Requirements Analysis and Specification for a Molecular Tumor Board Platform Based on cBioPortal

Abstract

Clinicians in molecular tumor boards (MTB) are confronted with a growing amount of genetic high-throughput sequencing data. Today, at German university hospitals, these data Diagnostics 2020, 10, 93 2 of 15 are usually handled in complex spreadsheets from which clinicians have to obtain the necessary information. The aim of this work was to gather a comprehensive list of requirements to be met by cBioPortal to support processes in MTBs according to clinical needs. Therefore, oncology experts at nine German university hospitals were surveyed in two rounds of interviews. To generate an interview guideline a scoping review was conducted. For visual support in the second round, screenshot mockups illustrating the requirements from the first round were created. Requirements that cBioPortal already meets were skipped during the second round. In the end, 24 requirements with sometimes several conceivable options were identified and 54 screenshot mockups were created. Some of the identified requirements have already been suggested to the community by other users or are currently being implemented in cBioPortal. This shows, that the results are in line with the needs expressed by various disciplines. According to our findings, cBioPortal has the potential to significantly improve the processes and analyses of an MTB after the implementation of the identified requirements.

FhirSpark – Implementing a Mediation Layer to Bring FHIR to the cBioPortal for Cancer Genomics

“…As the user interface of cBioPortal is written in TypeScript, the model for therapy recommendations is backed by type definitions and can be easily exported to objects using the JavaScript Object Notation (JSON). However, this format is not conformant to any standard and is driven by the prior requirements analysis of Buechner et al [5] and type definitions of the contained TypeScript objects.…”

“…cBioPortal is an open-source tool mainly developed by the Memorial Sloan Kettering Cancer Center that provides integrated access and interfaces to more than 300 public cancer studies [3,4]. As it is designed with a data warehousing approach in mind, it lacks various features for routine use in an MTB, as evaluated in a requirements analysis by Buechner et al [5]. Adding such features is possible, but not straight forward as pointed out after a more in-depth analysis of the cBioPortal architecture [6].…”

“…An essential functionality identified by Buechner et al [5] is documenting therapy recommendations for patients directly in cBioPortal. This feature is particularly challenging as its implementation impacts not only the codebase itself but also the persistence layer to store new recommendations.…”

Gene Expression and Data Analysis Pipeline Using Cancer BioPortal in the Classroom †

“…The cBioPortal for Cancer Genomics ( https://www.cbioportal.org ), known simply as cBioPortal, is an open-access collective cancer research resource for storing and exploring clinical, genomic, proteomic, and transcriptomic data across hundreds of cancer studies and includes thousands of individual samples ( 1 ). A graphical user interface (GUI) eliminates the barrier of having to work meticulously through large and complex genomic datasets ( 2 ). Readily interpretable visualizations provide robust data analysis leading to biological insights ( 1 ).…”

Overexpression of chaperonin containing TCP1 subunit 7 has diagnostic and prognostic value for hepatocellular carcinoma.

“…Then, we analyzed the correlation between CCT7 mRNA and DNA methylation and identi ed CpG sites that affect mRNA expression in the MethSurv database, which was A web tool to perform multivariable survival analysis using DNA methylation data [27]. Next, we investigated genetic alteration and mutation hotspots of CCT7 in the Liver Hepatocellular Carcinoma (TCGA, Firehose Legacy) dataset from the cBioPortal database (http://www.cbioportal.org/) [28]. Then, we analyzed the correlation between the genetic alteration of CCT7 and the prognosis of HCC patients.…”