Enhancing data integrity in Electronic Health Records: Review of methods for handling missing data

Abstract Introduction Electronic Health Records (EHRs) are vital repositories of patient information for medical research, but the prevalence of missing data presents an obstacle to the validity and reliability of research. This study aimed to review and category ise methods for handling missing data in EHRs, to help researchers better understand and address the challenges related to missing data in EHRs. Materials and Methods This study employed scoping review methodology. Through systematic searches on EMBASE up to October 2023, including review articles and original studies, relevant literature was identified. After removing duplicates, titles and abstracts were screened against inclusion criteria, followed by full-text assessment. Additional manual searches and reference list screenings were conducted. Data extraction focused on imputation techniques, dataset characteristics, assumptions about missing data, and article types. Additionally, we explored the availability of code within widely used software applications. Results We reviewed 101 articles, with two exclusions as duplicates. Of the 99 remaining documents, 21 underwent full-text screening, with nine deemed eligible for data extraction. These articles introduced 31 imputation approaches classified into ten distinct methods, ranging from simple techniques like Complete Case Analysis to more complex methods like Multiple Imputation, Maximum Likelihood, and Expectation-Maximization algorithm. Additionally, machine learning methods were explored. The different imputation methods, present varying reliability. We identified a total of 32 packages across the four software platforms (R, Python, SAS, and Stata) for imputation methods. However, it’s significant that machine learning methods for imputation were not found in specific packages for SAS and Stata. Out of the 9 imputation methods we investigated, package implementations were available for 7 methods in all four software platforms. Conclusions Several methods to handle missing data in EHRs are available. These methods range in complexity and make different assumptions about the missing data mechanisms. Knowledge gaps remain, notably in handling non-monotone missing data patterns and implementing imputation methods in real-world healthcare settings under the Missing Not at Random assumption. Future research should prioritize refining and directly comparing existing methods.