Leveraging error-prone algorithm-derived phenotypes: Enhancing association studies for risk factors in EHR data

Abstract

Objectives

It has become increasingly common for multiple computable phenotypes from electronic health records (EHR) to be developed for a given phenotype. However, EHR-based association studies often focus on a single phenotype. In this paper, we develop a method aiming to simultaneously make use of multiple EHR-derived phenotypes for reduction of bias due to phenotyping error and improved efficiency of phenotype/exposure associations.

Materials and Methods

The proposed method combines multiple algorithm-derived phenotypes with a small set of validated outcomes to reduce bias and improve estimation accuracy and efficiency. The performance of our method was evaluated through simulation studies and real-world application to an analysis of colon cancer recurrence using EHR data from Kaiser Permanente Washington.

Results

In settings where there was no single surrogate performing uniformly better than all others in terms of both sensitivity and specificity, our method achieved substantial bias reduction compared to using a single algorithm-derived phenotype. Our method also led to higher estimation efficiency by up to 30% compared to an estimator that used only one algorithm-derived phenotype.

Discussion

Simulation studies and application to real-world data demonstrated the effectiveness of our method in integrating multiple phenotypes, thereby enhancing bias reduction, statistical accuracy and efficiency.

Conclusions

Our method combines information across multiple surrogates using a statistically efficient seemingly unrelated regression framework. Our method provides a robust alternative to single-surrogate-based bias correction, especially in contexts lacking information on which surrogate is superior.