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Editorial Dear ACGT newsletter readers. As every project has an end, it is now time to say goodbye to ACGT as the project ends this summer, after four challenging and rewarding years. Building on the increasingly important ICT demand for innovative solutions for healthcare, ACGT has built a translational infrastructure for Clinical Trials for Cancer which will be resulting in applications that will increase the coherency of the entire system for building Clinical trials. Even if the Islandic Vulcano has showed no mercy to the project’s members scattered all around the world, ACGT demonstrates that willingness aligned with strong scientific orientation can make a project carry forward all of its intended results. From Legal and ethical aspects to purely ICT solutions, ACGT legacy will be seen under several EC co financed projects such as ANCCA and CONTRACT, projects that will support the platform created by the ACGT project. We know that many partnerships developed during the project lifetime will continue and we hope that many of you will take the opportunity of this newsletter to get in touch with the project management to engage in further innovative discussions and partnerships. [...] Clinical Trials The elaboration of guidelines and recommendations for integrating clinical data sources into the ACGT platform
An important challenge in carrying out post-genomic bio-medical research is to efficiently manage and retrieve all relevant data from many heterogeneous sources. A post-genomic clinical trial involves the collection, storage and management of a wide variety of data, including: clinical data collected on Case Report Forms (e.g. symptoms, histology, administered treatment, treatment response), imaging data, genomic data, pathology data and other lab data. Next to that, access to many external sources of data and knowledge is required. These store information about gene and protein sequences, pathways, genomic variation, microarray experiments, medical literature, etc. Seamless access to all these data repositories would greatly facilitate research. In order to provide seamless data access, syntactic and semantic integration needs to take place. Syntactic data integration handles differences in formats and mechanisms of data access, the fact that information can be represented in different ways, using different terms and identifiers. [...] Products and Services From Prototype to Production – Changes to the ObTiMA development to make it ready for clinical scenariosWhen the development of ObTiMA was launched early within the ACGT project, it was first intended to become a showcase application for the various innovative technologies created within that project. The main focus at that time was to highlight the novel possibilities for designing and managing the various parts of clinical trials based on ontological concepts and descriptions. But very soon it became obvious that ObTiMA has a much greater potential than just being a research prototype. And therefore the decision was taken to develop the system further into the direction of fulfilling the strict software requirements found in clinical settings. But to create such a production-ready application the previous research-focused development process had to be shifted towards a commercial software development methodology. Also different criteria gained focus that are of lesser importance in research but essential in everyday use, such as usability (since in clinical environments, easy-and-quick-to-use software is of utmost importance). In the following we describe some of the measures taken over the last year in light of the just said: [...] Grid news Proper launch of the EGI - A challenge for the European Grid CommunityWhile grids are commonly understood as distributed computing infrastructures, they are primary about the collaboration. It is therefore not surprising that the first international pusher for the large scale grid infrastructure was a community behind the high energy physics scientific experiments. A development that initially started as a support activity of one scientific community became soon a movement that attracted scientists from many other disciplines and a recognition at the highest national political levels. The initial efforts culminated in a series of the EGEE projects, run between 2004 and 2010 and supported by the European Commission within the 6th and 7th Framework Programmes. While successful, these projects also demonstrated the shortcomings of an infrastructure based on standard projects and taken care of by very heterogeneous group of supporting institutions, ranging from university departments to proper infrastructure building bodies. [...] Feature article ACGT links to the new EU funded projects: ENCCA and CONTRACT
The necessity of an environment that deals with the recent advances in high throughput genomics and post-genomics methods and technologies in molecular biology, which have resulted in an explosion of information and knowledge about cancer and its treatment, is more than evident today. As a result of this explosion in information and knowledge, our ability to characterize and understand the various forms of cancer is growing exponentially. Information arising from post-genomics research and combined genetic and clinical trials on one hand, and advances from high-performance computing and informatics on the other is rapidly providing the medical and scientific community with an enormous opportunity to improve prognosis of patients with cancer by individualizing treatment. Multi-level data collection within clinico-genomic trials and interdisciplinary analysis by clinicians, molecular biologists and others involved in life science is mandatory to further improve the outcome of cancer patients. It is essential to merge the research results of biomolecular findings, imaging studies and clinical data of patients and to enable users to easily join, analyze and share even great amounts of data. [...] Community views Enhancing Access to Cancer Clinical TrialsThe Education Network to Advance Cancer Clinical Trials (ENACCT) is a US-based nonprofit organization, founded 2004 with support from the Lance Armstrong Foundation. ENACCT’s mission is to improve access to cancer clinical trials through education and collaboration with communities, health care providers, and researchers. ENACCT helps patients, communities, and health care providers better understand the importance of cancer clinical trials—while also helping researchers communicate more effectively about these trials. In this article, I am pleased to share ENACCT’s perspective on what it takes to enhance access to cancer clinical trials. [...] Events VPH 201030th September to 1st October, 2010, The Virtual Physiological Human Network of Excellence (VPH NoE) will hold the first of a series of VPH Conferences (VPH2010) on 30th September to 1st October, 2010. The first meeting will be held in Brussels, Belgium, and is supported by the European Commission ICT for Health / DG Information Society and Media. The Virtual Physiological Human Network of Excellence is an umbrella project representing the Virtual Physiological Human Initiative set up by the European Commission with a budget of ~ 350 million Euros for the Framework 7 Program. The VPH NoE is also responsible for producing a ‘ VPH Vision and Strategy Document’ to inform the next calls for the VPH field for FP7, FP8 and for European large infrastructural actions. [...] Medinfo 201012 - 15 of September 2010 Cape Town, South Africa will host the 13th International Congress on Medical Informatics from the 12 - 15 of September 2010. The Medinfo conference is the premier triennial international meeting for the medical informatics community. It brings together world leaders in this field to share knowledge and experiences. Medinfo 2010 is a unique opportunity to meet these leaders and to hear of, and contribute to, advances in biomedical and health informatics. The Medinfo conference is the official conference of the International Medical Informatics Association (IMIA), a bridging organisation aiming at supporting stimulating high-quality translational communication, research, education, and practice in biomedical and health informatics. Medinfo 2010 is organised and coordinated by the South African Health Informatics Association. A number of governmental organisations, associations and businesses have agreed to be sponsors. The conference theme selected for Medinfo 2010 is a topic that most countries are currently addressing: Partnerships for effective eHealth solutions - Innovative collaborations promote solutions to health challenges. [...] Legal & Ethical ACGT: Risky Business?
Safeguarding the privacy of patients is an important task for anyone dealing with medical data as harming it can do tremendous damage to the individual involved (note that privacy breaches are irreparable as an information leak cannot be undone). With respect to the research itself, such incidents are likely to lead to patients withdrawing from participation (damaged trust) and could very well lead to prosecution of those responsible for the breach. The ACGT project has contributed considerable effort to solving the data protection-related issues which accompany the creation of a transnational biomedical research infrastructure. The project aimed to provide researchers with a convenient and easily implementable solution to deal with legal and regulatory compliance regarding data privacy. The solution has been defined in the form of a framework consisting of a combination of technical, organisational and legal measures. [...] Life in ACGT Project coordinator’s Farewell
ACGT (Advancing Clinico-Genomic Trials on cancer: Open Grid Services for improving Medical Knowledge Discovery) is an Integrated Project (IP) funded in the 6th Framework Program of the European Commission under the Action Line “Integrated biomedical information for better health”. Its high level objective has been the development of methods and systems for improved medical knowledge discovery and understanding through integration of biomedical information (e.g. using modeling, visualization, data mining and grid technologies). Biomedical data and information that have been considered include clinical information relating to tissues, organs or personal health-related information, but also information at the level of molecules and cells, as acquired from genomics and proteomics research. The project vision has been rooted in the realization that information arising from post-genomics research and genetic and clinical trials is rapidly providing the medical and scientific community with new insights, answers and capabilities when combined with advances in high-performance computing and informatics. [...] ACGT people Yannick Legréholds an Engineer Degree in Telecommunication and Networks. He is one of the co-founders and current president of the International HealthGrid Association. He works in the domain of Grid technologies applied to healthcare and biomedical research since August 2000 and he has been successfully involved in more than 15 projects. He is regularly acting as an expert for the European Commission. Since June 2008, he is Director of International Relationships for the maatG company (www.maatg.com) [...] Andreas Persidisis the CEO of Biovista, the ACGT partner responsible for the literature mining, ontology browsing and related ACGT applications. Andreas’ research interests focus on knowledge management and the development of tools for systematic knowledge discovery in the life-science domain. With a long career in artificial intelligence, ontology development and text mining but also significant business experience, he serves as an expert reviewer and advisor to national organizations, investment banks and the EC itself. Andreas has brought this experience to bear within ACGT, pushing the consortium to always take into account the true needs of the stakeholders and to develop solutions that make sense in actual environments rather than purely research contexts. Not being any longer able to program to save his life, Andreas instead works on spreading the word for the better exchange and use of data to address the complex issue of better health care. He believes that mining the information in patient records is a step in the right direction. Andreas shares his time between Europe and the US and what time remains free, he enjoys with his 5 year old daughter Leda who has yet to see tangible benefits for her from his ACGT work. [...] SPECIAL PROJECT CLOSING The TOP trial for the final ACGT Demonstration
The ultimate objective of the ACGT project is the provision of a unified technological infrastructure which will facilitate the seamless and secure access and analysis of multi-level clinical and genomic data enriched with high-performing knowledge discovery operations and services, in the concrete setting of clinical trials on Cancer. Pilot trials have been selected based on the presence of clear research objectives, raising the need to integrate data at all levels of the human being. This integrative view underlies the development of clinico-genomic models, showing that the combination of biomarkers and clinical factors are most relevant in terms of statistical fit and also, more practically, in terms of cross-validation predictive accuracy The TOP trial, a trial which aims at identifying molecular markers that predict response/resistance to one of the most commonly administered chemotherapies in breast cancer, is one of those pilot trials for ACGT and has been chosen for the final demonstration of ACGT. [...] |
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