Magister Scientiae - MSc / The aim of this study was to investigate the genetic diversity of the SLC22A1 gene and to deduce its possible pharmacogenetic implications within the Cape Coloured population of South Africa; a uniquely admixed population of immigrant Europeans, Asians and the indigenous populations. Recent studies have reported an abundance of polymorphic variants within this solute carrier transporter gene encoding for the organic cation transporter 1, as well as evidence linking these variants to an effect on metformin uptake. This study included establishing baseline frequency distribution of previously reported alleles for 20 SNP variants within the SLC22A1 gene, as well as the development of SNaPshot® and Multiplex AS-PCR genotyping assays, and also exploring the possibility of using High-resolution melt (HRM) analysis as a costeffective alternative for SNP genotyping. Ethics clearance was obtained from the Ethics Committee of the University of the Western Cape. Biological samples in the form of buccal (oral) swabs were collected from 132 unrelated voluntary donors from the Cape Coloured population residing in the Cape Metropolitan area. Two SNaPshot® Multiplex Systems were specifically designed for the study,successfully optimized and used for genotyping. Hundred genetic profiles were then generated for a total of 20 SNP variants on SLC22A1 gene, using this primer extension-based genotyping method that enables multiplexing up 10 SNPs. Population genetics data obtained for the investigated SNPs were analysed using various statistical analysis software. Important population genetic parameters were calculated, and possible pharmacogenetics implications were then discussed. Among others, allelic and genotypic frequencies, as well as linkage disequilibrium were determined and compared with world populations. Minor deviation from Hardy- Weinberg equilibrium was observed in the Cape Coloured population. No significantLinkage Disequilibrium between the investigated SNPs was observed in this population. A Multiplex allele specific – PCR (MAS-PCR) genotyping system was successfully designed and optimized for the genotyping of 10 SNPs from the SLC22A1. This system, also developed specifically for this study, was made of 2 multiplexes each covering 5 SNPs. It is an inexpensive genotyping assay that allows for efficient discrimination of SNP polymorphisms in one reaction tube with standard PCR conditions. A pilot study was conducted to explore the possibility of using High-resolution melt (HRM) analysis as a cost-effective alternative for SNP genotyping. In addition to genotyping, HRM analysis can be used to scan large numbers of samples for novel genetic variations. / South Africa

Cette thèse cherche à optimiser l’utilisation du génotypage et des scores de gravité dans la drépanocytose. L’aspect diagnostic génétique ne nous semblait pas poser problème jusqu’à ce que nous rencontrions un cas très atypique d’hétérozygotie A/S avec délétion en mosaïque du gène β-globine qui nous a conduits à réfléchir sur une nouvelle forme génétique potentielle de syndrome drépanocytaire majeur. Pour ce qui est des gènes modificateurs de drépanocytose, nous avons voulu faciliter leur l’accès en proposant, pour deux d’entre eux (haplotypes β-globine et G6PD), une méthode de génotypage rapide par HRM et/ou FRET. Notre travail a consisté ensuite en la validation d’un score de sévérité pédiatrique décrit initialement par Van den Tweel. De façon inattendue, les résultats nous ont amenés à nous interroger sur le rôle exact du génotype α-globine dans la drépanocytose avec un possible effet âge-dépendant. Enfin, nous avons étudié les fréquences alléliques des principaux polymorphismes influant sur l’activité des opiacés: une résistance pharmacologique (gènes OPRM1 et COMT) est apparue peu probable mais une proportion non négligeable de drépanocytaires pourrait avoir des génotypes ABCB1 et UGT2B7 défavorables à la biodisponibilité des opiacés / This work is submitted for a PhD thesis in the field of red cell haematology. Sickle cell disease (SCD) is a monogenic disorder under polygenic and environmental control. The aim of this work was to integrate genotyping results from patients' DNA into the determination of the disease severity scores. Through a large population of SCD patients, we have discovered an atypical case of βA / βS heterozygosity namely, a mosaicism deletion of the beta-globin gene. This represents a new SCD complex situation for molecular diagnosis. Further investigations have led to set up a new genotyping method by using HRM and/or FRET for the determination of two SCD modifiers (beta-globin haplotypes and G6PD deficiency). By using a paediatric severity score of the disease proposed by Van den Tweel, our results show that there is a possible age-dependent effect of the alpha-globin gene in the severity of SCD. Finally, we studied the allelic frequencies of the main opiate-related polymorphisms: a pharmacological resistance (OPRM1 and COMT genes) seemed unlikely but a quite important proportion of patients could have both an ABCB1 and a UGT2B7 genotype unfavorable for opiates bioavailability

Pharmacogenetics (PGx) and personalised medicine are new disciplines that, gathering the existing knowledge about the genetic and phenotypic factors that underpin drug response, aim to deliver more targeted therapies that avoid the existing problems of adverse drug reactions or lack of drug efficacy. PGx and personalised medicine imply a shift in the way drugs are prescribed, as they require introducing diagnostic tools and implementing pre-screening mechanisms that assess patients' susceptibility to new or existing drugs. The direct benefit is an improvement in drug safety and/or efficacy. However, neither pharmacogenetics nor personalised medicine, are widely used in clinical practice. Both technologies face a number of controversies that hamper their widespread use in clinical practice. This thesis investigates the scientific; technological; social; economic; regulatory and ethical implications of PGx and personalised medicine, to understand the enablers and barriers that drive the process of technology diffusion in three conditions: autoimmune diseases, acute lymphoblastic leukaemia and non-small cell lung cancer.The thesis uses concepts of the sociology of science and a qualitative approach, to explore the arguments for and against the use of the technology by different actors (pharmaceutical and biotechnology companies, researchers, clinicians, regulators and patient organisations). The core of this analysis lies in the understanding of how, diagnostic testing (TPMT testing in the case of autoimmune diseases, acute lymphoblastic leukaemia, and EGFR testing in the case of non-small-cell lung cancer) may affect the existing drug development and service delivery mechanisms, with a particular focus on the user-producer interactions and feedback mechanisms that underpin diffusion of medical innovations and technological change in medicine.The thesis concludes by identifying gaps in knowledge and common issues among TPMT and EGFR testing, which might be used, in the future, to inform policy on how to improve PGx service delivery through a public Health System such as the NHS.

Le traitement de la leucémie myéloïde chronique (LMC) par imatinib est un succès de thérapie ciblée en oncologie. Le principe de cette thérapie est de bloquer les processus biochimiques à l'origine du développement de la maladie, et de permettre à une majorité de patients de réduire leurs risques de progression mais aussi d'éviter des traitements lourds et risqués comme la greffe de cellules souches hématopoïétiques.Cependant, même si l'efficacité de l'imatinib à été prouvée dans un contexte clinique, il n'en demeure pas moins qu'une proportion non négligeable de patients n'obtient par de niveaux de réponse moléculaire jugés optimale. Le but de cette thèse est de tester l'hypothèse d'un lien entre des polymorphismes de gènes impliqués dans l'absorption des médicaments et de leurs métabolisme, et la réponse moléculaire dans la leucémie myéloïde chronique en phase chronique traitée par imatinib.Dans le but d'évaluer la réponse moléculaire des patients, des prélèvements sanguins sont réalisés tout les 3 mois afin de pratiquer le dosage d'un biomarqueur. Ce type particulier de suivi produit des données censurées par intervalles. Comme par ailleurs, les patients demeurent à risque de progression ou sont susceptible d'interrompre leurs traitements pour cause d'intolérance, il est possible que la réponse d'intérêt ne soit plus observable sous le traitement étudié. Les données ainsi produites sont censurées par intervalles dans un contexte de compétition (risques compétitifs).Afin de tenir compte de la nature particulière des données collectées, une méthode basée sur l'imputation multiple est proposée. L'idée est de transformer les données censurées par intervalles en de multiples jeux de données potentiellement censurées à droite et d'utiliser les méthodes disponibles pour l'analyser de ces données. Finalement les résultats sont assemblés en suivant les règles de l'imputation multiple. / Imatinib in the treatment of chronic myeloid leukemia is a success of targeted therapy in oncology. The aim of this therapy is to block the biochemical processes leading to disease development. This strategy results in a reduction of the risk of disease progression and allows patients to avoid extensive and hazardous treatments such as hematologic stem cell transplantation.However, even if imatinib efficacy has been demonstrated in a clinical setting, a significant part of patients do not achieve suitable levels of molecular response. The objective of this thesis, is to test the hypothesis of a correlation between polymorphisms of genes implied in drug absorption an metabolism and the molecular response in chronic myeloid leukemia in chronic phase treated by imatinib.In order to evaluate patients molecular response, blood biomarker assessments are performed every 3 months. This type of follow up produces interval censored data. As patients remain at risk of disease progression, or may interrupt their treatments due to poor tolerance, the response of interest may not be observable in a given setting. This situation produces interval censored competing risks data.To properly handle such data, we propose a multiple imputation based method.The main idea is to convert interval censored data into multiple sets of potentially right censored data that are then analysed using multiple imputation rules.

NADPH-P450 oxidoreductase (POR) is a membrane bound flavoprotein that donates electrons to a wide spectrum of heme-containing proteins, among which are several steroidogenic and many xenobiotics-metabolizing enzymes. Given the important role of POR protein in drug metabolism and pharmacogenomics, there is a particular need to understand the contributions of POR genetic variants to these processes. Mutations in POR gene cause a disorder called POR deficiency, which manifests with a wide phenotypic spectrum ranging from disordered steroidogenesis to skeletal malformation, namely, Antley-Bixler syndrome (ABS). The aim of the present work was to investigate the POR gene in patients suspected to have POR deficiency syndrome from Czech Republic and to perform genotyping in Czech and Jewish control populations. We analyzed 644 alleles in unrelated individuals from the general Czech population and 1128 alleles in Jewish population, where 330 alleles were of Askhenazi and 798 of Sephardic Jews. We have also studied the impact of selected new genetic variants on POR activity and identified fourteen amino acid variations, two of which we have studied in detail to establish their influence on POR activity. Using the available human POR three-dimensional structure, we then modelled the newly identified variants...

55 Abstract Frequency of selected genetic polymorphisms of cytochrome P450 in the Czech population and the influence of CYP2C9 genotype on the hypolipidemic effect of fluvastatin Introduction: One of the main factors of genetically determined variability in response of humans to administered drugs are differences in catalytic activity of metabolizing enzymes, which are caused mainly by genetic polymorphisms in cytochrom P450 family enzymes. This thesis consists of two parts and it is presented as a commentary to the original papers. The first aim was to investigate the frequency of functionally important variant alleles of three main isoenzymes of cytochrome P450 gene: CYP2D6, CYP2C9, CYP2C19, throughout the Czech population, predict the prevalence of poor metabolizer phenotypes, and then to compare the results to the data from other populations. Secondly, we analysed the correlation between the CYP2C9 genotype and cholesterol-lowering effect of fluvastatin in human hypercholesterolemic patients. Methods: Genotypes were determined by PCR-RFLP. The presence of alleles CYP2D6*1, *6, *5, *4, *3, and gene duplication was analysed in 233 healthy volunteers, CYP2C9*1, *2 and*3 in 254 subjects and CYP2C19*1, *2 and *2 in 218 subjects. Eighty seven patients on fluvastatin therapy, and 48 patients on monotherapy...

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Orientador: Roberta Okamoto / Resumo: Atualmente, com os avanços da Farmacogenética, estudos estão demonstrando que a resposta individual de medicamentos pode ser diretamente afetada pela alteração da farmacocinética induzida pela genética de cada paciente, e isto pode induzir à ausência, redução, alteração ou aumento da atividade enzimática associada. Esse fato pode modificar a eficácia clínica de determinados medicamentos e, nos casos de anti-inflamatórios não esteroidais (AINEs), alterar sua capacidade de lidar com a dor e até aumentar a frequência e a gravidade dos efeitos adversos. Este estudo teve como objetivo genotipar e fenotipar o gene CYP2C9 em 89 pacientes saudáveis submetidos à cirurgia de terceiro molar inferior, sob medicação de 20 mg de tenoxicam por dia durante 4 dias, comparando a influência do gene na dor pós-operatória, edema, trismo, quantidade de medicamentos de socorro consumidos pelos pacientes, avaliação global e satisfação do paciente em relação à ingestão do medicamento. Trata-se de um ensaio clínico randomizado, desenvolvido no Departamento de Cirurgia e Traumatologia Bucomaxilofacial da Faculdade de Odontologia de Araçatuba (FOA/UNESP) e na Disciplina de Farmacologia do Departamento Ciências Biológicas da Faculdade de Odontologia de Bauru (FOB/USP). Foi realizado o sequenciamento genético dos participantes do estudo, a fim de verificar polimorfismos do gene CYP2C9, e estes dados foram cruzados com as características pós-operatórias acima mencionadas. Oitenta e nove participantes foram... (Resumo completo, clicar acesso eletrônico abaixo) / Doutor

Indiana University-Purdue University Indianapolis (IUPUI) / Pharmacogenetic testing has the potential to improve pain management through addressing wide interindividual variations in responses to pharmacogenetically actionable opioids, ultimately decreasing costly adverse drug effects and improving responses to these medications. A recent review of pharmacogenomics in the nursing literature highlighted the need for nurses to more fully embrace the burgeoning field of pharmacogenomics in nursing research, clinical practice, and education. Despite the promise of pharmacogenetic testing, significant challenges exist for evaluating outcomes related to its implementation, including oversimplification of medication exposure, the complexity of patients' clinical profiles, and the characteristics of healthcare contexts in which medications are prescribed. A better understanding of these challenges could enhance the assessment and documentation of the benefits of pharmacogenetic testing in guiding opioid therapies. This dissertation is intended to address the challenges of evaluating outcomes of pharmacogenetic testing implementation and the need for nurses to lead pharmacogenomic-related research. The dissertation purpose was to advance the sciences of nursing, pain management, and pharmacogenomics through the development of a typology of common patterns of medication exposure to known pharmacogenetically actionable opioids (codeine & tramadol). A qualitative, person-oriented approach was used to retrospectively analyze six months of electronic health record and pharmacogenotype data in 30 underserved adult patients. An overarching typology with eight groups of patients that had one of five opioid prescription patterns (singular, episodic, switching, sustained, or multiplex) and one of three types of medical emphasis of care (pain, comorbidities, or both) were identified. This typology consisted of a description of multiple common patterns that compare and contrast salient factors of exposure and the emphasis of why individuals were seeking care. Furthermore, in an aggregate descriptive analysis evaluating key clinical profile factors, these patients had complex medical histories, extensive healthcare utilization, and experienced significant polypharmacy. These findings can aid in addressing challenges related to the implementation of pharmacogenetic testing in clinical practice and point to ways in which nurses can take the lead in pharmacogenomics research. Findings also provide a foundation for future studies aimed at developing medication exposure measures to capture its dynamic nature and identifying and tailoring interventions in this population.

Backgroun and aims: Pharmacokinetic variability is of paramount importance for sucessfull pharmacotherapy. The main purpose of this work was to study variability of pharmacokinetics in clinical and non-clinical setting with the aim to predict variability in target population. Specifically, three drugs were chosen, sufentanil, with relativelly narrow therapeutic index, and nabumeton and abirateron, both with known high variability. Methods: The study of pharmacokinetic variability of sufentanil was based on clinical samples taken from patients undergoing surgical cardiac procedure, where the sufentanil was used as a part of the drug coctail used during the procedure. New analytical method was necessary to prepare and validate to measure sufentanil concentrations and obtain pharmacokinetic parameters. These were compared between determined genotype groups of MDR1 and OPRM1. Similarly, clinical study was executed with nabumetone, in which nabumetone was administered in a group of 24 subjects on two separate occassions. Plazma samples were obtained and concentrations of nabumetone and its active metabolite, 6-methoxynaphtylacetic acid (6-MNA), were determined. Obtained pharmacokinetic profiles were compared between female and male volunteers, and genotypes for MDR1 and CYP2D6. Finaly for abiraterone,...