CC BY-NC-ND 4.0 · Appl Clin Inform 2022; 13(02): 363-369
DOI: 10.1055/s-0042-1743560
Research Article

Searching of Clinical Trials Made Easier in cBioPortal Using Patients' Genetic and Clinical Profiles

Philipp Unberath
1   Friedrich-Alexander University Erlangen-Nuremberg, Chair of Medical Informatics, Erlangen, Bayern, Germany
,
Lukas Mahlmeister
1   Friedrich-Alexander University Erlangen-Nuremberg, Chair of Medical Informatics, Erlangen, Bayern, Germany
,
Niklas Reimer
2   Universität zu Lübeck, Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Lübeck, Schleswig-Holstein, Germany
,
Hauke Busch
2   Universität zu Lübeck, Group for Medical Systems Biology, Lübeck Institute of Experimental Dermatology, Lübeck, Schleswig-Holstein, Germany
,
Melanie Boerries*
3   University of Freiburg Faculty of Medicine, Institute of Medical Bioinformatics and Systems Medicine, University Medical Center Freiburg, Freiburg, Baden-Württemberg, Germany
4   German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
,
Jan Christoph*
1   Friedrich-Alexander University Erlangen-Nuremberg, Chair of Medical Informatics, Erlangen, Bayern, Germany
5   Martin-Luther-University Halle-Wittenberg, Faculty of Medicine, Junior Research Group (Bio-)Medical Data Science, Halle, Sachsen-Anhalt, Germany
› Author Affiliations
Funding This research has been conducted within the MIRACUM project. MIRACUM is funded by the German Federal Ministry of Education and Research (BMBF), grant IDs 01ZZ1801A (P.U., L.M., and J.C.) and 01ZZ1801B (M.B.). This work was supported by the BMBF funded HiGHmed project, grant ID 01ZZ1802Z (H.B., N.R.) and by the German Research Foundation (DFG), grant IDs CRC 850 and CRC 1160 (M.B.).

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.

Protection of Human and Animal Subjects

The project was performed in compliance with the World Medical Association Declaration of Helsinki on Ethical Principles for Medical Research Involving Human Subjects. Ethical approval was not required.


* These authors contributed equally to this work.




Publication History

Received: 06 September 2021

Accepted: 15 November 2021

Publication Date:
30 March 2022 (online)

© 2022. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/)

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