Atypical hemolytic uremic syndrome (aHUS) is characterized by acute renal failure, thrombocytopenia, and microangiopathic hemolytic anemia. aHUS is far less common and more severe than typical HUS, which is caused by E. coli infection and manifests as diarrheal illness. The pathogenesis of the disease is linked to dysregulation of the alternative pathway of the complement cascade. Mutations in the complement regulators factor H (CFH), membrane cofactor protein (MCP), factor B (CFB), and factor I (CFI) have been implicated in aHUS. These loss or gain of function mutations lead to uncontrolled complement activity and immune-mediated host cell damage. Establishing a genetic etiology is important as it helps to direct treatment during the acute phase of disease and when transplantation is considered. It has been shown in previous studies that the age of onset as well the severity of the disease is correlated with the type of mutation a patient is found to carry. In forty percent of aHUS patients a mutation in CFH, MCP, CFB, CFI, C3 or THBD is not detected. These data strongly suggest that other genetic factors are involved in the pathogenesis of aHUS and that comprehensive mutation detection in aHUS patients is essential to provide diagnostic and prognostic information, and improve their clinical care. My thesis work has aimed to identify the other genetic contributors to this disease. To achieve this goal we began by screening the largest American cohort of aHUS patients for mutations in CFH, MCP, CFB, CFI, C3, THBD as well as CFHR5. This study identified over thirty novel mutations and suggests a more comprehensive genetic screening method that would better serve patients. To complement these studies multiplex ligation-dependent probe amplification was used to detect genetic rearrangements within the factor H related genes. A number of unique fusion proteins were seen in aHUS patients, all of which are predicted to affect the function of CFH. To discover mutations in novel genes that are causally related to aHUS, we have optimized a platform called CASCADE (Capture and Sequencing of Complement-Associated Disease Exons), which is based on targeted-genome capture and next-generation sequencing. This study revealed an unexpected role for ADAMTS13 and other genes in the coagulation pathway as modifiers of aHUS. Using functional assays we show two of the ADAMTS13 variants alter the behavior of this protein. This work has changed how we view this disease by identifying several novel candidate genes, for which we hope future analysis will lead to a better understanding of their role in aHUS. Using this knowledge we can provide better and more personalized treatments for patients.

High-throughput sequencing technologies have changed the way we identify, study and understand the role of rare variation in Mendelian diseases. Sequencing in complex diseases have proven to be more challenging to interpret, but methods and approaches are being developed to aid in our understanding of variation in these diseases.

The genome-wide association study (GWAS) approach has identified novel loci for a variety of complex diseases. However, for most of these disorder much of the heritability is not explained by this approach, which focuses on identifying common variants that are associated with disease risk. The unexplained heritability may be due to genetic or phenotypic heterogeneity or the influence of rare variants. The motivation behind this thesis was to uncover the unexplained heritability by applying joint analyses of sets of variants (gene-based association test) and multiple disease-related phenotypes (called multivariate gene-based association test). First, we evaluated multivariate gene-based methods for detecting association of common genetic variants with correlated phenotypes. An extensive simulation study showed that the method combining the MultiPhen and GATES software performed best for most tested scenarios especially when correlations among phenotypes are relatively low. We developed a new multivariate gene-based test using rare variants called VEMPHAS. A simulation study using VEMPHAS showed that this method correctly controls for type I error in all tested scenarios. We applied VEMPHAS to analysis of various phenotypes related to Alzheimer disease (AD) and found suggestive association (P < 4.15x10-6) with the gene TRIM22, which has been identified in a previous sequencing study of AD onset in PSEN1/2 mutation carriers. We also developed software with a graphical user interface which is designed for integrating information from different types of data sources including genetic data (from GWAS or sequencing), expression data (from RNA-Seq), and protein structures (from protein data banks). This software has several features including 1) testing associations between genetic variants and gene expressions; 2) locating amino acids, encoded by the variants, in a protein structure; and 3) retrieving genetic locations (chromosome and base pair positions) of amino acids of interest in the protein structure. The last feature can be applied for prioritizing coding variants for gene-based association testing. The methods and strategies developed for this dissertation project can effectively uncover a portion of the remaining heritability of complex diseases that is unexplained by traditional GWAS approaches.

Elevated risk of cardiometabolic disease is magnified by variation in body fat distribution, in particular increased accumulation of visceral fat. Genome-wide association studies have mainly focused on anthropometric indices such as WHR and BMI to assess adiposity. They successfully identified over 100 loci highlighting for total fat mainly pathways in the brain involved in the regulation of energy expenditure and appetite and for fat distribution genes expressed in adipose and the periphery. Although genetic variants affecting localised fat deposition are known, the functional mechanisms of regional fat accumulation remain poorly understood. Here, we aimed to explore the genetic contribution to body composition to gain further mechanistic insight, and increase our understanding of the role of such genetic variants in metabolic health. We focused on the isolated population of Orkney. 1,301 participants from the Orkney Complex Disease Study, ORCADES underwent DXA scans allowing direct assessment of fat mass in various depots around the body. Genetic data imputed to the 1000 Genomes Project enabled the investigation of 35 million genetic variants. We first used univariate and bivariate analysis to quantify the contribution of genetic factors to the variation of body composition and establish genetic correlations with metabolic traits. We carried out genome-wide association analyses for body composition to identify new underlying genetic loci. We sought to replicate these findings in the Icelandic AGES cohort and the UK Biobank, with 3,219 and 1,575 participants with body composition analysis, respectively. We investigated the coding variation or the regulatory landscape around the associated variants to understand their functional impact. We further focused on one of the associated loci in greater detail. To establish a potential, causal gene for the associated variants and understand the impact of genetic variation on the regulatory elements, we carried out chromatin conformation studies around ENPP6 by. We then explored the role of causal gene candidate on body composition and metabolic health in an animal mouse model. Individual fat depots were moderately heritable with heritability estimates ranging from 35-50% in ORCADES. The genetic correlations with metabolic traits were highest with android, and visceral fat and the ratio of android and gynoid fat percentage: Insulin (0.68-0.75), HOMA-B (0.58-0.70), HOMA-IR (0.69-0.75), CRP (0.47-0.55) and DBP (0.49-0.58). Genome-wide association analysis identified three regions associated with body composition: VRTN, EXOC6B and ENPP6. Low frequency variants on chromosome 4, mapping within the ENPP6 gene associated with the ratio of android and gynoid fat (p= 4.5x10-10), which replicated in abdominal fat by CT in AGES (p=0.003). Per allele, variant carriers show a reduction in android fat by 3% and visceral fat of 140g as well as lowered diastolic blood pressure of 10mmHg. Due to this evidence ENPP6 was chosen as a focus for further mechanistic and functional studies. The lead SNPs map to an ENCODE-predicted DNase1 hypersensitivity site within the second intron of the ENPP6 gene, suggesting a role in genome regulation. Marking the areas with sequence-specific probes by 3D fluorescent in situ hybridisation confirmed that the association interval co-localised more frequently with the ENPP6 promoter than with other gene promoters within the same chromosomal region in SH-SY5Y neurons (p=0.01) but not human SGBS adipocytes. This indicates ENPP6 as a possible causal gene. Consistent with this ENPP6 mRNA levels were extremely low in human subcutaneous and visceral adipose tissue. ENPP6 expression is highest in the brain and kidney, suggesting a neuronal/renal mediated mechanism driving body composition. To model the impact of Enpp6 on adiposity in vivo, Enpp6-/- mice were generated and their metabolic profile investigated. Enpp6-/- mice showed a decrease in visceral fat depot and improved glucose tolerance (n= 24, pfat=0.002, pGTT=0.001). However, no difference was found with regards to their feeding or physical activity behaviour, suggesting an intrinsic alternative to maintaining an energy balance. Using the advantage of genetic drift in a population isolate and direct fat phenotyping we confirmed the contribution of genetic variants to variation in body composition and describe the involvement of three particular loci VRTN, EXOC6B and ENPP6. In particular, we describe ENPP6 as a likely neuronal mechanism underlying selectively visceral adiposity in humans and mice. This study sets a starting point for the investigation into ENPP6 as an anti-obesity and anti-diabetes therapeutic.

<p>Linkage in the 2q37 region was evaluated using microsatellite markers in multi-case families from Sweden, Iceland and Norway. Both the two-point and the multipoint linkage analysis show highly significant LOD scores (Z=4.51 and 6.03, respectively). Linkage disequilibrium mapping indicates that some association exists in this region. The <i>PDCD1</i> gene was suggested as a candidate gene within the 2q37 locus due to its importance in immune regulation. Indeed, one haplotype, described by the presence of allele A of the PD1.3 SNP located within intron 4 of this gene, shows linkage to SLE in the Nordic families. The PD1.3A allele is also found to be strongly associated in familiar and sporadic cases of SLE in Europeans and Mexicans. Functional studies further support PD1.3A to be a susceptibility allele for SLE.</p><p>The 1q23 region, containing the genes for the low affinity Fcγ receptors, was fine mapped using single- and multi- case families of various origins. Genetic variants of those genes were analysed and association is found to both the risk alleles of <i>Fc</i>γ<i>RIIA</i> and <i>Fc</i>γ<i>RIIIA</i> in all families. In these families, a single haplotype carrying both risk alleles is predominantly transmitted to patients with SLE, suggesting a presence of linkage disequilibrium between those two genes. <i>Fc</i>γ<i>RIIA</i> and <i>Fc</i>γ<i>RIIIA</i> are also found to be associated to SLE and lupus nephritis in a case-control cohort from Sweden. In the same cohort, the PD1.3A allele shows strong association to lupus nephritis. We suggest that there may be an additive effect between <i>Fc</i>γ<i>RIIA</i> and <i>PDCD1</i>, since having the disease-associated genotypes at both loci gives an increased risk for developing lupus nephritis.</p><p>Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disorder with a complex multifactorial aetiology. Genetic studies suggest that several genes are involved in disease pathogenesis and that extended genetic heterogeneity is present.</p>

<p>The aim with this thesis has been to identify genes involved in the pathogenesis of Systemic Lupus Erythematosus (SLE). SLE is a systemic autoimmune disorder, most likely caused by both several genetic and environmental factors. </p><p>In order to identify susceptibility loci for the disease we performed linkage analyses on data from 70 families of various ethnic origins. Significant linkage was found in two regions. One region (chromosome 17p12-q11) was linked to SLE in a set of Argentine families. Since the same region had been previously identified in several linkage studies on Multiple Sclerosis patients, we propose that this locus may contain a genetic variant that affects not only SLE, but also autoimmunity in general. The second locus is located on chromosome 4p14-13 and has only been identified in a set of Icelandic families. We suggest that this locus contains a mutation that has been enriched in the Icelandic population due to its population history.</p><p>The <i>BCL2 </i>gene has been suggested as a candidate gene for SLE. Three markers in this gene were investigated for association with the disease in two different populations. However, no association could be found with any of the markers or when these markers were analysed together as a haplotype. We conclude that the <i>BCL2</i> gene is not associated with SLE in our material. This result contradicts previously published results of an association between <i>BCL2</i> and SLE. </p><p>We suggest that the PD-1 pathway (involved in inhibition of T- and B-cell responses) is an important component in SLE pathogenesis. A regulatory variant in the <i>PD-1</i> gene had previously been associated with SLE and here we show strong association (p<0.0001) to a haplotype containing SNPs in both <i>PD-L1</i> and <i>PD-L2</i>. </p><p>Our results indicate that SLE is a disease caused by several genetic variations that differ between families and populations.</p>

Linkage in the 2q37 region was evaluated using microsatellite markers in multi-case families from Sweden, Iceland and Norway. Both the two-point and the multipoint linkage analysis show highly significant LOD scores (Z=4.51 and 6.03, respectively). Linkage disequilibrium mapping indicates that some association exists in this region. The PDCD1 gene was suggested as a candidate gene within the 2q37 locus due to its importance in immune regulation. Indeed, one haplotype, described by the presence of allele A of the PD1.3 SNP located within intron 4 of this gene, shows linkage to SLE in the Nordic families. The PD1.3A allele is also found to be strongly associated in familiar and sporadic cases of SLE in Europeans and Mexicans. Functional studies further support PD1.3A to be a susceptibility allele for SLE. The 1q23 region, containing the genes for the low affinity Fcγ receptors, was fine mapped using single- and multi- case families of various origins. Genetic variants of those genes were analysed and association is found to both the risk alleles of FcγRIIA and FcγRIIIA in all families. In these families, a single haplotype carrying both risk alleles is predominantly transmitted to patients with SLE, suggesting a presence of linkage disequilibrium between those two genes. FcγRIIA and FcγRIIIA are also found to be associated to SLE and lupus nephritis in a case-control cohort from Sweden. In the same cohort, the PD1.3A allele shows strong association to lupus nephritis. We suggest that there may be an additive effect between FcγRIIA and PDCD1, since having the disease-associated genotypes at both loci gives an increased risk for developing lupus nephritis. Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disorder with a complex multifactorial aetiology. Genetic studies suggest that several genes are involved in disease pathogenesis and that extended genetic heterogeneity is present.

The aim of this thesis has been to identify genetic variants that increase the susceptibility for Systemic Lupus Erythematosus (SLE), an autoimmune disease caused by a complex interplay between various genetic and environmental factors. Five different candidate genes were selected through different strategies, and were analysed for association with SLE in an attempt to distinguish some of the underlying mechanisms of this disease. Two of these genes, PD-L1 and PD-L2, appeared not to contain any major risk factors for SLE in the analysed European and Latin American populations. In two other genes, CD24 and STAT4, there appeared to be population-specific effects. The A57V amino acid substitution in the CD24 gene, previously implicated with multiple sclerosis, was associated in a Spanish cohort, with a weak trend in German samples, and no association in Swedish. The previously reported and highly convincing association of the STAT4 transcription factor gene was confirmed in all our cohorts. Interestingly, the results indicate the presence of at least two independent risk variants: the first, represented by a previously reported SNP, was the strongest in individuals of Northern European ancestry, and the second was more pronounced in individuals from Southern Europe and Latin America. We also report the identification of a novel susceptibility gene. The BANK1 gene, encoding a scaffold protein involved in B-cell activation, contains functional variants affecting important domains, which are associated in all investigated cohorts from Europe and Latin America. These results confirm the existence of replicable associations between genetic variants and SLE, which are common and present in many populations. The results also illustrate a certain degree of heterogeneity, where some risk factors could have variable effect in different populations.

The aim with this thesis has been to identify genes involved in the pathogenesis of Systemic Lupus Erythematosus (SLE). SLE is a systemic autoimmune disorder, most likely caused by both several genetic and environmental factors. In order to identify susceptibility loci for the disease we performed linkage analyses on data from 70 families of various ethnic origins. Significant linkage was found in two regions. One region (chromosome 17p12-q11) was linked to SLE in a set of Argentine families. Since the same region had been previously identified in several linkage studies on Multiple Sclerosis patients, we propose that this locus may contain a genetic variant that affects not only SLE, but also autoimmunity in general. The second locus is located on chromosome 4p14-13 and has only been identified in a set of Icelandic families. We suggest that this locus contains a mutation that has been enriched in the Icelandic population due to its population history. The BCL2 gene has been suggested as a candidate gene for SLE. Three markers in this gene were investigated for association with the disease in two different populations. However, no association could be found with any of the markers or when these markers were analysed together as a haplotype. We conclude that the BCL2 gene is not associated with SLE in our material. This result contradicts previously published results of an association between BCL2 and SLE. We suggest that the PD-1 pathway (involved in inhibition of T- and B-cell responses) is an important component in SLE pathogenesis. A regulatory variant in the PD-1 gene had previously been associated with SLE and here we show strong association (p&lt;0.0001) to a haplotype containing SNPs in both PD-L1 and PD-L2. Our results indicate that SLE is a disease caused by several genetic variations that differ between families and populations.

Cervical cancer is the forth most commonly diagnosed cancer among women worldwide. It is caused by persistent infection with an oncogenic type of Human Papillomavirus (HPV). The HPV is a necessary but not sufficient cause of cervical cancer. Environmental factors such as smoking, high parity and long-term use of oral contraceptives increases the risk of cervical cancer. Genetic factors also affect the risk of developing the disease. The aim of this thesis is to search for and evaluate genetic risk factors for cervical cancer using both a candidate gene approach and a genome-wide association study (GWAS). Paper I examined the association of genetic variation in three Fanconi Anemia (FA) genes (FANCA, FANCC and FANCL), involved in DNA repair, with cervical cancer susceptibility in the Swedish population. No association was observed. Paper II evaluated the association of genetic variation in the TMC6 and TMC8 genes with susceptibility to cervical cancer in the Swedish population and an association of two SNPs (rs2290907 and rs16970849) with cervical cancer was observed.  In paper III the first GWAS performed in cervical cancer was reported. Three independent loci in the major histocompatibility complex (MHC) region at 6p21.3 were found to affect the susceptibility to cervical cancer. Paper IV examined the sequence variation in the TMC6 and TMC8 region and its association with cervical cancer. A highly polymorphic 21 bp sequence was identified and found to be repeated 5 to 42 times in both cases and controls. Lack of this repeat was associated with increased risk of cervical cancer. An intronic SNP (rs2926778) located in between the TNRC6C and TMC6 genes was also found to be associated with cervical cancer. The thesis provides evidence for the importance of genes in the immune system for cervical cancer susceptibility. The genetic risk factors identified explain only a part of the genetic susceptibility, implying that other risk factors remains to be identified