Advancing Clinico Genomic Trials on Cancer
Advancing Clinico Genomic Trials on Cancer (ACGT) is an Integrated Project (EU) funded by the European Commission in the Sixth Framework Programme (FP6) under the action line Integrated biomedical information for better health. The high level objective of the action line is the development of methods and systems for improved medical knowledge discovery and undertanding through integration of biomedical information (e.g. using modeling, visualization, data mining and grid technologies).
ACGT focuses on the domain of Cancer research and its ultimate objective is the design, development and validation of an integrated Grid enabled technological platform in support to post-genomic, multi-centric clinical trials on Cancer. The driving motivation behind the project is the belief that the breadth and depth of information already available in the research community at large, present an enormous opportunity for improving the ability to reduce mortality from cancer, improve therapies and meet the demanding individualization of care needs
Start date: Feb 1, 2006; End date: July 31, 2010; Partner institutions: 25
ACGT project objectives
In order to develop a Semantic Grid infrastructure offering high-level tools and techniques for the distributed mining and extraction of knowledge from data repositories available on the Grid, leveraging semantic descriptions of components and data and offering knowledge discovery services in the domain of cancer research, the project focuses on:
- Integration of Clinical Research Centers on Cancer
Centers with varying needs and capabilities are integrated in a common network for sharing data, application and technologies.
- Development of a useable and scalable biomedical grid
Clinical Research Centers on Cancer will actively use this grid for added value clinical trials.
- Implementation of data analysis, visualisation and grid-enabled knowledge discovery tools
Development of such tools and modification of existing ones will permit to utilise the advantages of grid computing, and enable high-performing data-mining and biomedical knowledge extraction operations.
- Implementation of Clinical trial management Systems
The system is based on an ontology driven software development process, which should result in semantically consistent clinical trial systems in the future.
- Sharing of biomedical information and data
It provides a uniform access to heterogeneous clinical trial, genetic as well as public biological databases, upon common standards protecting data privacy and security.
- Development, clinical adaptation and partial validation of the "Oncosimulator"
The Oncosimulator is a "top-down" multiscale tumour biology simulation system aiming at supporting clinico-genomic trial design and interpretation as well as treatment optimization in the patient individualized context. To this end imaging, histopathological, molecular and clinical data of the patient are exploited following appropriate preprocessing.Clinical adaptation and validation of the system are performed within the framework of clinico-genomic trials.
- The definition of an unified architecture
The unified architecture has a complex layered organization, integrating security, data anonymization, GRID-distributed computing, uniform database access, etc which enables the support of the advanced clinico- genomics clinical trials of the future.
ACGT project consortium
The partners of the consortium collectively bring to the table a multitude of skills and competencies as required by the multidisciplinary nature of the project (e.g. Clinical Researchers, Medical Informaticians and Bioinformaticians, GRID, Ontologies and semantic integration, Trust and Security, Legal, Ethical). Similarly, the necessary sectors (industry, including SMEs, healthcare organisations with strong clinical research, research organisations, and academia) all are present in the consortium. The organizations participating in project and their corresponding responsabilities are listed hereafter:
- ERCIM: Project Coordinator, with substantial involvement in the Dissemination Activities.
- FORTH: Clinico-Genomic Information System, Seamless Data Analysis, Grid-based tools, Ontologies, DNA microarrays, genotyping, integration of the ACGT technological platform. Responsible for the delivery of the Integrated ACGT technological Platform.
- INRIA: Code execution acceleration (grid, parallelization etc.) for biomedical applications including in silico oncology. Also involved in the specification of the ACGT Architecture and its services. Data Mining – Visualization.
- UVA: Virtual reality visualization of clinical data and simulation predictions. Also involved in GRID Interface and applications.
- Philips: Novel 3D MRI Visualization Tools.
- IJB: Clinical Trials in Breast Oncology and system evaluation.
- SIB: Formulate evaluation criteria, verification procedures and feedback report guidelines for the clinical trials. Coordinate with the local evaluation managers and report to management and steering group meetings on progresses achieved and remaining problems to be addressed wrt clinical trials.
- LundU: Data Management Proteomics, Transcriptomics.
- UMA: Data Mining – Knowledge discovery and design and development of the computational integration infrastructure at the project.
- UPM: Define the Ontologies needed for clinico-genomic integration and develop semantic mediation tools and services. UPM has also significant involvement in the data mining and knowledge discovery activities of the project.
- FhG: Biomedical data analysis and knowledge discovery (cellular level). Data Mining–Knowledge Discovery-Information Systems.
- Biovista: Data and Text Mining and Visualization.
- UoC: Clinical Trials in Breast Oncology, Tissue banks, clinico-genomic system specifications.
- LUH: Security, Ethics, Legislation and Quality Control assessment.
- PSNC: Development and support of the basic GRID technology layer in ACGT.
- Custodix: Contribution to specification and implementation of the trust and security related tools and technologies taking into consideration the ethical and legal aspects identified.
- HEALTHGRID: Dissemination and liaison of the ACGT with other HealthGRID projects for dissemination and concertation.
- ICCS: Development of the multiscale in silico cancer models and coordination of the "Oncosimulator" development. Models refer to the treatment response for both breast cancer and nephroblastoma. Contribution to the clinical adaptation and validation of the models.
- USAAR: Clinical Trials in children oncology.
- SIVECO: The ACGT Portals and their services, preparation of educational material for training.
- FUNDP: Study of the Legal Issues related to the work of the project and contribution to the specifications, especially of the trust and security requirements of the ACGT biomedical GRID infrastructure.
- UH: Study of the Ethical Issues related to the project, contribution to harmonisation and standards in the domain, contribution to specification of the technical aspects related to ethical constraints and requirements.
- UOXF.BP: Clinical Trials in Breast Oncology.
- UHok: Architecture and Standards, Development Biomedical Grid Technology Layer, Data Access , Knowledge Management.
- IEO: Providing breast cancer cases to be included in the study, validating the Grid infrastructure technology.
ACGT project achievements
- The ACGT Handbook wiki documents the use of the ACGT platform and the ACGT portal. The first goal of this wiki is to provide a documentation of the ACGT platform for end-users. The second objective is to provide a documentation of the ACGT platform for 3rd-party contributors.
- GridR is an R-Package that can be used to submit R functions for execution on remote computers, clusters or grids. In addition, users are provided with an interface to share variables and functions with other users
- The ACGT Master Ontologyis based on the semantic modelling of biomedical concepts using existing ontologies and ontologies developed for the needs of the project Brochhausen M, Weiler G, Martin L, Cocos C, Stenzhorn H, Graf N, Dörr M, Tsiknakis M, Smith B, "Applications of the ACGT Master Ontology on Cancer," In: R. Meersman, Z. Tari, P. Herrero (eds.): OTM 2008 Workshops, LNCS 5333, 2008, 1046-1055.
- The ACGT Ontology Based Trial Management (ObTiMA) supports the design phase of a clinical trial allowing to set up the Patient Data Management System for a trial in a standardized and user friendly way integrating the ACGT master ontology into the design process.