Impact of Terminology Mapping on Population Health Cohorts IMPaCt

Background and Objectives: The population health care delivery model uses phenotype algorithms in the electronic health record (EHR) system to identify patient cohorts targeted for clinical interventions such as laboratory tests, and procedures. The standard terminology used to identify disease cohorts may contribute to significant variation in error rates for patient inclusion or exclusion. The United States requires EHR systems to support two diagnosis terminologies, the International Classification of Disease (ICD) and the Systematized Nomenclature of Medicine (SNOMED). Terminology mapping enables the retrieval of diagnosis data using either terminology. There are no standards of practice by which to evaluate and report the operational characteristics of ICD and SNOMED value sets used to select patient groups for population health interventions. Establishing a best practice for terminology selection is a step forward in ensuring that the right patients receive the right intervention at the right time. The research question is, “How does the diagnosis retrieval terminology (ICD vs SNOMED) and terminology map maintenance impact population health cohorts?” Aim 1 and 2 explore this question, and Aim 3 informs practice and policy for population health programs. Methods Aim 1: Quantify impact of terminology choice (ICD vs SNOMED) ICD and SNOMED phenotype algorithms for diabetes, chronic kidney disease (CKD), and heart failure were developed using matched sets of codes from the Value Set Authority Center. The performance of the diagnosis-only phenotypes was compared to published reference standard that included diagnosis codes, laboratory results, procedures, and medications. Aim 2: Measure terminology maintenance impact on SNOMED cohorts For each disease state, the performance of a single SNOMED algorithm before and after terminology updates was evaluated in comparison to a reference standard to identify and quantify cohort changes introduced by terminology maintenance. Aim 3: Recommend methods for improving population health interventions The socio-technical model for studying health information technology was used to inform best practice for the use of population health interventions. Results Aim 1: ICD-10 value sets had better sensitivity than SNOMED for diabetes (.829, .662) and CKD (.242, .225) (N=201,713, p Aim 2: Following terminology maintenance the SNOMED algorithm for diabetes increased in sensitivity from (.662 to .683 (p Aim 3: Based on observed social and technical challenges to population health programs, including and in addition to the development and measurement of phenotypes, a practical method was proposed for population health intervention development and reporting

Processing of Electronic Health Records using Deep Learning: A review

Availability of large amount of clinical data is opening up new research avenues in a number of fields. An exciting field in this respect is healthcare, where secondary use of healthcare data is beginning to revolutionize healthcare. Except for availability of Big Data, both medical data from healthcare institutions (such as EMR data) and data generated from health and wellbeing devices (such as personal trackers), a significant contribution to this trend is also being made by recent advances on machine learning, specifically deep learning algorithms

Combining semantic web technologies with evolving fuzzy classifier eClass for EHR-based phenotyping : a feasibility study

In parallel to nation-wide efforts for setting up shared electronic health records (EHRs) across healthcare settings, several large-scale national and international projects are developing, validating, and deploying electronic EHR oriented phenotype algorithms that aim at large-scale use of EHRs data for genomic studies. A current bottleneck in using EHRs data for obtaining computable phenotypes is to transform the raw EHR data into clinically relevant features. The research study presented here proposes a novel combination of Semantic Web technologies with the on-line evolving fuzzy classifier eClass to obtain and validate EHR-driven computable phenotypes derived from 1956 clinical statements from EHRs. The evaluation performed with clinicians demonstrates the feasibility and practical acceptability of the approach proposed

Usage of Electronic Health Record Phenotyping in American Adult Patients with Schizophrenia to Improve Detection of Type II Diabetes Mellitus

Objective: Prevalence of type II diabetes is higher in diagnosed patients with schizophrenia when compared with the general adult population. With the propagation of electronic health records (EHR), we assess whether electronic health record phenotyping can improve diabetes mellitus type 2 (T2DM) screening when compared to conventional diabetic screening metrics in patients with schizophrenia.Method: EHR data from 1267 patients with schizophrenia was used to develop a pre-screening tool for current T2DM using logistic regression and random forest models. Three types of models were created: the first used conventional diabetic screening criteria (BMI, age, gender, etc.) and their interactions. The second utilized conventional factors plus prescribed medications. The thirdutilized conventional factors, prescriptions, and diagnoses as determined by ICD-9 codes.Results: EHR phenotyping models utilizing conventional factors, prescriptions, and diagnosis information (EHR-DX) had improved ability to detect T2DM, when compared to models containing conventional (EHR-conventional) or conventional & prescription metrics (EHR-RX). Conversely, there was not a statistically significant improvement in T2DM detection between models containing conventional metrics and models containing conventional & prescription metrics (likelihood ratio test, p < 0.001). The AUC for the full EHR DX, EHR RX, and conventional models using logistic regression were 85.8%, 74.8%, and 72.7% respectively.Several ICD codes were shown to have a significant association with diabetes diagnosis, including several from established predictors or comorbidities, such as prediabetes and heart disease. Associations between antipsychotic drugs and diabetes diagnosis were generally insignificant and lacked a discernible positive or negative association trend

Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review

Novel approaches that complement and go beyond evidence-based medicine are required in the domain of chronic diseases, given the growing incidence of such conditions on the worldwide population. A promising avenue is the secondary use of electronic health records (EHRs), where patient data are analyzed to conduct clinical and translational research. Methods based on machine learning to process EHRs are resulting in improved understanding of patient clinical trajectories and chronic disease risk prediction, creating a unique opportunity to derive previously unknown clinical insights. However, a wealth of clinical histories remains locked behind clinical narratives in free-form text. Consequently, unlocking the full potential of EHR data is contingent on the development of natural language processing (NLP) methods to automatically transform clinical text into structured clinical data that can guide clinical decisions and potentially delay or prevent disease onset

Design patterns for the development of electronic health record-driven phenotype extraction algorithms

AbstractBackgroundDesign patterns, in the context of software development and ontologies, provide generalized approaches and guidance to solving commonly occurring problems, or addressing common situations typically informed by intuition, heuristics and experience. While the biomedical literature contains broad coverage of specific phenotype algorithm implementations, no work to date has attempted to generalize common approaches into design patterns, which may then be distributed to the informatics community to efficiently develop more accurate phenotype algorithms.MethodsUsing phenotyping algorithms stored in the Phenotype KnowledgeBase (PheKB), we conducted an independent iterative review to identify recurrent elements within the algorithm definitions. We extracted and generalized recurrent elements in these algorithms into candidate patterns. The authors then assessed the candidate patterns for validity by group consensus, and annotated them with attributes.ResultsA total of 24 electronic Medical Records and Genomics (eMERGE) phenotypes available in PheKB as of 1/25/2013 were downloaded and reviewed. From these, a total of 21 phenotyping patterns were identified, which are available as an online data supplement.ConclusionsRepeatable patterns within phenotyping algorithms exist, and when codified and cataloged may help to educate both experienced and novice algorithm developers. The dissemination and application of these patterns has the potential to decrease the time to develop algorithms, while improving portability and accuracy

Precision Medicine: Viable Pathways to Address Existing Research Gaps

Precision Medicine (PM) seeks to customize medical treatments for patients based on measurable and identifiable characteristics. Unlike personalized medicine, this effort is not intended to result in tailored care for each patient. Instead, this effort seeks to improve overall care within the medical domain by shifting the focus from one-size-fits-all care to optimized care for specified subgroups. In order for the benefits of PM to be expeditiously realized, the diverse skills sets of the scientific community must be brought to bear on the problem. This research effort explores the intersection of quality engineering (QE) and healthcare to outline how existing methodologies within the QE field could support existing PM research goals. Specifically this work examines how to determine the value of patient characteristics for use in disease prediction models with select machine learning algorithms, proposes a method to incorporate patient risk into treatment decisions through the development of performance functions, and investigates the potential impact of incorrect assumptions on estimation methods used in optimization models