Automated Extraction of Tumor Staging and Diagnosis Information From Surgical Pathology Reports

Typically stored as unstructured notes, surgical pathology reports contain data elements valuable to cancer research that require labor-intensive manual extraction. Although studies have described natural language processing (NLP) of surgical pathology reports to automate information extraction, efforts have focused on specific cancer subtypes rather than across multiple oncologic domains. To address this gap, we developed and evaluated an NLP method to extract tumor staging and diagnosis information across multiple cancer subtypes.

The NLP pipeline was implemented on an open-source framework called Leo. We used a total of 555,681 surgical pathology reports of 329,076 patients to develop the pipeline and evaluated our approach on subsets of reports from patients with breast, prostate, colorectal, and randomly selected cancer subtypes.

Averaged across all four cancer subtypes, the NLP pipeline achieved an accuracy of 1.00 for International Classification of Diseases, Tenth Revision codes, 0.89 for T staging, 0.90 for N staging, and 0.97 for M staging. It achieved an F1 score of 1.00 for International Classification of Diseases, Tenth Revision codes, 0.88 for T staging, 0.90 for N staging, and 0.24 for M staging.

The NLP pipeline was developed to extract tumor staging and diagnosis information across multiple cancer subtypes to support the research enterprise in our institution. Although it was not possible to demonstrate generalizability of our NLP pipeline to other institutions, other institutions may find value in adopting a similar NLP approach-and reusing code available at GitHub-to support the oncology research enterprise with elements extracted from surgical pathology reports.