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MatchMiner: An open source computational platform for real-time matching of cancer patients to precision medicine clinical trials using genomic and clinical criteria

By James Lindsay, Catherine Del Vecchio Fitz, Zachary Zwiesler, Priti Kumari, Bernd Van Der Veen, Tamba Monrose, Tali Mazor, Susan Barry, Adem Albayrak, Michael Tung, Khanh Do, Suzanne Hector-Barry, Brian Beardslee, Geoffrey Shapiro, John Methot, Lynette Sholl, Laura E. MacConaill, Neil Lindeman, Bruce Johnson, Barrett Rollins, Chris Sander, Michael Hassett, Ethan Cerami

Posted 11 Oct 2017
bioRxiv DOI: 10.1101/199489

Background: Molecular profiling of cancers is now routine at many cancer centers, and the number of precision cancer medicine clinical trials, which are informed by profiling, is steadily rising. Additionally, these trials are becoming increasingly complex, often having multiple arms and many genomic eligibility criteria. Currently, it is a challenging for physicians to match patients to relevant clinical trials using the patient's genomic profile, which can lead to missed opportunities. Automated matching against uniformly structured and encoded genomic eligibility criteria is essential to keep pace with the complex landscape of precision medicine clinical trials. Results: To meet these needs, we built and deployed an automated clinical trial matching platform called MatchMiner at the Dana-Farber Cancer Institute (DFCI). The platform has been integrated with Profile, DFCI's enterprise genomic profiling project, which contains tumor profile data for >20,000 patients, and has been made available to physicians across the Institute. As no current standard exists for encoding clinical trial eligibility criteria, a new language called Clinical Trial Markup Language (CTML) was developed, and over 178 genomically-driven clinical trials were encoded using this language. The platform is open source and freely available for adoption by other institutions. Conclusion: MatchMiner is the first open platform developed to enable computational matching of patient-specific genomic profiles to precision cancer medicine clinical trials. Creating MatchMiner required developing clinical trial eligibility standards to support genome-driven matching and developing intuitive interfaces to support practical use-cases. Given the complexity of tumor profiling and the rapidly changing multi-site nature of genome-driven clinical trials, open source software is the most efficient, scalable, and economical option for matching cancer patients to clinical trials.

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