Idiopathic Parkinson’s disease (IPD) is the second most common neurodegenerative disease, yet effective disease modifying treatments are still lacking. Neurodegeneration involves multiple interacting pathological pathways. The extent to which neurovascular mechanisms are involved in IPD is not well defined. Indeed within the umbrella term of IPD great heterogeneity of motor (and non-motor) features exists, suggesting that different phenotypes may have differing underlying pathophysiologies. We aimed to determine whether novel magnetic resonance imaging (MRI) techniques can reveal changes in structural or physiological neurovascular measures, herein also referred to as ‘altered neurovascular status (NVS)’, in IPD.Based on preliminary data from our initial exploratory study in a small IPD cohort, phenotypic differences in structural and physiological MRI measures of NVS were investigated in a larger study. The 3 Tesla (3T) MRI protocol included T2-weighted fluid-attenuated inversion recovery (FLAIR) imaging to assess white matter lesion (WML) burden, arterial spin labelling (ASL) measurements of cerebral blood flow (CBF) and arterial arrival time (AAT) and dynamic contrast enhanced (DCE) measures of blood-brain barrier (BBB) integrity. Analysis was undertaken of IPD clinical phenotypes, by comparison with two control groups. In total, fifty-one patients with IPD (mean age 69.0 ± 7.7 years) (21 tremor dominant [TD], 24 postural instability and gait disorder [PIGD] and 6 intermediates) were compared with 2 control groups, the first comprising 18 control positive (CP) subjects with a history of clinical cerebrovascular disease (CVD) (mean age 70.1 ± 8.0 years) and the second comprising 34 control negative (CN) subjects without a history of clinical CVD (mean age 67.4 ± 7.6 years). IPD patients showed diffuse regions of significantly prolonged AAT and lower CBF by comparison with CN subjects, and a few regions of prolonged AAT by comparison with CP subjects, despite significantly fewer vascular risk factors. TD patients showed regions of significantly prolonged AAT and lower WML volume by comparison with PIGD patients. IPD patients also showed increased leakiness of the BBB in basal ganglia regions compared to the CN group, with a similar pattern in both IPD phenotypes. These data provide evidence of altered NVS in IPD, with IPD phenotype specific differences.

Whole-exome and genome sequencing are widely used to diagnose individual patients. However, despite its success, this approach leaves many patients undiagnosed. This could be due to the need to discover more disease genes and variants or because disease phenotypes are novel and arise from a combination of variants of multiple known genes related to the disease. Recent rapid increases in available genomic, biomedical, and phenotypic data enable computational analyses, reducing the search space for disease-causing genes or variants and facilitating the prediction of causal variants. Therefore, artificial intelligence, data mining, machine learning, and deep learning are essential tools that have been used to identify biological interactions, including protein-protein interactions, gene-disease predictions, and variant--disease associations. Predicting these biological associations is a critical step in diagnosing patients with rare or complex diseases. In recent years, computational methods have emerged to improve gene-disease prioritization by incorporating phenotype information. These methods evaluate a patient's phenotype against a database of gene-phenotype associations to identify the closest match. However, inadequate knowledge of phenotypes linked with specific genes in humans and model organisms limits the effectiveness of the prediction. Information about gene product functions and anatomical locations of gene expression is accessible for many genes and can be associated with phenotypes through ontologies and machine-learning models. Incorporating this information can enhance gene-disease prioritization methods and more accurately identify potential disease-causing genes. This dissertation aims to address key limitations in gene-disease prediction and variant prioritization by developing computational methods that systematically relate human phenotypes that arise as a consequence of the loss or change of gene function to gene functions and anatomical and cellular locations of activity. To achieve this objective, this work focuses on crucial problems in the causative variant prioritization pipeline and presents novel computational methods that significantly improve prediction performance by leveraging large background knowledge data and integrating multiple techniques. Therefore, this dissertation presents novel approaches that utilize graph-based machine-learning techniques to leverage biomedical ontologies and linked biological data as background knowledge graphs. The methods employ representation learning with knowledge graphs and introduce generic models that address computational problems in gene-disease associations and variant prioritization. I demonstrate that my approach is capable of compensating for incomplete information in public databases and efficiently integrating with other biomedical data for similar prediction tasks. Moreover, my methods outperform other relevant approaches that rely on manually crafted features and laborious pre-processing. I systematically evaluate our methods and illustrate their potential applications for data analytics in biomedicine. Finally, I demonstrate how our prediction tools can be used in the clinic to assist geneticists in decision-making. In summary, this dissertation contributes to the development of more effective methods for predicting disease-causing variants and advancing precision medicine.