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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - MedBioinformatics (Creating medically-driven integrative bioinformatics applications focused on oncology, CNS disorders and their comorbidities (MedBioinformatics))

Teaser

Summary

Progress in biomedical research and healthcare requires taking advantage of the huge amount of biological knowledge and clinical data. The management and exploitation of this information requires adequate bioinformatics approaches. The latest scientific advancement in bioinformatics methods and applications has been impressive, but their practical impact in the medical field is still limited due to: 1) the deficit of integrative approaches that combine different types of data from various sources; and 2) the lack of active involvement of the end-users in the design of the applications so they are easily actionable in clinical practice and translational research. MedBioinformatics addresses those issues by designing and developing bioinformatics applications for supporting knowledge-based activities in relevant clinical areas (oncology and CNS disorders), which cover an important percentage of the burden of chronic diseases and have a big impact in citizensâ€™ wellbeing, showing challenging comorbidities. The specific objectives of the MedBioinformatics project are:

1. To build a new generation of computational tools for the analysis of genotype-phenotype relationships on the basis of high throughput sequencing data (WP3).
2. To develop systems medicine tools able to mine, integrate, filter, prioritise, analyse and visualise relevant health data and scientific knowledge (WP4).
3. To tailor the tools for the needs of translational scientists and clinical practitioners in neuropsychiatry and oncology (WP4-5).
4. To develop specific bioinformatics applications addressing the characteristics of cancer, supporting its molecular diagnosis and personalised treatment (WP5).
5. To test the applications in relevant case studies in oncology and neuropsychiatry, selected due to their relevance and their intrinsic biomedical interest (WP5-7).
6. To implement a rigorous software engineering approach that intensively incorporates the potential end-users in the whole process with the aim of yielding useful and user-friendly applications (WP2).
7. To promote the use of the tools in translational research and clinical practice, expanding to other medical specialties (WP8).

Work performed

During the first half of the project significant progress has been achieved regarding the methods and applications to be developed, such as:

1. A new version of the Variant Effect Predictor (VEP) developed by EMBL-EBI, which is faster and more stable, flexible and precise than the preceding one (WP3).
2. A major improvement of DisGeNET, a comprehensive knowledge resource on gene-disease associations, developed by PSMAR-UPF. It incorporates extended and updated information, as well as new functionalities for the exploration and analysis of the information (WP4).
3. A new version of PsyGeNET, a curated knowledge base on gene-disease associations in the psychiatric field, developed by PSMAR-UPF. A computational curation pipeline and a community of experts have been devised for performing the curation of the associations (WP4).
4. UCPH is developing a Disease Trajectory Comorbidity Browser providing information on disease comorbidities taking into account their association along the time (WP4).
5. UPF is developing an extended version of the Cancer Genome Interpreter, which integrates knowledge in cancer genomics and pharmacogenomics to help oncologists and cancer researchers to interpret the genome, transcriptome and epigenome of tumours for accurate decision-making (WP5).
6. FIMM has implemented a computational pipeline composed by Drug Target Commons, TIMMA 2.0 and SynergyFinder for proposing personalised drug combinations in cancer therapy (WP5).

These bioinformatics tools are being applied to the following case studies:

â€¢ Analysis of a patient\'s tumour genomic alterations to support the allocation to the most appropriate clinical trial (WP5).
â€¢ In silico prescription identifying genomic vulnerabilities of the patient\'s tumour to explore drug repurposing opportunities (WP5).
â€¢ Analysis of the alteration landscape of a tumour cohort undergoing a therapeutic intervention for the discovery of novel biomarkers of drug response (WP5).
â€¢ Identification of the existing/investigational chemical compounds interacting with the genes in a tumour to guide the design of novel drug assays (WP5).
â€¢ Comparative analysis of the molecular bases of major depression and alcohol-induced major depression (WP6).
â€¢ Comparative study of the molecular basis of the major depression and Alzheimer disease comorbidity (WP6).
â€¢ Study of the comorbidity between Alzheimer disease and cancer (WP7).
â€¢ Study of the comorbidity between major depression and cancer (WP7).

Moreover, the project has carried out different horizontal activities in the framework of WP2: software development guidelines (D2.1), general guidelines to gather user feedback, two iterations of the investigation of the user requirements (D2.2, D2.3)

Final results

MedBioinformatics aims to generate significant impact in different dimensions:

ACCELERATE THE TRANSLATION OF THE RESULTS INTO CLINICAL RESEARCH.
MedBioinformatics incorporates clinical researchers from different medical specialities for developing bioinformatics methods and tools driven by clinical needs. The consortium\'s composition contributes to overcome communication barriers between bioinformaticians and clinical researchers. The project results will empower translational scientists and health professionals to perform information-related operations required for their daily work without the assistance of a bioinformatician, thus accelerating and optimising the translational research pipeline. Translational and clinical scientists are directly carrying out the case studies, making the translation of the results into clinical research an key part of the project.

WIDESPREAD DISSEMINATION OF THE NEW BIOINFORMATICS METHODS TO MAXIMISE THE ACCESSIBILITY AND UTILITY OF BIOMEDICAL DATA IN RESEARCH AND MEDICINE.
The first channel for dissemination of the project results are the scientific publications in high impact journals. Internet is another effective channel that is being intensively used. Moreover, the project is organising activities for collaborating with other related projects and consolidating a translational bioinformatics community.

INCREASED COMMERCIAL PRODUCTS IN BIOINFORMATICS. INCREASED RESEARCH & INNOVATION OPPORTUNITIES IN THIS SME-INTENSIVE FIELD.
MedBioinformatics is producing applications with commercial exploitation potential given their focus on satisfying current needs from translational scientists and clinical practitioners, and because of the attention given to high-quality standards and user-friendliness. Key aspects that are taken into account when developing these applications are the implementation of rigorous software engineering practices, and the filtering and prioritization of information to be shown.

BUILDING ON EUROPEAN EXCELLENCE TO MAKE THE EU A LOCATION OF CHOICE FOR ADVANCED BIOINFORMATICS RESEARCH.
Scientific excellence and management are driving the project activities for contributing to the European synergistic networking and competitiveness in translational bioinformatics, a trans-disciplinary approach combining advanced science, technological innovation and societal impact, thus increasing the centrality of Europe as a key location for both bioinformatics research and its transformation into business opportunities and social/economic development.