Next-generation sequencing: A frameshift in skeletal dysplasia gene discovery

In the last decade, huge breakthroughs in genetics - driven by new technology and different statistical approaches - have resulted in a plethora of new disease genes identified for both common and rare diseases. Massive parallel sequencing, commonly known as next-generation sequencing, is the latest advance in genetics, and has already facilitated the discovery of the molecular cause of many monogenic disorders. This article describes this new technology and reviews how this approach has been used successfully in patients with skeletal dysplasias. Moreover, this article illustrates how the study of rare diseases can inform understanding and therapeutic developments for common diseases such as osteoporosis. © International Osteoporosis Foundation and National Osteoporosis Foundation 2013.

Simultaneous genotyping of multiplex single nucleotide polymorphisms of the K-ras gene with a home-made kit

Accurate and fast genotyping of single nucleotide polymorphisms (SNPs) is important in the human genome project. Here an automated fluorescent method that can rapidly and accurately genotype multiplex known SNPs was developed by using a homemade kit, which has lower cost but higher resolution than commercial kit. With this method, oncogene K-ras was investigated, four known SNPs of K-ras gene exon 1 in 31 coloerctal cancer patients were detected. Results indicate that mutations were present in 8(26%) of 31 patients, and most mutations were localized in codon 12. The presence of these mutations is thought to be a critical step and plays an important role in human colorectal carcinogenesisas. (C) 2003 Elsevier B.V. All rights reserved.

DNA diagnosis by capillary electrophoresis and microfabricated electrophoretic devices

DNA diagnosis is experiencing an impressive progression towards the development of novel technology to identity various clinically relevant categories of genetic changes and to meet the exponential growth of genomics. The introduction of capillary electrophoresis has dramatically accelerated the completion of the first draft of the human DNA sequence in the Human Genome Project, and thus, has become the method of choice for analysis of various genetic variants. The recent development of microfabricated electrophoretic devices has led to the possibility of integrating multiple sample handling with the actual measurement steps required for automation of molecular diagnostics. This review highlights the most recent progress in capillary electrophoresis and electrophoretic microdevices for DNA-based diagnostics, including the important areas of genotyping for point mutation, single nucleotide polymorphisms, short tandem repeats and organism identification. The application of these techniques for infectious and genetic disease diagnosis, as well as forensic identification purpose, are covered. The promising development and the challenges for techinical problems are also discussed.

O papel do farmacêutico na implementação de estudos de farmacogenómica

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

Sequencing and its consequences:Path dependence and the relationships between genetics and medicalization

Both advocacy for and critiques of the Human Genome Project assume a self-sustaining relationship between genetics and. medicalization. However, this assumption ignores the ways in which the meanings of genetic research are conditional on its position in sequences of events. Based, on analyses of three conditions for which at least one putative gene or genetic marker has been identified, this article argues that critical junctures in the institutional stabilization of phenotypes and the mechanisms that sustain such classifications over time configure the practices and meanings of genetic research. Path dependence is critical to understanding the lack of consistent fit between genetics and medlcalization.

Molecular Medicine and Molecular Pathology for Haematologists:I. Gene Speak made Easy: An Overview of Genes and Gene Expression

Molecular Medicine and Molecular Pathology are integral parts of Haematology as we enter the new millennium. Their origins can be linked to fundamental developments in the basic sciences, particularly genetics, chemistry and biochemistry. The structure of DNA and the genetic code that it encrypts are the critical starting points to our understanding of these new disciplines. The genetic alphabet is a simple one, consisting of just 4 letters, buts its influence is crucial to human development and differentiation. The concept of a gene is not a new one but the Human Genome Project (a joint world-wide effort to characterise our entire genetic make-up) is providing an invaluable understanding of how genes function in normal cellular processes and pinpointing how disruption of these processes can lead to disease. Transcription and translation are the key events by which our genotype is converted to our phenotype (via a messenger RNA intermediate), producing the myriad proteins and enzymes which populate the cellular factory of our body. Unlike the bacterial or prokaryotic genome, the human genome contains a large amount of non coding DNA (less than 1% of our genome codes for proteins), and our genes are interrupted, with the coding regions or exons separated by non coding introns. Precise removal of the intronic material after transcription (though a process called splicing) is critical for efficient translation to occur. Incorrect splicing can lead to the generation of mutant proteins, which can have a dilaterious effect on the phenotype of the individual. Thus the 100,000-200,000 genes which are present in each cell in our body have a defined control mechanism permitting efficient and appropriate expression of proteins and enzymes and yet a single base change in just one of those genes can lead to diseases such as haemophilia or fanconis anaemia.

Le financement de la haute technologie dans le système de santé : le cas de la pharmacogénomique

L’exercice d’allocation de ressources en santé, relevant du Ministère de la santé, se voit fortement influencé autant par les besoins variés de la population que par les exigences des intervenants en santé. Quel rôle ces différents intérêts peuvent-ils jouer dans l’intégration de nouvelles technologies dans la distribution des soins de santé ? La pharmacogénomique, branche émergente de la pharmacologie intégrant les données issues du projet génome humain au processus de développement du médicament, est perçue comme une technologie qui permettrait de personnaliser la médecine. Son intégration aux processus de développement ou de prescription de médicaments promet de minimiser l’apparition d’effets secondaires néfastes découlant de la prise de médicaments. Serait-il alors judicieux pour le gouvernement du Québec, considérant la conjoncture actuelle d’allocation de ressources, d’investir dans la pharmacogénomique en tant que nouvel outil de développement du médicament ou nouveau mode pronostic de médication pour sa population ? Nous aborderons cette question à l’aide de critères de sélection dictés par Caulfield et ses collaborateurs (2001)[1] pour évaluer la pertinence de l’investissement public dans la mise sur pied d’un test génétique, soit l’acceptabilité, l’utilité, la non-malfaisance et la présence d’un bénéfice clair – à coût raisonnable – pour la population. La génomique avoisinant la génétique, ces facteurs s’avèrent applicables dans notre discussion.

Étude des anomalies du développement humain# un modèle d’analyse phénotypique

Depuis le début des années 90, le projet génome humain a permis l’émergence de nombreuses techniques globalisantes porteuses du suffixe –omique : génomique, transcriptomique, protéomique, épigénomique, etc.… L’étude globale de l’ensemble des phénotypes humains (« phénome ») est à l’origine de nouvelles technologies constituant la « phénomique ». L’approche phénomique permet de déterminer des liens entre des combinaisons de traits phénomiques. Nous voulons appliquer cette approche à l’étude des malformations humaines en particulier leurs combinaisons, ne formant des syndromes, des associations ou des séquences bien caractérisés que dans un petit nombre de cas. Afin d’évaluer la faisabilité de cette approche, pour une étude pilote nous avons décidé d’établir une base de données pour la description phénotypique des anomalies foetales. Nous avons effectué ces étapes : o Réalisation d’une étude rétrospective d’une série d’autopsies de foetus au CHU Sainte- Justine (Montréal, QC, Canada) entre 2001-2006 o Élaboration de trois thésaurus et d’une ontologie des anomalies développementales humaines o Construction une base de données en langage MySQL Cette base de données multicentrique accessible sur (http://www.malformations.org), nous permet de rechercher très facilement les données phénotypiques des 543 cas observés porteurs d’une anomalie donnée, de leur donner une description statistique et de générer les différents types d’hypothèses. Elle nous a également permis de sélectionner 153 cas de foetus malformés qui font l’objet d’une étude de micropuce d’hybridation génomique comparative (aCGH) à la recherche d’une anomalie génomique.

Phénomène de biohype dans des articles scientifiques rapportant des résultats issus de recherches cliniques en nutrigénétique/nutrigénomique : caractérisation et perception des chercheurs

Le développement de la nutrigénétique/nutrigénomique (NGx) a suscité de nombreuses attentes puisque les retombées qui lui sont associées s’avèrent potentiellement bénéfiques autant pour les individus en santé que pour les individus malades. De grandes attentes avaient également été associées au Projet de décryptage du Génome Humain (PGH). Aujourd’hui, seules quelques attentes de celles envisagées se sont concrétisées. Le PGH a donc évolué dans un contexte marqué par du biohype, soit la promotion d’attentes exagérées, voir irréalistes. Étant donné l’importance des attentes associées avec le développement de la NGx et des limites méthodologiques auxquelles fait encore face la recherche clinique conduite dans ce domaine, l’objectif principal de cette thèse est de déterminer si les publications scientifiques rapportant des résultats de recherches cliniques effectuées en NGx contribuent à l’émergence d’un phénomène de biohype. Plus spécifiquement, il s’agira également de documenter la perception des chercheurs oeuvrant dans le domaine de la NGx du phénomène de biohype, d’identifier certains facteurs qui pourraient expliquer son émergence dans la littérature scientifique propre à ce domaine et de proposer des pistes d’actions pour limiter les risques associés à ce phénomène. Nous avons tout d’abord procédé à une analyse documentaire d’articles scientifiques rapportant des résultats issus de recherches cliniques en NGx. Celle-ci nous a révélé que plusieurs bénéfices étaient promus dans cette littérature alors même que les limites méthodologiques n’étaient pas d’emblée présentées et discutées. Cette observation nous portait à croire que ces bénéfices étant potentiellement prématurés. Nous avons ensuite voulu valider notre constat auprès des chercheurs œuvrant principalement dans le domaine de la NGx. Cette enquête nous a permis de constater que les chercheurs étaient généralement en accord avec les bénéfices que nous avons recensés dans les articles scientifiques. Toutefois, ils n’envisageaient pas leur concrétisation à moyen terme. Par ailleurs, cette enquête nous a également révélé que les limitations méthodologiques actuellement rencontrées dans la conduite de recherches cliniques soulevaient des doutes quant à la faisabilité des bénéfices promut dans les articles scientifiques. Ces données viennent confirmer notre observation à savoir qu’un phénomène de biohype serait réellement en émergence dans les articles scientifiques rapportant des résultats de recherches cliniques en NGx. Outre des informations concernant les publics ciblés par les chercheurs et les éléments que doivent contenir un article scientifique, cette enquête nous a également aidés à mieux comprendre les avantages associés à la promotion de bénéfices. Selon la majorité des chercheurs interrogés, la promotion de bénéfices dans un article scientifique augmenterait les chances d’un manuscrit d’être publié et favoriserait la continuité du financement du domaine de recherche. Cette activité étant caractérisée par un environnement compétitif, la promotion de bénéfices semble être une avenue à envisager pour se démarquer. Quoique la promotion de bénéfices prématurés ou exagérés ne soit pas considérée comme de l’inconduite scientifique, elle peut causer entre autres un affaiblissement du sentiment de confiance entre le public et les chercheurs et ultimement, contrevenir à la continuité d’une saine activité de recherche. À la lumière de ces données, nous croyons qu’une des stratégies qui permettrait de prévenir l’apparition des risques associés au phénomène de biohype serait de sensibiliser les chercheurs et les éditeurs de journaux scientifiques à ces derniers. Plus particulièrement, nous encourageons l’intégration de lignes directrices portant sur la gestion du biohype dans les codes de conduites qui ont été mis en place pour favoriser les bonnes pratiques en recherche.

British Nutrition Foundation annual lecture: chips with everything? Nutritional genomics and the application of diet in disease prevention

The development of high throughput techniques ('chip' technology) for measurement of gene expression and gene polymorphisms (genomics), and techniques for measuring global protein expression (proteomics) and metabolite profile (metabolomics) are revolutionising life science research, including research in human nutrition. In particular, the ability to undertake large-scale genotyping and to identify gene polymorphisms that determine risk of chronic disease (candidate genes) could enable definition of an individual's risk at an early age. However, the search for candidate genes has proven to be more complex, and their identification more elusive, than previously thought. This is largely due to the fact that much of the variability in risk results from interactions between the genome and environmental exposures. Whilst the former is now very well defined via the Human Genome Project, the latter (e.g. diet, toxins, physical activity) are poorly characterised, resulting in inability to account for their confounding effects in most large-scale candidate gene studies. The polygenic nature of most chronic diseases offers further complexity, requiring very large studies to disentangle relatively weak impacts of large numbers of potential 'risk' genes. The efficacy of diet as a preventative strategy could also be considerably increased by better information concerning gene polymorphisms that determine variability in responsiveness to specific diet and nutrient changes. Much of the limited available data are based on retrospective genotyping using stored samples from previously conducted intervention trials. Prospective studies are now needed to provide data that can be used as the basis for provision of individualised dietary advice and development of food products that optimise disease prevention. Application of the new technologies in nutrition research offers considerable potential for development of new knowledge and could greatly advance the role of diet as a preventative disease strategy in the 21st century. Given the potential economic and social benefits offered, funding for research in this area needs greater recognition, and a stronger strategic focus, than is presently the case. Application of genomics in human health offers considerable ethical and societal as well as scientific challenges. Economic determinants of health care provision are more likely to resolve such issues than scientific developments or altruistic concerns for human health.

The use of proteomics to identify novel therapeutic targets for the treatment of disease

The completion of the Human Genome Project has revealed a multitude of potential avenues for the identification of therapeutic targets. Extensive sequence information enables the identification of novel genes but does not facilitate a thorough understanding of how changes in gene expression control the molecular mechanisms underlying the development and regulation of a cell or the progression of disease. Proteomics encompasses the study of proteins expressed by a population of cells, and evaluates changes in protein expression, post-translational modifications, protein interactions, protein structure and splice variants, all of which are imperative for a complete understanding of protein function within the cell. From the outset, proteomics has been used to compare the protein profiles of cells in healthy and diseased states and as such can be used to identify proteins associated with disease development and progression. These candidate proteins might provide novel targets for new therapeutic agents or aid the development of assays for disease biomarkers. This review provides an overview of the current proteomic techniques available and focuses on their application in the search for novel therapeutic targets for the treatment of disease.

An insight into the public acceptance of nutrigenomic-based personalised nutrition.

It is predicted that non-communicable diseases will account for over 73 % of global mortality in 2020. Given that the majority of these deaths occur in developed countries such as the UK, and that up to 80 % of chronic disease could be prevented through improvements in diet and lifestyle, it is imperative that dietary guidelines and disease prevention strategies are reviewed in order to improve their efficacy. Since the completion of the human genome project our understanding of complex interactions between environmental factors such as diet and genes has progressed considerably, as has the potential to individualise diets using dietary, phenotypic and genotypic data. Thus, there is an ambition for dietary interventions to move away from population-based guidance towards 'personalised nutrition'. The present paper reviews current evidence for the public acceptance of genetic testing and personalised nutrition in disease prevention. Health and clear consumer benefits have been identified as key motivators in the uptake of genetic testing, with individuals reporting personal experience of disease, such as those with specific symptoms, being more willing to undergo genetic testing for the purpose of personalised nutrition. This greater perceived susceptibility to disease may also improve motivation to change behaviour which is a key barrier in the success of any nutrition intervention. Several consumer concerns have been identified in the literature which should be addressed before the introduction of a nutrigenomic-based personalised nutrition service. Future research should focus on the efficacy and implementation of nutrigenomic-based personalised nutrition.

A parallel DNA fragment assembly algorithm based on eulerian superpath approach

Fragments assembly is among the core problems in the research of Genome. Although many assembly tools based on the "overlap-layout-consensus" paradigm are widely used such as in the Human Genome Project currently, they still can not resolve the "repeats problem" in the DNA sequencing. For the purpose of resolving such problem, Pevzner et al. put forward a new Euler Superpath assembly algorithm. But it needs a big and complex de Bruijin graph which consumes large amounts of memories i.e. becomes the bottleneck of the performance. We present a parallel DNA fragment assembly algorithm based on the Eularian Superpath theory and solve the bottleneck in the current assembly program. The experimental results demonstrate that our approach has a good scalability, and can be used in DNA assembly of middle and large size of eukaryote genome.