Une maladie est considérée comme étant rare si elle touche moins d’une personne sur 2000. Étant donné les connaissances limitées sur ces conditions médicales, les adultes atteints de maladies rares peinent à être diagnostiqués rapidement et à obtenir des traitements appropriés. Ces soins inadéquats leur occasionnent des difficultés importantes dans le milieu de la santé, leurs vies quotidiennes, leurs relations interpersonnelles ainsi que leurs carrières et leurs études. Plusieurs de ces difficultés peuvent être qualifiées de situations moralement problématiques selon l’éthique pragmatiste. L’éthique pragmatiste est une théorie en éthique qui reconnaît la place centrale de la moralité dans la vie humaine. Elle souligne l’importance existentielle de ces situations pour les personnes qui les vivent. Elle apprécie leur agentivité. Elle leur offre des outils pour mieux comprendre ces situations et les résoudre. Malgré la signification qu’ont ces situations pour les personnes qui les vivent, elles n’ont pas été étudiées précédemment. En parallèle, le concept de situation moralement problématique a seulement été décrit superficiellement dans la littérature. Pour répondre à ces lacunes dans la littérature, le projet de recherche décrit dans cette thèse avait quatre objectifs : (1) identifier des situations moralement problématiques vécues par les adultes atteints de maladies rares; (2) approfondir les situations moralement problématiques les plus significatives vécues par les adultes québécois atteints de maladies rares; (3) proposer un plan d’action de nature éthique qui soutient la résolution des trois situations moralement problématiques les plus significatives vécues par les adultes atteints de maladies rares; et (4) enrichir le concept de situation moralement problématique en précisant ses composantes. Pour répondre à ces objectifs, nous avons entrepris un projet de recherche-action participative compris d’étapes de recherche qualitatives. Nous avons formé le Groupe de travail sur l’éthique et les maladies rares pour nous appuyer dans la mise en œuvre du projet. Le groupe de travail était constitué de trois personnes atteintes de maladies rares, deux cliniciens-chercheurs, une représentante d’une association de patients, une assistante de recherche et un éthicien. Les étapes de recherche du projet étaient une revue de littérature, une collecte de témoignages sous la forme d’un sondage en ligne et le développement d’un plan d’action de nature éthique. Les membres du groupe de travail ont contribué au développement de ces étapes, à l’interprétation des résultats et à la rédaction des chapitres de résultats qui en découlent. Ces étapes de recherche révèlent que les adultes atteints de maladies rares vivent des situations moralement problématiques dans le milieu de la santé, la vie quotidienne, la carrière et les études ainsi que dans les interactions sociales et les relations interpersonnelles. Ces situations sont moralement problématiques parce qu’elles engendrent des tensions internes chez les personnes qui les vivent, contraignent leur agentivité et à l’occasion, les incitent à mobiliser des stratégies d’autonomisation pour les surmonter. Ces situations ont des causes et des répercussions affectives, elles évoluent et elles ont des impacts négatifs et positifs. Dans notre plan d’action de nature éthique, nous présentons des interventions prometteuses qui pourraient limiter l’émergence de ces situations dans le milieu de la santé. / A disease is considered rare if its prevalence is less than 1 in 2,000 people. Given the limited knowledge about these medical conditions, adults living with rare diseases struggle to be promptly diagnosed and receive appropriate treatment. This inadequacy in care causes them significant difficulties in the healthcare environment, their daily lives, their interpersonal relationships, and their careers and studies. Many of these difficulties can be qualified as morally problematic situations according to pragmatist ethics. Pragmatist ethics is a theory in ethics that recognizes the centrality of morality in human life. This theory underlines the existential importance of these situations for the people who experience them. It also appreciates their agency. Thus, it provides them with tools to better understand these situations and resolve them. Despite the significance that these situations have for those who experience them, they have not been studied previously. Moreover, the concept of the morally problematic situation has only been superficially described in the literature. To address these gaps in the literature, the research project described in this dissertation had four objectives: (1) to identify morally problematic situations experienced by adults living with rare diseases; (2) to understand in greater depth the most significant morally problematic situations experienced by adults living with rare diseases in the province of Québec; (3) to propose an ethics action plan that supports the resolution of the three most significant morally problematic situations experienced by adults living with rare diseases; and (4) to enrich the concept of the morally problematic situation by specifying its components. To meet these objectives, we undertook a participatory action research project that included qualitative research steps. We created the Ethics and Rare Diseases Working Group to support us in carrying out the project. The working group was made up of three individuals living with rare diseases, two clinician researchers, a representative of a patient association, a research assistant and an ethicist. The research stages of the project were a literature review, collecting testimonies through an online survey and the development of an ethics action plan. The members of the working group notably contributed to the development of these stages, the interpretation of the results, and the drafting of the chapters reporting these results. Our research reveals that adults with rare diseases experience morally problematic situations in the health environment, daily life, career and studies, and in social interactions and interpersonal relationships. These situations are morally problematic because they elicit internal tensions within the people who experience them, constrain their agency and, on occasion, prompt them to mobilize empowerment strategies to overcome them. These situations have causes and emotional repercussions, they evolve, and they have negative and positive impacts. In our ethical action plan, we present promising interventions that could limit the emergence of these situations in the health sector.

Im Frühjahr/Sommer 2002 wurde eine Befragung von 51 erwachsenen Patienten im Raum Berlin-Brandenburg mit seltenen Muskelerkrankungen bzw. neuromuskulären Erkrankungen zu verschiedenen Aspekten der medizinischen Versorgung durchgeführt. Angewandte Methoden waren ein standardisierter Fragebogen sowie ein Leitfadeninterview. Vom ersten Arztbesuch bis zur in 59% der Fälle im Krankenhaus erfolgten Diagnosestellung einer Muskelerkrankung vergingen durchschnittlich 4,1 Jahre (Median: 1 Jahr). Es fanden sich eine unzureichende Anamneseerhebung und körperliche Untersuchung sowie eine mangelnde Überweisungsbereitschaft an Neurologen. Eine signifikante Verzögerung erlitten Patienten, die anstelle eines Hausarztes zunächst einen anderen Facharzt als den Neurologen aufgesucht hatten. 43% der Patienten hatten Schwierigkeiten, im Anschluss einen kompetenten Arzt für die Langzeitbetreuung zu finden. Fragen der Vererbbarkeit sowie der respiratorischen und kardialen Komplikationen wurden unzu! reichend besprochen. Im Verlauf erfolgte eine mangelnde Überwachung der respiratorischen sowie kardialen Funktion. Die Verordnung von Physiotherapie und Hilfsmitteln wurde dagegen gut bewertet. Bei 51% der Patienten kam es auch nach der Diagnosestellung zu Krankenhausaufenthalten. 22% der Patienten mussten wegen Komplikationen stationär behandelt werden. Insgesamt zeigten sich Defizite in der medizinischen Versorgung, wie sie z.T. bereits in Expertenstellungnahmen bzw. wenigen anderen Studien berichtet wurden. Für den Bereich der seltenen Erkrankungen gilt eine Spezialambulanz als geeignetes Versorgungsmodell, welches die spezialisierte, multidisziplinäre Betreuung der Patienten sichern soll. Solche Einrichtungen existieren mittlerweile in Deutschland, Outcome-Studien fehlen jedoch bisher. / In spring/summer 2002 a group of 51 adult patients in Berlin-Brandenburg suffering from a muscle or a neuromuscular disease were questioned concerning various aspects of their medical care. The applied methods were a standardized questionnaire and a qualitative interview. The average time between the first consultation of a physician and the establishment of the diagnosis of a muscle disease was 4,1 years (median: 1 year). 59% of the patients received their diagnosis at a hospital. An insufficient history-taking, lacks in the physical examination and a reluctance to refer the patient to a neurologist could be identified. There was a significant delay for those patients who initially consulted a non-neurological specialist instead of a general physician. 43% of the patients had difficulties in finding a qualified physician for the long-time care. The patients were insufficiently informed about the heredity of their disease and about possible respiratory and cardiac complicati! ons. There was a lack in following up the respiratory and cardiac functions of the patients. The prescription of physiotherapy and aids was rated positively by the patients. 51% of the patients had hospital stays also after having their diagnosis. 22% were admitted to hospital due to complications of their disease. In general, deficits in the medical care for these patients were shown, similar to those described in expert opinions or few preview studies. A specialized hospital-based outpatient centre that should ensure the specialized multidisciplinary care for the patients is regarded as the model for the medical care in the area of rare diseases. Similar centres exist in Germany by now, but there are no outcome-studies yet.

Rare diseases represent a clinically and genetically heterogeneous group of diseases affecting various organs and presenting at different ages. Identification and functional characterization of genetic defects causing individual rare diseases represent unique opportunity to understand biological functions of human genes and gene products as well as to basic pathogenetic mechanisms of individual diseases. This knowledge is prerequisite for their effective diagnosis, specific treatment and prevention and it also opens up an avenue for better understanding of complex diseases. My thesis documents basic conceptual and methodological developments of biochemical genetics, functional cloning, genetic mapping, positional cloning, DNA microarrays and genomic sequencing, which have provided a universal framework for effective characterization of the genetic architecture of almost all human diseases. This conceptual and technological developments are demonstrated on several cases of rare genetic diseases - adenylosuccinate lyase deficiency, mucopolysacharidosis type IIIC, Rotor syndrome, deficiency of ATP synthase, neuronal ceroid lipofuscinosis, GAPO syndrome and X -linked restrictive cardiomyopathy, which genetic and molecular basis I have helped to elucidate.

The study of rare genetic diseases presents unique opportunity to uncover the genetic and molecular basis of human traits and greatly helped to the identification of genes, to the elucidation of their function and to the characterization of metabolic pathways and cellular processes. Over the past decades, linkage analysis has been appropriate approach to search for the genes causing Mendelian diseases and contributed to the identification of many genes, but the genetic cause of many diseases remains unknown. New methods of studying the human genome, microarray technology and massively parallel sequencing (next generation sequencing), represent a way to efficiently identify the cause of genetically determined diseases, based on direct observation of mutations in the genome of affected individuals. These techniques replaced the traditional method of disease gene identification represented by linkage analysis and sequencing of candidate genes and have become the standard approach to elucidate the molecular basis of diseases. In this work, i describe the the results achieved by using these methods - identification of the genes underlying mucopolysacharidosis type IIIC, isolated defect of ATP synthase, Rotor syndrome, autosomal dominat ANCL and GAPO syndrome.

La recherche dans le domaine des maladies sans traitement existant obéit à plusieurs impératifs définis par le législateur européen dans le règlement (CE) n° 141/2000 du 16 décembre 1999 concernant les médicaments orphelins. Les patients atteints de maladies rares et négligées ont le droit à « la même qualité de traitement que les autres » ce qui suppose de prendre les mesures d'incitation nécessaires pour « promouvoir la recherche, le développement et la commercialisation de traitements adéquats ». C'est un « domaine prioritaire ». Après avoir désigné les médicaments concernés, l'Union européenne veut « éviter la dispersion de ressources limitées » notamment par la promotion d'une « coopération transnationale ». Dans une démarche téléologique, cette recherche décrit les effets de la législation européenne sans ignorer la réception de ce droit par les États membres. Des fondements théoriques à même d'assurer une meilleure performativité du droit et des propositions concrètes en vue de conformer le droit positif à l'intention du législateur et aux attentes des parties prenantes sont proposés. En se focalisant sur le seul levier de la propriété intellectuelle, ce droit spécial et incitatif ne semble pas en mesure d'apporter aux patients la plupart des traitements attendus. La régulation de la concurrence et la compétence nationale sur le prix des médicaments perpétuent un seuil de rentabilité éloignant de nombreuses recherches de la phase du développement. L'accès aux médicaments orphelins demeure très restreint. Un changement de paradigme dans la construction de ce droit apparaît nécessaire afin qu'un modèle économique favorable se mette en place. Il convient que le profit des pharmaciens de l'industrie ne dépende plus de la conquête de parts de marché, mais de l'intérêt de leurs inventions pour les besoins de santé non satisfaits. / Research in the field of diseases without an existing treatment is governed by several requirements defined by the European legislator in Regulation (CE) No 141/2000 of 16 December 1999 on orphan medicinal products. Patients with rare and neglected diseases have the right to "the same quality of treatment as other patients" which means taking the necessary incentives to stimulate research, development and bringing to the market of appropriate medications". It is a "priority area". After designating the drugs concerned, the European Union wants to "avoid the dispersion of limited resources", in particular by promoting "cross national co-operation". In a teleological approach, this research analyses the positive law endeavouring to implement the objectives of Orphan Drug Law. It describes the effects of European legislation without ignoring the receipt of this law by the Member States. Theoretical foundations that can ensure a better performativity of the law, as well as concrete proposals to conform the positive law to the intention of the legislator and to the stakeholders' wills are proposed. By focusing solely on the leverage of intellectual property rights, this special and incentive law does not seem to be able to provide patients with many of the expected treatments. Competition regulation and setting of the price which is a national competency perpetuate a high profitability threshold, often withholding research projects from reaching the development phase. Access to orphan drugs remains very limited. A paradigm shift in the construction of this law appears necessary in order for a favorable economic model to emerge. The profit of the industry's pharmacists should no longer depend on the conquest of market shares, but on the value of their inventions for unmet health needs.

Introduction: Diagnosing inborn metabolic diseases, as a large subgroup of rare diseases, due to their rarity and wide variety of clinical manifestations, can be demanding and often prolonged. Objective: The aim of this work is, with the regard to clinical, biochemical and genetical aspects of selected rare diseases, to contribute to their rapid detection, widen the features of the natural course of the disease and contribute to their preventability. Material: This work includes cohort studies of patiens with cardiac manifestations in mitochondrial diseases, namely a group of 48 patients with TMEM70 protein deficiency, a group of 4 patients with Barth syndrome and individual cases of rare mitochondrial cardiomyopathies, thimidine kinase 2 deficiency and alanyl tRNA synthetase 2 deficiency. By determining the frequency, severity and type of heart disease, the phenotype was expanded, and the design of a therapeutic algorithm then made a positive impact on the prognosis of these patients. The work is also focused on the role of cardiac disease in the differential diagnosis of other genetically determined rare diseases, Marfan's syndrome and especially Pompe disease, where the emphasis is on early diagnosis, mainly due to the existence of an effective therapy. Focus on a broader differential diagnosis...

In my work, I want to focus on the perceived advantages and disadvantages of membership in the umbrella organization. This topic, I will discuss from the perspectives of the member organizations. This is a specific segment associations - the patient organizations focused to patients with rare diseases. It is clear that cooperation in the umbrella organization brings advantages, but it is probable that it can also bring some disadvantages. For my work I choose the Czech Association for rare diseases. In the Czech Republic is the only organization in the civil sector, focusing exclusively on rare diseases. The goal of the master thesis is to find out the perceived advantages and disadvantages, and how it is related to the level of activity of members of the umbrella organization. Further, I want to compare the data with the theoretical literature in order that differs. Theme of umbrella in the Czech Republic is almost unexplored. There are only a few expert papers in this area. That's why I decided to focus on cooperation in civil sector (organization focus on rare diseases), which is relatively unknown. Keys words: advantages of cooperation, disadvantages of cooperation, rare disease, advocacy function, information function, umbrella organizations, patient organizations, Czech Association for Rare...

Transaldolase-Mangel (TALDO) ist ein extrem seltener, angeborener Stoffwechseldefekt, von dem weltweit nur 34 Fälle bekannt sind. Der Defekt geht auf den Verlust des Enzyms Transaldolase 1 aus dem nicht-oxidativen Pentosephosphat-Weg (nicht-oxPPW) zurück und äußert sich in einem weiten Spektrum klinischer Symptome. Die schwerwiegendsten Folgen sind Leber- und Nierenmangelfunktionen, die zum sehr frühen Tod führen können. Desweiteren leiden 15 % der Patienten an wiederkehrenden Infektionen. Neutrophile Granulozyten (Neutrophile) sind die häufigsten weißen Blutkörperchen im Menschen und essentiell für die angeborene Immunantwort gegen Infektionserreger. Ich habe hier funktionale Aspekte von TALDO-Neutrophilen untersucht. Der oxidative Pentosephosphat-Weg (oxPPW) stellt das Reduktionsäquivalent NADPH bereit, welches indirekt für die Entstehung von reactive oxygen species (ROS)-abhängigen Neutrophil Extracellular Traps (NETs) verantwortlich ist. Der Beitrag des nicht-oxPPW zur ROS-abhängigen NET-Bildung ist bislang nicht bekannt. In dieser Arbeit konnte ich für Neutrophile aus drei TALDO-Patienten eine jeweils komplett abwesende Entstehung ROS-abhängiger NETs und einen deutlich verringerten oxidativen Burst nach PMA-Stimulation zeigen. Um diese Beobachtungen in einem unabhängigen Modelsystem zu bestätigen, habe ich mit Hilfe des CRISPR-Cas9-Systems, ‚knock-out‘ Mutanten von Transaldolase 1 und dessen Partnerenzym Transketolase in der Neutrophil-ähnlichen Zelllinie PLB-985 hergestellt. Die dergestalt genetisch manipulierten Zellen waren nicht mehr zu PMA-induziertem Zelltod in der Lage. Dies ist somit der erste genetische Beweis für die Abhängigkeit des oxidativen Burst und der Bildung von NETs vom nicht-oxPPW. Diese Erkenntnis trägt zum einen zum mechanistischen Verständnis der NET-Entstehung bei und liefert zum anderen eine potentielle Erklärung für einige der bei TALDO beobachteten Symptome. Desweiteren wurden einige der metabolischen Erfordernisse für die Bildung von NETs mit Hilfe von Inhibitoren untersucht. Die erhaltenen Erkenntnisse zeigen, dass das initiale Maximum des oxidativen Bursts für NET-Bildung unerheblich ist und vielmehr die ROS-Generierung nach ca. 50 Minuten entscheidende Bedeutung für diese hat. / Transdaldolase 1-deficiency (TALDO) is a rare genetic disease with only 34 described cases globally. Transaldolase 1 is part of the non-oxidative pentose phosphate pathway (PPP) and its deficiency results in many clinical symptoms including kidney and liver failure, which can lead to early child-mortality. Some of these patients suffer from recurrent infections, for example in the respiratory tract. Neutrophils are the most abundant white blood cells and essential for the innate immune defence against bacterial and fungal pathogens. The PPP generates reduced NADPH that is crucial for the generation of superoxide by the NADPH oxidase NOX2. In turn, NOX2 is essential for neutrophil extracellular trap (NET) formation. NETs occur through the neutrophil-specific cell death netosis and consist of chromatin decorated with granular proteins. Here I report that neutrophils of three TALDO patients did not make NETs. Deletion of transaldolase 1, and its partner enzyme transketolase, in the neutrophil-like PLB-985 cell line reduced ROS generation and cell death. This confirms that transaldolase 1 is required for NET formation. We present, to the best of our knowledge, the first genetic evidence that the non-oxidative PPP is required for ROS generation and NET formation. Furthermore, some of the metabolic requirements for NET formation were assessed. The obtained data indicate that the initial peak of the oxidative burst is irrelevant for NET formation but the ROS generation after 50 minutes on the contrary has crucial significance.

The study of rare genetic diseases presents unique opportunity to uncover the genetic and molecular basis of human traits and greatly helped to the identification of genes, to the elucidation of their function and to the characterization of metabolic pathways and cellular processes. Over the past decades, linkage analysis has been appropriate approach to search for the genes causing Mendelian diseases and contributed to the identification of many genes, but the genetic cause of many diseases remains unknown. New methods of studying the human genome, microarray technology and massively parallel sequencing (next generation sequencing), represent a way to efficiently identify the cause of genetically determined diseases, based on direct observation of mutations in the genome of affected individuals. These techniques replaced the traditional method of disease gene identification represented by linkage analysis and sequencing of candidate genes and have become the standard approach to elucidate the molecular basis of diseases. In this work, i describe the the results achieved by using these methods - identification of the genes underlying mucopolysacharidosis type IIIC, isolated defect of ATP synthase, Rotor syndrome, autosomal dominat ANCL and GAPO syndrome.

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.