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.

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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.

Genome-wide association studies in multifactorial diseases have contributed to our understanding of genetic risk and defined specific disease-associated loci in particular populations. However, risk cannot be fully explained by genetics and evidence points to both genetic and environmental factors being important in causation and pathophysiology. The role of vitamin D in calcium homeostasis is well established. Over the last 30 years it has become clear that vitamin D has a wider role in physiology and disease, notably in autoimmune, cancer and infectious conditions. However, the molecular mechanisms and possible causal role of these associations are poorly understood. Here I propose that the role of vitamin D in immune and inflammatory responses is significant, that genetic variation partly determines the response to vitamin D and that integrative analysis can yield important insights for disease mechanisms. For this I investigate the relationship between vitamin D and genetic risk involving the immune system by focusing on multiple sclerosis and sepsis, conditions classically defined as autoimmune and inflammatory respectively. I describe data resolving genetic variation associated with autoimmune diseases in vitamin D receptor binding sites; the association to multiple sclerosis of a genetic variant lying within a VDR binding site; the correlation of plasma vitamin D with genotype and cell specific transcriptomes in healthy volunteers; and the extent of vitamin D deficiency in severe sepsis and septic shock, its association with survival, correlation with gene expression and use in sub-classification to identify patients at higher risk of death. The limitations of each study and future work are discussed. Integrating epidemiological and clinical observations with genetic and functional genomics techniques has the potential to reveal interactions in population specific disease susceptibility that may lead to an improved understanding of disease mechanisms and clinical translation. The work I present here bridges molecular analysis, candidate and genome- wide, with phenotypic observations that are important in our understanding of disease.

Tumor-like proliferative vascular lesions manifest in several diseases such as peripheral arterial disease (PAD) and atherosclerosis (AS) after arterial injury. The cause of the vascular cell dysfunction in PAD patients is not known. Our recent novel discovery shows that inhibitor of differentiation 3 (ID3) is highly expressed in intimal lesions of clinical vascular disease samples. The central hypothesis of our study is: estrogenic chemical induced dysregulation of ID3 target genes is involved in the development of vascular disease. NHANES data analysis demonstrated higher geometric levels of all 6 PCB congeners in both PAD diagnosed participants and participants at risk of AS when compared to the rest of the population. Adjusted models showed association between higher exposure of PCBs, phthalates, BPA, and increased risk of PAD. Furthermore PCB153 was shown to have the highest geometric mean amongst all PCB congeners in both participants diagnosed with PAD and at risk of AS. Gene expression of ID3 & ID3 candidate targets in blood & tissue studies identified ID3 & ID3 candidate target genes as a driver of vascular disease. Overlapping ID3 & ID3 candidate target genes included: ABCB6, ACP1, BYSL, CAD, CDH15, DCBLD2, DHRS3, DNMT1, ID3, MCM4, and NDUFA7. The ID3 target genes involved in the: focal adhesion pathway were ACTN1, COL1A2, COL3A1, COL6A1, CTNNB1, IBSP, ID3, ITGA8, and MYL2; ECM-receptor interaction were COL1A2, COL3A1, COL6A1, IBSP, ID3, and ITGA8; oxidative phosphorylation pathway ATP5D, ATP5H, ATP6V0B, ATP6V0D1, ATP6V1B2, COX5A, COX7C, COX8A, CYC1, ID3, NDUFA1, NDUFA7, NDUFS4, NDUFV1, NDUFV2; and cell cycle pathway ANAPC10, ATM, CDKN2B, E2F5, MCM3, and MCM4. In summary our results showed an association between exposure to PCBs, phthalates, BPA, and increased risk of PAD and AS, and possible molecular mechanisms of interaction of ID3 target genes and estrogenic chemicals involved in PAD and AS.

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.

The aim of this study is to evaluate the outcome of adoptions and to study the gene-environment influences on psychiatric illness as well as sick-leave patterns. The material consists of 2 966 adopted persons born between 1917 and 1949, their 5 932 adoptive parents and 5 438 identified biological parents.Adopted persons had a higher incidence of personality disorders and substance abuse than non-adopted controls. Adopted men also had an increased incidence of neuroses. Adopted women had an increased sick-leave because of somatic complaints, especially upper respiratory tract infections and abdominal complaints of short duration. Somatization i.e. more than 2 sick-leaves/year because of somatic complaint together with nervous complaints was more frequent among adopted women. Women with somatization could be separated into 2 types according to the pattern of sick-leave. Type 1 ("high frequency") had frequent sick-leaves for psychiatric, abdominal and back complaints. They also had a high frequency of alcohol abuse. Type 2 ("diversiform") had more diverse complaints and had fewer sick-leaves because of nervous complaints.High frequency somatizers had biological fathers with teenage onset of criminality and frequent registrations for alcohol abuse. Diversiform somatizers had the same genetic background as adopted men with petty criminality or male limited alcoholism.No specific genetic influences on treated depression or substance abuse were found in this study. However, a non-specific vulnerability of the biological mother influenced on the risk of depression and substance abuse among adopted women.There were some indications that placement in the adoptive home between 6 and 12 months of age was associated with reactive neurotic depression in adult life. Otherwise early negative experiences in term of unstable placements before adoption did not significantly influence on psychiatric illness in adulthood.Affective disorders in the adoptive father were associated with treatment for depressions or substance abuse in the adoptee. Low social status in the part of the adoptive father increased the risk of somatization of both types in the adoptee. / <p>S. 1-80: sammanfattning, s. 81-236: 6 uppsatser</p> / digitalisering@umu

The variability in caffeine consumption and inconsistencies among studies linking caffeine to heart disease may be explained by genetic variation. Caffeine antagonizes adenosine receptors with downstream effects on dopamine and serotonin. The objectives of this thesis were to determine whether the DRD2 957C>T or HTR2A 102C>T polymorphisms are associated with caffeine consumption or modify the association between coffee consumption and risk of myocardial infarction (MI). DRD2 genotype was associated with caffeine consumption among non-smokers and CYP1A2 -163C allele carriers. HTR2A genotype was associated with caffeine consumption among non-smokers and subjects with the ADORA2A TT genotype. Neither polymorphism modified the association between coffee consumption and risk of MI; however, a significant coffee x HTR2A interaction was seen among subjects with the CYP1A2 -163C allele. The results suggest caffeine’s reinforcing effects may be mediated by the dopamine and serotonin receptors and implicate serotonin in caffeine’s effect on risk of MI.

The variability in caffeine consumption and inconsistencies among studies linking caffeine to heart disease may be explained by genetic variation. Caffeine antagonizes adenosine receptors with downstream effects on dopamine and serotonin. The objectives of this thesis were to determine whether the DRD2 957C>T or HTR2A 102C>T polymorphisms are associated with caffeine consumption or modify the association between coffee consumption and risk of myocardial infarction (MI). DRD2 genotype was associated with caffeine consumption among non-smokers and CYP1A2 -163C allele carriers. HTR2A genotype was associated with caffeine consumption among non-smokers and subjects with the ADORA2A TT genotype. Neither polymorphism modified the association between coffee consumption and risk of MI; however, a significant coffee x HTR2A interaction was seen among subjects with the CYP1A2 -163C allele. The results suggest caffeine’s reinforcing effects may be mediated by the dopamine and serotonin receptors and implicate serotonin in caffeine’s effect on risk of MI.