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. 2021 Dec 20;21(1):358.
doi: 10.1186/s12911-021-01719-z.

cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board

Affiliations

cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board

Arsenij Ustjanzew et al. BMC Med Inform Decis Mak. .

Abstract

Background: Extensive sequencing of tumor tissues has greatly improved our understanding of cancer biology over the past years. The integration of genomic and clinical data is increasingly used to select personalized therapies in dedicated tumor boards (Molecular Tumor Boards) or to identify patients for basket studies. Genomic alterations and clinical information can be stored, integrated and visualized in the open-access resource cBioPortal for Cancer Genomics. cBioPortal can be run as a local instance enabling storage and analysis of patient data in single institutions, in the respect of data privacy. However, uploading clinical input data and genetic aberrations requires the elaboration of multiple data files and specific data formats, which makes it difficult to integrate this system into clinical practice. To solve this problem, we developed cbpManager.

Results: cbpManager is an R package providing a web-based interactive graphical user interface intended to facilitate the maintenance of mutations data and clinical data, including patient and sample information, as well as timeline data. cbpManager enables a large spectrum of researchers and physicians, regardless of their informatics skills to intuitively create data files ready for upload in cBioPortal for Cancer Genomics on a daily basis or in batch. Due to its modular structure based on R Shiny, further data formats such as copy number and fusion data can be covered in future versions. Further, we provide cbpManager as a containerized solution, enabling a straightforward large-scale deployment in clinical systems and secure access in combination with ShinyProxy. cbpManager is freely available via the Bioconductor project at https://bioconductor.org/packages/cbpManager/ under the AGPL-3 license. It is already used at six University Hospitals in Germany (Mainz, Gießen, Lübeck, Halle, Freiburg, and Marburg).

Conclusion: In summary, our package cbpManager is currently a unique software solution in the workflow with cBioPortal for Cancer Genomics, to assist the user in the interactive generation and management of study files suited for the later upload in cBioPortal.

Keywords: Bioconductor; Clinical data; Data management; File generation; Genomic data; Molecular Tumor Board; Patient management; R; Shiny; cBioPortal.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The study folder acts as a link between cbpManager and the local cBioPortal instance. cbpManager reads, generates and modifies study files stored in the study folder. The study upload to cBioPortal is an independent process of cbpManager and can be handled with the native script metaImport.py provided by cBioPortal
Fig. 2
Fig. 2
IT-Architecture of dockerized services enhancing security. The user authenticates via Keycloak and is redirected to the Docker-container of cbpManager via ShinyProxy. Behind the scene, the study files are stored in the respective subfolders of the study directory. The studies are uploaded to cBioPortal via automated upload processes. cBioPortal provides mechanisms for handling user and group rights and supports Keycloak as Identity Provider
Fig. 3
Fig. 3
Role of cbpManager in use case of a MTB. For the discussion of a patient in MTB, a molecular analysis of the tumor is performed and clinical information such as diagnosis and previous therapies are retrieved from the medical records (MR). A medical documentalist applies cbpManager to create data files suitable for the upload in cBioPortal. For this, molecular data should be prepared in a MAF format, while samples and clinical data are added via the cpbManager interface. Once imported in cBioPortal, molecular aberrations are automatically annotated and previous therapies are visualized. This facilitates the patient-specific selection of a therapy in MTB
Fig. 4
Fig. 4
Common workflow for the use of the cbpManager. The blue arrows symbolize the individual pages of the cbpManager from top to bottom. The text boxes explain the function of the respective page. At the beginning, there are the pages that have to be edited compulsorily. Afterwards, the pages follow, which can be supplemented depending upon existing data
Fig. 5
Fig. 5
Study page of cbpManager. A An overview over cbpManager’s first page allowing the user to create new studies or select and load existing ones. The text fields for the addition of a new study represent meta information of the study and are later written to the meta study file. B A close up of the page showing the OncoTree table used for the cancer type selection
Fig. 6
Fig. 6
Patient page of the cbpManager representing the Patient Data of the example study Testpatient provided with the cbpManager. Three main panels contain a description, an exemplary representation of how the data is displayed in cBioPortal (Sample from cBioPortal), and the table representing Patient Data of the currently loaded study, accompanied by several buttons that allow editing the table. Only the column PATIENT_ID is mandatory, the remaining optional columns are a mix of pre-defined and customized ones
Fig. 7
Fig. 7
Exemplary dialog windows. A Dialog window triggered by the button Add patient showing an input field per existing attribute in the Patient manager table enables the user to add a new row with patient data. B Dialog window triggered by the button Import patient enables the import of patients from other studies by importing data of the selected patients into the currently loaded study. C Dialog window triggered by the button Add column(s) provides the user the possibility to add a custom column to the Patient manager table. A custom column requires a column name, a short name, a long name, and the data type of the column. The data type can be numeric, boolean, or a character string. D The dialog window triggered by the button Add column(s) alternatively enables the user to add predefined columns to the Patient manager table
Fig. 8
Fig. 8
Timeline page of the cbpManager representing the Timeline Data. The page is divided in six panels containing 1) a description (collapsed panel—blue box), 2) an exemplary image of the cBioPortal representation (red box), 3) a panel for managing dates of first diagnosis (green box), 4) a panel containing tab separated timeline track manager (yellow box), 5) a panel for the addition and selection of further timeline tracks (violet box), and 6) a panel where the table of the selected custom timeline track is shown (brown box)

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