Using Large Language Models to Determine Reasons for Missed Colon Cancer Screening Follow-Up

Abstract

Abstract Importance Identifying reasons for missed preventive care, such as follow-up colonoscopy after an abnormal stool-based colon cancer screening test, is critical for quality improvement initiatives. However, manual chart review to extract this information from unstructured clinical notes is time-consuming and costly. Objective To determine whether a large language model (LLM) can accurately extract reasons for a lack of follow-up colonoscopy after abnormal outpatient fecal immunohistochemical test (FIT) or fecal occult blood test (FOBT). Design Cross-sectional study. Setting University of California, San Francisco (UCSF). Participants Adult patients aged 45 years or older with an abnormal outpatient FIT/FOBT between 2012 and 2024 who did not undergo a colonoscopy within 90 days of the abnormal test. Exposure We investigate the potential of an LLM to determine whether reasons for a lack of follow-up colonoscopy are documented in the clinical notes and whether an LLM can accurately classify those reasons into clinically meaningful categories. Main Outcomes and Measures Accuracy score was calculated to evaluate LLM performance against a 10% subsample manually classified by a physician reviewer. Results From a total of 2164 patients with abnormal FIT/FOBTs performed at UCSF during the study period, 355 (16.4%) underwent a colonoscopy within 90 days of the abnormal test. Among those who did not receive a colonoscopy within 90 days, 846 patients were eligible for the main analysis. Based on LLM categorization of patient note content, 270 (31.9%) patients did not have any reference to colonoscopy/colorectal cancer screening in their notes, 379 (44.8%) patients had mentions of colonoscopy/colorectal cancer screening without explicit reasons for not having a colonoscopy provided, and 197 (23.3%) patients had notes detailing explicit reasons for not having a colonoscopy. Overall LLM classification accuracy was 89.3%. The most common reasons for not having a colonoscopy included: Refused/not interested (n = 96; 35.2%), Comorbidities (n = 51; 18.7%), and Patient Unavailable (n = 46; 16.8%). Conclusions and Relevance This study suggests that an LLM can accurately identify and categorize reasons for the absence of follow-up colonoscopy after an abnormal FIT/FOBT. Our results suggest that LLMs have the potential to automate chart review for quality improvement initiatives.

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