Back from New York City

ByMIRACUM

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.