Epidermolysis Bullosa simplex (EBS) is a rare genetic disorder that is typically inherited in an autosomal dominant fashion and affects approximately 1 out of 20 000 individuals. This disease is caused by mutations in either the KRT14, KRT5 or PLEC genes. These genes code for proteins involved in the formation of the cytoskeleton in basal keratinocytes, which form the basal layer of the epidermis. The cytoskeleton provides structural support to the basal keratinocytes and mutations in these genes cause cytoskeletal malformations, making these cells more susceptible to physical stress. This results in the cells undergoing lysis under trivial mechanical stress and causing the epidermis to detach from the dermis, the layer immediately below the epidermis. This leads to the primary symptom of EBS: the formation of blisters. The goal of this project is to recreate EBS in zebrafish using transgenesis and to create stable mutant transgenic line. In the future, high throughput drug screening will be done on mutant zebrafish embryos to find potential drug candidates that can alleviate the symptoms of EBS. To accomplish this, missense and deletion mutations in zebrafish krt5 cDNA using site-directed mutagenesis were performed. It was previously shown that mice models for this disease die shortly after birth and thus no stable mutant lines were able to be created. To ensure embryo survival and avoid a similar fate, mutant krt5 cDNA was expressed in non-essential tissue, such as the embryonic fin fold using a fin epithelial-specific enhancer named epi. These constructs were injected into one-cell stage zebrafish embryos, which were raised and screened for integration of the construct in their germ cells. While results from injected embryos were promising, mutant transgenic zebrafish did not demonstrate any blistering. In an attempt to induce blistering, mutant zebrafish embryos were placed under various environmental stressors known to worsen the symptoms of EBS. This was not successful. Expression of mutant keratin 5 in the basal epidermis of the entire embryo using the 2.3kb upstream region of the zebrafish krt5 gene to drive expression also did not yield any results. More investigations are needed to determine if it will be possible to use the zebrafish to model EBS.

Rare diseases caused by single-gene mutations affect almost one million Canadians. According to the Online Mendelian Inheritance in Man database, ~4,500 rare monogenic diseases have a known cause; but less than 5% of patients have access to disease-modifying drugs. The dearth of accessible drugs for patients suffering from rare genetic diseases is partly due to the astronomical costs of traditional drug development which, when combined with the small target population, make rare disease therapeutics unattractive ventures for the pharmaceutical establishment. The paucity of cost-effective treatments for rare diseases has resulted in the promotion of clinic-ready drug repurposing as a tenable strategy for rare disease therapeutics. To identify repurposed candidates for rare neurogenetic diseases, I conducted a transcriptome-wide drug screen in mouse primary cerebrocortical cultures. RNA sequencing was used to develop a database of transcriptome-wide differential expression for 218 clinic-tested drugs. The “Neuron Screen” database was queried to identify drugs that upregulate ~60 rare neurogenetic disease genes (type I hits). Gene set enrichment pathway analysis by Ingenuity Pathway Analysis (IPA) was used to identify network associated drug-gene interactions (type II hits). Both types of drug-gene hits were further assessed in vitro and in vivo by qRT-PCR and western blot analysis. This analysis showed that the IPA-based network-associated approach reduces the false positive rate when identifying differentially expressed genes in transcriptome-wide data-sets. The analysis also identified two drug-gene interactions with genes that cause rare neurogenetic disease, thyroid hormone-Pmp22 and dexamethasone-Mfsd2a, that merit further investigation. This work proves the utility of the Neuron Screen database to connect rare disease genes with transcript-modulating drugs and provides a starting point to understand the transcriptional effects of pharmacologic agents on the mammalian brain.

Objectives: 1) To evaluate the quality of randomized clinical trials (RCTs) in rare diseases using Juvenile Idiopathic Arthritis (JIA) as an example, 2) to evaluate the time to treatment response in patients with rheumatic diseases, 3) to evaluate the power of the Randomized Placebo-Phase Design (RPPD) under various response time distributions, and 4) to examine the use of Value of Information (VOI) methodology in the optimal design of clinical trials for rare disease using hemophilia prophylaxis with factor VIII as an example. Methods. The methods include a systematic review, a secondary analysis of data from an RCT and from a patient registry, a computer simulation study, and an evaluation of hypothetical RCT scenarios with VOI methodology. Results. The quality of RCTs in JIA based on selected quality indicators was poor with some positive changes over time. In the data sets used for the assessment of hazard distributions, the response times followed mostly generalized gamma or lognormal distributions. The impact of time-to-event distribution on the power of RCTs was assessed in computer simulations. Based on the simulation results, the highest sample sizes were observed for response times following the exponential distribution. In most scenarios, the parallel groups RCT design had higher power than the RPPD. The conclusion of the VOI analyses indicated that at threshold values lower than 400,000 the current evidence supported the use of on-demand therapy. Threshold values higher than 1,000,000 supported the use of tailored or alternate day prophylaxis. At threshold values between 400,000 - 1,000,000 the optimal decision varied from on-demand to prophylaxis therapies. Conclusions. New, more powerful and acceptable designs should be developed for rare diseases. When time-to-event outcomes are used, investigators should use various sources of information to evaluate response time distributions before the new trial is designed, and consider this information in sample size calculation and analysis. VOI methodology should be used in the planning stage of studies to determine the relevant costs and benefits of future research, and to determine the optimal trial parameters that maximize the cost-benefit trade-off.

Objectives: 1) To evaluate the quality of randomized clinical trials (RCTs) in rare diseases using Juvenile Idiopathic Arthritis (JIA) as an example, 2) to evaluate the time to treatment response in patients with rheumatic diseases, 3) to evaluate the power of the Randomized Placebo-Phase Design (RPPD) under various response time distributions, and 4) to examine the use of Value of Information (VOI) methodology in the optimal design of clinical trials for rare disease using hemophilia prophylaxis with factor VIII as an example. Methods. The methods include a systematic review, a secondary analysis of data from an RCT and from a patient registry, a computer simulation study, and an evaluation of hypothetical RCT scenarios with VOI methodology. Results. The quality of RCTs in JIA based on selected quality indicators was poor with some positive changes over time. In the data sets used for the assessment of hazard distributions, the response times followed mostly generalized gamma or lognormal distributions. The impact of time-to-event distribution on the power of RCTs was assessed in computer simulations. Based on the simulation results, the highest sample sizes were observed for response times following the exponential distribution. In most scenarios, the parallel groups RCT design had higher power than the RPPD. The conclusion of the VOI analyses indicated that at threshold values lower than 400,000 the current evidence supported the use of on-demand therapy. Threshold values higher than 1,000,000 supported the use of tailored or alternate day prophylaxis. At threshold values between 400,000 - 1,000,000 the optimal decision varied from on-demand to prophylaxis therapies. Conclusions. New, more powerful and acceptable designs should be developed for rare diseases. When time-to-event outcomes are used, investigators should use various sources of information to evaluate response time distributions before the new trial is designed, and consider this information in sample size calculation and analysis. VOI methodology should be used in the planning stage of studies to determine the relevant costs and benefits of future research, and to determine the optimal trial parameters that maximize the cost-benefit trade-off.

Thanks to the affordability of DNA sequencing, hundreds of thousands of individuals with rare disorders are undergoing whole-genome sequencing in an effort to reveal novel disease aetiologies, increase our understanding of biological processes and improve patient care. However, the power to discover the genetic causes of many unexplained rare diseases is hindered by a paucity of cases with a shared molecular aetiology. This thesis presents research into statistical and computational methods for determining the genetic causes of rare diseases. Methods described herein treat important aspects of the nature of rare diseases, including genetic and phenotypic heterogeneity, phenotypes involving multiple organ systems, Mendelian modes of inheritance and the incorporation of complex prior information such as model organism phenotypes and evolutionary conservation. The complex nature of rare disease phenotypes and the need to aggregate patient data across many centres has led to the adoption of the Human Phenotype Ontology (HPO) as a means of coding patient phenotypes. The HPO provides a standardised vocabulary and captures relationships between disease features. I developed a suite of software packages dubbed 'ontologyX' in order to simplify analysis and visualisation of such ontologically encoded data, and enable them to be incorporated into complex analysis methods. An important aspect of the analysis of ontological data is quantifying the semantic similarity between ontologically annotated entities, which is implemented in the ontologyX software. We employed this functionality in a phenotypic similarity regression framework, 'SimReg', which models the relationship between ontologically encoded patient phenotypes of individuals and rare variation in a given genomic locus. It does so by evaluating support for a model under which the probability that a person carries rare alleles in a locus depends on the similarity between the person's ontologically encoded phenotype and a latent characteristic phenotype which can be inferred from data. A probability of association is computed by comparison of the two models, allowing prioritisation of candidate loci for involvement in disease with respect to a heterogeneous collection of disease phenotypes. SimReg includes a sophisticated treatment of HPO-coded phenotypic data but dichotomises the genetic data at a locus. Therefore, we developed an additional method, 'BeviMed', standing for Bayesian Evaluation of Variant Involvement in Mendelian Disease, which evaluates the evidence of association between allele configurations across rare variants within a genomic locus and a case/control label. It is capable of inferring the probability of association, and conditional on association, the probability of each mode of inheritance and probability of involvement of each variant. Inference is performed through a Bayesian comparison of multiple models: under a baseline model disease risk is independent of allele configuration at the given rare variant sites and under an alternate model disease risk depends on the configuration of alleles, a latent partition of variants into pathogenic and non-pathogenic groups and a mode of inheritance. The method can be used to analyse a dataset comprising thousands of individuals genotyped at hundreds of rare variant sites in a fraction of a second, making it much faster than competing methods and facilitating genome-wide application.

Introduction: The scarcity of rigorous evidence regarding rare disease therapies contributes to uncertainty for stakeholders who make decisions about the use, prescription, or funding of such therapies. My dissertation objective was to integrate stakeholder perspectives and evidence related to how rare disease therapies are evaluated to better understand drivers of uncertainty in decision making and develop an evaluation framework for future evidence generation, synthesis, and decision support. Methods: To better understand the perceived challenges in generating robust treatment effectiveness evidence, and describe various methods for mitigating these challenges, I used a meta-narrative literature review. I also conducted focus group interviews with key rare disease stakeholders (patients/caregivers, physicians, and policy advisors) to elicit different perspectives on how evidence is generated, evaluated, and synthesized in the context of health care decision making, both at a personal and population level. Finally, I integrated the focus group findings with a targeted literature review to identify characteristics of rare diseases and their candidate therapies that may warrant special consideration in health technology assessment (HTA) and health care decision making. Findings: My dissertation data revealed three fundamental challenges in generating robust treatment effectiveness evidence for rare diseases: limitations in recruiting a sufficient sample; inability to account for clinical heterogeneity; and reliance on outcomes with unclear clinical relevance. Several methodological solutions have been proposed to overcome these challenges. In addition, study participants described different perspectives on how they choose to participate in and use research in their roles as health care users, care providers, and policy advisors. Notably, conventional wisdom that patients/caregivers participate in clinical research studies because of therapeutic misconception was not supported. Finally, focus group and literature review findings identified information that potentially warrants special consideration in future HTA specific to rare diseases, including characteristics of the disease, understanding of causal hypotheses relevant to the therapy, and complexities of cost-effectiveness given the high price of many rare disease therapies. Discussion: Together, the findings from this dissertation support an evaluation framework with eight key principles that aim to mitigate important aspects of uncertainty from various stakeholder perspectives and promote evidence-informed decision making about rare disease therapies.

Evaluating Drugs for Rare Diseases (DRDs) for the purpose of reimbursement and beyond represents a tremendous challenge for most health care priorities. A consensus is set about the irrelevance of cost e ectiveness analysis to evaluate such drugs. The appeal for multi criteria decision aid models seems reasonable as the evaluation of DRDs is indeed multifaceted. However, the application of MCDA for the purpose of evaluating DRDs is yet primitive and simplistic. The present work tries to tackle the issue of evaluating DRDs from a decision maker angle by adopting an innovative robust ordinal regression MCDA method, UTADIS-GMS, that helps the decision maker discern between the DRDs based on their multi criteria value.

The number of known monogenic rare diseases (~7000) exceeds the number of effective treatments (~500) by more than an order of magnitude underlining the pressing need for generalizable therapeutic approaches for this class of conditions. In this regard, the majority of recessive and x-linked recessive disorders are caused by missense mutations encoding proteins that frequently have residual function but are rapidly degraded by the 26S proteasome. Bortezomib is a small molecule that inhibits the 26S proteasome and has been approved for use in patients for an unrelated condition; multiple myeloma. Previous work has shown that, for a small number of disorders, bortezomib can inhibit the degradation of the mutant protein, thereby increasing the protein level and activity, holding out the promise of a beneficial therapeutic effect by the repurposing of this agent. We present here a high level western blot based survey of nine recessive disorders to characterize the general effectiveness of such an approach. Thirteen patient fibroblast cell lines comprising 9 different diseases with 19 known mutations were selected on the basis of missense mutations protein expression data when available. The cell lines were incubated with bortezomib (10 nM and 50 nM; 24 hrs) and levels of the mutated protein were quantified by western blot. Unfortunately, no consistent, appreciable increase was observed for any of the conditions tested. The general therapeutic value of re-purposing bortezomib for recessive and x-linked diseases appears limited at best. The few reported cases of bortezomib successfully working in increasing mutated protein levels appear to be the exceptions and not the norm. Moreover successes are more often limited to cell lines carrying a transgene expressing the mutated protein rather than endogenous mutated protein in patient cell lines.

Rasmussen's encephalitis is a rare neurological disease first described in 1958 that is characterized by medico-refractory seizures, focal unilateral cerebral inflammation, and deficits such as hemiparesis. While we still do not have a full understanding of this disease, proposed theories behind its etiology include auto-immune manifestations, immune attack by T cells, and malfunctional alterations in genetic expression. It is classically considered a rare childhood malady with a median age of onset of six years, and cases in adolescents and adults are even rarer, representing up to 10% of all cases to date. In this report, we would like to share a rare case of Rasmussen's encephalitis that occurred in an adolescent. Our 17-year-old male patient presented with signs and symptoms beginning at age 14 and was initially diagnosed with cerebral palsy only to later present with additional symptoms and characteristic EEG and MRI findings that ultimately led to a diagnosis of Rasmussen's encephalitis. Thus, with this case report, our intent is twofold: to shed light on an atypical presentation of an already rare disease, even rarer in adolescents and adults, and to underscore the importance of keeping a broad differential when it comes to evaluating a patient with seizures.

Abstract : Rare diseases are debilitating conditions often leading to severe clinical manifestations for affected patients. Orphan drugs have been developed to treat these rare diseases affecting a small number of individuals. Incentives in the legal framework aimed to recoup the research and development cost of orphan drugs for pharmaceutical companies have been implemented in the United States and the European Union. At the present time, Canada is still lacking a legal and policy framework for orphan drugs. Several problems at the federal and provincial levels remain: lack of research funds for rare diseases, discrepancies on orphan drug policies between provinces, difficulties to access and reimburse these high price drugs. Recommendations and measures are proposed, such as a pan-Canadian (national) scientific committee to establish evidence-based guidelines for patients to access orphan drugs uniformly in all provinces with a disease specific registry, a formal agreement for a centralized Canadian public funding reimbursement procedure, and increasing the role of “guardian” for prices by the Patented Medicines Review Board in Canada. These recommendations and measures will be beneficial for the implementation of a policy framework for orphan drugs in Canada. / Résumé : Les maladies rares sont des maladies sérieuses pouvant causer des manifestations cliniques sévères chez les patients atteints. Les médicaments orphelins ont été développés pour le traitement de ces maladies rares qui touchent un petit nombre d’individus. Un cadre légal permettant des incitatifs pour les compagnies pharmaceutiques aux États-Unis et au niveau de l’Union Européenne a favorisé la recherche et le développement desdits médicaments. Présentement, il n’existe pas de cadre juridique et de politiques spécifiques au Canada entourant les médicaments orphelins. Ceci a mené à plusieurs problèmes tant au niveau fédéral que provincial dont: un manque de support financier consacré à la recherche pour les maladies rares, des disparités entre les provinces concernant les politiques pour les médicaments orphelins, des difficultés d’accès et de remboursement desdits médicaments dont les coûts sont élevés. Des recommandations et mesures sont proposées, telles l’implantation d’un comité scientifique pancanadien (national) afin d’établir des lignes directrices fondées sur des données probantes pour faciliter un accès uniforme aux médicaments orphelins pour les patients, y compris un registre spécifique élaboré pour chaque maladie, établir une entente formelle centralisée pour tout le Canada pour un financement public de remboursement des médicaments orphelins, augmenter le rôle de « gardien » des prix par le Conseil d’examen du prix des médicaments brevetés au Canada. Ces recommandations et mesures serviront à l’implantation d’un cadre de politiques pour les médicaments orphelins au Canada.