ClinicalOmicsDB: Exploring Molecular Associations of Oncology Drug Responses in Clinical Trials

Authors

Chang In Moon
John Michael Elizarraras
Jonathan Thomas Lei
Byron Jia
Bing Zhang

Publication Date

1-5-2024

Journal

Nucleic Acids Research

DOI

10.1093/nar/gkad871

PMID

37811874

PMCID

PMC10767859

PubMedCentral® Posted Date

10-9-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

Humans, Databases, Factual, Gene Expression Profiling, Neoplasms, Software, Tumor Microenvironment, Clinical Trials as Topic

Abstract

Matching patients to optimal treatment is challenging, in part due to the limited availability of real-world clinical datasets for predictive biomarker identification. The growing integration of omics profiling into clinical trials presents a new opportunity to tackle this challenge. Here, we introduce ClinicalOmicsDB, a web application for exploring molecular associations of oncology drug responses in clinical trials. This database includes transcriptomic data from 40 clinical trial studies, with 5913 patients spanning 11 cancer types. These studies include 67 treatment arms with a variety of chemotherapy, targeted therapy and immunotherapy drugs, and their combinations, which we organize based on an established ontology for easier navigation. The web application provides users with three options to explore molecular associations of oncology drug responses, focusing on studies, treatments or genes, respectively. Gene set analysis further connects treatment response to pathway activity and tumor microenvironment attributes. The user-friendly web interface of ClinicalOmicsDB streamlines interactive analysis. A Rust-based backend speeds up response time, and application programming interfaces and an R package enable programmatic access. We use three case studies to demonstrate the utility of this resource in human cancer studies. ClinicalOmicsDB is freely available at http://trials.linkedomics.org/