Abstract
BackgroundExtensive 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.ResultscbpManager 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).ConclusionIn 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.
Highlights
Extensive sequencing of tumor tissues has greatly improved our understanding of cancer biology over the past years
CBioPortal enables to collect and visualize the clinical data of the patient, including previous therapies, which are required for the final selection of a personalized therapy. cBioPortal can be run as a local instance and could be used in individual institutions for the documentation and interpretation of molecular aberrations in Molecular Tumor Boards (MTB)
Workflow of cbpManager In the context of an MTB use-case, cbpManager serves as a tool to manage and prepare clinical and molecular data for upload to cBioPortal, where new patients need to be added continuously and new data is generated during the course of treatment
Summary
Extensive sequencing of tumor tissues has greatly improved our understanding of cancer biology over the past years. One of the most important findings of this massive analysis of tumor samples is that molecular aberrations are not specific to tumor entities, but can be shared between different cancer types This knowledge has led to a widespread application of off-label therapies in personalized protocols. For this purpose, molecular data of single patients can be uploaded e.g. in the Mutation Annotation Format (MAF) and clinical data as plain text files with values separated by a delimiter. In order to improve the MTB workflow, facilitating the import of clinical and molecular data into a local instance of cBioPortal, we have developed the R package cbpManager
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