Rozprawy doktorskie na temat „Human Genome Project”

Thesis (Ph. D.)--University of Adelaide, Dept. of Paediatrics, Women's and Children's Hospital, 1995.
Includes publications and manuscripts by the author. Includes bibliographical references (leaves 196-215).

The Human Genome Project (HGP), the name given to the scientific program to map and decode all of human genetic material, has been projected to revolutionize the conduct of biological science in the twenty-first century. For several years before its formation in 1990, a federally-funded, systematic study of the human genome was discussed first in the scientific arena and then in the public arena. The central thesis of this dissertation is that the arguments supporting or rejecting creation of the HGP and the rhetorical devices used to further those arguments had a major influence on the shape the HGP took in 1991. The argumentation used both for and against the creation of the HGP before the public as well as on the border between the public and scientific arenas is studied. The rhetorical devices such as metaphor, narrative, and selective word choices used to further these arguments are also examined. In particular, a rhetorical content analysis was performed on the 1986-1991 argumentation available to the most crucial audience for such persuasion: the members of Congress who ultimately voted for or against the program's funding and its establishment as a part of U.S. science policy. The proponents of the HGP, especially after the first year of public debate, presented their arguments in a wider arena of discussion and presented more and more varied arguments to advocate the project. The opposition raised questions that had for the most part been answered earlier in the debate. Often anti-HGP arguments focused on less effective audiences (scientists instead of members of Congress). Opposition to the project didn't become organized until near the end of the time frame studied, too late to have much of an impact on the outcome of the debate. The rhetorical devices studied served to magnify the impact of arguments used: in particular, the metaphor served as a boundary object to bridge discussions between the scientific and the public arenas. Ultimately the victory in the debate over the establishment of the HGP was awarded to the promulgators of the strongest underlying metaphor--the idealized excitement and profit of exploration of unknown territory--and the benefits to come from filling in and conquering the unknown areas of the human genetic map, territory the U.S. was eager to claim for its own.
Ph. D.

This thesis examines one of the premier "big science" projects of the contemporary era - the globalised genetic mapping and sequencing initiative known as the Human Genome Project (HGP), and how Australia has responded to it. The study focuses on the relationship between the HGP, the biomedical model of health, and globalisation. It seeks to examine the ways in which the HGP shapes ways of thinking about health; the influence globalisation has on this process; and the implications of this for smaller nations such as Australia. Adopting a critical perspective grounded in political economy, the study provides a largely structuralist analysis of the emergent health context of the HGP. This perspective, which embraces an insightful nexus drawn from the literature on biomedicine, globalisation and the HGP, offers much utility by which to explore the basis of biomedical dominance, in particular, whether it is biomedicine's links to the capitalist infrastructure, or its inherent efficacy and efficiency, that sustains the biomedical paradigm over "other" or non-biomedical health approaches. Additionally, the perspective allows for an assessment of whether there should be some broadening of the way health is conceptualised and delivered to better account for social, economic, and environmental factors that affect living standards and health outcomes, and also the capacity of globalisation to promote such change. These issues are at the core of the study and provide the theoretical frame to examine the processes by which Australian policy makers have given an increasing level of support to human genomic research over the past decade and also the implications of those discrete policy choices. Overall, the study found that globalisation is renewing and extending the dominance of the biomedical model, which will further marginalise other models of health while potentially consuming greater resources for fewer real health outcomes. While the emerging genomic revolution in health care may lead to some wondrous innovations in the coming decades, it is also highly likely to exacerbate the problems of escalating costs and diminishing returns that characterise health care systems in industrialised countries, and to lead to greater health inequities both within and between societies. The Australian Government has chosen to underwrite human genomic research and development. However, Australia's response to the HGP has involved both convergences and variations from the experiences of more powerful industrial nations. The most significant divergence has been in industry and science policy, where until the mid-1990s, the Australian Government displayed no significant interest in providing dedicated research funding, facilities, or enabling agencies to the emerging field. Driven by the threat of economic marginalisation and cultural irrelevance, however, a transformation occurred. Beginning with the Major National Research Facilities Program of the Department of Industry, Science and Technology, and then the landmark Health and Medical Research Strategic Review, support for human genomic research grew strongly. Comprehensive policy settings have recently been established to promote the innovation, commercialisation, promotion and uptake of the products of medical biotechnology and genomics. As such, local advocates of a broader model of health will be forced to compete on the political and economic stage with yet another powerful new area of biomedicine, and thus struggle to secure resources for perhaps more viable and sustainable approaches to health care in the 21st century.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Science
Faculty of Science
Full Text

The way in which scientific research is conceived, organized and practiced in the context of shifting policies and institutional structures is the main focus of this thesis. The empirical component examines the development of the UK Human Genome Mapping Project (HGMP), the British contribution to the international plan to locate all of the genes in the human species. A comparative case-study examines the unsuccessful attem pts by Australian scientists to establish a national genome mapping initiative. Two main sets of research questions are posed. Why was the HGMP set up in the UK at the end of the 1980s when, prima facie, a number of factors suggested that an organized project would not be established? Allied to this question is the comparative one of how and why a project was successfully established in the UK but not in Australia? The second major question asks how policy subsequently developed for the UK programme: what factors shaped policy-making, what aspects of science did the programme shape? Drawing on recent developments in sociology of science and science policy studies, it is argued that in both Australia and the UK debates over whether to have a genome project, and the subsequent developments in UK policy towards the project, were not straightforward administrative choices. In both countries, the question of what was the best science to support was translated into debates over the best way to do science, what scientific knowledge was for and even what was to count as worthwhile knowledge. The implicit and explicit answers to those questions by various groups were embodied in policies and policy recommendations. The thesis concludes that differing expectations concerning the role of science had to be orchestrated together in order to mobilize, and subsequently maintain, support for gene mapping and sequencing.

Understanding our evolutionary history as a species has since long been one of the most attracting and controversial themes of the scientific investigation. From its geographical position, outstanding fossil record and richness of human diversity, the Horn of Africa and, particularly, the Ethiopian region offers an unmatched opportunity to investigate our origins from a genetic perspective. To carry out a genome-wide survey of this region, 13 out of the estimated 80 extant Ethiopian populations were typed on an Illumina Omni 1M SNP array. The results showed a good concordance between genetic and linguistic stratification and, overall, a complex population structure placing the Ethiopians in between North and Sub Saharan Africans, due to the recent non African gene flow which was dated at around 3000 years ago. Furthermore the SNP array data unveiled putative traces of the out of Africa migrations as well as, in two of the typed populations, signatures of genetic adaptation to high altitude. To obtain an unbiased, high resolution representation of the Ethiopian genetic landscape, 25 individuals from each of five populations were newly collected and sequenced on an Illumina HiSeq platform. These populations were chosen, from among the ones typed on the SNP array, to represent the main components of Ethiopian genetic diversity. Of the 25 samples per population, 24 were sequenced at low depth to generate a broad list of genetic variants, while one sample from each was sequenced at high depth to provide a higher resolution list of variants peculiar to each analysed population. The 125 Ethiopian genomes thus sequenced, while overall consistent with the genotyping results, described the Ethiopian populations in a less biased way than the SNP array data. Furthermore estimation of past effective population size fluctuations from the individual genomes unveiled a unique pattern in the ancestry of the Ethiopian populations in the early stages of human evolution. These results provide a data resource which can be used in future analyses.

As pesquisas envolvendo seres humanos geram preocupações éticas, pois os voluntários aceitam riscos e inconveniências com o objetivo de contribuir para o avanço do conhecimento científico e beneficiar outrem. A disposição para participar de pesquisas clínicas se mostra quando o paciente adere ao Termo de Consentimento Livre e Esclarecido (TCLE), compreendendo-o, assinando-o e comprometendo-se a cumprir todas as normas estabelecidas nesse documento, embora consciente de que, a qualquer momento, poderá suspender sua adesão. O TCLE aborda informações que precisam estar descritas de forma clara e de fácil compreensão, destacando riscos, possíveis benefícios e procedimentos. Além disso, garantir a participação voluntária e sua desistência em qualquer momento da pesquisa. Atualmente discute-se a possibilidade de sujeitos de pesquisa não entenderem totalmente o texto do TCLE nem seus direitos como participantes, mesmo tendo assinado o TCLE e aderido à pesquisa. A presente casuística analisa os dados de 793 pacientes, que foram convidados a participar de diferentes protocolos de pesquisa clínica, como especifica a seguir: 380 pacientes, que foram convidados a participar do grupo controle do projeto Genoma Clínico do Câncer; 365 pacientes, que foram convidados a participar do projeto Genoma Clínico do Câncer do Aparelho do Digestivo por apresentarem tumor em uma das seguintes localizações: câncer colorretal, câncer esofágico, câncer de cárdia ou câncer gástrico.; 48 pacientes que foram convidados a participar do Estudo Multicêntrico, Internacional, Randomizado, de Grupos Paralelos, Controlado por Placebo, Duplo-Cego, com subsidiária cega, para determinar o efeito de 156 semanas de tratamento com MK-966(antiinflamatório Anti-COX 2) na recorrência de pólipo adenomatoso de intestino grosso, em pacientes com histórico de adenoma colorretal ressecado por colonoscopia. Coletaram-se dados dos fichários de pesquisa científica para avaliar a aderência do sujeito de pesquisa ao protocolo, correlacionando-a com fatores demográficos (raça, sexo e idade), sociais (local de nascimento, morada atual e instituição de tratamento), relação risco/beneficio envolvida e nível de escolaridade. O grau de dificuldade dos textos que compõem os TCLE foi avaliado, aplicando-se os Índices de Legibilidade Flesch Reading Ease e Flesch- Kincaid. Aplicou-se questionário aos entrevistadores para avaliar, a posteriori, a postura do sujeito de pesquisa à adesão ao TCLE no momento de sua assinatura ou discordância. A adesão dos sujeitos de pesquisa aos protocolos propostos não teve influência dos fatores demográficos e sociais, no entanto, verificou-se maior adesão entre os pacientes de instituição de tratamento público (99,7%) em comparação com instituição de tratamento privada (93,7%). A adesão foi maior entre os pacientes que participaram de protocolos com menor risco (99,73%) em comparação com os pacientes que participaram de protocolos com maior risco (81,3%). Apesar de a adesão não ter tido influência do nível de escolaridade, este foi menor ou igual a 8 anos de estudo para 462 pacientes (58,26%), entre os quais 444 (96,1%) pacientes eram de instituição de tratamento público. Os índices de legibilidade obtidos variaram de 9.9 12 para o teste de Flesch-Kincaid e 33,1 51,3 para o teste de Flesch Reading Ease. Os resultados encontrados na aplicação dos testes de legibilidade classificaram todos os textos avaliados em nível de difícil compreensão, exigindo maior nível de escolaridade para o seu entendimento Os entrevistadores estimaram, através do questionário aplicado a eles, que 90% dos pacientes do hospital público preferem ouvir a explicação do TCLE a ler o texto. Na instituição privada esta estimativa foi de 40%. Apenas onze sujeitos de pesquisa não aderiram ao TCLE. A adesão não recebeu influência de fatores demográficos e sociais. O risco inerente aos protocolos apresentados influenciou a adesão dos sujeitos de pesquisa. Os textos avaliados não se constituíram em linguagem escrita de fácil entendimento, necessitando mais de 9 anos de estudo para sua compreensão. Esta pesquisa sugere que, apesar da alta incidência de adesão, a avaliação de novos métodos de aplicação do TCLE é necessária para que o sujeito de pesquisa menos instruído tenha condições de compreender adequadamente todo o conteúdo do texto proposto no TCLE.
Researches engaging human beings pose ethical concerns since volunteers take on risks and inconveniences aiming to contribute to advanced scientific knowledge and to benefit others. The moment patients sign the term of voluntary and informed consent TCLE (Termo de Consentimento Livre e Esclarecido) they show they are willing to participate in clinical trials and that they understand the term and commit to complying with all rules in the document, aware that they can, at any moment, withdraw acceptance. The TCLE addresses all issues in the research process and are therefore important to the study participants. The information given at the TCLE must be clearly stated and easily understood, highlighting risks, possible benefits and procedures in addition to guaranteeing volunteer participation and consent withdrawal at any time during the trial. Lately, it has been speculated that the study participants do not totally understand the TCLEs text content and their participants rights before accepting the TCLE and joining the trial. This study analyzes the data from 793 patients, invited to take part in different protocols of clinical trials, as follows: 380 patients, invited to join the Clinic Cancer Genome Project Control Group; 365 patients, invited to join the Genome Clinic Cancer Genome of the Digestive System since they had one of the four tumors: colorectal cancer, cancer of the esophagus, cardia adenocarcinoma and gastric cancer; 48 patients were invited to join the International Multicenter double-blind, randomized, parallel-group, placebocontrolled study, with undisclosed sponsor, to determine the outcome of a 156-week treatment with MK-966(anti-inflammatory Anti-COX 2) in recurrent adenomatous polyp of the large bowel, in patients with a history of colorectal resection for adenoma at colonoscopy. Data were collected from previous scientific studies to assess study participants acceptance, correlating it to demographic factors (ethnic group, gender and age), social (birthplace, home place, health institution), cost/benefit and schooling. The level of difficulty in the TCLE texts was assessed with Flesch Reading Ease and Flesch-Kincaid readability measures. Interviewers answered a questionnaire a posteriori, to evaluate the study participants attitude toward the TCLE acceptance at the moment they signed it or did not accept it. The study participants acceptance of the suggested protocols was not influenced by demographic and social factors. However, patients from public health institutions (99,7%) outnumbered those from private health institutions (93,7%). Acceptance was higher among patients taking part in low-risk protocols (99,73%) than in high-risk protocols (81,3%). Although schooling did not influence acceptance, it was 8 years or less in 462 patients (58,26%), among who 444 (96,1%) were patients from public health institutions. The indices of legibility had varied of 9.9 - 12 for the test of Flesch-Kincaid and 33.1 - 51,3 for the test of Flesch Reading Ease. The results found in the application of the legibility tests had classified all the texts evaluated in level of difficult understanding, demanding higher school level for its agreement. Interviewers reported in questionnaires that 90% of the patients from public hospitals would rather listen to an explanation of the TCLE than read the text whereas in patients from private institution the percentage dropped to 40%. Only eleven study participants did not join the TCLE. Acceptance was not influenced by social and demographic factors, but the protocols risk levels influenced the study participants decisions. The evaluated texts proved to be difficult to understand, demanding over 9 years of schooling to be understood. This study suggests that, in spite of being highly accepted, the TCLE requires new application methods so that less educated people can properly understand its text contents.

The EBV has been linked to multiple human disease phenotypes and has been associated with cancers and other infections. Recently single gene analysis and genome-wide analysis studies have been exploited to uncover the human genetic variants that are linked with EBV diseases. It also suggested the substantial role of individual host genetics and also provided a clue in understanding the interaction between virus and human. Furthermore, the outcome of the EBV infection is a complex phenomenon governs by the variation in the genetic architecture of the viral and human genomes and/or the interacting environmental factors. Therefore, this PhD work is mainly a large-scale effort towards the understanding of the human and EBV genetic architecture to uncover the role of genetic variation in EBV associated infections, disease susceptibility, immune recognition and invasion. Our results also provide a framework on the impact of human and EBV genetic variation and their unusual interactions that highlight the human genetic influence affecting viral load reflecting the clinical behavior of EBV in LCLs and the other side viral antigenic variation modulating immune response to sustain persistence infection. This EBV-human perturbation is essential to follow-up in the context of the susceptibility of individual populations to a specific EBV associated pathology.

Etiquetas de sequências expressas (ESTs) são fundamentais para a identificação de genes no genoma humano e para definir características de expressão gênica. Neste trabalho, descrevemos uma nova abordagem para a geração de bibliotecas de cDNA, utilizando iniciadores arbitrários para a produção, por PCR, de mini-bibliotecas a partir de mRNA derivado de câncer de mama. Clones destas bibliotecas foram sequenciadas para gerar 6029 ESTs. Utilizando esta abordagem, foi possível observar uma significante normalização das diferentes sub-populações de mRNA e amplificação preferencial de porções centrais dos genes. Análise bioinformática destas sequências mostra que 3.350 ESTs (56%) tem similaridade significante a sequências de DNA e/ou cDNA já conhecidas (sequências anotadas) descritas em diferentes organismos, e 1509 ESTs (25%) não possuem qualquer similaridade a diferentes bancos de dados. Dentre as sequências anotadas, identificamos algumas sequências com alta similaridade a genes conhecidos em diferentes organismos, indicando a descoberta de alguns genes homólogos possivelmente envolvidos com processos carcinogênicos. Como exemplo, isolamos e caracterizamos parcialmente (i) uma nova isoforma do gene NABC1 (novel amplified sequence in breast carcinoma 1), o qual é pouco expresso em tumores coloretais, (ii) um novo gene da família de semaforinas (moléculas de motilidade axonal) que apresenta uma baixa expressão em linhagens celulares de glioblastoma tratadas com ácido retinóico, um agente antitumoral e (iii) o gene ortólogo humano Notch 2, aparentemente superexpresso em tumores mamários com maior malignidade.
Expressed sequence tags (ESTs) are of fundamental importance for the identification of genes within the human genome and defining gene expression characteristics. In this work, we describe a new approach for generating cDNA libraries using essentially arbitrary primers to construct PCR-based minilibraries from breast tumor mRNA. Clones from these libraries were sequenced to generate 6,029 ESTs. Using this approach, we were able to observe a significant normalization of the different mRNA subpopulations and a preferential amplification of the central portions of the genes. Bioinformatic analysis of these sequences shows that 3,350 ESTs (56%) have significant similarity to known DNA and/or cDNA sequences (annotated sequences) from different organisms and 1,509 ESTs (25%) show no similarity to any sequences on different databases. From the annotated sequences, we have identified some sequences with high similarity to known genes from different organisms, indicating the discovery of some homologous genes possibly correlated with carcinogenic processes. For instance, we have isolated and partially characterized (i) a new NABC1 (novel amplified sequence in breast carcinoma 1) isoform which is downregulated in colorectal tumors, (ii) a novel semaphorin member of axon guidance molecules that is down-regulated in glioblastoma cell lines treated with all-trans-retinoic acid, an anti-tumor agent and (iii) the ortolog Notch 2 human gene, apparenty overexpressed in breast tumors with higher malignancy.

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas
Nos dias de hoje existe uma preocupação acrescida de aumentar a segurança, efetividade e racionalização dos fármacos, pretendendo com isto otimizar as terapêuticas. Muitas vezes utiliza-se erradamente a Farmacogenómica como sinónimo de Farmacogenética. A Farmacogenómica é uma ciência promissora e em expansão, tendo como objetivo a terapêutica individualizada, diminuindo o risco das RAMs e da ineficácia do tratamento. Devido à sua formação, o papel do farmacêutico poderá ser uma mais-valia para esta área da terapia personalizada, prestando o seu conhecimento em fármacos. Esta dissertação divide-se em parte teórica e parte prática. Esta última consiste num estudo realizado através de um inquérito via-online, cujo objetivo é apurar o conhecimento de estudantes universitários sobre a Farmacogenómica. Nowadays there is a heightened concern of increasing safety, effectiveness and rationalization of drugs, intending to optimize this therapeutic. Often it is used incorrectly as a synonym for the Pharmacogenomics Pharmacogenetics. The Pharmacogenomics is a science promising and expanding, aiming to individualized therapy, reducing the risk of ADRs and treatment failure. Because of their training, the role of the pharmacist can be an asset to this area of personalized therapy, paying their knowledge in pharmaceuticals. This thesis is divided into theoretical and practical part. The latter consists of a study conducted through a survey via online-whose goal is to determine the knowledge of university students on Pharmacogenomics.

The beginning of the new millennium has witnessed the completion of the first DNA reference sequence for Homo sapiens (Human Genome Project) and the establishment of a human SNP haplotype map (International HapMap Project). In particular, these advancements have revolutionised our understanding of the role of genes and genetic variation in the study of human traits and disease. Although a plethora of genes underlying complex phenotypes have been characterised, many are family specific or only explain a portion of the total underlying genetic component. Increasingly, researchers are turning to population isolates to dissect the genetic and non-genetic components underlying common, complex human disorders. Isolates are populations that have expanded in severe geographical or cultural isolation from a limited number of original founders. Genetic and non-genetic heterogeneity are limited or even reduced in isolates due to the presence of various genetic, environmental and societal factors. Norfolk Island is a young, South Pacific population isolate whose origins are intertwined with the fate of Her Majesty’s Armed Ship, the Bounty. The majority of permanent residents are descended from 9 Isle of Man, Bounty Mutineers and 6 Tahitian women who colonised Pitcairn Island (then uninhabited) in 1790 and relocated to the then uninhabited Norfolk Island in 1856. These historical origins have been confirmed with ancestry informative markers.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Medical Science
Griffith Health
Full Text

Now that the human genome project has been completed, the race is on to improve the existing sequencing techniques, or develop new ones, to allow affordable and reasonably quick personal DNA testing. This would help predict personal response to drugs and disease predisposition. The standard sequencing method is based on electrophoresis, which allows a sorting of molecules according to their size. In the first part of this thesis, I develop a new numerical method to rapidly obtain the continuum limit mobility of a migrating molecule, using results obtained on a lattice. I then use this technique to re-examine the theoretical foundation of the current model (the Ogston-Morris-Rodbard-Chrambach or OMRC model) used to describe the molecular size dependence of the electrophoresic mobility of small molecules during gel electrophoresis. I consider three-dimensional gels and electric field lines similar to the ones used in electrophoresis and show that the OMRC model could not reliably predict the mobility of a molecule in a gel. In the second part of this thesis, I present a computational study of a new technique that could be used to provide alternatives to electrophoresis-based sequencing. This technique, named solid phase DNA amplification, allows for the parallelization of DNA amplification (and ultimately, a new sequencing method). I use Monte Carlo and Brownian Dynamics simulations to model this new experimental technique. I show that it leads to a geometrical amplification of DNA molecules and sharp population size distributions.

This thesis examines one of the premier "big science" projects of the contemporary era - the globalised genetic mapping and sequencing initiative known as the Human Genome Project (HGP), and how Australia has responded to it. The study focuses on the relationship between the HGP, the biomedical model of health, and globalisation. It seeks to examine the ways in which the HGP shapes ways of thinking about health; the influence globalisation has on this process; and the implications of this for smaller nations such as Australia. Adopting a critical perspective grounded in political economy, the study provides a largely structuralist analysis of the emergent health context of the HGP. This perspective, which embraces an insightful nexus drawn from the literature on biomedicine, globalisation and the HGP, offers much utility by which to explore the basis of biomedical dominance, in particular, whether it is biomedicine's links to the capitalist infrastructure, or its inherent efficacy and efficiency, that sustains the biomedical paradigm over "other" or non-biomedical health approaches. Additionally, the perspective allows for an assessment of whether there should be some broadening of the way health is conceptualised and delivered to better account for social, economic, and environmental factors that affect living standards and health outcomes, and also the capacity of globalisation to promote such change. These issues are at the core of the study and provide the theoretical frame to examine the processes by which Australian policy makers have given an increasing level of support to human genomic research over the past decade and also the implications of those discrete policy choices. Overall, the study found that globalisation is renewing and extending the dominance of the biomedical model, which will further marginalise other models of health while potentially consuming greater resources for fewer real health outcomes. While the emerging genomic revolution in health care may lead to some wondrous innovations in the coming decades, it is also highly likely to exacerbate the problems of escalating costs and diminishing returns that characterise health care systems in industrialised countries, and to lead to greater health inequities both within and between societies. The Australian Government has chosen to underwrite human genomic research and development. However, Australia's response to the HGP has involved both convergences and variations from the experiences of more powerful industrial nations. The most significant divergence has been in industry and science policy, where until the mid-1990s, the Australian Government displayed no significant interest in providing dedicated research funding, facilities, or enabling agencies to the emerging field. Driven by the threat of economic marginalisation and cultural irrelevance, however, a transformation occurred. Beginning with the Major National Research Facilities Program of the Department of Industry, Science and Technology, and then the landmark Health and Medical Research Strategic Review, support for human genomic research grew strongly. Comprehensive policy settings have recently been established to promote the innovation, commercialisation, promotion and uptake of the products of medical biotechnology and genomics. As such, local advocates of a broader model of health will be forced to compete on the political and economic stage with yet another powerful new area of biomedicine, and thus struggle to secure resources for perhaps more viable and sustainable approaches to health care in the 21st century.

Orientador: Laymert Garcia dos Santos
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Filosofia e Ciencias Humanas
Made available in DSpace on 2018-08-05T01:28:26Z (GMT). No. of bitstreams: 1 Leite_Marcelo_D.pdf: 18137235 bytes, checksum: d2ccf296709649c706ae95e568a4a4e8 (MD5) Previous issue date: 2005
Resumo: A tese central deste trabalho é que a aceitação pública despertada pelo Projeto Genoma Humano só se explica pelo uso político e retórico de um determinismo genético crescentemente irreconciliável com os resultados empíricos da pesquisa genômica atual. A complexidade verificada no genoma humano e em suas interações com o meio desautoriza a manutenção de uma noção simples e unidirecional de causalidade, contrariamente ao pressuposto na idéia de gene como único portador de informação, esteio da doutrina do determinismo genético. Um complexo de metáforas informacionais e/ou lingüísticas continuo vivo nos textos publicados por biólogos moleculares na literatura científica, notadamente nos artigos veiculados nos periódicos de alto impacto Nature e Science de 15 e 16 fevereiro de 2001, respectivamente. Tais metáforas inspiram um tipo de discurso ambíguo que modula nuances variadas de retórica determinista, conforme se dirija aos próprios pares ou ao público leigo" O campo da genômica ainda está longe de rejeitar a conjunção problemática das noções de gene pré-formacionista e de gene como recurso desenvo/vimenta/ na base da metáfora do gene como informação. Essa fusão inspirada pela terminologia cibernética propicia uma versão asséptica de gene, distanciada da natureza, puramente sintática, móvel e virtual o bastante para circular desimpedida nos circuitos de produção de valor como recurso genético passível de garimpagem e de patenteamento. Críticos dã tecnociência devem desafiar o campo da genômica a reformular drasticamente as metáforas que dão suporte a seu programa hegemônico de pesquisa
Abstract: The central thesis of this work is that the public support generated for the Human Genome Project and the hype surrounding it can be explained only by the political and rhetorical uses of genetic determinism, a notion which increasingly cannot be reconciled with the empirical results of on-going genomic research. The complexity that has been uncovered in the human genome and in its interactions with the environment implies that a simple and unidirectional notion of causality cannot be maintained, contrary to a presupposition of the idea of the gene as the sole carrier of iliformation, an idea that contributes to sustain the doctrine of genetic determinism. A complex of informational and/or linguistic metaphors lives on in the texts published by molecular biologists in the scientific press, most notably in the issues published February 15thand 16thof 2001 ofthe high impact journals Nature and Science, respectively. These metaphors generate an ambiguous type of discourse that modulates various nuances of deterministic rhetoric, depending on whether it addresses peers or the lay publico The field of genomics is still a long way ITom rejecting the questionable conflation of the notions of gene as preformation and gene as developmental resource which underpins the metaphor of gene as information. This conflation inspired by cybernetics terminology enables an aseptic version of the gene, separated ITom nature, portable and virtual enough to flow unimpeded through the channels ofvalue production as genetic resource suitable for mining and patenting. Critics of technoscience should challenge the field of genomics to drastically reshape the metaphors which have supported its hegemonic research agenda
Doutorado
Doutor em Ciências Sociais

Dissertação (mestrado) - Pontifícia Universidade Católica do Paraná, Curitiba, 2007
Inclui bibliografia
O presente trabalho tem como escopo analisar algumas transformações da sociedade no campo das ciências biomédicas, demonstrando que o Direito deve agir como uma ferramenta eficaz para regulamentar as inovações biotecnológicas relacionadas à Genética e ao
Il presente lavoro ha per scopo analizzare alcune trasformazioni della società nel campo delle scienze biomediche, dimostrando che il Diritto deve operare come uno strumento efficace a regolare le innovazioni biotecnologiche riguardanti la Genetica ed il

Les génomes du cancer présentent une mosaïque de types de mutations. Trente signatures mutationnelles ont été identifiées à partir d'un grand nombre de tumeurs humaines primaires. Déchiffrer l'origine de ces signatures mutationnelles pourrait aider à identifier les causes du cancer humain. Environ 40% des signatures décrites sont d'origine inconnue, soulignant la nécessité de modèles expérimentaux contrôlés pour étudier l'origine de ces signatures. Au cours de mon travail de doctorat, j'ai caractérisé et utilisé des modèles in vitro et in vivo d'exposition aux cancérogènes, caractériser les signatures mutationnelles au niveau de génome entier de plusieurs composés cancérogènes pour lesquels le spectre de mutations n'était pas connu ou controversé. Tout d'abord, les conditions de cytotoxicités et genotoxicités pour chaque composé ont été établies et la formation d'adduits d'ADN a été évaluée. Suite au séquençage du gène TP53, on a effectué un séquençage au niveau du génome des clones MEF immortalisés dérivés de l'exposition à l'acrylamide, au glycidamide et à l'ochratoxine A. Le travail suggère une nouvelle signature mutationnelle unique pour l'acrylamide et médiée par son métabolite actif, le glycidamide. En fait, le motif des mutations de glycidamide, correspondant au profil de sa signature mutationnelle, a récapitulé les types de mutations attendus en fonction de l'analyse des adduits d'ADN. En outre, une analyse intégrée utilisant des modèles in vitro et in vivo suggère un manque de mutagénicité directe pour l'OTA avec une contribution potentielle d'un mode d'action lié à la production des radicaux libres à la signature mutationnelle OTA dans les MEF. Cette stratégie expérimentale simple et puissante peut faciliter l'interprétation des empreintes de mutations identifiées dans les tumeurs humaines, élucider l'étiologie du cancer et finalement soutenir la classification des cancers du CIRC en fournissant des preuves mécanistes
Cancer genomes harbour a mosaic of mutation patterns from which thirty mutational signatures have been identified, each attributable to a particular known or yet undetermined causal process. Deciphering the origins of these global mutational signatures in full could help identify the causes of human cancer, especially for about 40% of those signatures identified thus far that remain without a known etiological factor. Thus, well-controlled experimental exposure models can be used to assign particular mutational signatures to various mutagenic factors.During the time frame of my PhD work, I characterized and employed innovative in vitro and in vivo models of carcinogen exposure, namely, primary Hupki MEF cells, HepaRG and lymphoblastoid cell lines as well as rodent tumors. The cytotoxic and genotoxic conditions for each tested exposure compound were established and DNA adduct formation was assessed in select cases. Following a pre-screen by TP53 gene sequencing, genome-wide sequencing of immortalized Hupki MEF clones derived from exposure to acrylamide, glycidamide and ochratoxin A was performed, alongside whole genome sequencing of ochratoxin A induced rat renal tumors. The results reveal a novel mutational signature of acrylamide mediated by its active metabolite, glycidamide, a pattern that can be explained by the parallel analysis of individual glycidamide-DNA adducts. In addition, an integrative mutation analysis using in vitro and in vivo models suggests a lack of direct mutagenicity for OTA and possible indirect effects due to the ROS-mediated mode-of-action in MEF cells. The presented robust experimental strategy can facilitate the interpretation of mutation fingerprints identified in human tumors, thereby elucidating cancer etiology, elucidating the relationship between mutagenesis and carcinogenesis and ultimately providing mechanistic evidence for IARC’s carcinogen classification

Made available in DSpace on 2019-03-29T23:34:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-08-31
Advances in biological research, especially in genetics, have a direct influence on medicine. The development of these surveys, especially those under the Human Genome Project, allows man can not only cure or prevent diseases through curative and preventive medicines, but also predict the disease, creating a predictive medicine, which generates information that may be used positively or negatively, with important repercussions in the legal universe. This study, entitled "Discrimination on grounds genetic" examines the consequences of using the so-called predictive medicine, having been developed through a literature review, aiming to identify the rights that may be effected by applying positive knowledge of human genetic data and rights that may be injured due to poor enforcement, seeking legal alternatives within the current legal system. Keywords: Genetic Discrimination, the Human Genome Project; Predictive Medicine; Biological determinism; Privacy genetics; Eugenia.
Os avanços das pesquisas biológicas, em especial da genética, têm influência direta na medicina. O desenvolvimento dessas pesquisas, principalmente as desenvolvidas no âmbito do Projeto Genoma Humano, permite que o homem possa não apenas curar ou prevenir doenças através das medicinas curativa e preventiva, mas também prever as doenças, criando a medicina preditiva, que gera informações que podem ser utilizadas de forma positiva ou negativa, com importantes repercussões no campo jurídico. O presente trabalho, intitulado O Papel dos Direitos de Personalidade no combate à Discriminação por Motivos Genéticos analisa as consequências da utilização da chamada medicina preditiva, tendo sido desenvolvido através de pesquisa bibliográfica, tendo como objetivos identificar os direitos que possam ser efetivados através da aplicação positiva do conhecimento dos dados genéticos humanos e os direitos que possam ser feridos em decorrência de sua má aplicação, buscando alternativas jurídicas dentro do ordenamento jurídico vigente. Palavras - chave: Discriminação genética; Projeto Genoma Humano; Medicina preditiva; Determinismo biológico; Privacidade genética; Eugenia.

Une pathologie est dite rare lorsqu'elle affecte moins d'une personne sur 2.000. On dénombre plus de 8.000 maladies rares dont environ 80% seraient d'origine génétique. Parmi les maladies rares, environ 3.000 sont des anomalies du développement (AD). Le déploiement du séquençage haut débit d’exome (ES), a mené à l'identification d’un grand nombre de gènes nouvellement associés à des anomalies du développement rares ou ultra-rares Cependant, un certain nombre d’individus restent sans identification de la cause génétique de leur pathologie. Plusieurs raisons contribuent à la limite de l’ES et le séquençage de génome (GS) permettrait de circonvenir ces problèmes. Nous avons réalisé différentes stratégies d’optimisation de l’ES avant d’entreprendre un GS chez les patients restés sans explication moléculaire.Dans une série de 70 patients sans diagnostic après ES-solo l’analyse en trio a permis d’identifier des variations candidates chez 18/70 patients (26%), dont 11 gènes nouvellement impliqués en pathologie humaine (dont IRF2BPL). Nous avons ensuite décidé d’évaluer l’intérêt d’une approche par pool parental. Chez 57 patients avec ES solo négatif, l’analyse rétrospective des pools parentaux a permis d’identifier des variations pathogènes chez 12 patients (21%). Chez 122 patients avec analyse prospective, les pools parentaux de première intention ont permis d’identifier des variations pathogènes chez 40 patients (33%). Ensuite, 36 patients sans explication moléculaire identifiée après ACPA et ES trio ont bénéficié d’un GS en trio. Chez 11/36 patients (31%), 7 variations ponctuelles et 4 variations de structure ont été considérées comme causales.Une première approche par ES-trio s’avère donc efficace mais onéreuse du fait des surcoûts liés à l’ES parental. Le déploiement de l’ES avec pools parentaux semble représenter une alternative intéressante et efficace puisqu’elle a obtenu un taux diagnostique de 21% pour la cohorte rétrospective et de 33% pour la cohorte prospective. Le GS a permis d’identifier un évènement pathogène chez 11/36 patients (31%) dont 4 SVs. Chez les patients avec AD, l’analyse des données de GS ciblée sur les variations exoniques et les variations de structures s’avère très intéressante pour identifier de nouvelles causes moléculaires et apparaît plus adaptée pour le diagnostic
A disease is considered rare when affecting less than 1/2,000 individuals. Currently, there are more than 8,000 rare disseases of which approximately 80% are of genetic origin. Among them, 3,000 are developmental anomalies (DA). Deployment of exome sequencing (ES) led to identify many different genes associated to rare or ultra-rare diseases. However, some patients remain without any explanation about the genetic cause of their pathology. Several reasons contribute to the limitation of ES but genome sequencing (GS) is expected to overcome them. We have performed various strategies for ES before undertaking GS in patients remaining undiagnosed at the molecular level.In a series of 70 patients without diagnosis after solo-ES, trio analysis allowed to identify candidate variants in 18/70 patients (26%), including 11 genes newly involved in human disorders (including IRF2BPL). We then evaluated the interest of a parental pool approach. In 57 patients with negative solo ES, retrospective parental pool analysis allowed to identify causal variants in 12 patients (21%). In 122 patients with prospective analysis, first-step parental pool ES allowed to identify causal variants in 40 patients (33%). Then, 36 patients with no molecular diagnosis after array-CGH and trio-ES benefited from trio-GS. In 11/36 patients (31%), 7 SNVs and 4 SVs were considered pathogenic.Therefore, a first approach with trio-ES is effective but expansive because of the additional costs of parental sequencing. Deployment of parental pool sequencing seems to represent an interesting alternative since it obtained a retrospective and prospective diagnostic rate of 21% and 33% respectively. GS identified pathogenic events in 11/36 patients (31%) including 4 SVs. In patients with AD, analysis of GS data focused on exonic variants and SVs is interesting for identifying new molecular causes and appears suitable for diagnostic purposes

This thesis explores the ontologies of planning, science, and politics underlying the tunnel project at Hallandsås. Four such foundational (universal) views are identified – absolute conceptions of space, linear notions of time, binary logic and anthropocentrism. The thesis examines the subsequent re-workings of the foundational philosophies of space, time, environment, nature and the human behind the initial project in the aftermath of the environmental scandal. The basic aim of the thesis has been to argue for alternative ontologies of planning, science, and politics. In this regard, it is argued that a recasting of the foundational notions of mainstream planning, science and politics is a crucial first step. The thesis contends that perspectives based on hybrid geographies offer an alternative foundation for policy, planning and science that is closely adjusted to a more than human world. The issue of whether one can distinguish signs of a de facto shift to a hybrid geographic perspective in the post-Hallandsås tunnel project is also explored. The methodology of the study is inspired by the precepts of ANT (Actor Network Theory) of following actors in their networks, events and processes. In as much as humans and non-humans participate in the construction of the world in multiple or complex ways the thesis has tried to give voice to these different actors. As such, the study of the tunnel project follows a hybrid method, one that includes humans and non-humans. The thesis makes the case for discussing hybrid geographies as one possible alternative perspective in planning. Hybrid geographies propose a multifaceted perspective that argues for an inclusive geography and one that is adjusted to a more than human world. The experiences from the project at Hallandsås should therefore be applied to other projects and planning. In times of complex ecological and environmental problems, alternatives to mainstream planning are both desirable and required. Hybrid geographies involve issues of altering our ways of thinking, acting and being in the world, for our own good. In this regard, hybrid geographical perspectives could be a basis for alternatives to mainstream planning.

Based on research primarily conducted in a molecular biology laboratory working on the Human Genome Project (HGP), this dissertation focuses-upon how genomic research, as an emerging form of scientific knowledge, stands to affect the fashioning of subjectivity. This study argues that as a biomedical project which claims to be capable of understanding "what it means to be human," the HGP stands to have profound consequences upon the way in which modern subjects know themselves. The life sciences have increasingly moved away from the mastery of nature towards knowledge and control over human nature. The HGP represents an emerging model in which human nature and life have become objects and categories of knowledge and control for the life sciences. The focus of this project is the investigation of how the HGP incorporates an understanding of human nature and life into its realm of study and how that knowledge in turn is incorporated into the understanding human beings have of themselves. This research centers upon the HGP as the site in which to draw out, counterpose and resolve some of the issues at stake in the scientific remaking of human subjects. The HGP represents an expansion of the domain of the life sciences into the control of life itself and the psychological as well as material expression of that life in human beings, known as human nature. Finally, this study characterizes the HGP as a biomedical research project that is essentially religious in how it perceives itself and claims to provide ultimate knowledge on being human. This project argues that such knowledge is religious and therefore inaccessible through modern science. Therefore it questions the ability of the HGP to provide valid knowledge on the ultimate understanding of human beings through religious, philosophical and scientific discourses that contest and subvert this claim.

According to Human Genome Project humans contains nearly 25,000 genes. Humans differs from each other just because of 0.1% of DNA. Since all the cells of an individual contains similar genetic material still they differ among one another in function and this is because of the differential gene expression. Since cells respond differently to different stimulus it is interesting to note their response. Gene expression is the main reason how cell gone a respond to different stimuli. In this study we have taken sequenced mRNA from human cell lines which was treated with TNF-alpha for some time period and try to identify all the differential expressed genes using RNA-Seq. We will extend our study to find out the pathways in which these genes have involved. In this study we have used DESeq2 package for normalization, statistical analysis and for visualization of dataset. Genes obtained at the end of the analysis can be act as biomarkers for the cancer treatment.

Includes publications and manuscripts by the author.
Bibliography: leaves 196-215.
1 v. : ill. (some col.) ; 30 cm.
Title page, contents and abstract only. The complete thesis in print form is available from the University Library.
The goal of the human genome project addressed in this thesis, was the construction of a genetric linkage map with a resolution of between 2-5 cM by the year 1995.
Thesis (Ph.D.)--University of Adelaide, Dept. of Paediatrics, Women's and Children's Hospital, 1995

abstract: In the past century, a number of technological projects have been undertaken as grand solutions to social problems. In the so called century of biology, this technological world view focuses on biomedical advances. The President of the United States, who once called for nuclear weapons and space exploration, now calls for new biotechnologies, such as genomics, individualized medicine, and nanotechnology, which will improve the world by improving our biological lives. Portrayed as the Manhattan Project of the late 20th Century, the Human Genome Project (HGP) not only undertook the science of sequencing the human genome but also the ethics of it. For this thesis I ask how the HGP did this; what was the range of possibilities of goods and evils imagined by the HGP; and what, if anything, was left out. I show that the Ethical, Legal, and Social Implications (ELSI) research program of the HGP was inscribed with the competencies of the professional field of bioethics, which had lent itself useful for governing biomedical science and technology earlier in the 20th century. Drawing on a sociological framework for understanding the development of professional bioethics, I describe the development of ELSI, and I note how the given-in-advance boundaries between authorized/unauthorized questions shaped its formation and biased technologically based conceptualizations of social problems and potential solutions. In this sense, the HGP and ELSI served both as the ends of policy and as instruments of self-legitimation, thus re-inscribing and enacting the structures for these powerful sociotechnical imaginaries. I engage the HGP and ELSI through historical, sociological, and political philosophical analysis, by examining their immediate context of the NIH, the meso level of professional/disciplinary bioethics, and the larger context of American democracy and modernity. My argument is simultaneously a claim about how questions are asked and how knowledge and expertise are made, exposing the relationship between the HGP and ELSI as a mutually constitutive and reciprocally related form of coproduction of knowledge and social structures. I finish by arguing that ELSI is in a better position than bioethics to carry out the original project of that field, i.e., to provide a space to elucidate certain institutionally authorized questions about science and technology. Finally, I venture into making a prophecy about the future of ELSI and bioethics: that the former will replace the latter as a locus for only formally rational and thin ethical debates.
Dissertation/Thesis
M.S. Biology 2012

Submitted to the faculty of the Informatics Graduate Program in partial fulfillment of the requirements for the degree Master of Science in Bioinformatics in the School of Informatics Indiana University May 2006
A plethora of genomic and proteomic information was uncovered by the U.S Human Genome Project (HGP) – mostly by means of bioinformatics tools and techniques. Despite the impact that bioinformatics and pharmacogenomics were projected to have in the drug discovery and development process, the challenges facing the pharmaceutical industry, such as the high cost and the slow pace of drug development, appear to persist. Socio-economic barriers exist that mitigate the full integration of bioinformatics and pharmacogenomics into the drug discovery and development process, hence limiting the desired and expected effects.

M.Comm.
A revolution in genetic research, known as the Human Genome Project (HGP), is taking place. This project, initiated in 1984, is a twenty-year, six billion-dollar science project designed to map the entire genetic structure (Genome) of the human species (Brockett and Tankersley, 1995). In 1998, the HGP leaders expected to complete the project by 2003 (Lowden, J. A., 1999:33). The Human Genome Project is designed to sequence the human genome (the blue print of genetic information) and to identify the estimated 100000 genesherein. This has added a new dimension to the technology available to underwriters in the life and health insurance industry for the selection of medical risks. Genetic testing can identify inherited diseases and predict illnesses that might not manifest for decades (Brackenridge & Elder, 1998:89). Genome research has opened up new opportunities for diagnosis and in some cases, early treatment of medical conditions. This new basis of knowledge is referred to as the advent of the molecular age in medicine. Medical journals, the mass media and genetic interest groups are treating human genetics and the opportunities it presents as a high-profile issue, with great attention being paid to the complex and emotive topics of life insurance and genetic testing (Regenauer & Schmidtke, 1998:5). The Insurance Industry can use genetic testing to identify high-risk applicants more accurately and price products accordingly, thereby improving risk assessment and profitability. These potential advantages, however, are counter-balanced by ethical considerations that are much more difficult to address (Lowden, J. A., 1999:33). Many consumers, ethicists and geneticists fear that insurers will use this data for unfair discriminatory purposes, identifying a genetic underclass of people who, although clinically well, will be uninsurable. Genetic testing could invade the privacy of applicants and their families. There are concerns about the confidential handling of genetic information as well as the accurate interpretation of genetic tests. The uncertainty about the predictive value of genetic tests, the shortage of trained geneticists and counsellors and the psychological impact of that knowledge of a predictable serious disease might have, have lead to much opposition to the use of genetic information by third parties. In the United States most Americans receive health insurance through their place of employment. There are fears that genetic testing will be used to discriminate against prospective employees and render many people unemployable and uninsurable (Council for responsible Genetics, 1997: http://www.gene-watch.org/genclisc htuil Consumer groups have lobbied effectively for the prohibition of testing or the use of testing by insurers in the United States and Europe and legislators aim to ban the use of genetic information on a broad basis. Insurers, on the other hand, are assuming that the new laws will cause untold damage to the fiscal stability of their companies (Lowden, J. A., 1999:33). However, it seems inevitable that genetic testing will affect risk classification sooner rather than later and to a greater extent than most believe (Chambers, 1997: http://www.Inrc.com/epirr/issues/143/143-4.htm).

Atualmente existe uma enorme preocupação com a utilização racional do medicamento e consequente otimização de terapêuticas. Para esta otimização é necessário focar em dois pontos essenciais, a segurança e a efetividade. Os seres humanos podem apresentar respostas terapêuticas diferentes quando administrado o mesmo fármaco. Isto acontece devido a diferenças na idade, peso, género, estado de saúde, dieta e também pelo genéticos. A farmacogenética está, neste momento, em rápida expansão, sendo uma disciplina que estuda as variações hereditárias que condicionam a resposta individual aos fármacos, particularmente por processos farmacocinéticos e farmacodinâmicos. Esta considera não só os mecanismos moleculares originários das reações adversas aos medicamentos, mas também os biomarcadores que permitem identificar as pessoas de risco. Considera-se então que a farmacogenética tem as ferramentas necessárias que possibilitam a construção de respostas terapêuticas dirigidas ao perfil genético dos indivíduos, permitindo respeitar a variabilidade inter-individual. A medicina personalizada tem assim como objetivo principal, a maximização da eficácia e a minimização dos riscos de toxicidade das terapêuticas para cada indivíduo. Um dos grandes estímulos para o avanço da farmacogenética foi a sequenciação do genoma humano, facilitando o estudo do efeito das variações genéticas. Esta revisão bibliográfica tem como objetivo mostrar uma visão geral da farmacogenética, introduzir os conceitos básicos e mostrar as aplicações que já são executadas nesta área. Para elaborar esta revisão foi realizada uma pesquisa bibliográfica em bases de dados como a Pubmed e a ScienceDirect.
Currently, there is an enormous concern regarding the rational use of the medication with the consequent optimization of therapeutics. To achieve this, it is necessary to focus on two essential points: safety and effectiveness. Human beings can present different therapeutic responses when administered the same drug. This happens due to differences in age, weight, gender, health state, diet and also to genetics. Pharmacogenetics is currently facing a rapid expansion, being a discipline which studies the heritable variations that condition the individual response to drugs, particularly through pharmacokinetic and pharmacodynamic processes. This discipline contemplates not only the molecular mechanisms in the origin of the adverse reactions to medications, but also the biomarkers that allow the identification of people at risk. Accordingly, it is considered that pharmacogenetics has the tools that enable the construction of therapeutic responses directed towards the genetic profile of the individuals, taking the inter-individual variability. It is the main goal of personalized medicine to maximize the efficiency and minimize the risks of toxicity of the therapeutics for each individual. One of the great catalysts for the advancement of pharmacogenetics was the sequencing of the human genome, facilitating the study of the effect of genetic variations. This literature review aims at exhibiting a general vision of pharmacogenetics, introducing the basic concepts and show the applications already being executed in this area. To elaborate this review, a bibliographic research was conducted on databases such as Pubmed and ScienceDirect.