low or high social status had increased risks of physical aggression or depression, whereas medium social status seemed to have a protective effect. Gene-environment interactions were found between experiences of maltreatment and the MAOA-VNTR in relation to delinquent behaviour. Moreover, the direction of the gene-environment interaction differed depending on sex: boys with the short (S) variant of the MAOA-VNTR, in contrast to girls with the long (LL) variant, had the highest risk of delinquency in combination with maltreatment. Gene-environment interactions were also found between experiences of maltreatment and the 5HTTLPR in relation to depression among girls. The girls that were homozygous for the S allele (SS) had the highest risk of depression in combination with maltreatment. Among boys however, no gene-environment interaction was found between the 5HTTLPR and maltreatment in relation to depression. In conclusion, it is important to consider both genetic effects, and psychosocial factors such as social status, shaming experiences, and experiences of maltreatment when investigating different aspects of health and behaviour among adolescents.