Natural Language Processing Combined with ICD-9-CM Codes as a Novel Method to Study the Epidemiology of Allergic Drug Reactions

Natural Language Processing Combined with ICD-9-CM Codes as a Novel Method to Study the Epidemiology of Allergic Drug Reactions:

Publication date: Available online 16 December 2019

Source: The Journal of Allergy and Clinical Immunology: In Practice

Author(s): Aleena Banerji, Kenneth H. Lai, Yu Li, Rebecca R. Saff, Carlos A. Camargo, Kimberly G. Blumenthal, Li Zhou

Abstract

Background

Allergic drug reaction epidemiologic data are sparse because it remains difficult to identify true cases in large datasets using manual chart review.

Objective

To develop and validate a novel informatics method based on natural language processing (NLP) in combination with ICD-9-CM codes that identifies allergic drug reactions in the electronic health record (EHR).

Methods

Previously studied and high-yield ICD-9-CM codes were used to screen for possible allergic drug reactions among all inpatients admitted in 2007 and 2008. A random sample was selected for manual chart review to identify true cases of allergic drug reactions. A rule-based NLP algorithm was then developed to identify allergic drug reactions using free-text clinical notes and discharge summaries from the filtered cases. The performance of using manual chart review of ICD-9-CM codes alone was compared to ICD-9-CM codes in combination with NLP.

Results

Of 3,907 cases identified by ICD-9-CM codes, 725 (19%) were randomly selected for manual chart review; 335 were confirmed as allergic drug reactions, resulting in a positive predictive value (PPV) of 46% (range: 18%-79%) when using ICD-9-CM codes alone. Our NLP algorithm in combination with ICD-9-CM codes achieved a PPV of 86% (range: 69% -100%). Among the 335 confirmed positive cases, NLP identified 259 true cases, resulting in a recall/sensitivity of 77% (range: 26%-100%). Among the 390 negative cases, NLP achieved a specificity of 89% (range: 69%-100%).

Conclusion

Using NLP with ICD-9-CM codes improved identification of allergic drug reactions. The resulting decrease in manual chart review effort will facilitate large epidemiology studies of this understudied area.