Dataset Information

Applying computable phenotypes within a common data model to identify heart failure patients for an implantable cardiac device registry.

ABSTRACT:

Background

Use of existing data in electronic health records (EHRs) could be used more extensively to better leverage real world data for clinical studies, but only if standard, reliable processes are developed. Numerous computable phenotypes have been validated against manual chart review, and common data models (CDMs) exist to aid implementation of such phenotypes across platforms and sites. Our objective was to measure consistency between data that had previously been manually collected for an implantable cardiac device registry and CDM-based phenotypes for the condition of heart failure (HF).

Methods

Patients enrolled in an implantable cardiac device registry at two hospitals from 2013 to 2018 contributed to this analysis wherein registry data were compared to PCORnet CDM-formatted EHR data. Seven different phenotype algorithms were used to search for the presence of HF and compare the results with the registry. Sensitivity, specificity, predictive value and congruence were calculated for each phenotype.

Results

In the registry, 176 of 319 (55%) patients had history of HF, compared with different phenotypes estimating between 96 (30%) and 188 (59%). The least-restrictive phenotypes (any diagnosis) had high sensitivity and specificity (90%/80%), but more restrictive phenotypes had higher specificity (e.g., code present in problem list, 94%). Differences were observed using time-based criteria (e.g., days between visit diagnoses) and between participating hospitals.

Conclusions

Consistency between manually-collected registry data and CDM-based phenotypes for history of HF was high overall, but use of different phenotypes impacted sensitivity and specificity, and results may differ depending on the medical condition of interest.

SUBMITTER: Graham J

PROVIDER: S-EPMC8861122 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Publications

Applying computable phenotypes within a common data model to identify heart failure patients for an implantable cardiac device registry.

Graham Jove J Iverson Andy A Monteiro Joao J Weiner Katherine K Southall Kara K Schiller Katherine K Gupta Mudit M Simard Edgar P EP

International journal of cardiology. Heart & vasculature 20220219

<h4>Background</h4>Use of existing data in electronic health records (EHRs) could be used more extensively to better leverage real world data for clinical studies, but only if standard, reliable processes are developed. Numerous computable phenotypes have been validated against manual chart review, and common data models (CDMs) exist to aid implementation of such phenotypes across platforms and sites. Our objective was to measure consistency between data that had previously been manually collect ...[more]

PMID: 35242997

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Project description:The purpose of this analysis was to develop and validate computable phenotypes for heart failure (HF) with preserved ejection fraction (HFpEF) using claims-type measures using the Rochester Epidemiology Project. This retrospective study utilized an existing cohort of Olmsted County, Minnesota residents aged ≥ 20 years diagnosed with HF between 2007 and 2015. The gold standard definition of HFpEF included meeting the validated Framingham criteria for HF and having an LVEF ≥ 50%. Computable phenotypes of claims-type data elements (including ICD-9/ICD-10 diagnostic codes and lab test codes) both individually and in combinations were assessed via sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) with respect to the gold standard. In the Framingham-validated cohort, 2,035 patients had HF; 1,172 (58%) had HFpEF. One in-patient or two out-patient diagnosis codes of ICD-9 428.3X or ICD-10 I50.3X had 46% sensitivity, 88% specificity, 84% PPV, and 54% NPV. The addition of a BNP/NT-proBNP test code reduced sensitivity to 35% while increasing specificity to 91% (PPV = 84%, NPV = 51%). Broadening the diagnostic codes to ICD-9 428.0, 428.3X, and 428.9/ICD-10 I50.3X and I50.9 increased sensitivity at the expense of decreasing specificity (diagnostic code-only model: 87% sensitivity, 8% specificity, 56% PPV, 30% NPV; diagnostic code and BNP lab code model: 61% sensitivity, 43% specificity, 60% PPV, 45% NPV). In an analysis conducted to mimic real-world use of the computable phenotypes, any one in-patient or out-patient code of ICD-9 428/ICD-10 150 among the broader population (N = 3,755) resulted in lower PPV values compared with the Framingham cohort. However, one in-patient or two out-patient instances of ICD-9 428.0, 428.9, or 428.3X/ICD-10 150.3X or 150.9 brought the PPV values from the two cohorts closer together. While some misclassification remains, the computable phenotypes defined here may be used in claims databases to identify HFpEF patients and to gain a greater understanding of the characteristics of patients with HFpEF.

Project description:ObjectivesAsthma is a heterogenous condition with significant diagnostic complexity, including variations in symptoms and temporal criteria. The disease can be difficult for clinicians to diagnose accurately. Properly identifying asthma patients from the electronic health record is consequently challenging as current algorithms (computable phenotypes) rely on diagnostic codes (e.g., International Classification of Disease, ICD) in addition to other criteria (e.g., inhaler medications)-but presume an accurate diagnosis. As such, there is no universally accepted or rigorously tested computable phenotype for asthma.MethodsWe compared two established asthma computable phenotypes: the Chicago Area Patient-Outcomes Research Network (CAPriCORN) and Phenotype KnowledgeBase (PheKB). We established a large-scale, consensus gold standard (n = 1,365) from the University of California, Los Angeles Health System's clinical data warehouse for patients 5 to 17 years old. Results were manually reviewed and predictive performance (positive predictive value [PPV], sensitivity/specificity, F1-score) determined. We then examined the classification errors to gain insight for future algorithm optimizations.ResultsAs applied to our final cohort of 1,365 expert-defined gold standard patients, the CAPriCORN algorithms performed with a balanced PPV = 95.8% (95% CI: 94.4-97.2%), sensitivity = 85.7% (95% CI: 83.9-87.5%), and harmonized F1 = 90.4% (95% CI: 89.2-91.7%). The PheKB algorithm was performed with a balanced PPV = 83.1% (95% CI: 80.5-85.7%), sensitivity = 69.4% (95% CI: 66.3-72.5%), and F1 = 75.4% (95% CI: 73.1-77.8%). Four categories of errors were identified related to method limitations, disease definition, human error, and design implementation.ConclusionThe performance of the CAPriCORN and PheKB algorithms was lower than previously reported as applied to pediatric data (PPV = 97.7 and 96%, respectively). There is room to improve the performance of current methods, including targeted use of natural language processing and clinical feature engineering.

Dataset Information

Applying computable phenotypes within a common data model to identify heart failure patients for an implantable cardiac device registry.

Background

Methods

Results

Conclusions

Publications

Applying computable phenotypes within a common data model to identify heart failure patients for an implantable cardiac device registry.

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