Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure.

Hector Countouris,Anita Burgun,Vincent Canuel,Pierre Laurent-Puig,Bastien Rance

doi:10.4338/aci-2015-09-ra-0125

Abstract

SummaryCancer research involves numerous disciplines. The multiplicity of data sources and their heterogeneous nature render the integration and the exploration of the data more and more complex. Translational research platforms are a promising way to assist scientists in these tasks. In this article, we identify a set of scientific and technical principles needed to build a translational research platform compatible with ethical requirements, data protection and data-integration problems. We describe the solution adopted by the CARPEM cancer research program to design and deploy a platform able to integrate retrospective, prospective, and day-to-day care data. We designed a three-layer architecture composed of a data collection layer, a data integration layer and a data access layer. We leverage a set of open-source resources including i2b2 and tranSMART.

Highlights

Cancer research ranges from epidemiology, basic research and molecular bioscience to translational research and analysis of routine care data used to evaluate and compare applications of the various therapies
Major medical research centers such as Vanderbilt [3] or Harvard [4] have demonstrated the research opportunities opened by secondary use of data
We describe the solution adopted by the CARPEM cancer research program to design, implement and deploy a translational research platform able to face the technical and scientific challenges, and the issues underlined by the CTSA survey

Summary

Introduction

Cancer research ranges from epidemiology, basic research and molecular bioscience to translational research and analysis of routine care data used to evaluate and compare applications of the various therapies. Cancer care involves multiple fields including ‘omics’ sciences, such as genomics. High-throughput technologies are part of the everyday care in most hospitals [1, 2]. The increasing adoption of EHRs worldwide provides a steady flow of structured clinical data for care and research. Major medical research centers such as Vanderbilt [3] or Harvard [4] have demonstrated the research opportunities opened by secondary use of data. The global movement toward an increased secondary use of care data opens new perspectives for researchers and clinicians, and raises new technical and ethical questions [5]

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