Integrative Cancer Research Through Innovative Biomedical Infrastructures

Integrative Cancer Research Through Innovative Biomedical Infrastructures

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INTEGRATE was a project co-funded by the European Commission within the Seventh Framework Programme (2007-2013) that aimed to empower clinical researcherswith the unique opportunity to access breast-cancer multi-scale data from 29 European cancer centres and develop breast cancer predictive model methodologies related to specific clinical questions for optimising therapy and identifying high-risk patients, among others.  An additional aim was to enable clinical researchers to retrieve temporal (e.g., before and after therapy), multi-level (e.g., from microarray to MRI/PET) data from specific population groups (e.g., postmenopausal women), with specific characteristics (e.g., who had received specific therapy regimens) and then extract/develop predictive biomarkers/models (e.g., based combination of imaging/genetic biomarkers) that could answer questions such as “can these models/biomarkers help predict the specific therapy outcome for a patient in order to avoid unnecessary/costly treatment?”

This involved integrating available data and knowledge into comprehensive models supported by interoperable infrastructures and tools, standardising methodologies, achieving wide-scale data sharing and reuse, and fostering multidisciplinary collaboration.

Despite the healthcare industry having improved its electronic data capture capabilities, IT systems fail to deliver knowledge and insight back to researchers and clinicians, resulting in inefficiency and duplication of data and effort. Low integration, lack of interoperability, and low adoption of common standards and terminologies create a challenge in accessing sufficient and high-quality data for basic and clinical research, and the lack of accurate predictive models integrating data and knowledge at different scales hinders the selection of the most suitable therapy yielding the best possible patient outcome.

In this context, the INTEGRATE project aimed to:

  • Build infrastructure components and tools for the storage, sharing and management of data, information, knowledge and models
  • Build tools to enable collaboration
  • Build predictive models and a modelling methodology and framework
  • Enable semantic interoperability to existing research and clinical infrastructures
  • Prototype and validate the INTEGRATE infrastructure components and tools.

INTEGRATE provided tools to streamline the screening phase of breast cancer clinical trials. Eligibility criteria such as age, cancer type and stage, or previous or concomitant treatments, are managed through lists and evaluated through automated electronic data capture. Therefore, an interface was created to easily link and extract clinical data from EHRs, acquire molecular testing data from central laboratories, and track biological samples.

INTEGRATE also facilitated central review of data across trials, enabling the definition of panels of experts and creating a framework for accessing and annotating data. Digital pathology images were visualised and annotated using integrated tools.

Statistical and bioinformatics analyses of data were also incorporated and resulted in a collaborative environment for researchers to share and annotate statistical models built from the data. The architecture was designed to be modular, allowing for easy integration of analytical components on top of the data querying component.

INTEGRATE project developed flexible infrastructure components and tools for data and knowledge sharing and large scale collaboration in biomedical research.

The infrastructure brings together heterogeneous multi-scale biomedical data generated through standard and novel technologies within post-genomic clinical trials and seamlessly links to existing research and clinical infrastructures, such as clinical trials management systems, eCRFs (electronic case report forms), and hospital EHRs (electronic health records). 

INTEGRATE encompasses a core platform, featuring a state of the art semantic interoperability solution embedded in a Service Oriented Architecture approach. This core platform provides the basis for innovative, semantic enabled clinical research and care application. Many applications that can run in this platform require the selection of patient cohorts – sets of patients that share similar characteristics – defined by the clinical user by means of filters. Within INTEGRATE, a tool was developed enabling users to construct patient cohorts in an intuitive manner. 

Several additional tools were developed as well: one for rapidly analysing and assessing the quality of certain clinical characteristics across patient populations; the “central review for pathology Images” tool enables multiple users to access and review over the web the same set of digital pathology images simultaneously; and the “patient screening” application impacts clinical care by efficiently evaluating the eligibility of a patient for a set of clinical trials.

  • Philips Electronics Nederland BV
  • Breast International Group – BIG
  • Foundation for research and technology Hellas-FORTH
  • Institut Jules Bordet-IJB
  • Universidad Politecnica de Madrid -UPM

The project ran from 01/02/2011 to 31/01/2014.

The initiative brought together 6 partner organisations from 4 different countries within Europe.

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INTEGRATE was a project co-funded by the European Commission within the Seventh Framework Programme.

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