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

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.

MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

“…cBioPortal is an open platform for exploring, visualizing, and analyzing multidimensional cancer genomics data and thus supports the translation of large data sets into biological insights and clinical applications [ 56 , 57 ]. For this reason, we have extended cBioPortal according to the needs of the MTB stakeholders [ 13 ] within the context of the MIRACUM consortium [ 60 , 61 , 62 ]. The upload is performed as follows: variants are exported in the mutation annotation format, the copy number variations as discrete copy number values and segmented data, and RNA fusions as structural variants.…”

“…Cancers 2023, 15, x FOR PEER REVIEW 9 of 14 information on the approval status of a given drug based on the European Medicines Agency (EMA). The extended cBioPortal even offers the possibility to search directly for clinical trials involving the patient's genetic alterations through an extension of Clincal-Trials.gov (Figure S2) [60]. Furthermore, the clinician can use cBioPortal's powerful virtual trial options to identify similar patients who have already been discussed with the option of documenting therapy recommendations based on the genetic findings generated by MIRACUM-Pipe, thus creating evidence for further similar individual therapeutic trials.…”

Construction of diagnostic and prognostic models based on gene signatures of nasopharyngeal carcinoma by machine learning methods

“…To further explore the value of prognostic gene signatures, the cBioPortal online website ( http://www.cbioportal.org/ ; accessed 4 February 2023) was used to analyze the mutation profile of prognostic gene signatures in patients ( 29 ).…”

Increased expression and immune cell infiltration of E2F1/2 collerate with better prognosis in thyroid cancer

“…cBioPortal (https://www.cbioportal.org) is a comprehensive web resource for analyzing cancer genomics based on TCGA database [14]. Genetic alterations and survival module of E2Fs family members were obtained from cBioPortal.…”