Tissue banks are thought to be an essential resource for medical research in the post-genomic age. Collections of tissue, usually removed in the course of diagnostic or therapeutic procedures, enable laboratory-based epidemiological studies to be carried out, linking abnormalities in the tissue to disease aetiology, prognosis and treatment responsiveness. There are, however, a number of technical, regulatory and ethical concerns that challenge those wishing to engage in tissue banking research. It is becoming increasingly apparent that tissue banking research is not without risk of harms, even though there is no direct physical risk to donors. This is because, in order to be most useful, banked specimens need to be linked to personal information about tissue donors and this poses the risk of inadvertent disclosure of personal─ particularly genetic─ information to those who might exploit such information (eg. insurance companies and employers). Furthermore, the long-term storage of specimens, and the impossibility of predicting all potential types of research programs for which they might be useful, raises the possibility that future projects will be carried out that are unacceptable to some (past) tissue donors. The ethical principles of autonomy and respect for persons demand that research subjects be informed of such risks and of the nature of the research, and that they participate willingly. On the other hand, there is a desire for science to progress unhindered by stringent consent requirements. For these reasons, a debate has emerged in the academic (bioethical and biomedical) literature and in the legal (law reform) sphere over what would constitute adequate consent. Despite an extensive discourse, it is still unclear whether it is permissible to carry out research on archival tissue that was originally taken for diagnostic purposes and whether project-specific (as opposed to open-ended) consent is required for research on tissue collected today. This lack of clarity is of concern to researchers, ethics committees and research subjects, all of whom recognise the importance of tissue banking research, yet fear that current consent procedures may be ethically or legally inadequate. Thus it is important that the consent dilemma be resolved as quickly and definitively as possible. Ongoing controversy and regulatory ambiguity are appropriate when morally contentious issues are at stake, and their existence does not, on its own, signal any flaws in the discourse process. There are, however, two reasons to suspect that the current �consent to tissue banking� debate, as portrayed in the academic literature and law reform documentation, is problematic. Firstly, the debate appears to be mired in an intractable conflict between those who want to maximise personal autonomy through stringent consent requirements, and those who want the scientific endeavour to progress in a manner that is unconstrained by what are viewed as arduous consent procedures. Secondly, the possible practical options (consent models) being generated by the debate are all limited because they are underpinned by a restricted notion of consent as an individualistic, legalistic and static activity, without consideration of any alternative conceptualisations of consent. Through a thematic analysis of the current �consent to tissue banking� debate in the academic and law reform literature (Section 3), this thesis shows that debate is essentially occurring between those who see individual autonomy (and stringent consent) as being of primary importance, and those who see unimpeded, market-driven scientific progress as the more important social good, which should not be impeded by unnecessarily stringent consent. Thematic analysis also confirms the existence of the two problems described above, and a failure of those engaged in the debate to reflect on, and challenge, the value-level assumptions underpinning their arguments and those of their opponents. It is argued that this lack of reflection accounts for the two problems: � Firstly, it precludes recognition of the cause of─ and, therefore, ways of resolving─ the intractable conflict at the centre of the debate. Value-level reflection shows that this is a result of the logical and moral conflict within western liberalism, between two modernist goods: individual freedom and scientific progress. � Secondly, it precludes the generation of varied conceptions of consent. Value-level reflection shows that the current range of consent models is restricted to procedures which are individualistic, abstract, static and legalistic, since they are underpinned by western liberal notions of autonomy and scientific progress. This recognition paves the way to consideration of alternative notions of autonomy, scientific progress and, therefore, consent, such as those derived from communitarian and feminist systems of values. A conceptually enriched model of tissue banking consent is then developed (Section 4). This model incorporates dominant (liberal) conceptions of autonomy and scientific progress as well as alternative notions of autonomy and scientific progress espoused by communitarian and feminist systems of values. It is argued that this conceptually-enriched model provides a practical solution to the two problems associated with the standard �consent to tissue banking� debate. In relation to the philosophically intractable conflict─ or what is termed the �modernist dilemma�─ between those privileging autonomy and those privileging scientific progress, it shows how the two apparently conflicting �modernist� goods can both be accommodated at a practical level, thus making the �consent to tissue banking� debate more tractable and fruitful. In relation to the restricted range of consent models being generated by the current debate, it provides new insights into the ways in which consent might be obtained such that a broader range of community values can be accommodated. More specifically, it stimulates the construction of a model that 1) involves communities, as opposed to merely individuals, in all stages of the scientific process; 2) is flexible and able to adapt consent procedures to specific contexts, rather than predefining procedures in abstract terms; and 3) is transactional and relational rather than static and legalistic. This outcome has interesting philosophical as well as practical implications. It shows that despite apparently unresolved, and possibly irresolvable, normative-level conflicts between the two modernist elements of western liberalism (autonomy and scientific progress), and between liberal, feminist and communitarian systems of values, a multi-perspectival, inclusive, model-building approach provides a practical solution that circumvents these normative-level conflicts.

Tissue banks are thought to be an essential resource for medical research in the post-genomic age. Collections of tissue, usually removed in the course of diagnostic or therapeutic procedures, enable laboratory-based epidemiological studies to be carried out, linking abnormalities in the tissue to disease aetiology, prognosis and treatment responsiveness. There are, however, a number of technical, regulatory and ethical concerns that challenge those wishing to engage in tissue banking research. It is becoming increasingly apparent that tissue banking research is not without risk of harms, even though there is no direct physical risk to donors. This is because, in order to be most useful, banked specimens need to be linked to personal information about tissue donors and this poses the risk of inadvertent disclosure of personal─ particularly genetic─ information to those who might exploit such information (eg. insurance companies and employers). Furthermore, the long-term storage of specimens, and the impossibility of predicting all potential types of research programs for which they might be useful, raises the possibility that future projects will be carried out that are unacceptable to some (past) tissue donors. The ethical principles of autonomy and respect for persons demand that research subjects be informed of such risks and of the nature of the research, and that they participate willingly. On the other hand, there is a desire for science to progress unhindered by stringent consent requirements. For these reasons, a debate has emerged in the academic (bioethical and biomedical) literature and in the legal (law reform) sphere over what would constitute adequate consent. Despite an extensive discourse, it is still unclear whether it is permissible to carry out research on archival tissue that was originally taken for diagnostic purposes and whether project-specific (as opposed to open-ended) consent is required for research on tissue collected today. This lack of clarity is of concern to researchers, ethics committees and research subjects, all of whom recognise the importance of tissue banking research, yet fear that current consent procedures may be ethically or legally inadequate. Thus it is important that the consent dilemma be resolved as quickly and definitively as possible. Ongoing controversy and regulatory ambiguity are appropriate when morally contentious issues are at stake, and their existence does not, on its own, signal any flaws in the discourse process. There are, however, two reasons to suspect that the current �consent to tissue banking� debate, as portrayed in the academic literature and law reform documentation, is problematic. Firstly, the debate appears to be mired in an intractable conflict between those who want to maximise personal autonomy through stringent consent requirements, and those who want the scientific endeavour to progress in a manner that is unconstrained by what are viewed as arduous consent procedures. Secondly, the possible practical options (consent models) being generated by the debate are all limited because they are underpinned by a restricted notion of consent as an individualistic, legalistic and static activity, without consideration of any alternative conceptualisations of consent. Through a thematic analysis of the current �consent to tissue banking� debate in the academic and law reform literature (Section 3), this thesis shows that debate is essentially occurring between those who see individual autonomy (and stringent consent) as being of primary importance, and those who see unimpeded, market-driven scientific progress as the more important social good, which should not be impeded by unnecessarily stringent consent. Thematic analysis also confirms the existence of the two problems described above, and a failure of those engaged in the debate to reflect on, and challenge, the value-level assumptions underpinning their arguments and those of their opponents. It is argued that this lack of reflection accounts for the two problems: � Firstly, it precludes recognition of the cause of─ and, therefore, ways of resolving─ the intractable conflict at the centre of the debate. Value-level reflection shows that this is a result of the logical and moral conflict within western liberalism, between two modernist goods: individual freedom and scientific progress. � Secondly, it precludes the generation of varied conceptions of consent. Value-level reflection shows that the current range of consent models is restricted to procedures which are individualistic, abstract, static and legalistic, since they are underpinned by western liberal notions of autonomy and scientific progress. This recognition paves the way to consideration of alternative notions of autonomy, scientific progress and, therefore, consent, such as those derived from communitarian and feminist systems of values. A conceptually enriched model of tissue banking consent is then developed (Section 4). This model incorporates dominant (liberal) conceptions of autonomy and scientific progress as well as alternative notions of autonomy and scientific progress espoused by communitarian and feminist systems of values. It is argued that this conceptually-enriched model provides a practical solution to the two problems associated with the standard �consent to tissue banking� debate. In relation to the philosophically intractable conflict─ or what is termed the �modernist dilemma�─ between those privileging autonomy and those privileging scientific progress, it shows how the two apparently conflicting �modernist� goods can both be accommodated at a practical level, thus making the �consent to tissue banking� debate more tractable and fruitful. In relation to the restricted range of consent models being generated by the current debate, it provides new insights into the ways in which consent might be obtained such that a broader range of community values can be accommodated. More specifically, it stimulates the construction of a model that 1) involves communities, as opposed to merely individuals, in all stages of the scientific process; 2) is flexible and able to adapt consent procedures to specific contexts, rather than predefining procedures in abstract terms; and 3) is transactional and relational rather than static and legalistic. This outcome has interesting philosophical as well as practical implications. It shows that despite apparently unresolved, and possibly irresolvable, normative-level conflicts between the two modernist elements of western liberalism (autonomy and scientific progress), and between liberal, feminist and communitarian systems of values, a multi-perspectival, inclusive, model-building approach provides a practical solution that circumvents these normative-level conflicts.

Recentemente estudos demonstraram que os SNPs (polimorfismos de base única) rs8099917 e rs12979860 localizados próximos ao gene da IL28B explicam a variação de resposta à infecção e tratamento do paciente contra o genótipo 1 do HCV, porém não para o genótipo 3 deste vírus. Este trabalho encontrou associação significativa entre resposta à infecção devida ao genótipo 3 pelo tratamento (PEG-INF e RBV) e o polimorfismo rs8099917 em uma amostra da população de Santos - SP. Para o polimorfismo rs12979860, esta associação somente foi encontrada ao se parear indivíduos para sexo, idade e grau de fibrose hepática, demonstrando a importância da retirada de efeitos de estratificação neste tipo de análise. Estes resultados se confirmam ao se agregar dados de uma população proveniente da Bahia em uma meta-análise. Além disso, fez-se um estudo GWAS a fim de se conhecer outras variações genéticas envolvidas nessa resposta. Esta análise indicou a existência de alguns SNPs candidatos com sugestão de associação, dentre eles a tiroglobulina, relacionada aos hormônios da tireóide. / Recently, studies have shown that SNPs (single nucleotide polymorphisms) rs8099917 and rs12979860, located near the gene IL28B explain the changes in the response to infection and treatment of a patient against the HCV genotype 1, but not for the genotype 3 of the virus. This study found a significant association between response to infection due to treatment by genotype 3 (PEG-INF and RBV) and the rs8099917 polymorphism in a population sample from Santos - SP. To the rs12979860 polymorphism, this association was only found when individuals are paired for sex, age and degree of hepatic fibrosis, demonstrating the importance of the withdrawal effects of stratification in this type of analysis. These results confirm the aggregate data from a population of Bahia in a meta-analysis. In addition, a GWAS was made in order to search other genetic variations involved in this response. This analysis indicated the existence of some candidate SNPs with suggestion of association, including thyroglobulin, thyroid hormones related to.

Recentemente estudos demonstraram que os SNPs (polimorfismos de base única) rs8099917 e rs12979860 localizados próximos ao gene da IL28B explicam a variação de resposta à infecção e tratamento do paciente contra o genótipo 1 do HCV, porém não para o genótipo 3 deste vírus. Este trabalho encontrou associação significativa entre resposta à infecção devida ao genótipo 3 pelo tratamento (PEG-INF e RBV) e o polimorfismo rs8099917 em uma amostra da população de Santos - SP. Para o polimorfismo rs12979860, esta associação somente foi encontrada ao se parear indivíduos para sexo, idade e grau de fibrose hepática, demonstrando a importância da retirada de efeitos de estratificação neste tipo de análise. Estes resultados se confirmam ao se agregar dados de uma população proveniente da Bahia em uma meta-análise. Além disso, fez-se um estudo GWAS a fim de se conhecer outras variações genéticas envolvidas nessa resposta. Esta análise indicou a existência de alguns SNPs candidatos com sugestão de associação, dentre eles a tiroglobulina, relacionada aos hormônios da tireóide. / Recently, studies have shown that SNPs (single nucleotide polymorphisms) rs8099917 and rs12979860, located near the gene IL28B explain the changes in the response to infection and treatment of a patient against the HCV genotype 1, but not for the genotype 3 of the virus. This study found a significant association between response to infection due to treatment by genotype 3 (PEG-INF and RBV) and the rs8099917 polymorphism in a population sample from Santos - SP. To the rs12979860 polymorphism, this association was only found when individuals are paired for sex, age and degree of hepatic fibrosis, demonstrating the importance of the withdrawal effects of stratification in this type of analysis. These results confirm the aggregate data from a population of Bahia in a meta-analysis. In addition, a GWAS was made in order to search other genetic variations involved in this response. This analysis indicated the existence of some candidate SNPs with suggestion of association, including thyroglobulin, thyroid hormones related to.

Multiple sclerosis is a complex immune mediated condition of the central nervous system characterized by myelin loss and progressive neurodegeneration. The risk of developing MS is influenced by both genetic and environmental agents and, among them, several lines of evidence support a role for vitamin D deficiency, Epstein-Barr virus (EBV) infection and smoking in the aetiology of this disease. The aim of this work was to further elucidate how nature and nurture act in the causal cascade leading to MS. In chapter 1, I show that the main genetic factor in adult MS (the HLA-DRB1*1501 allele) plays an equally important role in paediatric cases of MS (PMS) and that EBV negative PMS patients represent a separate entity characterized by lower age at disease onset, lower female to male ratio and a trend towards a lower frequency of the HLA-DRB1*1501 allele. In chapter 2, I provide evidence in support of month of birth having a role on MS risk and T cell production and that vitamin D may underlie this effect. In chapter 3 I demonstrate the presence of a link between vitamin D deficiency and the immune response against EBV, whereby the proportion of EBV seropositive MS patients and controls increases with increasing latitude and high dose vitamin D supplementation appears to reduce the level of antibodies against this virus. In chapter 4, I show that MS associated genetic variants are located in genomic regions that exert a regulatory function and are active in immune cell types. In chapter 5, I illustrate how vitamin D receptor binding is also located within active regulatory regions in immune cells and that this is particularly evident near MS associated genes. Finally, in chapter 6, I use chromatin data on more than 100 different cell types and conclude that MS associated genetic variants are particularly active in T helper, T cytotoxic and B cells. Further work is needed to elucidate how genetic and environmental agents play a role in the cause of MS and to develop effective strategies for disease treatment and prevention.

The tumour suppressor p53 is at the centre of the signalling pathway that controls cellular processes crucial in tumourogenesis, cancer progression and tumour clearance. Alterations in the p53 pathway that lead to cancer progression can be good candidates for molecular biomarkers that would assist in the identification of patients with different prognoses, but also serve as good predictors of appropriate targeted therapies. Patient cohorts and cancer cell panels are utilised to seek associations with the attenuation of the p53 pathway and cancer progression. Firstly, the alternatively spliced transcript of the p53 inhibitor HDMX, which is frequently found in tumours with poor prognosis, is studied. The high ratio of the alternatively spliced HDMX-S transcript over the full-length HDMX-FL transcript (HDMX-S/FL) is demonstrated to associate with p53 pathway attenuation in cancer cells and breast carcinomas, and with faster metastatic progression of osteosarcoma and breast cancer patients. Secondly, inherited polymorphism in the HDMX gene is investigated and demonstrated as a unique and highly reproducible eQTL, which identifies patients with different prognoses for metastatic disease in breast cancer and melanoma cohorts. Lastly, a screening approach to identify novel inherited polymorphisms in the p53 pathway genes that associate with metastatic progression of melanoma is developed and implemented, and subsequently in silico and in vitro functional analyses are performed to investigate a mechanism behind the FOXO3 SNP, identified as the strongest candidate, whereby the experimental evidence demonstrate that the causal SNP in the FOXO3 haplotype is controlled by the GATA3 transcription factor. Together, the work presented in this thesis provides strong support for the role of the p53 pathway in the metastatic progression of cancer, and suggests that molecular biomarkers that can detect changes in the activity of p53 pathway genes could offer a robust set of biomarkers for cancer progression applicable to different types of cancer.

Whole genome sequencing (WGS) has transformed molecular infectious diseases epidemiology in the last five years, and represents a high resolution means by which to catalogue the genetic content and variation in bacterial pathogens. This thesis utilises WGS to enhance our understanding of antimicrobial resistance in two clinically important members of the Enterobacteriaceae family of bacteria, namely Escherichia coli and Klebsiella pneumoniae. These organisms cause a range of clinical infections globally, and are increasing in incidence. The rapid emergence of multi-drug resistance in association with infections caused by them represents a major threat to the effective management of a range of clinical conditions. The reliability of sequencing and bioinformatic methods in the analysis of E. coli and K. pneumoniae sequence data is assessed in chapter 4, and provides a context for the subsequent study chapters, investigating resistance genotype prediction, outbreak epidemiology in two different contexts, and population structure of an important global drug-resistant E. coli lineage, ST131 (5-8). In these, the advantages (and limitations) of short-read, high-throughput, WGS in defining resistance gene content, associated mobile genetic elements and host bacterial strains, and the relationships between them, are discussed. The overarching conclusion is that the dynamic between all the components of the genetic hierarchy involved in the transmission of important antimicrobial resistance elements is extremely complicated, and encompasses almost every imaginable scenario. Complete/near-complete assessment of the genetic content of both chromosomal and episomal components will be a prerequisite to understanding the evolution and spread of antimicrobial resistance in these organisms.

Viral sequence data has great potential for answering questions about the epidemiological dynamics and evolution of viruses. Classical approaches have sought amino acid changes that alter pathogenesis or transmissibility by influencing a virus's ability to enter or replicate within cells. However, this approach rarely recognises the fundamental impact of heterogeneous host contact structures and existing immunological responses on viral transmission. This thesis draws heavily on ecological and immunological concepts to explore the epidemiological dynamics, diversity and evolution of viruses using molecular sequence data. A number of different research approaches and study systems are used in this thesis. I begin by describing a novel polyomavirus in a European badger, and apply phylogenetic techniques to analyze the evolutionary history of the Polyomaviridae. I subsequently describe a large metaviromic study in a population of wild mute swans, for which host demographic data are available. I describe nine new viral species and test whether age and season are associated with differences in abundance and prevalence of different viral taxonomic groups. The study highlights the potential of metaviromics for investigating viral epidemiological dynamics in natural populations. Influenza A viruses of avian origin (AIV) threaten human and animal health. Using phylogeographic methods, I reconstruct the spatial spread of an H5N8 virus at a regional scale, and investigate how bird density and migration shaped this dispersal. Despite the importance of acquisition of humoral immunity to different strains throughout the lifespan of wild birds for epidemiological dynamics, this topic is poorly understood. I assess the accumulation of immune responses to AIV with age in mute swans. I consider how ecological factors, including age-structured immunity, might have affected the epidemiology of an H5N8 outbreak in the population.

Lowering LDL-cholesterol with statin therapy produces substantial reductions in cardiovascular events, and larger cholesterol reductions may produce larger benefits. Rarely, myopathy occurs with statins, especially at higher doses and in combination with certain medications. Similarly strong associations might exist between myopathy with high-dose statin regimens and genetic variants, especially those affecting blood statin levels. This study aimed to find genetic variants associated with statin-induced myopathy. A feasibility study was completed to assess whether plausible effect sizes of 5 to10-fold higher risks per genetic variants could be detected among 50-100 cases with statin-induced myopathy and to consider the best study design. A genome-wide association study was then carried out using approximately 300,000 genetic markers (and additional fine-mapping) in 85 people with definite or incipient myopathy and 90 controls, who were all taking 80mg simvastatin daily in a 12,000 participant trial of 80mg vs 20mg simvastatin daily. The cases were also compared to 2,300 additional controls who had not been exposed to intensive-dose statin therapy. Replication of the myopathy result and lipid-lowering associations were tested in a 20,000 participant trial of 40mg simvastatin daily versus placebo. The genome-wide scan yielded a single strong association (p = 4x10^-9) of myopathy with the rs4363657 single nucleotide polymorphism (SNP) located within the SLCO1B1 gene on chromosome 12. This non-coding SNP was in nearly complete linkage disequilibrium (r²=0.97) with the non-synonymous rs4149056 SNP. The population prevalence of the rs4149056 C allele was 15%, and the odds ratio for myopathy was 4.5 (95% confidence interval 2.6 to 7.7) for each copy of the C allele and 16.9 (4.7 to 61.1) for CC vs TT homozygotes. Over 60% of these myopathy cases could be attributed to the C variant. The SLCO1B1 gene encodes the organic anion transport polypeptide OATP1B1, which has been shown to regulate hepatic uptake of statins. In literature reports, rs4149056 reduced statin transport and was associated with 37% (31% to 44%) higher systemic statin acid levels per C allele. The association of rs4149056 with myopathy was replicated in the trial of 40mg simvastatin daily, which also showed that it was associated with the cholesterol-lowering effects of simvastatin. No SNPs in any other region were clearly associated with myopathy (although comparison of the myopathy cases with the 2,300 controls identified a region of chromosome 1p12 that warrants further study). This study identified common variants in SLCO1B1 that influence the risks of statin-induced myopathy substantially. Genotyping these variants may be useful for tailoring both the statin dose and safety monitoring. More generally, such studies of the genetic determinants of serious adverse reactions with other drug classes may help to improve the balance between treatment efficacy and safety.

Vascular disease is the leading cause of global disease burden, but substantial gaps in our knowledge regarding family history of vascular disease, peripheral arterial disease (PAD) and acute aortic disease persist. Prospective, population-based data in these neglected areas may be useful in diagnosis, risk prediction, prognosis and clinical management of vascular disease. The Oxford Vascular Study (OXVASC) is an ongoing prospective, population-based study of vascular disease in all territories in Oxfordshire, UK, which started in 2002. The study population comprises all 91,106 individuals registered with nine general practices. Multiple overlapping methods of “hot” and “cold” pursuit are used to identify all patients with acute vascular events. I have shown that patients with acute coronary syndromes (ACS) and a history of myocardial infarction (MI) in both parents are 6 times more likely to have siblings with MI than those ACS patients with no parental history of MI, whereas, parental stroke does not predict stroke in siblings among TIA/stroke patients. Maternal history of MI is more common in women than men with ACS. Premature maternal MI is strongly associated with premature MI in females and males. I have also shown that maternal stroke is more common than paternal stroke in female ACS patients, and that family history of stroke is as common in patients with ACS as in patients with TIA/stroke. However, I showed that these associations between family history and MI or stroke cannot be explained by disease localisation or disease severity on coronary angiography. In both primary and secondary prevention settings, PAD indicates a high risk of future events. I have shown that, although acute PAD events account for only 7% of acute vascular events at 1 year, they account for 12% of acute vascular deaths. Acute peripheral arterial events are more aggressive in terms of risk factor profile, mortality and morbidity than other vascular disease. Half of patients with incident PAD had history of vascular disease. Incidence and severity of PAD events generally increases with age, and severity of disease predicts mortality. I have shown that incidence of ruptured abdominal aortic aneurysm (RAAA) and aortic dissection increased steeply with age, and 5-year mortality rates were 74% and 65% for RAAA and aortic dissection respectively. I have also shown that the true population-based incidence of acute aortic dissection is similar to previous estimates of incidence, implying that it is accurately diagnosed and coded, and that retrospective data analysis produces valid estimates of incidence.