Category Archive:News

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Back from New York City

Jan Christoph and Marc Hinderer of the MIRACUM team spent 10 days in New York City for an intense research visit and have just returned with lots of input for some of our use cases. They also opened the door for future cooperations with three distinguished U.S. biomedical informatics and cancer research centers.

First they had the chance to visit the Memorial Sloan Kettering Cancer Center (MSKCC) for several days to join the molecular oncology and bioinformatics groups of Dr. Michael F. Berger (developer of the powerful and new MSK-IMPACT genome-sequencing test) and Dr. Ahmet Zehir. Especially the interviews with key scientists as well as the participation in the  sign-out meetings of the MSKCC team and the quality control meetings provided valuable input for the MIRACUM use case on precision medicine. Together with our MIRACUM members, Michael Berger illustrated the opportunities of identifing actionable targets with a large gene panel rather than performing whole-exome-sequencing or even whole-genome-sequencing. In several meetings with Ahmet Zehir (Director of Clinical Bioinformatics at MSKCC) they learned about the “Clinical Variation and Result” database which is extensively used for moleculargenetic diagnostics within MSKCC. He invited our MIRACUM members to join him for several sign-out meetings of the MSKCC team and for quality control meetings in order to learn about the advantages of this database. Furthermore, he described how to modify and integrate such a database within the MIRACUM consortium. Moreover, our MIRACUM members met Dr. Sumit Middha and his team in order to understand and analyze the omics pipeline of MSKCC. This pipeline comprises automated and streamlined workflows for DNA sequencing, which has the chance to help taking genomic sequencing in Germany to the next level. Since the development and integration of a pharmacogenomic clinical decision support system is one of MIRACUM’s main goals for the upcoming phase, our MIRACUM members met Dr. Debyani Chakravarty and Dr. Jianjiong Gao, two of the leading scientists for knowledge bases at MSKCC and the main developers of two powerful and well-known tools regarding cancer genomics data. They offered our MIRACUM members a comprehensive insight into OncoKB and cBioPortal. OncoKB is the precision oncology knowledge base of MSKCC, which also comprises a pharmacogenomic clinical decision support system. cBioPortal is a “web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data” (Gao et al. 2016). In addition to that, next steps in order to design and implement both OncoKB and cBioPortal into a German clinical environment were discussed and determined.

MarcA photo showing Hinderer and Jan Christoph in front of the building of the "Memorial Sloan-Kettering Cancer Center"

A photo showing Ahmet Zehir, Michael F. Berger, Jan Christoph and Marc Hinderer (standing in front of the office door)

At the Department of Biomedical Informatics of the Columbia University, our MIRACUM members met the two leading scientists in biomedical informatics – Dr. George Hripcsak and Dr. Noemie Elhadad. George Hripcsak is Professor and Chair of the Department of Biomedical Informatics of Columbia University and Director of Medical Informatics Services at the Presbyterian Hospital/Columbia Campus in New York. Our MIRACUM members discussed with him both the cooperation with the OHDSI consortium and possible approaches to apply the OMOP common data model within MIRACUM. A presentation of the newest version of the Achilles and Atlas tools illustrated the potential of these particular tools for the analysis of cross-network data both within the MIRACUM project and for Germany. Noemie Elhadad is an Associate Professor of Biomedical Informatics at Columbia University and the main developer of the HARVEST tool. She offered the MIRACUM members a comprehensive insight into HARVEST – an innovative tool for the summarization and visualization of care processes. Moreover, she showed potential ways in which HARVEST could support the MIRACUM consortium in its project regarding the visualization of patient timelines.

A photo showing Jan Christoph, George Hripsak and Marc Hinderer standing on the roof deck of the Presbyterian Building

At last, Jan and Marc met leading scientists in clinical health informatics of the Weil Cornell Medical College: Dr. Jyotishman Pathak, Dr. Thomas CampionDr. David R. Artz and Dr. Olivier Elemento. They gave our MIRACUM members an insight into their omics pipeline and discussed potential options for the implementation of their Precision Medicine Knowledgebase (PMKB) into the MIRACUM infrastructure. Since the Weil Cornell Medical College extensively uses i2b2 and OMOP for data integration, the scientists outlined the purpose of the application both within their clinical and their research environment. Furthermore, they described their current pharmacogenomic Clinical Decision Support System and explained the technical mechanisms behind this system.

During all these visits the architecture of the MIRACUM data integration center and the interoperability between similar US initiatives/projects was extensively discussed and opportunities for future cooperations have been outlined.

 

 

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7th new Medical Informatics/Medical Data Science Professorship announced from MIRACUM members

We are happy to announce the seventh  newly established professorship in the context of the MIRACUM consortium. The Faculty of Medicine Mannheim of Heidelberg University invites applicants for a W3 Professorship for Medical Informatics Detailed information is provided in the job advertisement in English and German. We are looking forward to receiving your applications and a future cooperation in the MIRACUM consortium!

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3rd MIRACUM Steering Board Meeting in Frankfurt

The MIRACUM Steering Board, together with the University hospital´s CIOs and team members from the participating medical informatics, biometrics and bioinformatics groups met for two days (29th/30th of March) at Frankfurt University Hospital for rounding up their grant proposal for the development and networking phase. The status of pilot projects was demonstrated and workplans for the future defined. While two members of the Erlangen Medical Informatics department in parallel pursued a 10 day research visit at three research groups in New York City, the input from those international cooperation partners and scientific advisors was directly transferred into the concepts for use case implementation.

The MIRACUM Steering Board congratulated the Medical Faculty of Gießen Universities and the Medical Faculty Mannheim of Heidelberg University for their recent announcement of new professorships in Medical Informatics. Finally the MIRACUM Steering Board initiated the planning of their first Scientific Symposium in February 2018.

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Erlangen´s tranSMART projects at the eHealth Summit 2017

For many years now Erlangen´s Chair of Medical Informatics has committed itself to the support of translational research. Since the i2b2 Toolkit has been successfully deployed in various projects for more than five years now, Erlangen´s section of medical informatics also faced the challenge of supporting the integration and -with it- the evaluation of molecular and genomic analysis data by providing clinical data. To this end the platform tranSMART, which evolved from i2b2 and was developed further by the Transmart Foundation, has been established at the medical faculty of the FAU Erlangen-Nürnberg. It has been refined and evaluated both for its application in medical teaching and for its usability regarding its use by basic researchers in medicine. Two of these projects have now been accepted for a presentation at the eHealth Summit 2017 in Vienna (23th/24th May 2017). The detailed results of the project will soon be published in the conference proceedings of the IOS series “Studies in Health Technologies and Informatics” as well.

  • Christoph Jan, Knell Christian, Nachberger Elisabeth, Stürzl Michael, Maier Christian, Prokosch Hans-Ulrich, Sedlmayr Martin. Two Years of tranSMART in a University Hospital for Translational Research and Education.
  • Knell Christian, Sedlmayr Martin, Christoph Jan. Developing interactive plug-ins for for tranSMART using the SmartR fram ework workwork: The case of survival analysis.
ByMIRACUM

First MIRACUM publication accepted for eHealth 2017 summit in Vienna

The first joint project results of the MIRACUM consortium will be presented by Marc Hinderer at the eHealth Summit Austria (23./24.5.2017) in Vienna. A project team from six of our MIRACUM partners has conducted semi-structured interviews with experts of five university hospitals concerning organizational structure and procedures which are currently established around the molecular tumor boards at those university hospitals. Even though this processes and structures are currently still quiet heterogeneous in those hospitals, three options to support those processes were identified: (1) standardized pipelines to integrate automated variant calling and annotation; (2) tools supporting the experts in creating their reports and presentations and (3) implementing pharmacogenomic CDSS into therapeutic recommendations. The resulting publication “Hinderer M, Boerries M, Haller F, Wagner S, Sollfranke S, Acker T, Prokosch HU. Christoph J. Supporting Molecular Tumor Boards in Molecular-guided Decision-making – the Current Status of Five German University Hospitals” will be published in the IOS Press open access Studies in Health Technologies and Informatics series and provide details of the current situation as well as the recommended IT support.

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Call for applications: W2 Professorship for Biomedical Informatics and Systematic Medicine

We are happy to announce a newly established professorship in the context of the MIRACUM consortium. The Faculty of Medicine of the Justus-Liebig-University of Giessen invites applicants for a W2 Professorship for Biomedical Informatics and Systematic Medicine; the application deadline expires on April 20th 2017. Detailed information is provided in the job advertisement in English and German. We are looking forward to receiving your applications!

ByMIRACUM

MIRACUM welcomes new partner from Magdeburg

In order to support the interest of the Federal Ministry of Education and Research to expand the planned data integration centre networks across all German university hospitals, MIRACUM had defined a set of rules and requirements for adding a new partner to the consortium. Within the last months researchers  of the Medical Faculty of the Otto-von-Guericke-University and the University Hospital Magdeburg have shown great interest in such a future participation and have already started to contribute effectively to the MIRACUM pilot projects and thus shown that they fulfill the defined criteria. Thus, within the recent two-day MIRACUM workshop the Dean of the Medical Faculty (Prof. Dr. Rothkötter), supported by the Director of the Department for Biometrics and Medical Informatics (Prof. Dr. Bernarding), presented their status and potential contributions as a future MIRACUM partner.

As a result we have the pleasure to announce a new member in the MIRACUM consortium: the Medical Faculty of the Otto-von-Guericke-University together with the University Hospital Magdeburg.

Prof. Dr. Prokosch, the MIRACUM coordinator, and the whole MIRACUM Steering Board gave a warm welcome to Prof. Dr. Hermann-Josef Rothkötter, the dean of the medical faculty, and Prof. Dr. Johannes Bernarding, the director of the Institute for Biometry and Medical Informatics, who have already joined the second MIRACUM Steering Board workshop in Erlangen.

Prof. Prokosch shaking hands with the representative of the new MIRARCUM partner Magdeburg

participants of the second MIRACUM workshop in their meeting room

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2. MIRACUM Workshop in Erlangen

30 MIRACUM members gathered in Erlangen from 6th to 7th February to present the status of ongoing pilot projects and to discuss the projects and aims for the development and networking phase of the medical informatics initiative. One highlight: we welcomed the University Hospital of Magdeburg as a new partner in our consortium. Furthermore, we discussed different topics for our use cases and pilot projects and received updates from our team members who participated in the National Steering Committee´s workgroups on Broad Consent, Data Sharing and Interoperability. The next meeting will be held in Frankfurt at the end of March.

The MIRACUM partners at work in their meeting roomProf. Prokosch shaking hands with the representative of the new MIRACUM partner Magdeburg

ByMIRACUM

Omics Workshop in Freiburg

New insights into the relationship between changes in genomic sequences and diseases can be gained even faster and more reliably if the genomic information of the respective patient is included in the analysis and evaluation of the medical data of a university hospital. Therefore it is necessary to enable researchers to access these so-called Omics data and, at the same time, to provide the necessary tools for a holistic analysis. The MIRACUM Consortium addresses this issue and has already conducted two workshops, during which potential solutions were discussed which are meant to enable the afore-said access/tools not only within an institution but also beyond in order to facilitate collaborative research.5 participants of the MIRACUM consortium in their meeting room in Freiburg.

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MIRACUM Workshops in Frankfurt, Freiburg and Erlangen

The first 2-day workshop of the MIRACUM consortium was hosted by the University Hospital of Frankfurt from 27th to 28th October 2016 and around 30 consortium members followed the invitation to Frankfurt. The agenda was fully packed – beginning with lively discussions on the lessons learned from the USA visiting tour and followed by presentations on the results of our first pilot projects (pharmacogenomic clinical decision support, analysis workflow for heterogeneous omics data and proof-of-concept data integration) in preparation of the full use-case projects planned for the development and networking phase. Potential partners from industry were invited as well; they presented their solutions and concepts in the field of data integration, clinical/pharmacogenomics decision support and natural language processing.

A second technical workshop was held on 22nd December in Frankfurt. The major topic of this workshop was the elaboration of the detailed technical concept of the various components of the data integration centre. A further workshop focusing on omics data workflow will be hosted by the University Hospital of Freiburg on 13th January 2017.

The next steering board workshop will be held on 6th/7th February 2017. Its venue will be the University Hospital of Erlangen.