Abstract A024: MatchMiner: An open-source computational platform for genomically-driven matching of cancer patients to precision medicine clinical trials
Authors: Mazor Tali , Keller Rachel B , Kumari Priti , Lindsay James , Marriott Eric , Ovalle Andrea , Siegel Ethan , Williams Elizabeth H , Yu Joyce , Hassett Michael , Cerami Ethan 
Published: March 2020

To facilitate interpretation of complex tumor sequencing data and clinical trial genomic eligibility criteria, we developed MatchMiner, an open-source platform to computationally match cancer patients to precision medicine clinical trials based on clinical and genomic features. MatchMiner supports two distinct workflows: (1) a patient-centric mode, in which an oncologist can find clinical trial matches for a specific patient, and (2) a trial-centric mode, in which a clinical trial investigator can identify and recruit patients for a specific trial. MatchMiner has been operational at Dana-Farber Cancer Institute since early 2017. There are currently 250+ trials curated in the system and genomic data from 24,000+ patients. Over 82% of living patients match to at least one open clinical trial, with an average of 6 trial matches per patient. At least 85 patients have enrolled on a clinical trial as a result of MatchMiner. The MatchMiner open-source software package is available through GitHub (https://github.com/dfci/matchminer). MatchMiner is a two-tier web application with a Python-based REST application programming interface (API) server and an AngularJS front-end. MatchMiner utilizes Security Assertion Markup Language (SAML)-based authentication and, when hosted behind a secure institutional firewall, is fully HIPAA-compliant. MatchMiner can connect to existing clinical systems, including clinical trial management systems for real-time trial status. To enable computational matching to clinical trials, we developed clinical trial markup language (CTML), a structured format to encode detailed information about a trial. CTML utilizes boolean logic to define clinical (e.g. cancer type), demographic (e.g. age) and genomic (e.g. specific mutations, copy number alterations, structural variants or mutational signatures) eligibility, which can be applied to individual arms of a trial. We recently refactored the core matching algorithm (the matchengine), which improves upon the original matchengine in several ways. While the original matchengine reported the reason for a patient-trial match, the refactored matchengine provides additional, more granular details. In addition, the original matchengine ran at the cohort level, matching all patients to all trials, whereas the refactored matchengine can also run against individual patients or trials, speeding up the matching process. The refactored matchengine is also easily extensible to match based on additional data types. In summary, we have defined a standard for encoding clinical trial information in a structured and computable form, and we have developed an open-source computational trial matching platform to support patient-specific trial identification as well as trial-specific patient recruitment. We are actively collaborating with clinical groups at Dana-Farber Cancer Institute to understand the role of MatchMiner in their clinical workflows, and we are committed to continuing to evolve MatchMiner to meet clinical needs.

Citation Format: Tali Mazor, Rachel B Keller, Priti Kumari, James Lindsay, Eric Marriott, Andrea Ovalle, Ethan Siegel, Elizabeth H Williams, Joyce Yu, Michael Hassett, Ethan Cerami. MatchMiner: An open-source computational platform for genomically-driven matching of cancer patients to precision medicine clinical trials [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A024. doi:10.1158/1535-7163.TARG-19-A024