Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts

• Published in: PloS one Vol. 10; no. 8; p. e0136651
• Main Authors: Liao, Katherine P., Ananthakrishnan, Ashwin N., Kumar, Vishesh, Xia, Zongqi, Cagan, Andrew, Gainer, Vivian S., Goryachev, Sergey, Chen, Pei, Savova, Guergana K., Agniel, Denis, Churchill, Susanne, Lee, Jaeyoung, Murphy, Shawn N., Plenge, Robert M., Szolovits, Peter, Kohane, Isaac, Shaw, Stanley Y., Karlson, Elizabeth W., Cai, Tianxi
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 24.08.2015; Public Library of Science (PLoS)
• Subjects: Adult; Aged; Algorithms; Analysis; Arthritis; Arthritis, Rheumatoid - complications; Arthritis, Rheumatoid - epidemiology; Arthritis, Rheumatoid - physiopathology; Cardiology; Cardiovascular disease; Cardiovascular diseases; Chronic diseases; Classification; Computerized physician order entry; Coronary artery; Coronary artery disease; Coronary Artery Disease - complications; Coronary Artery Disease - epidemiology; Coronary Artery Disease - physiopathology; Coronary heart disease; Coronary vessels; Diabetes; Diabetes mellitus; Diabetes Mellitus - epidemiology; Diabetes Mellitus - physiopathology; Electronic Health Records; Electronic medical records; Electronic records; Female; Genetic aspects; Genotype & phenotype; Health informatics; Health risks; Heart; Heart diseases; Hospitals; Humans; Hyperlipidemias - complications; Hyperlipidemias - epidemiology; Hyperlipidemias - physiopathology; Inflammatory bowel disease; Inflammatory bowel diseases; Inflammatory Bowel Diseases - complications; Inflammatory Bowel Diseases - epidemiology; Inflammatory Bowel Diseases - physiopathology; Intestine; Laboratories; Male; Medical electronics; Medical records; Medical schools; Middle Aged; Natural Language Processing; Patients; Phenotype; Phenotypes; Population studies; Populations; Rheumatic diseases; Rheumatism; Rheumatoid arthritis; Rheumatoid factor; Rheumatology; Risk analysis; Risk Factors; Sensitivity; Studies; Systematic review; Womens health; United States; United States > US; Massachusetts
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0136651

Typically, algorithms to classify phenotypes using electronic medical record (EMR) data were developed to perform well in a specific patient population. There is increasing interest in analyses which can allow study of a specific outcome across different diseases. Such a study in the EMR would require an algorithm that can be applied across different patient populations. Our objectives were: (1) to develop an algorithm that would enable the study of coronary artery disease (CAD) across diverse patient populations; (2) to study the impact of adding narrative data extracted using natural language processing (NLP) in the algorithm. Additionally, we demonstrate how to implement CAD algorithm to compare risk across 3 chronic diseases in a preliminary study. We studied 3 established EMR based patient cohorts: diabetes mellitus (DM, n = 65,099), inflammatory bowel disease (IBD, n = 10,974), and rheumatoid arthritis (RA, n = 4,453) from two large academic centers. We developed a CAD algorithm using NLP in addition to structured data (e.g. ICD9 codes) in the RA cohort and validated it in the DM and IBD cohorts. The CAD algorithm using NLP in addition to structured data achieved specificity >95% with a positive predictive value (PPV) 90% in the training (RA) and validation sets (IBD and DM). The addition of NLP data improved the sensitivity for all cohorts, classifying an additional 17% of CAD subjects in IBD and 10% in DM while maintaining PPV of 90%. The algorithm classified 16,488 DM (26.1%), 457 IBD (4.2%), and 245 RA (5.0%) with CAD. In a cross-sectional analysis, CAD risk was 63% lower in RA and 68% lower in IBD compared to DM (p<0.0001) after adjusting for traditional cardiovascular risk factors. We developed and validated a CAD algorithm that performed well across diverse patient populations. The addition of NLP into the CAD algorithm improved the sensitivity of the algorithm, particularly in cohorts where the prevalence of CAD was low. Preliminary data suggest that CAD risk was significantly lower in RA and IBD compared to DM.