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Singer F, Irmisch A, Toussaint NC, Grob L, Singer J, Thurnherr T, Beerenwinkel N, Levesque MP, Dummer R, Quagliata L, Rothschild SI, Wicki A, Beisel C, Stekhoven DJ. SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics. BMC Med Inform Decis Mak 2018; 18:89. [PMID: 30373609 PMCID: PMC6206832 DOI: 10.1186/s12911-018-0680-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/18/2018] [Indexed: 12/18/2022] Open
Abstract
Background Molecular precision oncology is an emerging practice to improve cancer therapy by decreasing the risk of choosing treatments that lack efficacy or cause adverse events. However, the challenges of integrating molecular profiling into routine clinical care are manifold. From a computational perspective these include the importance of a short analysis turnaround time, the interpretation of complex drug-gene and gene-gene interactions, and the necessity of standardized high-quality workflows. In addition, difficulties faced when integrating molecular diagnostics into clinical practice are ethical concerns, legal requirements, and limited availability of treatment options beyond standard of care as well as the overall lack of awareness of their existence. Methods To the best of our knowledge, we are the first group in Switzerland that established a workflow for personalized diagnostics based on comprehensive high-throughput sequencing of tumors at the clinic. Our workflow, named SwissMTB (Swiss Molecular Tumor Board), links genetic tumor alterations and gene expression to therapeutic options and clinical trial opportunities. The resulting treatment recommendations are summarized in a clinical report and discussed in a molecular tumor board at the clinic to support therapy decisions. Results Here we present results from an observational pilot study including 22 late-stage cancer patients. In this study we were able to identify actionable variants and corresponding therapies for 19 patients. Half of the patients were analyzed retrospectively. In two patients we identified resistance-associated variants explaining lack of therapy response. For five out of eleven patients analyzed before treatment the SwissMTB diagnostic influenced treatment decision. Conclusions SwissMTB enables the analysis and clinical interpretation of large numbers of potentially actionable molecular targets. Thus, our workflow paves the way towards a more frequent use of comprehensive molecular diagnostics in Swiss hospitals. Electronic supplementary material The online version of this article (10.1186/s12911-018-0680-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Franziska Singer
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Anja Irmisch
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Linda Grob
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Jochen Singer
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Thomas Thurnherr
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Niko Beerenwinkel
- SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Luca Quagliata
- Department of Pathology, University Hospital Basel, Schönbeinstrasse 40, 4056, Basel, Switzerland
| | - Sacha I Rothschild
- Division of Oncology, Department of Biomedicine, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Andreas Wicki
- Division of Oncology, Department of Biomedicine, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Daniel J Stekhoven
- NEXUS Personalized Health Technologies, ETH Zurich, Otto-Stern-Weg 7, 8093, Zurich, Switzerland. .,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland.
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