There is a wide variation in the phenotypic expression, progression rates, therapy response and complications in Parkinson’s disease (PD). The primary research objective in this thesis was to analyse the variation in the 4 domains of phenotypic expression i.e. motor, non-motor, cognitive, and quality of life in a subset of early onset Parkinson’s disease (EOPD) patients from the PRoBaND study, in the United Kingdom. The secondary objective was to explore the factors responsible for this variation or heterogeneity in the clinical characteristics. Linking genotypes with phenotypes, besides evaluating environmental risk factors and iatrogenic influences, represents one mechanism of understanding this variation in the phenotypic expression of PD. We found subtle but significant variation across all domains of symptoms examined in this thesis by classifying patients into groups according to motor subtype, gender, age at diagnosis and heritability of the parkinsonian trait, despite statistically insignificant differences in risk factors such as head trauma, exposure to pesticides (including herbicides, insecticides, fungicides and fumigants), heavy metals, caffeine and a past history of oophorectomy (in females) with the exception of smoking (p=0.046) and exposure to solvents, which were more common in males compared to females (p<0.001). There were differences in the prevalence of motor symptoms such as balance problems being more prevalent in the postural instability gait difficulty (PIGD) subtype compared to the tremor dominant PD (TDPD) and ‘Mixed’ motor subtypes both subjectively (p<0.001) and objectively (p<0.001). Other axial problems such as speech difficulties and freezing were also more prevalent in those with the PIGD phenotype compared to the other motor subtypes both subjectively (p=0.004, p<0.001) and objectively (p=0.002, p<0.001). There was also variation in the prevalence of motor complications such as dyskinesia (p<0.001) and dystonia (p=0.020), being more prevalent in the PIGD subtype compared to other motor subtypes. 8 The prevalence of certain non-motor symptoms such as pain (p=0.022) and features of gastrointestinal dysfunction e.g. prandial bloating (p=0.024) and constipation (p=0.022) were more commonly reported by females compared to males. There were also differences in the prevalence of cognitive impairment (p=0.049) and neurobehavioural characteristics such as anxiety (p=0.002) and depression (p=0.006), after the diagnosis of PD, being more prevalent in PIGD compared to other motor subtypes. Finally, these differences contributed to the variation in the independence of activities of daily living scores which were lower in those with the PIGD phenotype compared to other motor subtypes (p<0.001). There were some differences in exposure to environmental risk factors for PD but not sufficient to explain all the variation. Iatrogenic influences from drugs contributed in part to the phenotypic variation. 10% of the cases in the EOPD cohort tested positive for mutations in one of three genes screened i.e. LRRK2, GBA and Parkin; their DNA remains banked and there is scope to test these cases for mutations in other genes, relevant to PD, in the future. There were too small numbers of cases in each subgroup to draw definite conclusions about the exact influence of genes on the overall phenotypic variation but differences between Parkin mutation carriers and gene test negative ‘controls’ such as early age of onset and long disease duration were obvious. PRoBaND is linked to other similar research studies in the UK, with the stated aim of sharing datasets, in the hope that larger numbers of patients and their DNA samples will increase the power, in statistical terms, to test hypotheses about the role of genetic markers in influencing the course and expression of symptoms. Our current understanding of PD as a complex trait suggests both genetic and environmental influences (including iatrogenic factors if patients are treated) play a role in the phenotypic expression of this condition. A lot more remains to be explored to improve our understanding of the finer details and molecular mechanisms underlying the variation in this disease.

The spinal cord dorsal horn is involved in the processing and transmission of sensory information to the brain. There are several distinct populations of dorsal horn projection cells that constitute the major output of the spinal cord. These cells are mostly found in lamina I and are scattered throughout the deep dorsal horn. There is a population of large lamina III projection cells that expresses the neurokinin 1 receptor (NK1r), which is the main target for substance P released by nociceptive primary afferents. These cells are densely innervated by peptidergic nociceptive afferents and more sparsely by low-threshold myelinated afferents. In addition, they also receive selective innervation from neuropeptide Y-containing inhibitory interneurons. However, not much is known about their input from glutamatergic spinal neurons. It has already been reported that the great majority of large lamina III NK1r expressing cells project to caudal ventrolateral medulla (CVLM) therefore in this study these cells were easily identified without retrograde tracer injection. Preliminary observations showed that these cells received contacts from preprodynorphin (PPD)-containing excitatory axons. The first part of the study tested the hypothesis that lamina III projection cells are selectively targeted by PPD-containing excitatory spinal neurons. Spinal cord sections from lumbar segments of the rat underwent immunocytochemical processing including combined confocal and electron microscopy to look for the presence of synapses at the sites of contact. The results showed that lamina III NK1r cells received numerous contacts from non-primary boutons that expressed vesicular glutamate transporter 2 (VGLUT2), and formed asymmetrical synapses on their dendrites and cell bodies. These synapses were significantly smaller than those formed by peptidergic afferents but provided a substantial proportion of the glutamatergic input to lamina III NK1r projection cells. Furthermore, it was observed that PPD was found to be present in ~58% of the VGLUT2 boutons that contacted these cells while a considerably smaller proportion of (5-7%) VGLUT2 boutons in laminae I-IV expressed PPD. These results indicate a highly selective targeting of the lamina III projection neurons by glutamatergic neurons that express PPD. Fine myelinated (Aδ) nociceptors are responsible for the perception of fast, well-localised pain. Very little is known about their postsynaptic targets in the spinal cord, and therefore about their roles in the neuronal circuits that process nociceptive information. In the second part of the study, Fluorogold injections were made into the lateral parabrachial region (LPb) of the rat brain on one side and cholera toxin B subunit (CTb) was injected into the sciatic nerve on the contralateral side to assess whether Aδ nociceptors provide input to lamina I projection cells. The vast majority of lamina I projection neurons belong to the spinoparabrachial tract, and these can be divided into two major groups: those that express NK1r, and those that do not. The results suggested that CTb labelled a distinct set of Aδ nociceptors, most of which lack neuropeptides. CTb-labelled Aδ afferents formed contacts on 43% of the spinoparabrachial lamina I neurons that lacked the NK1r, but on a significantly smaller proportion (26%) of NK1r projection cells. Combined confocal and electron microscopy established that the contacts were associated with synapses. Furthermore, the contact density of CTb labelled boutons was considerably higher on the NK1r- cells than on those with the NK1r. These results provide further evidence that primary afferents input to projection cells is organized in a specialized way and that both NK1r+ and NK1r- lamina I projection neurons are directly innervated by Aδ nociceptors, thus may have an important role in the perception of fast pain. Lamina I of the rat spinal cord dorsal horn contains a population of large spinoparabrachial projection neurons (giant cells) that receive numerous synapses from both excitatory (VGLUT2) and inhibitory (VGAT) interneurons. The giant cells are selectively innervated by GABAergic axons that express neuronal-nitric oxide synthase (nNOS) and are thought to originate from local inhibitory interneurons. In the rat, the nNOS inhibitory cells belong to a distinct functional population that differs from other inhibitory interneurons in terms of somatostatin receptor (sst2A) expression and also in responsiveness to painful stimuli. There is a population of inhibitory interneurons that express green fluorescent protein (GFP) in lamina II of mice in which GFP is under control of the prion promoter (PrP) and the great majority of these cells also express nNOS. In this part of the study, the inhibitory synaptic input from nNOS-containing GFP boutons to giant lamina I cells was investigated. The great majority of lamina I projection neurons express NK1 receptor; therefore, the possibility that lamina I NK1r-expressing projection neurons received innervation from GFP+/nNOS+ axons was also tested. Since retrograde tracing technique was not used in this part of the study, lamina I projection cells were identified based on the observations made in the previous studies in the rat. Lamina I giant cells were recognized with antibodies against glycine receptor associated protein gephyrin as well as VGLUT2 and VGAT boutons, all of which provide dense innervation to these cells while only those lamina I NK1cells were included in the sample that were large and strongly immunoreactive for NK1r. The results indicated that although GFP axons accounted for only 7-9% of the GABAergic boutons in superficial dorsal horn, they provided over 70% of the inhibitory synapses on most of the giant cells in the PrP-GFP mouse and the great majority of these boutons also contained nNOS. Moreover, a subset of large lamina I NK1r-expressing cells (18/60) received a substantial inhibitory input (> 30%) from GFP+ boutons while the majority of these neurons showed sparse (< 15%) synaptic input. Recently, it has been reported that loss of some inhibitory interneurons in mice lacking the transcription factor Bhlhb5 results in exaggerated itch, and the cells that are lost include many of those that would normally express nNOS. Therefore, in the final set of experiments was designed to test whether there is a reduction in the inhibitory synaptic input to the giant cells in Bhlhb5-/- mouse. Spinal cord sections from Bhlhb5-/- mice and the wild type littermates were processed and analysed to determine any difference in the inhibitory nNOS input to lamina I giant cells belonging to either group. The giant cells from the knockout mice showed a substantial reduction (~80%) in their inhibitory nNOS input; with a moderate reduction in their overall GABAergic input (~35%). There was a considerable increase in nNOS-/VGAT+ boutons in the Bhlhb5-/- mouse (18 ± 4.6 and 37.7 ± 8.2/100 µm of the dendrite in WT and KO, respectively), suggesting some compensation from other nNOS-negative inhibitory interneurons. These results suggest that the loss of nNOS-containing inhibitory synaptic input to lamina I projection cells may contribute to the abnormal scratching behaviour seen in the Bhlhb5-/- mouse. This raises the possibility that the giant cells and a subset of large lamina I NK1r-expressing cells are involved in perception of itch.

Parkinson’s disease (PD) is commonly treated with L-DOPA. Long-term treatment is associated with the development of motor side effects such as L-DOPA induced dyskinesia (LID), and pathological changes in the striatal circuitry. However, while this circuitry is implicated in both motor and non-motor behaviour, little is known about the effects of long-term L-DOPA treatment on non-motor function. This thesis used a rat model of PD and LID to test the hypothesis that long-term L-DOPA treatment also affects non-motor behaviour. Pharmacological studies typically utilise albino rats, while pigmented rats are preferred for operant studies. To guide later methodological decisions, Experiment 1 compared pigmented Listed Hooded and albino Sprague Dawley rats’ motor, dyskinetic, or operant response to L-DOPA. As there were no gross strain differences, and Lister Hooded rats are preferred in operant studies, they were used in later experiments measuring both LID and operant behaviour. Experiment 2 aimed to identify appropriate lesion screening tests. Success of unilateral 6-OHDA lesions is commonly measured using amphetamine-induced rotations. However, amphetamine interferes with goal-directed behaviour. The ability of amphetamine-induced rotations and four non-pharmacological motor tests to accurately identify lesion rats was therefore compared. The non-pharmacological spontaneous rotations and cylinder tests were identified as robust screening tests and used in later experiments. L-DOPA competes with dietary amino acids for transport across the blood-brain barrier, and chronic L-DOPA treatment sensitises dopamine receptors. It was therefore hypothesised that food restriction and chronic L-DOPA would both decrease the L-DOPA dose required to alleviate motor symptoms in the rat 6-OHDA model. Chapter 4 describes two dose response curves testing the effect of food restriction and chronic L-DOPA on the motor response to acute L-DOPA in rats with intra-striatal or MFB lesions. Chronic L-DOPA increased the motor response to acute L-DOPA in the MFB, but not intra-striatal, lesion model. Conversely, food restriction increased the motor response to acute L-DOPA in the intra-striatal, but not MFB, lesion model. Chapter 5 used microdialysis to test the hypothesis that the increased motor response following food restriction was caused by an increased influx of L-DOPA to the striatum. The data did not support the hypothesis but suggested that food restriction affects baseline neurotransmitter levels in the 6-OHDA lesion rat. Chapter 6 tested the hypothesis that LID onset, by disrupting cortico-striatal synaptic plasticity which is implicated in motor skill learning, impairs acquisition of novel motor skills by measuring rats’ performance on the staircase task. While an initial experiment suggested that chronic LID onset impaired lesion rats’ acquisition of the task, the phenomenon could not be replicated. Chapters 7 and 8 further explored the effect of chronic L-DOPA on non-motor function using a lateralized choice reaction time task reliant on the striatal system. Chronic L-DOPA exacerbated a lesion induced accuracy deficit that has been hypothesised to reflect extinction. This deficit was linked to LID onset, rather than L-DOPA exposure per se. The data therefore expand on current knowledge by suggesting that the effects of chronic L-DOPA extends beyond inducing motor side effects to also affect non-motor function.

interventions are recommended for people with bipolar disorder to enable them to effectively self-manage their health, prevent relapse and improve their long-term outcomes. Psychoeducation comprises expert information (on topics such as monitoring mood, lifestyle and medication) and is commonly presented by health care professionals in structured individual or group face-to-face sessions. This thesis reviewed the evidence from randomised controlled trials and qualitative studies that psychoeducational approaches in different formats may or may not be beneficial for patients with bipolar disorder, and consequently found the evidence base to be sparse, particularly with regard to the benefits and drawbacks of different formats of delivery. This thesis explores the feasibility, acceptability and impact of a group-based psychoeducation programme for people with bipolar disorder in Wales (Bipolar Education Programme – Cymru) and a novel internet-based psychoeducation programme (Beating Bipolar) for participants of a randomised controlled trial. Adopting a pragmatic approach, and using both qualitative and quantitative research methods in a predominantly qualitative study, I explored and compared both interventions from the perspectives of patients and facilitators, using qualitative interviews, data from the Beating Bipolar online discussion forum and quantitative outcome data from questionnaires. Findings principally describe the facilitators and barriers to delivery in different formats, what participants liked and disliked about the programmes, the potential impact of the programmes and recommendations for future use, and identify the potential therapeutic mechanisms of psychoeducation. Receiving social support from the groups and enhanced knowledge and understanding of bipolar disorder from the educational content and shared experiences were found to improve many participants’ self-reported confidence in their ability to manage their bipolar disorder, and many made beneficial changes to their lifestyles, coping strategies and their attitudes towards medication and bipolar disorder in general as a result. Future research should focus on widening access to both interventions.

Individuals with schizophrenia have severe cognitive impairments that impact upon their ability to function within society. Better understanding the genetic mechanisms underlying schizophrenia and cognition provides an opportunity for targeted pharmacological intervention. This thesis investigates common and rare genetic variation in schizophrenia and their associations with cognitive ability in schizophrenia cases and healthy controls. Polygenic risk of schizophrenia and bipolar disorder predicted ability on tests of cognitive domains affected in schizophrenia, performance, verbal and full scale IQ in healthy controls. Increased polygenic risk of schizophrenia was robustly associated with lower performance IQ at different training thresholds in two independent cognition samples. There was no consistent association between bipolar polygenic risk and cognition. Common genetic differences between schizophrenia and bipolar disorder were associated with verbal and full scale IQ. I investigated the hypothesis that 155 gene-sets across six biological categories relating to cognition, brain function and structure were enriched for SNPs influencing general cognitive ability. Schizophrenia polygenic pathway scores for gene-sets were not associated with general cognitive ability in schizophrenia patients, or performance IQ in healthy individuals. Separately, neither gene-sets vi nor general categories were enriched for common SNPs showing association with general cognitive ability in schizophrenia cases. Associations between rare CNVs and general cognitive ability were tested in schizophrenia cases. Cases with a known pathogenic CNV performed approximately one standard deviation below other schizophrenia cases on the MATRICS composite score. In addition, increases in the number of genes hit by large (>100kb) and rare (frequency <1%) CNVs were associated with lower general cognitive ability. However, the number of genes hit in gene-sets previously mentioned was not associated with the MATRICS composite score. These findings indicate genetic variation in schizophrenia is associated with cognitive ability in schizophrenia cases and healthy controls, providing direction for future research.

Disease (HD) is an autosomal dominant neurodegenerative disease caused by a CAG expansion on the HD gene on chromosome 4, which gives rise to an expanded polyglutamine (polyQ) tract in the huntingtin protein. HD is characterised primarily by motor abnormalities, but is also commonly associated with cognitive impairments and psychiatric disturbances. Huntingtin (HTT) dynamically shuttles between subcellular compartments, however the mutant huntingtin protein (mHTT) is mislocalised to cell nuclei, where it may interfere with nuclear functions, such as transcription. The phosphorylation of HTT has been implicated with the regulation of its subcellular localisation; however the mechanism by which the mislocalisation of mHTT occurs is currently unknown. The localisation of HTT in an immortalised embryonic striatal cell model of HD (StHdhQ111) was identified as being more nuclear with a longer polyQ length. Additionally, stimulation of StHdhQ111 lines with a panel of growth factors alters the apparent subcellular localisation of HTT in a polyQ length-dependent manner. Aberrant kinase responses to growth factor stimulation were identified by ELISA assay. Inhibition of AKT1 and MEK1 phosphorylation indicated that their activation may be involved in mHTT mislocalisation and immediate-early gene expression. Transcriptional dysregulation is a characteristic feature of HD pathogenesis that may be directly influenced by HTT localisation. Microarray analysis of differential gene expression responses to growth factor stimulation uncovered a potential role for SMAD transcription factor activity and the transforming growth factor-β pathway in HD pathogenesis. Primary embryonic striatal cells from the HdhQ111 and HdhQ150 mouse models of HD showed similarities to the StHdhQ111 cell model in terms of HTT localisation, kinase signalling and gene expression. Cellular dysfunction may therefore be an early HD phenotype that is present from embryogenesis, and potentially alters HD development and progression; aberrant control of kinase signalling may regulate mHTT mislocalisation, which in turn modulates transcriptional dysregulation and contributes to HD pathogenesis.

Huntington’s disease (HD) is an inherited neurodegenerative condition characterised by progressive motor, cognitive and psychiatric symptoms. The most frequent cause of death is respiratory failure, yet little is known about respiratory function through the progression of the disease or the underlying causes of respiratory failure. A thorough exploration of the relevant literature led to the development of a conceptual framework for respiratory failure in people with HD. Within this framework respiratory failure was characterised as type 1 hypoxaemic and type2 hypercapnic failure and further evaluated through (i) an observational study to investigate respiratory function in people with HD, and (ii) the benefit and feasibility of inspiratory muscle training in people with HD. In order to develop understanding of potential underlying causes of type 1 hypoxaemic and type 2 hypercapnic respiratory failure, the observation study aimed to investigate if there was a difference in respiratory function between healthy controls and people with HD at different stages of the disease, and to explore factors that may influence or be influenced by respiratory function. The framework was further evaluated through the intervention study which investigated the feasibility and benefit of inspiratory muscle training in people with HD as a method of increasing capacity of the respiratory system. Method In the observation study 67 people with HD and 39 healthy control participants underwent a series of measurements of respiratory function based on underlying causes of type 1 hypoxaemic respiratory failure and type 2 hypercapnic respiratory failure. These included measurement of lung volume, respiratory muscle strength and endurance. Exercise capacity, physical activity, swallow and posture as potential influencing factors were also measured in people with HD. In the intervention study 20 people with HD were randomly allocated either to inspiratory muscle training at 50% of maximal inspiratory pressure, or to training against a load suggested to have no effect, completed in the home. The training protocol was 30 breaths, twice daily for six weeks, which was preceded by a habituation period of one week. Sniff nasal inspiratory pressure, peak cough flow and 30 second sit to stand were measured before and after the intervention. The programme was supported by alternate weekly phone calls and home visits. Results All measures of respiratory function, except FEV1/FVC were significantly decreased (p <0.001) in people with manifest HD compared to healthy control participants and people with pre-manifest HD. There was no difference between healthy control participants and people with pre-manifest HD. Respiratory function demonstrated a significant linear decline with disease progression measured by the total functional capacity scale (p<0.001). In particular, peak cough flow was abnormal at the middle stage of the disease. Exercise capacity, physical activity, swallow and posture were significantly related to respiratory function in people with manifest HD (p range 0.016-0.001). In people with manifest HD, exercise capacity was 27.73% ±26.29 predicted and swallow capacity was abnormal in 84.80% of participants. In the intervention study, five participants completed the intervention arm and 7 completed the sham arm. Adherence to the inspiratory muscle training programme ranged from 37-100% across both groups, with mean adherence rates of 70.67% ±26.35 and 74.53% ±21.03 for intervention and sham groups respectively. There was no difference in inspiratory muscle strength, peak cough flow or 30 second sit to stand as a result of the intervention. Participants and their carers identified carer support as a key enabler and life events as a barrier for carrying out the exercises. Conclusion The findings from this study indicate that people with HD are susceptible to type 1 hypoxaemic respiratory failure and predisposed to type 2 hypercapnic respiratory failure due to increased elastic and resistive loads and decreased capacity of respiratory muscles. The risk of type 1 hypoxaemic respiratory failure is high due to decreased swallow capacity and concomitant decreased cough efficacy. Decreased lung volume leading to hypoventilation may be impact on both type 1 hypoxaemic respiratory failure and lead on to type 2 hypercapnic respiratory failure. The predisposition to type 2 hypercapnic respiratory failure is due to decreased respiratory muscle capacity and increased elastic and resistive load. The study also highlighted the complex relationship between respiratory function, exercise capacity and physical activity. Although inspiratory muscle strength, cough efficacy and functional activity remained unchanged in this small sample, the results of the intervention study suggest that inspiratory muscle training is feasible in people with HD. Further studies should use protocols that are directly related to the primary outcome measure e.g. a power based protocol to improve cough efficacy or an endurance based protocol to improve physical activity. A model of respiratory failure in people with HD incorporating both type 1 hypoxaemic and type 2 hypercapnic respiratory failure can be proposed based from the findings of the studies that informs future research and clinical management of people with HD.

Absence seizures (ASs) are the predominant form of seizure featuring in the idiopathic generalised epilepsies, and are the only seizure type of childhood absence epilepsy. They are characterised by behavioural arrest, impairment of consciousness and an electrographic signature of spike-and-wave discharges (SWDs) and are associated with psychosocial and cognitive impairment of development. The seizures are known to arise in the thalamocortical network, but the firing dynamics of thalamic neurones during seizure is not known. In vivo and in vitro studies have yielded contradictory results, suggesting predominant silence and regular burst firing respectively, but no studies have previously recorded from intact, single thalamic neurones in a freely moving model of absence epilepsy. In this thesis it has been shown that, in Genetic Absence Epilepsy Rats from Strasbourg, thalamocortical (TC) neurones are mostly either silent or fire single spikes irregularly but synchronously during AS. T-type calcium channel-mediated bursts in neurones of the reticular thalamic nucleus (nRT) were frequently observed during full seizure expression. These cells expressed varied firing patterns ranging from regular burst firing to predominant silence, with similarly varying degrees of synchrony. It is also suggested that the nRT burst firing observed may be required for seizure generation. T-type calcium channel-mediated burst firing of TC neurones is neither necessary for, nor commonly observed in, the full generation or propagation of absence seizures These results suggest that TC neurones are predominantly silent during AS. This is compatible with the idea of a cortical seizure initiator and driver, as suggested by the cortical initiation site and cortical abnormalities observed in multiple experimental AS models. The observations herein also confirm that the temporal relationship between thalamic firing and SWDs previously observed in anaesthetised animals is maintained in the freely moving condition, but suggest that there is a greater incidence of asynchronous thalamic activity during AS (particularly of nRT neurones) than previously suggested. The firing dynamics of thalamic neurones observed are a crucial step towards understanding TC network activity during AS, and provide a significant insight into the role of the thalamus in alterations of sensation, movement, and consciousness associated with these seizures.

This thesis encompasses a range of experiments designed to characterise and validate a method of desensitising rodent hosts in the neonatal period to human tissue in order to promote the survival of human striatal grafts in the adult host. Thus, the successful application of this method is important to allow the preclinical testing of potential human donor cells for therapeutic transplantation, specifically in neurological disease. Demonstrating safety and functionality of transplanted human cells in rodent hosts requires long term assessment of surviving grafts, for which current immune suppression methods are insufficient. The experiments presented in this thesis were therefore designed to determine the optimum parameters of a previously described method of desensitising rats to human tissue and to validate this method in mice. The findings provide further support for the neonatal desensitisation method in rat hosts, and suggest the potential for use of non-neural tissue types for desensitisation of neonates. The data presented in this thesis also has implications for the mechanisms underlying the success of the method in the rat. However interpretation was difficult as graft survival was generally poor and even mouse to mouse allografts did not survive to the level expected. Thus this highlights the need to reassess standard immunosuppression protocols in mice, and determine what differs between the rat and mouse rejection response to xenografts.

Disease loci underlying complex disorders such as schizophrenia(SCZ)are likely to exist as variants of multiple typesbeyond the single nucleotide polymorphisms(SNPs) typically surveyed in genome-­‐wide association studies(GWAS). Large copy number variants (CNV), small insertions and deletions (INDELS),rare compound heterozygous mutations and other classes of genetic variation are all expected to contribute to disease risk. A true understanding of disease genetics cannot be attained without careful consideration of each class of variation and how they are related. Additionally, it is often the case that no or few single variants have strong enough effect sizes to attain the level of statistical significance required to offset the large number of tests performed in a genome-­‐wide single locus survey of any variant type. It has been shown that a cumulative burden of risk alleles is correlated with disease risk, indicating true biological signal within those variants. However, this approach merely implicates that class of variation across the genome and does not refine variants to a subset of risk regions or genes. Defining sets of genes within biological pathways and testing them as a group will allow for both the power of aggregating loci of small effect and interpretation of the underlying biology. This dissertation assesses the role of multiple classes of variation from different technologies in risk to schizophrenia with a particular focus on brain related biological pathways.