IMPaCT-Data, medical data integration to boost precision medicine

IMPaCT, the Infrastructure for Precision Medicine associated with Science and Technology, is an innovative programme that aims to revolutionise medical care. Coordinated and funded by the Carlos III Health Institute, it aims to boost the effective deployment of personalised precision medicine.

Personalised medicine is a medical approach that recognises that each patient is unique. By analysing the genetic, physiological and lifestyle characteristics of each person, more efficient and safer tailor-made treatments with fewer side effects are developed.  Access to this information is also key to making progress in prevention and early detection, as well as in research and medical advances.

IMPaCT consists of 3 strategic axes:

• Axis 1 Predictive medicine: COHORTE Programme. It is an epidemiological research project consisting of the development and implementation of a structure for the recruitment of 200,000 people to participate in a prospective study. 
• Strand 2 Data science: DATA Programme. It is a programme focused on the development of a common, interoperable and integrated system for the collection and analysis of clinical and molecular data. It develops criteria, techniques and best practices for the collection of information from electronic medical records, medical images and genomic data.
• Axis 3 Genomic medicine: GENOMICS Programme. It is a cooperative infrastructure for the diagnosis of rare and genetic diseases. Among other issues, it develops standardised procedures for the correct development of genomic analyses and the management of the data obtained, as well as for the standardisation and homogenisation of the information and criteria used.

In addition to these axes, there are two transversal strategic lines: one focused on ethics and scientific integrity and the other on internationalisation, as summarised in the following visual.

Source: IMPaCT-Data

In the following, we will focus on the functioning and results of IMPaCT-Data, the project linked to axis 2.

IMPaCT-Data, an integrated environment for interoperable data analysis

IMPaCT-Data is oriented towards the development and validation of an environment for the integration and joint analysis of clinical, molecular and genetic data, for secondary use, with the ultimate goal of facilitating the effective and coordinated implementation of personalised precision medicine in the National Health System. It is currently made up of a consortium of 45 entities associated by an agreement that runs until 31 December 2025.

Through this programme, the aim is to create a cloud infrastructure for medical data for research, as well as the necessary protocols to coordinate, integrate, manage and analyse such data. To this end, a roadmap with the following technical objectives is followed:

Source: IMPaCT-Data.

Results of IMPaCT-Data

As we can see, this infrastructure, still under development, will provide a virtual research environment for data analysis through a variety of services and products:

• IMPaCT-Data Federated Cloud. It includes access to public and access-controlled data, as well as tools and workflows for the analysis of genomic data, medical records and images. At this video shows how federated user access and job execution is realised through the use of shared computational resources. This allows for viewing and accessing the results in HTML and raw format, as well as their metadata. For those who want to go deeper into the user access options, please see this video another video where the linking of institutional accounts to the IMPaCT-Data account and the use of passports and visas for local access to protected data is shown.
• Compilation of software tools for the analysis of IMPaCT-Data. These tools are publicly accessible through the iMPaCT-Data domain  domain at bio.tools a registry of software components and databases aimed at researchers in the field of biological and biomedical sciences. It includes a wide range of tools. On the one hand, we find general solutions, for example, focused on privacy through actions related to data de-identification and anonymisation (FAIR4Health Data Privacy Tool). On the other hand, there are specific tools, focused on very specific issues, such as gene expression meta-analysis (ImaGEO).
• Guidelines with recommendations and good practices for the collection of medical information. There are currently three guides available: "IMPaCT-Data recommendations on data and software", "IMPaCT-Data additional considerations to the IMPaCT 2022 call for projects" and "IMPaCT-Data recommendations on data and software" .

In addition to these, there are a number of deliverables related to technical aspects of the project, such as comparisons of techniques or proofs of concept, as well as scientific publications.

Driving use cases through demonstrators

One of the objectives of IMPaCT-Data is to contribute to the evaluation of technologies associated with the project's developments, through an ecosystem of demonstrators. The aim is to encourage contributions from companies, organisations and academic groups to drive improvements and achieve large-scale implementation of the project.

To meet this objective, different activities are organised where specific components are evaluated in collaboration with members of IMPaCT-Data. One example is the oRBITS terminology server for the encoding of clinical phenotypes into HPO (Human Phenotype Ontology) aimed at automatically extracting and encoding information contained in unstructured clinical reports using natural language processing. It uses the HPO terminology, which aims to standardise the collection of phenotypic data, making it accessible for further analysis.

Another example of demonstrators refers to the sharing of virtualised medical data between different centres for research projects, within a governed, efficient and secure environment, where all data quality standards defined by each entity are met within a governed, efficient and secure environment, where all data quality standards defined by each entity are met.

A strategic project aligned with Europe

IMPaCT-Data fits directly into the National Strategy for the Secondary Use of National Health System Data, as described in the PERTE on health (Strategic Projects for Economic Recovery and Transformation), with its knowledge, experience and input being of great value for the development of the National Health Data Space.

Furthermore, IMPaCT-Data's developments are directly aligned with the guidelines proposed by GAIA-X both at a general level and in the specific health environment.

The impact of the project in Europe is also evidenced by its participation in the european project GDI (Genomic Data Infrastructure) which aims to facilitate access to genomic, phenotypic and clinical data across Europe, where IMPaCT-Data is being used as a tool at national level.

This shows that thanks to IMPaCT-Data it will be possible to promote biomedical research projects not only in Spain, but also in Europe, thus contributing to the improvement of public health and individualised treatment of patients.