The Use of Electronic Health Records for Behavioral Phenotyping of School-Age Children With Unilateral Hearing Loss: A Methodological Approach.

PURPOSE: This methodological study describes a technique for extracting information from de-identified electronic health records (EHRs) to identify occurrences of permanent unilateral hearing loss (UHL) and associated educational comorbidities. METHOD: This was an exploratory methodological study utilizing approximately 3.3 million de-identified medical records. Structured and unstructured data were extracted using both automated and manual methods. When both methods were available, positive and negative predictive values were calculated to evaluate the utility of using automated methods. RESULTS: We defined a cohort of 471 records that met our criteria of school-age children with permanent UHL and no additional significant disabilities/diagnoses. Fifty-one percent of the children reflected in this cohort had indicators of adverse educational progress, defined as documentation of receiving educational services, speech-language therapy, and/or parental/teacher concern, with 12% of records reflecting overlapping services/concerns. Negative predictive values were generally high and positive predictive values were generally low, suggesting automated searches are useful for excluding factors of interest, but not finding them. CONCLUSIONS: This study demonstrates the feasibility of using EHRs in examining UHL in school-age children. By restricting our cohort to individuals who were seen in audiology clinic, we were able to capture variables such as educational difficulty that are not routinely ascertained in medical contexts. The proportion of children in this cohort demonstrating a marker of adverse educational progress is consistent with numerous prior observational studies, thus providing validity to this ascertainment approach. We describe challenges encountered in creating this cohort and detail our hybrid approach to ascertaining key variables accurately.

Using Natural Language Processing to Predict Fatal Drug Overdose From Autopsy Narrative Text: Algorithm Development and Validation Study.

BACKGROUND: Fatal drug overdose surveillance informs prevention but is often delayed because of autopsy report processing and death certificate coding. Autopsy reports contain narrative text describing scene evidence and medical history (similar to preliminary death scene investigation reports) and may serve as early data sources for identifying fatal drug overdoses. To facilitate timely fatal overdose reporting, natural language processing was applied to narrative texts from autopsies. OBJECTIVE: This study aimed to develop a natural language processing-based model that predicts the likelihood that an autopsy report narrative describes an accidental or undetermined fatal drug overdose. METHODS: Autopsy reports of all manners of death (2019-2021) were obtained from the Tennessee Office of the State Chief Medical Examiner. The text was extracted from autopsy reports (PDFs) using optical character recognition. Three common narrative text sections were identified, concatenated, and preprocessed (bag-of-words) using term frequency-inverse document frequency scoring. Logistic regression, support vector machine (SVM), random forest, and gradient boosted tree classifiers were developed and validated. Models were trained and calibrated using autopsies from 2019 to 2020 and tested using those from 2021. Model discrimination was evaluated using the area under the receiver operating characteristic, precision, recall, F1-score, and F2-score (prioritizes recall over precision). Calibration was performed using logistic regression (Platt scaling) and evaluated using the Spiegelhalter z test. Shapley additive explanations values were generated for models compatible with this method. In a post hoc subgroup analysis of the random forest classifier, model discrimination was evaluated by forensic center, race, age, sex, and education level. RESULTS: A total of 17,342 autopsies (n=5934, 34.22% cases) were used for model development and validation. The training set included 10,215 autopsies (n=3342, 32.72% cases), the calibration set included 538 autopsies (n=183, 34.01% cases), and the test set included 6589 autopsies (n=2409, 36.56% cases). The vocabulary set contained 4002 terms. All models showed excellent performance (area under the receiver operating characteristic ≥0.95, precision ≥0.94, recall ≥0.92, F1-score ≥0.94, and F2-score ≥0.92). The SVM and random forest classifiers achieved the highest F2-scores (0.948 and 0.947, respectively). The logistic regression and random forest were calibrated (P=.95 and P=.85, respectively), whereas the SVM and gradient boosted tree classifiers were miscalibrated (P=.03 and P<.001, respectively). "Fentanyl" and "accident" had the highest Shapley additive explanations values. Post hoc subgroup analyses revealed lower F2-scores for autopsies from forensic centers D and E. Lower F2-score were observed for the American Indian, Asian, ≤14 years, and ≥65 years subgroups, but larger sample sizes are needed to validate these findings. CONCLUSIONS: The random forest classifier may be suitable for identifying potential accidental and undetermined fatal overdose autopsies. Further validation studies should be conducted to ensure early detection of accidental and undetermined fatal drug overdoses across all subgroups.

Real-time clinical note monitoring to detect conditions for rapid follow-up: A case study of clinical trial enrollment in drug-induced torsades de pointes and Stevens-Johnson syndrome.

Identifying acute events as they occur is challenging in large hospital systems. Here, we describe an automated method to detect 2 rare adverse drug events (ADEs), drug-induced torsades de pointes and Stevens-Johnson syndrome and toxic epidermal necrolysis, in near real time for participant recruitment into prospective clinical studies. A text processing system searched clinical notes from the electronic health record (EHR) for relevant keywords and alerted study personnel via email of potential patients for chart review or in-person evaluation. Between 2016 and 2018, the automated recruitment system resulted in capture of 138 true cases of drug-induced rare events, improving recall from 43% to 93%. Our focused electronic alert system maintained 2-year enrollment, including across an EHR migration from a bespoke system to Epic. Real-time monitoring of EHR notes may accelerate research for certain conditions less amenable to conventional study recruitment paradigms.

Prescribing Prevalence of Medications With Potential Genotype-Guided Dosing in Pediatric Patients.

Importance: Genotype-guided prescribing in pediatrics could prevent adverse drug reactions and improve therapeutic response. Clinical pharmacogenetic implementation guidelines are available for many medications commonly prescribed to children. Frequencies of medication prescription and actionable genotypes (genotypes where a prescribing change may be indicated) inform the potential value of pharmacogenetic implementation. Objective: To assess potential opportunities for genotype-guided prescribing in pediatric populations among multiple health systems by examining the prevalence of prescriptions for each drug with the highest level of evidence (Clinical Pharmacogenetics Implementation Consortium level A) and estimating the prevalence of potential actionable prescribing decisions. Design, Setting, and Participants: This serial cross-sectional study of prescribing prevalences in 16 health systems included electronic health records data from pediatric inpatient and outpatient encounters from January 1, 2011, to December 31, 2017. The health systems included academic medical centers with free-standing children's hospitals and community hospitals that were part of an adult health care system. Participants included approximately 2.9 million patients younger than 21 years observed per year. Data were analyzed from June 5, 2018, to April 14, 2020. Exposures: Prescription of 38 level A medications based on electronic health records. Main Outcomes and Measures: Annual prevalence of level A medication prescribing and estimated actionable exposures, calculated by combining estimated site-year prevalences across sites with each site weighted equally. Results: Data from approximately 2.9 million pediatric patients (median age, 8 [interquartile range, 2-16] years; 50.7% female, 62.3% White) were analyzed for a typical calendar year. The annual prescribing prevalence of at least 1 level A drug ranged from 7987 to 10 629 per 100 000 patients with increasing trends from 2011 to 2014. The most prescribed level A drug was the antiemetic ondansetron (annual prevalence of exposure, 8107 [95% CI, 8077-8137] per 100 000 children). Among commonly prescribed opioids, annual prevalence per 100 000 patients was 295 (95% CI, 273-317) for tramadol, 571 (95% CI, 557-586) for codeine, and 2116 (95% CI, 2097-2135) for oxycodone. The antidepressants citalopram, escitalopram, and amitriptyline were also commonly prescribed (annual prevalence, approximately 250 per 100 000 patients for each). Estimated prevalences of actionable exposures were highest for oxycodone and ondansetron (>300 per 100 000 patients annually). CYP2D6 and CYP2C19 substrates were more frequently prescribed than medications influenced by other genes. Conclusions and Relevance: These findings suggest that opportunities for pharmacogenetic implementation among pediatric patients in the US are abundant. As expected, the greatest opportunity exists with implementing CYP2D6 and CYP2C19 pharmacogenetic guidance for commonly prescribed antiemetics, analgesics, and antidepressants.

Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease.

OBJECTIVE: The Phenotype Risk Score (PheRS) is a method to detect Mendelian disease patterns using phenotypes from the electronic health record (EHR). We compared the performance of different approaches mapping EHR phenotypes to Mendelian disease features. MATERIALS AND METHODS: PheRS utilizes Mendelian diseases descriptions annotated with Human Phenotype Ontology (HPO) terms. In previous work, we presented a map linking phecodes (based on International Classification of Diseases [ICD]-Ninth Revision) to HPO terms. For this study, we integrated ICD-Tenth Revision codes and lab data. We also created a new map between HPO terms using customized groupings of ICD codes. We compared the performance with cases and controls for 16 Mendelian diseases using 2.5 million de-identified medical records. RESULTS: PheRS effectively distinguished cases from controls for all 15 positive controls and all approaches tested (P < 4 × 1016). Adding lab data led to a statistically significant improvement for 4 of 14 diseases. The custom ICD groupings improved specificity, leading to an average 8% increase for precision at 100 (-2% to 22%). Eight of 10 adults with cystic fibrosis tested had PheRS in the 95th percentile prio to diagnosis. DISCUSSION: Both phecodes and custom ICD groupings were able to detect differences between affected cases and controls at the population level. The ICD map showed better precision for the highest scoring individuals. Adding lab data improved performance at detecting population-level differences. CONCLUSIONS: PheRS is a scalable method to study Mendelian disease at the population level using electronic health record data and can potentially be used to find patients with undiagnosed Mendelian disease.

Breadcrumbs: Assessing the Feasibility of Automating Provider Documentation Using Electronic Health Record Activity.

This study assessed the feasibility of automating the generation of the outpatient encounter summary. We reviewed screen tracking video and log-file metadata from electronic health record (EHR) interactions based on two simulated encounters. We mapped the sequence of metadata to key concepts in the video to assess the precision with which the log files aligned with user activity and to generate the Breadcrumbs encounter summary (BES). The BES captured all interactions documented in clinical notes with the exception of the physical exam. The videos addressed all Evaluation and Management (E/M) requirements, while the log files did not contain the physical exam. The BES was as comprehensive as the gold standard visit summary. The BES offers a promising method for the collection and compilation of necessary elements of outpatient clinical documentation. The combination of log files and video could provide evidence of EHR activity satisfying documentation requirements.