Development of Phenotyping Algorithms for the Identification of Organ Transplant Recipients: Cohort Study.

Lee Wheless,Laura Baker,Nimay Anand,Allison Hanlon,Mary-Margaret Chren,Kelly Birdwell,Lavar Edwards

doi:10.2196/18001

Abstract

BackgroundStudies involving organ transplant recipients (OTRs) are often limited to the variables collected in the national Scientific Registry of Transplant Recipients database. Electronic health records contain additional variables that can augment this data source if OTRs can be identified accurately.ObjectiveThe aim of this study was to develop phenotyping algorithms to identify OTRs from electronic health records.MethodsWe used Vanderbilt’s deidentified version of its electronic health record database, which contains nearly 3 million subjects, to develop algorithms to identify OTRs. We identified all 19,817 individuals with at least one International Classification of Diseases (ICD) or Current Procedural Terminology (CPT) code for organ transplantation. We performed a chart review on 1350 randomly selected individuals to determine the transplant status. We constructed machine learning models to calculate positive predictive values and sensitivity for combinations of codes by using classification and regression trees, random forest, and extreme gradient boosting algorithms.ResultsOf the 1350 reviewed patient charts, 827 were organ transplant recipients while 511 had no record of a transplant, and 12 were equivocal. Most patients with only 1 or 2 transplant codes did not have a transplant. The most common reasons for being labeled a nontransplant patient were the lack of data (229/511, 44.8%) or the patient being evaluated for an organ transplant (174/511, 34.1%). All 3 machine learning algorithms identified OTRs with overall >90% positive predictive value and >88% sensitivity.ConclusionsElectronic health records linked to biobanks are increasingly used to conduct large-scale studies but have not been well-utilized in organ transplantation research. We present rigorously evaluated methods for phenotyping OTRs from electronic health records that will enable the use of the full spectrum of clinical data in transplant research. Using several different machine learning algorithms, we were able to identify transplant cases with high accuracy by using only ICD and CPT codes.

Highlights

The Scientific Registry for Transplant Recipients (SRTR) is an outstanding resource for studies of organ transplant recipients (OTRs)
We present rigorously evaluated methods for phenotyping OTRs from electronic health records that will enable the use of the full spectrum of clinical data in transplant research
Most studies seeking broader data have attempted to link electronic health record (EHR) data to the SRTR [9,10,11]. This approach can be problematic because to protect patient privacy according to the Health Insurance Portability and Accountability Act, the linkage is done by the SRTR management team, with new identifiers returned to the investigator

Summary

Introduction

The Scientific Registry for Transplant Recipients (SRTR) is an outstanding resource for studies of organ transplant recipients (OTRs). Most studies seeking broader data have attempted to link EHR data to the SRTR [9,10,11] This approach can be problematic because to protect patient privacy according to the Health Insurance Portability and Accountability Act, the linkage is done by the SRTR management team, with new identifiers returned to the investigator. These new identifiers preclude linkage back for updating or correcting records or linking to deidentified genetic databases. Studies involving organ transplant recipients (OTRs) are often limited to the variables collected in the national Scientific Registry of Transplant Recipients database. Electronic health records contain additional variables that can augment this data source if OTRs can be identified accurately

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Conclusion