Characterizing variability of electronic health record-driven phenotype definitions

OBJECTIVE

The aim of this study was to analyze a publicly available sample of rule-based phenotype definitions to characterize and evaluate the variability of logical constructs used.

MATERIALS AND METHODS

A sample of 33 preexisting phenotype definitions used in research that are represented using Fast Healthcare Interoperability Resources and Clinical Quality Language (CQL) was analyzed using automated analysis of the computable representation of the CQL libraries.

RESULTS

Most of the phenotype definitions include narrative descriptions and flowcharts, while few provide pseudocode or executable artifacts. Most use 4 or fewer medical terminologies. The number of codes used ranges from 5 to 6865, and value sets from 1 to 19. We found that the most common expressions used were literal, data, and logical expressions. Aggregate and arithmetic expressions are the least common. Expression depth ranges from 4 to 27.

DISCUSSION

Despite the range of conditions, we found that all of the phenotype definitions consisted of logical criteria, representing both clinical and operational logic, and tabular data, consisting of codes from standard terminologies and keywords for natural language processing. The total number and variety of expressions are low, which may be to simplify implementation, or authors may limit complexity due to data availability constraints.

CONCLUSIONS

The phenotype definitions analyzed show significant variation in specific logical, arithmetic, and other operators but are all composed of the same high-level components, namely tabular data and logical expressions. A standard representation for phenotype definitions should support these formats and be modular to support localization and shared logic.

Prediction of left ventricular ejection fraction changes in heart failure patients using machine learning and electronic health records: a multi-site study

Left ventricular ejection fraction (EF) is a key measure in the diagnosis and treatment of heart failure (HF) and many patients experience changes in EF overtime. Large-scale analysis of longitudinal changes in EF using electronic health records (EHRs) is limited. In a multi-site retrospective study using EHR data from three academic medical centers, we investigated longitudinal changes in EF measurements in patients diagnosed with HF. We observed significant variations in baseline characteristics and longitudinal EF change behavior of the HF cohorts from a previous study that is based on HF registry data. Data gathered from this longitudinal study were used to develop multiple machine learning models to predict changes in ejection fraction measurements in HF patients. Across all three sites, we observed higher performance in predicting EF increase over a 1-year duration, with similarly higher performance predicting an EF increase of 30% from baseline compared to lower percentage increases. In predicting EF decrease we found moderate to high performance with low confidence for various models. Among various machine learning models, XGBoost was the best performing model for predicting EF changes. Across the three sites, the XGBoost model had an F1-score of 87.2, 89.9, and 88.6 and AUC of 0.83, 0.87, and 0.90 in predicting a 30% increase in EF, and had an F1-score of 95.0, 90.6, 90.1 and AUC of 0.54, 0.56, 0.68 in predicting a 30% decrease in EF. Among features that contribute to predicting EF changes, baseline ejection fraction measurement, age, gender, and heart diseases were found to be statistically significant.

Design and validation of a FHIR-based EHR-driven phenotyping toolbox

OBJECTIVES

To develop and validate a standards-based phenotyping tool to author electronic health record (EHR)-based phenotype definitions and demonstrate execution of the definitions against heterogeneous clinical research data platforms.

MATERIALS AND METHODS

We developed an open-source, standards-compliant phenotyping tool known as the PhEMA Workbench that enables a phenotype representation using the Fast Healthcare Interoperability Resources (FHIR) and Clinical Quality Language (CQL) standards. We then demonstrated how this tool can be used to conduct EHR-based phenotyping, including phenotype authoring, execution, and validation. We validated the performance of the tool by executing a thrombotic event phenotype definition at 3 sites, Mayo Clinic (MC), Northwestern Medicine (NM), and Weill Cornell Medicine (WCM), and used manual review to determine precision and recall.

RESULTS

An initial version of the PhEMA Workbench has been released, which supports phenotype authoring, execution, and publishing to a shared phenotype definition repository. The resulting thrombotic event phenotype definition consisted of 11 CQL statements, and 24 value sets containing a total of 834 codes. Technical validation showed satisfactory performance (both NM and MC had 100% precision and recall and WCM had a precision of 95% and a recall of 84%).

CONCLUSIONS

We demonstrate that the PhEMA Workbench can facilitate EHR-driven phenotype definition, execution, and phenotype sharing in heterogeneous clinical research data environments. A phenotype definition that integrates with existing standards-compliant systems, and the use of a formal representation facilitates automation and can decrease potential for human error.

Development of a repository of computable phenotype definitions using the clinical quality language

OBJECTIVE

The objective of this study is to create a repository of computable, technology-agnostic phenotype definitions for the purposes of analysis and automatic cohort identification.

MATERIALS AND METHODS

We selected phenotype definitions from PheKB and excluded definitions that did not use structured data or were not used in published research. We translated these definitions into the Clinical Quality Language (CQL) and Fast Healthcare Interoperability Resources (FHIR) and validated them using code review and automated tests.

RESULTS

A total of 33 phenotype definitions met our inclusion criteria. We developed 40 CQL libraries, 231 value sets, and 347 test cases. To support these test cases, a total of 1624 FHIR resources were created as test data.

DISCUSSION AND CONCLUSION

Although a number of challenges were encountered while translating the phenotypes into structured form, such as requiring specialized knowledge, or imprecise, ambiguous, and conflicting language, we have created a repository and a development environment that can be used for future research on computable phenotypes.

CQL4NLP: Development and Integration of FHIR NLP Extensions in Clinical Quality Language for EHR-driven Phenotyping

Lack of standardized representation of natural language processing (NLP) components in phenotyping algorithms hinders portability of the phenotyping algorithms and their execution in a high-throughput and reproducible manner. The objective of the study is to develop and evaluate a standard-driven approach - CQL4NLP - that integrates a collection of NLP extensions represented in the HL7 Fast Healthcare Interoperability Resources (FHIR) standard into the clinical quality language (CQL). A minimal NLP data model with 11 NLP-specific data elements was created, including six FHIR NLP extensions. All 11 data elements were identified from their usage in real-world phenotyping algorithms. An NLP ruleset generation mechanism was integrated into the NLP2FHIR pipeline and the NLP rulesets enabled comparable performance for a case study with the identification of obesity comorbidities. The NLP ruleset generation mechanism created a reproducible process for defining the NLP components of a phenotyping algorithm and its execution.

Toward cross-platform electronic health record-driven phenotyping using Clinical Quality Language

INTRODUCTION

Electronic health record (EHR)-driven phenotyping is a critical first step in generating biomedical knowledge from EHR data. Despite recent progress, current phenotyping approaches are manual, time-consuming, error-prone, and platform-specific. This results in duplication of effort and highly variable results across systems and institutions, and is not scalable or portable. In this work, we investigate how the nascent Clinical Quality Language (CQL) can address these issues and enable high-throughput, cross-platform phenotyping.

METHODS

We selected a clinically validated heart failure (HF) phenotype definition and translated it into CQL, then developed a CQL execution engine to integrate with the Observational Health Data Sciences and Informatics (OHDSI) platform. We executed the phenotype definition at two large academic medical centers, Northwestern Medicine and Weill Cornell Medicine, and conducted results verification (n = 100) to determine precision and recall. We additionally executed the same phenotype definition against two different data platforms, OHDSI and Fast Healthcare Interoperability Resources (FHIR), using the same underlying dataset and compared the results.

RESULTS

CQL is expressive enough to represent the HF phenotype definition, including Boolean and aggregate operators, and temporal relationships between data elements. The language design also enabled the implementation of a custom execution engine with relative ease, and results verification at both sites revealed that precision and recall were both 100%. Cross-platform execution resulted in identical patient cohorts generated by both data platforms.

CONCLUSIONS

CQL supports the representation of arbitrarily complex phenotype definitions, and our execution engine implementation demonstrated cross-platform execution against two widely used clinical data platforms. The language thus has the potential to help address current limitations with portability in EHR-driven phenotyping and scale in learning health systems.

Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms

With the increased adoption of electronic health records, data collected for routine clinical care is used for health outcomes and population sciences research, including the identification of phenotypes. In recent years, research networks, such as eMERGE, OHDSI and PCORnet, have been able to increase statistical power and population diversity by combining patient cohorts. These networks share phenotype algorithms that are executed at each participating site. Here we observe experiences with phenotype algorithm portability across seven research networks and propose a generalizable framework for phenotype algorithm portability. Several strategies exist to increase the portability of phenotype algorithms, reducing the implementation effort needed by each site. These include using a common data model, standardized representation of the phenotype algorithm logic, and technical solutions to facilitate federated execution of queries. Portability is achieved by tradeoffs across three domains: Data, Authoring and Implementation, and multiple approaches were observed in representing portable phenotype algorithms. Our proposed framework will help guide future research in operationalizing phenotype algorithm portability at scale.

Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study

While natural language processing (NLP) of unstructured clinical narratives holds the potential for patient care and clinical research, portability of NLP approaches across multiple sites remains a major challenge. This study investigated the portability of an NLP system developed initially at the Department of Veterans Affairs (VA) to extract 27 key cardiac concepts from free-text or semi-structured echocardiograms from three academic edical centers: Weill Cornell Medicine, Mayo Clinic and Northwestern Medicine. While the NLP system showed high precision and recall easurements for four target concepts (aortic valve regurgitation, left atrium size at end systole, mitral valve regurgitation, tricuspid valve regurgitation) across all sites, we found moderate or poor results for the remaining concepts and the NLP system performance varied between individual sites.