CUSTOM-SEQ: A prototype for oncology rapid learning in a comprehensive EHR environment

Jeremy L. Warner*, Lucy Wang, William Pao, Jeffrey A. Sosman, Ravi V. Atreya, Pam Carney, Mia A. Levy

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Background: As targeted cancer therapies and molecular profiling become widespread, the era of "precision oncology" is at hand. However, cancer genomes are complex, making mutation-specific outcomes difficult to track. We created a proof-of-principle, CUSTOM-SEQ: Continuously Updating System for Tracking Outcome by Mutation, to Support Evidence-based Querying, to automatically calculate and display mutation-specific survival statistics from electronic health record data. Methods: Patients with cancer genotyping were included, and clinical data was extracted through a variety of algorithms. Results were refreshed regularly and injected into a standard reporting platform. Significant results were highlighted for visual cueing. A subset was additionally stratified by stage, smoking status, and treatment exposure. Results: By August 2015, 4310 patients with a median follow-up of 17 months had sufficient data for survival calculation. As expected, epidermal growth factor receptor (EGFR) mutations in lung cancer were associated with superior overall survival, hazard ratio (HR)=0.53 (P <. 001), validating the approach. Guanine nucleotide binding protein (G protein), q polypeptide (GNAQ) mutations in melanoma were associated with inferior overall survival, a novel finding (HR=3.42, P < .001). Smoking status was not prognostic for epidermal growth factor receptor-mutated lung cancer patients, who also lived significantly longer than their counterparts, even with advanced disease (HR=0.54, P=.001). Interpretation: CUSTOM-SEQ represents a novel rapid learning system for a precision oncology environment. Retrospective studies are often limited by study of specific time periods and can lead to incomplete conclusions. Because data is continuously updated in CUSTOM-SEQ, the evidence base is constantly growing. Future work will allow users to interactively explore populations by demographics and treatment exposure, in order to further investigate significant mutation-specific signals.

Original languageEnglish (US)
Pages (from-to)692-700
Number of pages9
JournalJournal of the American Medical Informatics Association
Issue number4
StatePublished - Jul 2016


  • Electronic health records
  • Genomics
  • Health information management
  • Information science
  • Neoplasms
  • Precision medicine

ASJC Scopus subject areas

  • Health Informatics

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