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Kondylakis H, Claerhout B, Keyur M, Koumakis L, van Leeuwen J, Marias K, Perez-Rey D, De Schepper K, Tsiknakis M, Bucur A. The INTEGRATE project: Delivering solutions for efficient multi-centric clinical research and trials. J Biomed Inform 2016; 62:32-47. [PMID: 27224847 DOI: 10.1016/j.jbi.2016.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/05/2016] [Accepted: 05/17/2016] [Indexed: 10/21/2022]
Abstract
The objective of the INTEGRATE project (http://www.fp7-integrate.eu/) that has recently concluded successfully was the development of innovative biomedical applications focused on streamlining the execution of clinical research, on enabling multidisciplinary collaboration, on management and large-scale sharing of multi-level heterogeneous datasets, and on the development of new methodologies and of predictive multi-scale models in cancer. In this paper, we present the way the INTEGRATE consortium has approached important challenges such as the integration of multi-scale biomedical data in the context of post-genomic clinical trials, the development of predictive models and the implementation of tools to facilitate the efficient execution of postgenomic multi-centric clinical trials in breast cancer. Furthermore, we provide a number of key "lessons learned" during the process and give directions for further future research and development.
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Affiliation(s)
- Haridimos Kondylakis
- Computational BioMedicine Laboratory, FORTH-ICS, N. Plastira 100, Heraklion, Greece.
| | - Brecht Claerhout
- Custodix NV, Kortrijksesteenweg 214b3, Sint-Martens-Latem, Belgium
| | - Mehta Keyur
- German Breast Group, GBG Forschungs GmbH, Geschaeftsfuehrer: Prof. Dr. med. Gunter von Minckwitz, Handelsregister: Amtsgericht Offenbach, HRB 40477 Sitz der Gesellschaft ist Neu-Isenburg, Germany
| | - Lefteris Koumakis
- Computational BioMedicine Laboratory, FORTH-ICS, N. Plastira 100, Heraklion, Greece
| | | | - Kostas Marias
- Computational BioMedicine Laboratory, FORTH-ICS, N. Plastira 100, Heraklion, Greece
| | - David Perez-Rey
- Biomedical Informatics Group, DLSIIS & DIA, Facultad de Informática, Universidad Politécnica de Madrid, Campus de Montegancedo S/N, 28660 Boadilla del Monte, Madrid, Spain
| | | | - Manolis Tsiknakis
- Computational BioMedicine Laboratory, FORTH-ICS, N. Plastira 100, Heraklion, Greece; Department of Informatics Engineering, Technological Educational Institute of Crete, Estavromenos 71004, Hearklion, Crete, Greece
| | - Anca Bucur
- PHILIPS Research Europe, High Tech Campus 34, Eindhoven, Netherlands
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Li SC, Tachiki LML, Kabeer MH, Dethlefs BA, Anthony MJ, Loudon WG. Cancer genomic research at the crossroads: realizing the changing genetic landscape as intratumoral spatial and temporal heterogeneity becomes a confounding factor. Cancer Cell Int 2014; 14:115. [PMID: 25411563 PMCID: PMC4236490 DOI: 10.1186/s12935-014-0115-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/24/2014] [Indexed: 02/06/2023] Open
Abstract
The US National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI) created the Cancer Genome Atlas (TCGA) Project in 2006. The TCGA’s goal was to sequence the genomes of 10,000 tumors to identify common genetic changes among different types of tumors for developing genetic-based treatments. TCGA offered great potential for cancer patients, but in reality has little impact on clinical applications. Recent reports place the past TCGA approach of testing a small tumor mass at a single time-point at a crossroads. This crossroads presents us with the conundrum of whether we should sequence more tumors or obtain multiple biopsies from each individual tumor at different time points. Sequencing more tumors with the past TCGA approach of single time-point sampling can neither capture the heterogeneity between different parts of the same tumor nor catch the heterogeneity that occurs as a function of time, error rates, and random drift. Obtaining multiple biopsies from each individual tumor presents multiple logistical and financial challenges. Here, we review current literature and rethink the utility and application of the TCGA approach. We discuss that the TCGA-led catalogue may provide insights into studying the functional significance of oncogenic genes in reference to non-cancer genetic background. Different methods to enhance identifying cancer targets, such as single cell technology, real time imaging of cancer cells with a biological global positioning system, and cross-referencing big data sets, are offered as ways to address sampling discrepancies in the face of tumor heterogeneity. We predict that TCGA landmarks may prove far more useful for cancer prevention than for cancer diagnosis and treatment when considering the effect of non-cancer genes and the normal genetic background on tumor microenvironment. Cancer prevention can be better realized once we understand how therapy affects the genetic makeup of cancer over time in a clinical setting. This may help create novel therapies for gene mutations that arise during a tumor’s evolution from the selection pressure of treatment.
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Affiliation(s)
- Shengwen Calvin Li
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Neurology, University of California Irvine School of Medicine, Irvine, CA 92697-4292 USA ; Department of Biological Science, California State University, Fullerton, CA 92834 USA
| | - Lisa May Ling Tachiki
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; University of California Irvine School of Medicine, Irvine, CA 92697 USA
| | - Mustafa H Kabeer
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Pediatric Surgery, CHOC Children's Hospital, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Surgery, University of California Irvine School of Medicine, 333 City Blvd. West, Suite 700, Orange, CA 92868 USA
| | - Brent A Dethlefs
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA
| | | | - William G Loudon
- CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave, Orange, CA 92868 USA ; Department of Neurological Surgery, Saint Joseph Hospital, Orange, CA 92868 USA ; Department of Neurological Surgery, University of California Irvine School of Medicine, Orange, CA 92862 USA ; Department of Biological Science, California State University, Fullerton, CA 92834 USA
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