OCTANE: Oncology Clinical Trial Annotation Engine.

Abstract

PURPOSE:

Many targeted therapies are currently available only via clinical trials. Therefore, routine precision oncology using biomarker-based assignment to drug depends on matching patients to clinical trials. A comprehensive and up-to-date trial database is necessary for optimal patient-trial matching.

METHODS:

We describe processes for establishing and maintaining a clinical trial database, focusing on genomically informed trials. Furthermore, we present OCTANE (Oncology Clinical Trial Annotation Engine), an informatics framework supporting these processes in a scalable fashion. To illustrate how the framework can be applied at an institution, we describe how we implemented an instance of OCTANE at a large cancer center. OCTANE consists of three modules. The data aggregation module automates retrieval, aggregation, and update of trial information. The annotation module establishes the database schema, implements data integration necessary for automation, and provides an annotation interface. The update module monitors trial change logs, identifies critical change events, and alerts the annotators when manual intervention may be needed.

RESULTS:

Using OCTANE, we annotated 5,439 oncology clinical trials (4,438 genomically informed trials) that collectively were associated with 1,453 drugs, 779 genes, and 252 cancer types. To date, we have used the database to screen 4,220 patients for trial eligibility. We compared the update module with expert review, and the module achieved 98.5% accuracy, 0% false-negative rate, and 2.3% false-positive rate.

CONCLUSION:

OCTANE is a general informatics framework that can be helpful for establishing and maintaining a comprehensive database necessary for automating patient-trial matching, which facilitates the successful delivery of personalized cancer care on a routine basis. Several OCTANE components are publically available and may be useful to other precision oncology programs.

• Authors: Jia Zeng, Md Abu Shufean, Yekaterina Khotskaya, Dong Yang, Michael Kahle, Amber Johnson, Vijaykumar Holla, Nora Sánchez, Kenna R Mills Shaw, Elmer V Bernstam, Funda Meric-Bernstam
• Journal: JCO clinical cancer informatics (JCO Clin Cancer Inform) Vol. 3 Pg. 1-11 (07 2019) ISSN: 2473-4276 [Electronic] United States
• PMID: 31265323 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Topics

• Clinical Trials as Topic
• Databases, Factual
• Decision Support Systems, Clinical
• Humans
• Medical Informatics (methods)
• Medical Oncology (methods)
• Neoplasms (diagnosis, etiology, therapy)
• Precision Medicine (methods)
• Search Engine
• Software
• Software Design
• Web Browser