Abstract
The rise of precision medicine combined with the variety of biomedical data sources and their heterogeneous nature make the integration and exploration of information that they retain more complicated. In light of these issues, translational research platforms were developed as a promising solution. Research centers have used translational tools for the study of integrated data for hypothesis development and validation, cohort discovery and data-exploration. For this article, we reviewed the literature in order to determine the use of translational research platforms in precision medicine. These tools are used to support scientists in various domains regarding precision medicine research. We identified eight platforms: BRISK, iCOD, iDASH, tranSMART, the recently developed OncDRS, as well as caTRIP, cBio Cancer Portal and G-DOC. The last four platforms explore multidimensional data specifically for cancer research. We focused on tranSMART, for it is the most broadly used platform, since its development in 2012.
Keywords
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Canuel, V., B. Rance, P. Avillach, P. Degoulet, and A. Burgun. 2014. Translational Research Platforms Integrating Clinical and Omics Data: A Review Of Publicly Available Solutions. Briefings in Bioinformatics 16 (2): 280–290.
Fenstermacher, D., C. Street, T. McSherry, V. Nayak, C. Overby, and M. Feldman. 2005. The cancer biomedical informatics grid (caBIG™). Conference Proceedings IEEE Engineering in Medicine and Biology Society 1: 743–746.
McConnell, P., R.C. Dash, R. Chilukuri, R. Pietrobon, K. Johnson, R. Annechiarico, and A.J. Cuticchia. 2008. The Cancer Translational Research Informatics Platform. BMC Medical Informatics and Decision Making 8 (1): 60.
NIH Report. 2011. An Assessment of the Impact of the NCI Cancer Biomedical Informatics Grid (caBIG). Available at http://deainfo.nci.nih.gov/advisory/bsa/archive/
Cerami, E., J. Gao, U. Dogrusoz, B.E. Gross, S.O. Sumer, B.A. Aksoy, A. Jacobsen, C.J. Byrne, M.L. Heuer, E. Larsson, Y. Antipin, B. Reva, A.P. Goldberg, C. Sander, and N. Schultz. 2012. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer Discovery 2 (5): 401–404.
Gao, J., B.A. Aksoy, U. Dogrusoz, G. Dresdner, B. Gross, S.O. Sumer, Y. Sun, A. Jacobsen, R. Sinha, E. Larsson, E. Cerami, C. Sander, and N. Schultz. 2013. Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal. Science Signaling 6 (269): pl1.
Madhavan, S., Y. Gusev, M. Harris, D.M. Tanenbaum, R. Gauba, K. Bhuvaneshwar, A. Shinohara, K. Rosso, L.A. Carabet, L. Song, R.B. Riggins, S. Dakshanamurthy, Y. Wang, S.W. Byers, R. Clarke, and L.M. Weiner. 2011. G-DOC: A Systems Medicine Platform for Personalized Oncology. Neoplasia 13 (9): 771–783.
Madhavan, S., Y. Gusev, T.G. Natarajan, L. Song, K. Bhuvaneshwar, R. Gauba, A. Pandey, B.R. Haddad, D. Goerlitz, A.K. Cheema, H. Juhl, B. Kallakury, J.L. Marshall, S.W. Byers, and L.M. Weiner. 2013. Genome-Wide Multi-Omics Profiling of Colorectal Cancer Identifies Immune Determinants Strongly Associated with Relapse. Frontiers in Genetics 4: 236.
Luo, L., P. McGarvey, S. Madhavan, R. Kumar, Y. Gusev, and G. Upadhyay. 2016. Distinct Lymphocyte Antigens 6 (Ly6) Family Members Ly6D, Ly6E, Ly6K and Ly6H Drive Tumorigenesis and Clinical Outcome. Oncotarget 7 (10): 11165–11193.
Rhodes, D.R., J. Yu, K. Shanker, N. Deshpande, R. Varambally, D. Ghosh, T. Barrette, A. Pander, and A.M. Chinnaiyan. 2004. ONCOMINE: A Cancer Microarray Database and Integrated Data-Mining Platform. Neoplasia 6 (1): 1–6.
Bhuvaneshwar, K., A. Belouali, V. Singh, R.M. Johnson, L. Song, A. Alaoui, M.A. Harris, R. Clarke, L.M. Weiner, Y. Gusev, and S. Madhavan. 2016. G-DOC Plus – An Integrative Bioinformatics Platform for Precision Medicine. BMC Bioinformatics 17 (1): 193.
Tan, A., B. Tripp, and D. Daley. 2011. BRISK—Research-Oriented Storage Kit for Biology-Related Data. Bioinformatics 27 (17): 2422–2425.
Schuetz, J.M., D. Daley, S. Leach, L. Conde, B.R. Berry, R.P. Gallagher, J.M. Connors, R.D. Gascoyne, P.M. Bracci, C.F. Skibola, J.J. Spinelli, and A.R. Brooks-Wilson. 2013. Non-Hodgkin Lymphoma Risk and Variants in Genes Controlling Lymphocyte Development. PLoS ONE 8 (9): e75170.
Shimokawa, K., K. Mogushi, S. Shoji, A. Hiraishi, K. Ido, H. Mizushima, and H. Tanaka. 2010. ICOD: An Integrated Clinical Omics Database Based on the Systems-Pathology View of Disease. BMC Genomics 11: S19.
Dropmann, A., T. Dediulia, K. Breitkopf-Heinlein, H. Korhonen, M. Janicot, S.N. Weber, M. Thomas, A. Piiper, E. Bertran, I. Fabregat, K. Abshagen, J. Hess, P. Angel, C. Coulouarn, S. Dooley, and N.M. Meindl-Beinker. 2016. TGF-β1 and TGF-β2 Abundance in Liver Diseases of Mice and Men. Oncotarget 7 (15): 19499–19518.
Itzel, T., P. Scholz, T. Maass, M. Krupp, J.U. Marquardt, S. Strand, D. Becker, F. Staib, H. Binder, S. Roessler, X.W. Wang, S. Thorgeirsson, M. Muller, P.R. Galle, and A. Teufel. 2014. Translating Bioinformatics in Oncology: Guilt-by-Profiling Analysis and Identification of KIF18B and CDCA3 as Novel Driver Genes in Carcinogenesis. Bioinformatics 31 (2): 216–224.
Ohno-Machado, L., V. Bafna, A.A. Boxwala, B.E. Chapman, W.W. Chapman, K. Chaudhuri, M.E. Day, C. Farcas, N.D. Heintzman, X. Jiang, H. Kim, J. Kim, M.E. Matheny, F.S. Resnic, and S.A. Vinterbo. 2012. IDASH: Integrating Data for Analysis, Anonymization, and Sharing. Journal of the American Medical Informatics Association 19 (2): 196–201.
Orechia, J., A. Pathak, Y. Shi, A. Nawani, A. Belozerov, C. Fontes, C. Lakhiani, C. Jawale, C. Patel, D. Quinn, D. Botvinnik, E. Mei, E. Cotter, J. Byleckie, M. Ullman-Cullere, P. Chhetri, P. Chalasani, P. Karnam, R. Beaudoin, S. Sahu, Y. Belozerova, and J.P. Mathew. 2015. OncDRS: An Integrative Clinical and Genomic Data Platform for Enabling Translational Research and Precision Medicine. Applied & Translational Genomics 6: 18–25.
Bierkens, M., W. van der Linden, K. van Bochove, W. Weistra, R.J.A. Fijneman, R. Azevedo, J.-W. Boiten, J. Beliën, and G.A. Meijer. 2015. TranSMART. Journal of Clinical Bioinformatics 5 (Suppl 1): S9.
Guo, Y., M. Braxenthaler, B.D. Athey, and M. Haas. 2013. tranSMART: An Open Source and Community-Driven Informatics and Data Sharing Platform for Clinical and Translational Research. AMIA 2013: 6–8.
Barash, C.I., K. Elliston, and R. Potenzone. 2015. TranSMART Foundation Datathon 1.0: The Cross Neurodegenerative Diseases Challenge. Applied & Translational Genomics 6: 42–44.
Jonnagaddala, J., J.L. Croucher, T.R. Jue, N.S. Meagher, L. Caruso, R. Ward, and N.J. Hawkins. 2016. Integration and Analysis of Heterogenous Colorectal Cancer Data for Translational Research. Nursing Informatics: 387–391.
Schumacher, A., T. Rujan, and J. Hoefkens. 2014. A Collaborative Approach to Develop a Multi-Omics Data Analytics Platform for Translational Research. Applied & Translational Genomics 3 (4): 105–108.
Firnkorn, D., S. Merker, M. Ganzinger, T. Muley, and P. Knaup. 2011. Unlocking Data for Statistical Analyses and Data Mining: Generic case Extraction of Clinical Items from i2b2 and tranSMART. Studies in Health Technology and Informatics 228: 567–571.
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Skolariki, K., Avramouli, A. (2017). The Use of Translational Research Platforms in Clinical and Biomedical Data Exploration. In: Vlamos, P. (eds) GeNeDis 2016. Advances in Experimental Medicine and Biology, vol 988. Springer, Cham. https://doi.org/10.1007/978-3-319-56246-9_25
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DOI: https://doi.org/10.1007/978-3-319-56246-9_25
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