Periodic Reporting for period 1 - PharmGenHUB (Pharmacogenomics Hub in a strengthened IMGGE)
Período documentado: 2022-07-01 hasta 2023-09-30
Personalized medicine uses pharmacogenomics (PGX) to individualize therapy upon patients’ unique DNA profiles. With ~200,000 deaths/year in Europe due to adverse drug reactions, it has become an imperative to improve treatment. In Western Balkans (WB), individualization of therapy is done sporadically. IMGGE (Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Serbia) is a pioneer in the PGX in WB. PharmGenHUB will strengthen IMGGE’s PGX R&I potential by exchanging knowledge between IMGGE and EU partnering institutions: University of Patras, Greece (UPAT), University of Ljubljana, Slovenia (UL), University of Trieste, Italy (UNITS). Through collaboration and knowledge sharing with 3 EU partners, IMGGE will become WB central place for PGX diagnostics and R&I, education and trainings, and translation of PGX knowledge into clinically applicable digital solutions. IMGGE’s research project, high-throughput DNA sequencing of WB populations, with support of UPAT and UL, will identify WB specific drug-PGX marker pairs and enable design of electronic tool for better decision-making in clinical practice, electronic PGX assistant for WB (ePGA-WB). iPSC model for validation of novel PGX markers relevant for Europe will be introduced at IMGGE with support of UNITS. IMGGE will renew, reinforce and establish new connections through networking with WB institutions. Project will be realized through short-term visits of IMGGE staff to EU partner institutions, staff exchanges, on-site trainings, experimental laboratory work. Outreach activities will include PGX days, WB conference and joint summer schools. To strengthen research management capacities and administrative skills of IMGGE staff, a research management unit will be established with assistance from UPAT. As focal point of PGX translational research, IMGGE will impact on WB health-care cost benefits and facilitate WB integration to EU-PGX research area through R&I activities and digitalization.
In order to accomplish the main objectives of PharmGenHUB project, work planned in the tasks defined in the WPs is performed as follows:
1. Bioinformatics on-site training of the IMGGE staff at UPAT as well as advanced statistics on-site training at UL have been carried out.
2. Most activities in the gaining knowledge to apply iPS cells model system for personalized pharmacogenomics research have been realized through intensive on- line communication with researchers from UNITS. Researchers from UNITS visited IMGGE in order to translate iPSC technology from UNITS to IMGGE.
3. The original bioinformatics tool for WGS analysis leading to the pipeline for pharmacogenomics analysis, has been designed and tested.
4. Communication with WB partners has been established and ethical issues regarding the Pilot project have been resolved.
5. Samples of 250 individuals from Western Balkans have been collected and the chemistry for WGS analysis is purchased. Most samples have been transferred to IMGGE. The WGS analysis is ongoing.
6. One paper has already been published and two more research papers, as a result of PharmGenHUB project have been submitted.
7. A Summer school in Trieste, Italy and a Pharmacogenomics Day in Skopje, Northern Macedonia have been organized. Other numerous dissemination activities have been carried out.
8. Web site has been activated and updated regularly. Social networks (Facebook, LinkedIn, Twitter) have been activated and the activities are posted. Leaflets have been distributed. Other means of communication were also used.
9. The Research Management Unit (RMU) has been established and has started to work at IMGGE. Reinforcement of the research supporting structures and offices of the IMGGE has been achieved through training of 5 IMGGE administrative staff and a senior researcher at UPAT.
10. Data Management Plan and the Plan for dissemination, exploitation and communication have been created.
1. Bioinformatics on-site training of the IMGGE staff at UPAT as well as advanced statistics on-site training at UL have been carried out.
2. Most activities in the gaining knowledge to apply iPS cells model system for personalized pharmacogenomics research have been realized through intensive on- line communication with researchers from UNITS. Researchers from UNITS visited IMGGE in order to translate iPSC technology from UNITS to IMGGE.
3. The original bioinformatics tool for WGS analysis leading to the pipeline for pharmacogenomics analysis, has been designed and tested.
4. Communication with WB partners has been established and ethical issues regarding the Pilot project have been resolved.
5. Samples of 250 individuals from Western Balkans have been collected and the chemistry for WGS analysis is purchased. Most samples have been transferred to IMGGE. The WGS analysis is ongoing.
6. One paper has already been published and two more research papers, as a result of PharmGenHUB project have been submitted.
7. A Summer school in Trieste, Italy and a Pharmacogenomics Day in Skopje, Northern Macedonia have been organized. Other numerous dissemination activities have been carried out.
8. Web site has been activated and updated regularly. Social networks (Facebook, LinkedIn, Twitter) have been activated and the activities are posted. Leaflets have been distributed. Other means of communication were also used.
9. The Research Management Unit (RMU) has been established and has started to work at IMGGE. Reinforcement of the research supporting structures and offices of the IMGGE has been achieved through training of 5 IMGGE administrative staff and a senior researcher at UPAT.
10. Data Management Plan and the Plan for dissemination, exploitation and communication have been created.
Several achievements beyond DoA are worth to be emphasized in the First Periodic Report.
1. The most critical part of the realization of the Project was the non-existence of publicly available bioinformatics pipeline for the analysis of WGS raw data. Since IMGGE had already introduced WGS methodology in house, and obtained 48 WGS raw sequences, EU partner UPAT with expertise in pharmacogenomics bioinformatics has been actively involved in intensive online communication regarding developing and testing bioinformatics WGS pipeline. The original tool for WGS analysis has been designed by UPAT staff and IMGGE staff.
2. IMGGE has acquired two key sequencing instruments- NextSeq 550 Dx and NextSeq 2000 (Illumina) from other projects and services, so that NGS analysis, including WGS can be performed in IMGGE. Also, ELTA d.o.o. a representative of Illumina in Serbia has supported the PharmGenHUB project by the installation of the robot for library preparation for NGS: Beckman Coulter Biomek i5 at IMGGE.
3. With the support of the researchers from UNITS, translation of iPSC technology from UNITS to IMGGE has been enabled through the establishment of new iPSC facility in IMGGE. This is one of the main achievements of the PharmGenHUB project related to iPSC research because it enables sustainability of the PharmGenHUB project.
4. PharmGenHUB team has been approached by TAKEDA and Novartis pharmaceutical companies. Project dedicated to the application of pharmacogenomics and artificial intelligence in inflammatory bowel diseases treatment has been approved by TAKEDA as investigator-initiated research (IISR) to be realized by 2025. Also, the PharmGenHUB team has applied for the grant of Novartis in May 2023. The project is dedicated to the pharmacogenomics of Hypercholesterolemia treatment. Both projects are based on population pharmacogenomics.
5. Several pharmacogenomics studies are initiated by PharmGenHUB project. Two manuscripts have already been submitted, and two more studies are ongoing.
6. Pharmacoeconomics studies, initiated in the PharmGenHUB project, will contribute to the Project impact on health care system and society as well.
1. The most critical part of the realization of the Project was the non-existence of publicly available bioinformatics pipeline for the analysis of WGS raw data. Since IMGGE had already introduced WGS methodology in house, and obtained 48 WGS raw sequences, EU partner UPAT with expertise in pharmacogenomics bioinformatics has been actively involved in intensive online communication regarding developing and testing bioinformatics WGS pipeline. The original tool for WGS analysis has been designed by UPAT staff and IMGGE staff.
2. IMGGE has acquired two key sequencing instruments- NextSeq 550 Dx and NextSeq 2000 (Illumina) from other projects and services, so that NGS analysis, including WGS can be performed in IMGGE. Also, ELTA d.o.o. a representative of Illumina in Serbia has supported the PharmGenHUB project by the installation of the robot for library preparation for NGS: Beckman Coulter Biomek i5 at IMGGE.
3. With the support of the researchers from UNITS, translation of iPSC technology from UNITS to IMGGE has been enabled through the establishment of new iPSC facility in IMGGE. This is one of the main achievements of the PharmGenHUB project related to iPSC research because it enables sustainability of the PharmGenHUB project.
4. PharmGenHUB team has been approached by TAKEDA and Novartis pharmaceutical companies. Project dedicated to the application of pharmacogenomics and artificial intelligence in inflammatory bowel diseases treatment has been approved by TAKEDA as investigator-initiated research (IISR) to be realized by 2025. Also, the PharmGenHUB team has applied for the grant of Novartis in May 2023. The project is dedicated to the pharmacogenomics of Hypercholesterolemia treatment. Both projects are based on population pharmacogenomics.
5. Several pharmacogenomics studies are initiated by PharmGenHUB project. Two manuscripts have already been submitted, and two more studies are ongoing.
6. Pharmacoeconomics studies, initiated in the PharmGenHUB project, will contribute to the Project impact on health care system and society as well.