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Renner C, Reimer N, Christoph J, Busch H, Metzger P, Boerries M, Ustjanzew A, Boehm D, Unberath P. Extending cBioPortal for Therapy Recommendation Documentation in Molecular Tumor Boards: Development and Usability Study. JMIR Med Inform 2023; 11:e50017. [PMID: 38079196 PMCID: PMC10750236 DOI: 10.2196/50017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/02/2023] [Accepted: 09/17/2023] [Indexed: 12/28/2023] Open
Abstract
BACKGROUND In molecular tumor boards (MTBs), patients with rare or advanced cancers are discussed by a multidisciplinary team of health care professionals. Software support for MTBs is lacking; in particular, tools for preparing and documenting MTB therapy recommendations need to be developed. OBJECTIVE We aimed to implement an extension to cBioPortal to provide a tool for the documentation of therapy recommendations from MTB sessions in a secure and standardized manner. The developed extension should be embedded in the patient view of cBioPortal to enable easy documentation during MTB sessions. The resulting architecture for storing therapy recommendations should be integrable into various hospital information systems. METHODS On the basis of a requirements analysis and technology analysis for authentication techniques, a prototype was developed and iteratively refined through a user-centered development process. In conclusion, the tool was evaluated via a usability evaluation, including interviews, structured questionnaires, and the System Usability Scale. RESULTS The patient view of cBioPortal was extended with a new tab that enables users to document MTB sessions and therapy recommendations. The role-based access control was expanded to allow for a finer distinction among the rights to view, edit, and delete data. The usability evaluation showed overall good usability and a System Usability Scale score of 83.57. CONCLUSIONS This study demonstrates how cBioPortal can be extended to not only visualize MTB patient data but also be used as a documentation platform for therapy recommendations.
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Affiliation(s)
- Christopher Renner
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Niklas Reimer
- Group for Medical Systems Biology, Lübeck Institute of Experimental, Universität zu Lübeck, Lübeck, Germany
- Campus Lübeck, University Cancer Center Schleswig-Holstein, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Jan Christoph
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
- Junior Research Group (Bio-) Medical Data Science, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Hauke Busch
- Group for Medical Systems Biology, Lübeck Institute of Experimental, Universität zu Lübeck, Lübeck, Germany
- Campus Lübeck, University Cancer Center Schleswig-Holstein, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine, University of Freiburg Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, University of Freiburg Faculty of Medicine, University Medical Center Freiburg, Freiburg, Germany
- Partner Site Freiburg, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Arsenij Ustjanzew
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Dominik Boehm
- Medical Center for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Philipp Unberath
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
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Witte HM, Riedl J, Künstner A, Fähnrich A, Ketzer J, Fliedner SMJ, Reimer N, Bernard V, von Bubnoff N, Merz H, Busch H, Feller A, Gebauer N. Molecularly Stratified Treatment Options in Primary Refractory DLBCL/HGBL with MYC and BCL2 or BCL6 Rearrangements (HGBL, NOS with MYC/BCL6). Target Oncol 2023; 18:749-765. [PMID: 37488307 PMCID: PMC10517902 DOI: 10.1007/s11523-023-00983-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND There is growing evidence supporting multidisciplinary molecular tumor boards (MTB) in solid tumors whereas hematologic malignancies remain underrepresented in this regard. OBJECTIVE The present study aimed to assess the clinical relevance of MTBs in primary refractory diffuse large B-cell lymphomas/high-grade B-cell lymphomas with MYC and BCL2 rearrangements (prDLBCL/HGBL-MYC/BCL2) (n = 13) and HGBL, not otherwise specified (NOS), with MYC and BCL6 rearrangements (prHGBL, NOS-MYC/BCL6) (n = 6) based on our previously published whole-exome sequencing (WES) cohort. PATIENTS AND METHODS For genomic analysis, the institutional MTB WES pipeline (University Cancer Center Schleswig-Holstein: UCCSH), certified for routine clinical diagnostics, was employed and supplemented by a comprehensive immunohistochemical work-up. Consecutive database research and annotation according to established evidence levels for molecularly stratified therapies was performed (NCT-DKTK/ESCAT). RESULTS Molecularly tailored treatment options with NCT-DKTK evidence level of at least m2A were identified in each case. We classified mutations in accordance with biomarker/treatment baskets and detected a heterogeneous spectrum of targetable alterations affecting immune evasion (IE; n = 30), B-cell targets (BCT; n = 26), DNA damage repair (DDR; n = 20), tyrosine kinases (TK; n = 13), cell cycle (CC; n = 7), PI3K-MTOR-AKT pathway (PAM; n = 2), RAF-MEK-ERK cascade (RME; n = 1), and others (OTH; n = 11). CONCLUSION Our virtual MTB approach identified potential molecularly targeted treatment options alongside targetable genomic signatures for both prDLBCL/HGBL-MYC/BCL2 and prHGBL, NOS-MYC/BCL6. These results underline the potential of MTB consultations in difficult-to-treat lymphomas early in the treatment sequence.
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Affiliation(s)
- Hanno M Witte
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
- Department of Hematology and Oncology, Federal Armed Forces Hospital Ulm, Bundeswehrkrankenhaus Ulm, Oberer Eselsberg 40, 89081, Ulm, Germany.
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany.
| | - Jörg Riedl
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
| | - Axel Künstner
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Anke Fähnrich
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Julius Ketzer
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
- Department of Pediatrics, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Stephanie M J Fliedner
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Straße 3, 24105, Kiel, Germany
| | - Niklas Reimer
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Veronica Bernard
- Hämatopathologie Lübeck, Reference Centre for Lymph Node Pathology and Hematopathology, Maria-Goeppert-Straße 9a, 23562, Lübeck, Germany
| | - Nikolas von Bubnoff
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
| | - Hartmut Merz
- Hämatopathologie Lübeck, Reference Centre for Lymph Node Pathology and Hematopathology, Maria-Goeppert-Straße 9a, 23562, Lübeck, Germany
| | - Hauke Busch
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Alfred Feller
- Hämatopathologie Lübeck, Reference Centre for Lymph Node Pathology and Hematopathology, Maria-Goeppert-Straße 9a, 23562, Lübeck, Germany
| | - Niklas Gebauer
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Alee 160, 23538, Lübeck, Germany
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Metzger P, Hess ME, Blaumeiser A, Pauli T, Schipperges V, Mertes R, Christoph J, Unberath P, Reimer N, Scheible R, Illert AL, Busch H, Andrieux G, Boerries M. MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making. Cancers (Basel) 2023; 15:3456. [PMID: 37444566 DOI: 10.3390/cancers15133456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
(1) Background: Next-generation sequencing (NGS) of patients with advanced tumors is becoming an established method in Molecular Tumor Boards. However, somatic variant detection, interpretation, and report generation, require in-depth knowledge of both bioinformatics and oncology. (2) Methods: MIRACUM-Pipe combines many individual tools into a seamless workflow for comprehensive analyses and annotation of NGS data including quality control, alignment, variant calling, copy number variation estimation, evaluation of complex biomarkers, and RNA fusion detection. (3) Results: MIRACUM-Pipe offers an easy-to-use, one-prompt standardized solution to analyze NGS data, including quality control, variant calling, copy number estimation, annotation, visualization, and report generation. (4) Conclusions: MIRACUM-Pipe, a versatile pipeline for NGS, can be customized according to bioinformatics and clinical needs and to support clinical decision-making with visual processing and interactive reporting.
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Affiliation(s)
- Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Maria Elena Hess
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Blaumeiser
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79110 Freiburg, Germany
| | - Thomas Pauli
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Vincent Schipperges
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Ralf Mertes
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Christoph
- Junior Research Group (Bio-)Medical Data Science, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, 06122 Halle, Germany
- Medical Informatics, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Philipp Unberath
- Medical Informatics, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Niklas Reimer
- Medical Systems Biology Group, Lübeck Institute Für Experimental Dermatology, University of Lübeck, Ratzeburger Alle 160, 23538 Lübeck, Germany
| | - Raphael Scheible
- Institute for AI and Informatics in Medicine, University Hospital Rechts der Isar, Technical University Munich, 81675 Munich, Germany
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Anna L Illert
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79110 Freiburg, Germany
- Department of Medicine III, Klinikum Rechts der Isar, Faculty of Medicine, Technical University of Munich, 81675 Munich, Germany
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Munich, 81675 Munich, Germany
- Center for Personalized Medicine, Klinikum Rechts der Isar, Faculty of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute Für Experimental Dermatology, University of Lübeck, Ratzeburger Alle 160, 23538 Lübeck, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Freiburg, 79110 Freiburg, Germany
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Witte HM, Fähnrich A, Künstner A, Riedl J, Fliedner SMJ, Reimer N, Hertel N, von Bubnoff N, Bernard V, Merz H, Busch H, Feller A, Gebauer N. Primary refractory plasmablastic lymphoma: A precision oncology approach. Front Oncol 2023; 13:1129405. [PMID: 36923431 PMCID: PMC10008852 DOI: 10.3389/fonc.2023.1129405] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Introduction Hematologic malignancies are currently underrepresented in multidisciplinary molecular-tumor-boards (MTB). This study assesses the potential of precision-oncology in primary-refractory plasmablastic-lymphoma (prPBL), a highly lethal blood cancer. Methods We evaluated clinicopathological and molecular-genetic data of 14 clinically annotated prPBL-patients from initial diagnosis. For this proof-of-concept study, we employed our certified institutional MTB-pipeline (University-Cancer-Center-Schleswig-Holstein, UCCSH) to annotate a comprehensive dataset within the scope of a virtual MTB-setting, ultimately recommending molecularly stratified therapies. Evidence-levels for MTB-recommendations were defined in accordance with the NCT/DKTK and ESCAT criteria. Results Median age in the cohort was 76.5 years (range 56-91), 78.6% of patients were male, 50% were HIV-positive and clinical outcome was dismal. Comprehensive genomic/transcriptomic analysis revealed potential recommendations of a molecularly stratified treatment option with evidence-levels according to NCT/DKTK of at least m2B/ESCAT of at least IIIA were detected for all 14 prPBL-cases. In addition, immunohistochemical-assessment (CD19/CD30/CD38/CD79B) revealed targeted treatment-recommendations in all 14 cases. Genetic alterations were classified by treatment-baskets proposed by Horak et al. Hereby, we identified tyrosine-kinases (TK; n=4), PI3K-MTOR-AKT-pathway (PAM; n=3), cell-cycle-alterations (CC; n=2), RAF-MEK-ERK-cascade (RME; n=2), immune-evasion (IE; n=2), B-cell-targets (BCT; n=25) and others (OTH; n=4) for targeted treatment-recommendations. The minimum requirement for consideration of a drug within the scope of the study was FDA-fast-track development. Discussion The presented proof-of-concept study demonstrates the clinical potential of precision-oncology, even in prPBL-patients. Due to the aggressive course of the disease, there is an urgent medical-need for personalized treatment approaches, and this population should be considered for MTB inclusion at the earliest time.
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Affiliation(s)
- Hanno M Witte
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Lübeck, Germany.,Department of Hematology and Oncology, Federal Armed Forces Hospital, Ulm, Germany
| | - Anke Fähnrich
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,University Cancer Center Schleswig-Holstein, University Hospital of Schleswig- Holstein, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,University Cancer Center Schleswig-Holstein, University Hospital of Schleswig- Holstein, Lübeck, Germany
| | - Jörg Riedl
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Lübeck, Germany.,Hämatopathologie Lübeck, Reference Centre for Lymph Node Pathology and Hematopathology, Lübeck, Germany
| | - Stephanie M J Fliedner
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Lübeck, Germany.,University Cancer Center Schleswig-Holstein, University Hospital of Schleswig- Holstein, Lübeck, Germany
| | - Niklas Reimer
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,University Cancer Center Schleswig-Holstein, University Hospital of Schleswig- Holstein, Lübeck, Germany
| | - Nadine Hertel
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Lübeck, Germany
| | - Nikolas von Bubnoff
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Lübeck, Germany.,University Cancer Center Schleswig-Holstein, University Hospital of Schleswig- Holstein, Lübeck, Germany
| | - Veronica Bernard
- Hämatopathologie Lübeck, Reference Centre for Lymph Node Pathology and Hematopathology, Lübeck, Germany
| | - Hartmut Merz
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig- Holstein, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.,University Cancer Center Schleswig-Holstein, University Hospital of Schleswig- Holstein, Lübeck, Germany
| | - Alfred Feller
- Hämatopathologie Lübeck, Reference Centre for Lymph Node Pathology and Hematopathology, Lübeck, Germany
| | - Niklas Gebauer
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Lübeck, Germany.,University Cancer Center Schleswig-Holstein, University Hospital of Schleswig- Holstein, Lübeck, Germany
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Unberath P, Mahlmeister L, Reimer N, Busch H, Boerries M, Christoph J. Searching of Clinical Trials Made Easier in cBioPortal Using Patients' Genetic and Clinical Profiles. Appl Clin Inform 2022; 13:363-369. [PMID: 35354211 PMCID: PMC8967483 DOI: 10.1055/s-0042-1743560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background
Molecular tumor boards (MTBs) cope with the complexity of an increased usage of genome sequencing data in cancer treatment. As for most of these patients, guideline-based therapy options are exhausted, finding matching clinical trials is crucial. This search process is often performed manually and therefore time consuming and complex due to the heterogeneous and challenging dataset.
Objectives
In this study, a prototype for a search tool was developed to demonstrate how cBioPortal as a clinical and genomic patient data source can be integrated with ClinicalTrials.gov, a database of clinical studies to simplify the search for trials based on genetic and clinical data of a patient. The design of this tool should rest on the specific needs of MTB participants and the architecture of the integration should be as lightweight as possible and should not require manual curation of trial data in advance with the goal of quickly and easily finding a matching study.
Methods
Based on a requirements analysis, interviewing MTB experts, a prototype was developed. It was further refined using a user-centered development process with multiple feedback loops. Finally, the usability of the application was evaluated with user interviews including the thinking-aloud protocol and the system usability scale (SUS) questionnaire.
Results
The integration of ClinicalTrials.gov in cBioPortal is achieved by a new tab in the patient view where the genomic profile for the search is prefilled and additional parameters can be adjusted. These parameters are then used to query the application programming interface (API) of ClinicalTrials.gov. The returned search results subsequently are ranked and presented to the user. The evaluation of the application resulted in an SUS score of 83.5.
Conclusion
This work demonstrates the integration of cBioPortal with ClinicalTrials.gov to use clinical and genomic patient data to search for appropriate trials within an MTB.
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Affiliation(s)
- Philipp Unberath
- Friedrich-Alexander University Erlangen-Nuremberg, Chair of Medical Informatics, Erlangen, Bayern, Germany
| | - Lukas Mahlmeister
- Friedrich-Alexander University Erlangen-Nuremberg, Chair of Medical Informatics, Erlangen, Bayern, Germany
| | - Niklas Reimer
- Universität zu Lübeck, Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Lübeck, Schleswig-Holstein, Germany
| | - Hauke Busch
- Universität zu Lübeck, Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Lübeck, Schleswig-Holstein, Germany
| | - Melanie Boerries
- University of Freiburg Faculty of Medicine, Institute of Medical Bioinformatics and Systems Medicine, University Medical Center Freiburg, Freiburg, Baden-Württemberg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Jan Christoph
- Friedrich-Alexander University Erlangen-Nuremberg, Chair of Medical Informatics, Erlangen, Bayern, Germany.,Martin-Luther-University Halle-Wittenberg, Faculty of Medicine, Junior Research Group (Bio-)Medical Data Science, Halle, Sachsen-Anhalt, Germany
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Reimer N, Hafke R, Wrensch M, Horst P, Bloch W, Hahn T, Kirchhoff A, Kluck KL, Stein J, Baumann F. Influence of a 12-month supervised, intensive resistance, aerobic and impact exercise intervention on muscle strength in prostate cancer patients undergoing anti-hormone therapy: Study protocol for the randomized, controlled Burgdorf study. Contemp Clin Trials 2022; 114:106685. [DOI: 10.1016/j.cct.2022.106685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 12/09/2021] [Accepted: 01/14/2022] [Indexed: 11/12/2022]
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Reimer N, Unberath P, Busch H, Börries M, Metzger P, Ustjanzew A, Renner C, Prokosch HU, Christoph J. Challenges and Experiences Extending the cBioPortal for Cancer Genomics to a Molecular Tumor Board Platform. Stud Health Technol Inform 2021; 287:139-143. [PMID: 34795098 DOI: 10.3233/shti210833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In Molecular Tumor Boards (MTBs), therapy recommendations for cancer patients are discussed. To aid decision-making based on the patient's molecular profile, the research platform cBioPortal was extended based on users' requirements. Additionally, a comprehensive dockerized workflow was developed to support the deployment of cBioPortal and connected services. In this work, we present the challenges and experiences of nearly two years of implementing and deploying an MTB platform based on cBioPortal and compare those to findings of a previous study.
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Affiliation(s)
- Niklas Reimer
- Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Universität zu Lübeck, Germany
| | - Philipp Unberath
- Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Universität zu Lübeck, Germany
| | - Hauke Busch
- Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Universität zu Lübeck, Germany
| | - Melanie Börries
- Institute of Medical Bioinformatics and Systems Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) Partner Site Freiburg and Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Arsenij Ustjanzew
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Johannes Gutenberg-University School of Medicine, Mainz, Germany
| | - Christopher Renner
- Department of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Ulrich Prokosch
- Department of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jan Christoph
- Department of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Junior Research Group (Bio-)Medical Data Science, Martin-Luther-University Halle-Wittenberg, Faculty of Medicine, Halle, Germany
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Reimer N, Unberath P, Busch H, Ingenerf J. FhirSpark - Implementing a Mediation Layer to Bring FHIR to the cBioPortal for Cancer Genomics. Stud Health Technol Inform 2021; 281:303-307. [PMID: 34042754 DOI: 10.3233/shti210169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
cBioPortal is a commonly used data warehousing solution for genomic cancer studies. The software is being extended for patient care application in a molecular tumor board by the MIRACUM consortium within the Medical Informatics Initiative Germany. A key feature for this use case is the ability to enter therapy recommendations for individual patients, which requires interoperability with the hospital information system. A RESTful interface between cBioPortal and an external mediation layer was selected from the different implementation options. It achieves interoperability by using a FHIR capable server to store data and applying the HL7 FHIR Genomics Reporting implementation guide. For systems not supporting the FHIR standard, the well-established HL7 Version 2 standard is available as a fallback export format.
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Affiliation(s)
- Niklas Reimer
- Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, University of Lübeck, Germany
| | - Philipp Unberath
- Department of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hauke Busch
- Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, University of Lübeck, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Germany
- Institute of Medical Informatics, University of Lübeck, Germany
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Dähnert L, Conraths FJ, Reimer N, Groschup MH, Eiden M. Molecular and serological surveillance of Hepatitis E virus in wild and domestic carnivores in Brandenburg, Germany. Transbound Emerg Dis 2018; 65:1377-1380. [PMID: 29655214 DOI: 10.1111/tbed.12877] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 12/23/2022]
Abstract
Hepatitis E virus (HEV) is a zoonotic virus which circulates in pigs and wild boars as main reservoir species. To reveal the infection rate in carnivores, we have carried out a monitoring study of raccoons, raccoon dogs, dogs and cats sampled in Brandenburg, Germany. In summary, 53.8% (43 of 80) of the raccoons, 34.3% (25 of 73) of the raccoon dogs, 56.6% (47 of 83) of dogs and 32.3% (21 of 65) of cats were tested positive for HEV-specific antibodies. No viral RNA could be detected. This first description of anti-HEV antibodies in raccoons and raccoon dogs worldwide and in dogs and cats in Germany highlights the natural host range expansion of HEV.
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Affiliation(s)
- L Dähnert
- Institute of Novel and Emerging Infectious Diseases at the Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - F J Conraths
- Institute of Epidemiology at the Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - N Reimer
- Institute of Epidemiology at the Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - M H Groschup
- Institute of Novel and Emerging Infectious Diseases at the Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - M Eiden
- Institute of Novel and Emerging Infectious Diseases at the Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Petersen CE, Scottolini AG, Cody LR, Mandel M, Reimer N, Bhagavan NV. A point mutation in the human serum albumin gene results in familial dysalbuminaemic hyperthyroxinaemia. J Med Genet 1994; 31:355-9. [PMID: 8064810 PMCID: PMC1049864 DOI: 10.1136/jmg.31.5.355] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using DNA samples obtained from two unrelated patients, diagnosed as having familial dysalbuminaemic hyperthyroxinaemia (FDH), exons 1-14 which span the entire coding region of the human serum albumin (HSA) gene were amplified by the polymerase chain reaction. The sequence of each of the 14 DNA fragments was then determined. In each case a point mutation was identified at nucleotide 653 which causes an Arg to His substitution at amino acid position 218. The substitution was confirmed by amino acid sequencing of a mutant peptide resulting from tryptic digestion of the protein. Abnormal affinity of FDH HSA for a thyroxine (T4) analogue was verified by an adaptation of the procedure used in routine free T4 measurement. The location of the mutation is discussed in relation to other studies on the binding properties of HSA.
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Affiliation(s)
- C E Petersen
- Department of Biochemistry and Biophysics, John A Burns School of Medicine, University of Hawaii, Honolulu 96822
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