Periodic Reporting for period 2 - MedBioinformatics (Creating medically-driven integrative bioinformatics applications focused on oncology, CNS disorders and their comorbidities (MedBioinformatics))
Periodo di rendicontazione: 2016-11-01 al 2018-04-30
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. From May 2015 to April 2018, MedBioinformatics contributed to address those issues by designing and developing seven bioinformatics applications for supporting knowledge-based activities in two relevant clinical areas (oncology and CNS disorders), which cover an important percentage of the burden of chronic diseases and have a big impact in citizens’ wellbeing and show challenging comorbidities.
The specific objectives of the MedBioinformatics project were:
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).
The specific objectives of the MedBioinformatics project were:
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).
During the second half of the project significant achievements have been reached:
• Release of seven bioinformatics tools supporting translational research:
- CGI, Cancer Genome Interpreter
- DisGeNET, Diseases Gene association NETwork
- PsyGeNET, Psychiatric disorders Gene association NETwork
- GePhEX, Genome-Phenome Explorer
- DTC, Drug Target Commons
- DTCB, Danish Disease Trajectory Comorbidity Browser
- VeP, Ensemblli Variant Effect Predictor
• 44 scientific publications.
• Organization of the 2nd and 3rd editions of the European Conference on Translational Bioinformatics.
• Definition of a Business development plan by an expert service support granted by the European Commission.
• The institutions involved in the development of some of the MedBioinformatics applications (DisGeNET, PsyGeNET) have been approached by some investors interested in participating in their commercial exploitation. There are ongoing negotiations on the matter.
The aforementioned bioinformatics tools have been applied to the following case studies:
• Analysis of a patient's tumour genomic alterations to support the allocation to the most appropriate clinical trial (WP5).
• In silico prescription identifying genomic vulnerabilities of the patient's tumour to explore drug repurposing opportunities (WP5).
• Analysis of the alteration landscape of a tumour cohort undergoing a therapeutic intervention for the discovery of novel biomarkers of drug response (WP5).
• Identification of the existing/investigational chemical compounds interacting with the genes in a tumour to guide the design of novel drug assays (WP5).
• Comparative analysis of the molecular bases of major depression and alcohol-induced major depression (WP6).
• Comparative study of the molecular basis of the major depression and Alzheimer disease comorbidity (WP6).
• Study of the comorbidity between Alzheimer disease and cancer, and 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).
• Release of seven bioinformatics tools supporting translational research:
- CGI, Cancer Genome Interpreter
- DisGeNET, Diseases Gene association NETwork
- PsyGeNET, Psychiatric disorders Gene association NETwork
- GePhEX, Genome-Phenome Explorer
- DTC, Drug Target Commons
- DTCB, Danish Disease Trajectory Comorbidity Browser
- VeP, Ensemblli Variant Effect Predictor
• 44 scientific publications.
• Organization of the 2nd and 3rd editions of the European Conference on Translational Bioinformatics.
• Definition of a Business development plan by an expert service support granted by the European Commission.
• The institutions involved in the development of some of the MedBioinformatics applications (DisGeNET, PsyGeNET) have been approached by some investors interested in participating in their commercial exploitation. There are ongoing negotiations on the matter.
The aforementioned bioinformatics tools have been applied to the following case studies:
• Analysis of a patient's tumour genomic alterations to support the allocation to the most appropriate clinical trial (WP5).
• In silico prescription identifying genomic vulnerabilities of the patient's tumour to explore drug repurposing opportunities (WP5).
• Analysis of the alteration landscape of a tumour cohort undergoing a therapeutic intervention for the discovery of novel biomarkers of drug response (WP5).
• Identification of the existing/investigational chemical compounds interacting with the genes in a tumour to guide the design of novel drug assays (WP5).
• Comparative analysis of the molecular bases of major depression and alcohol-induced major depression (WP6).
• Comparative study of the molecular basis of the major depression and Alzheimer disease comorbidity (WP6).
• Study of the comorbidity between Alzheimer disease and cancer, and 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).
The MedBioinformatics outcomes (computational tools and scientific publications) can accelerate the translation of the results of biomedical research into the clinical research, giving support to translational scientists and health professionals to perform information-related operations required for their daily work without the assistance of bioinformatics experts, thus accelerating and optimising the translational research pipeline.
In order to maximise the accessibility and utility of the biomedical data in research and medicine progress, the new bioinformatics methods developed by MedBIoinformatics have been reported in scientific articles published in high impact journals and widely disseminated by participation in scientific events. The dissemination activities have been addressed to the potential users of the applications.
MedBioinformatics has produced software applications with commercial exploitation potential given the focus on satisfying current needs from translational scientists and clinical practitioners, and because of the attention given to high-quality standards and user-friendliness. To increase the applicability of the applications, surveys to potential users provided hints for improving the software functionalities.
The scientific excellence and complementarity between the MedBioinformatics partners constituted the basis for a synergic and fruitful collaboration, which paved the way for future joint projects that they are planning. The results obtained from this collaborative framework could had not been the same carried out individually. Initiatives like MedBioinformatics show up the remarkable benefit of a trans-disciplinary approach combining advanced science, technological innovation and societal impact, thus increasing the centrality of Europe as a key location for bioinformatics research, its practical implementation and its transformation into business opportunities and social/economic development.
In order to maximise the accessibility and utility of the biomedical data in research and medicine progress, the new bioinformatics methods developed by MedBIoinformatics have been reported in scientific articles published in high impact journals and widely disseminated by participation in scientific events. The dissemination activities have been addressed to the potential users of the applications.
MedBioinformatics has produced software applications with commercial exploitation potential given the focus on satisfying current needs from translational scientists and clinical practitioners, and because of the attention given to high-quality standards and user-friendliness. To increase the applicability of the applications, surveys to potential users provided hints for improving the software functionalities.
The scientific excellence and complementarity between the MedBioinformatics partners constituted the basis for a synergic and fruitful collaboration, which paved the way for future joint projects that they are planning. The results obtained from this collaborative framework could had not been the same carried out individually. Initiatives like MedBioinformatics show up the remarkable benefit of a trans-disciplinary approach combining advanced science, technological innovation and societal impact, thus increasing the centrality of Europe as a key location for bioinformatics research, its practical implementation and its transformation into business opportunities and social/economic development.