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Electronic health record (EHR) datasets are statistically powerful but are subject to ascertainment bias and missingness. Using the Mass General Brigham multi-institutional EHR, we approximated a community-based cohort by sampling patients receiving longitudinal primary care between 2001-2018 (Community Care Cohort Project [C3PO], n  = 520,868). We utilized natural language processing (NLP) to recover vital signs from unstructured notes. We assessed the validity of C3PO by deploying established risk models for myocardial infarction/stroke and atrial fibrillation. We then compared C3PO to Convenience Samples including all individuals from the same EHR with complete data, but without a longitudinal primary care requirement. NLP reduced the missingness of vital signs by 31%. NLP-recovered vital signs were highly correlated with values derived from structured fields (Pearson r range 0.95–0.99). Atrial fibrillation and myocardial infarction/stroke incidence were lower and risk models were better calibrated in C3PO as opposed to the Convenience Samples (calibration error range for myocardial infarction/stroke: 0.012–0.030 in C3PO vs. 0.028–0.046 in Convenience Samples; calibration error for atrial fibrillation 0.028 in C3PO vs. 0.036 in Convenience Samples). Sampling patients receiving regular primary care and using NLP to recover missing data may reduce bias and maximize generalizability of EHR research.

A fundamental challenge in diagnostics is integrating multiple modalities to develop a joint characterization of physiological state. Using the heart as a model system, we develop a cross-modal autoencoder framework for integrating distinct data modalities and constructing a holistic representation of cardiovascular state. In particular, we use our framework to construct such cross-modal representations from cardiac magnetic resonance images (MRIs), containing structural information, and electrocardiograms (ECGs), containing myoelectric information. We leverage the learned cross-modal representation to (1) improve phenotype prediction from a single, accessible phenotype such as ECGs; (2) enable imputation of hard-to-acquire cardiac MRIs from easy-to-acquire ECGs; and (3) develop a framework for performing genome-wide association studies in an unsupervised manner. Our results systematically integrate distinct diagnostic modalities into a common representation that better characterizes physiologic state. A challenge in diagnostics is integrating different data modalities to characterize physiological state. Here, the authors show, using the heart as a model system, that cross-modal autoencoders can integrate and translate modalities to improve diagnostics and identify associated genetic variants.

A Woman with a Racing Heart, Fatigue, and Dyspnea A 70-year-old woman presented with a racing heart, fatigue, dyspnea, and leg edema. One month earlier, percutaneous catheter ablation for atrial fibrillation had been performed. A diagnosis was made.

Left ventricular mass is a risk marker for cardiovascular events, and may indicate an underlying cardiomyopathy. Cardiac magnetic resonance is the gold-standard for left ventricular mass estimation, but is challenging to obtain at scale. Here, we use deep learning to enable genome-wide association study of cardiac magnetic resonance-derived left ventricular mass indexed to body surface area within 43,230 UK Biobank participants. We identify 12 genome-wide associations (1 known at TTN and 11 novel for left ventricular mass), implicating genes previously associated with cardiac contractility and cardiomyopathy. Cardiac magnetic resonance-derived indexed left ventricular mass is associated with incident dilated and hypertrophic cardiomyopathies, and implantable cardioverter-defibrillator implant. An indexed left ventricular mass polygenic risk score ≥90 th percentile is also associated with incident implantable cardioverter-defibrillator implant in separate UK Biobank (hazard ratio 1.22, 95% CI 1.05-1.44) and Mass General Brigham (hazard ratio 1.75, 95% CI 1.12-2.74) samples. Here, we perform a genome-wide association study of cardiac magnetic resonance-derived indexed left ventricular mass to identify 11 novel variants and demonstrate that cardiac magnetic resonance-derived and genetically predicted indexed left ventricular mass are associated with incident cardiomyopathy. A genome-wide association study of cardiac magnetic resonance-derived left ventricular mass index including 43,000 UK Biobank participants reveals 12 associations (11 novel), implicating genes involved in cardiac contractility and cardiomyopathy.

Increased left atrial volume and decreased left atrial function have long been associated with atrial fibrillation. The availability of large-scale cardiac magnetic resonance imaging data paired with genetic data provides a unique opportunity to assess the genetic contributions to left atrial structure and function, and understand their relationship with risk for atrial fibrillation. Here, we use deep learning and surface reconstruction models to measure left atrial minimum volume, maximum volume, stroke volume, and emptying fraction in 40,558 UK Biobank participants. In a genome-wide association study of 35,049 participants without pre-existing cardiovascular disease, we identify 20 common genetic loci associated with left atrial structure and function. We find that polygenic contributions to increased left atrial volume are associated with atrial fibrillation and its downstream consequences, including stroke. Through Mendelian randomization, we find evidence supporting a causal role for left atrial enlargement and dysfunction on atrial fibrillation risk. In this study, a deep learning-based model of left atrial size in UK Biobank enabled genome-wide association studies in 35,049 healthy participants. Several lines of evidence, including the PITX2 locus, linked left atrial dysfunction to atrial fibrillation risk.

Coronary artery disease (CAD) is the leading cause of death among adults worldwide. Accurate risk stratification can support optimal lifetime prevention. Current methods lack the ability to incorporate new information throughout the life course or to combine innate genetic risk factors with acquired lifetime risk. We designed a general multistate model (MSGene) to estimate age-specific transitions across 10 cardiometabolic states, dependent on clinical covariates and a CAD polygenic risk score. This model is designed to handle longitudinal data over the lifetime to address this unmet need and support clinical decision-making. We analyze longitudinal data from 480,638 UK Biobank participants and compared predicted lifetime risk with the 30-year Framingham risk score. MSGene improves discrimination (C-index 0.71 vs 0.66), age of high-risk detection (C-index 0.73 vs 0.52), and overall prediction (RMSE 1.1% vs 10.9%), in held-out data. We also use MSGene to refine estimates of lifetime absolute risk reduction from statin initiation. Our findings underscore our multistate model’s potential public health value for accurate lifetime CAD risk estimation using clinical factors and increasingly available genetics toward earlier more effective prevention. Coronary artery disease is the leading cause of death among adults worldwide, however current risk stratification methods lack the ability to incorporate new information throughout the life-course or to combine innate genetic risk factors with acquired lifetime risk. Here the authors introduce a multistate model to address these limitations.

Prediction models are commonly used to estimate risk for cardiovascular diseases, to inform diagnosis and management. However, performance may vary substantially across relevant subgroups of the population. Here we investigated heterogeneity of accuracy and fairness metrics across a variety of subgroups for risk prediction of two common diseases: atrial fibrillation (AF) and atherosclerotic cardiovascular disease (ASCVD). We calculated the Cohorts for Heart and Aging in Genomic Epidemiology Atrial Fibrillation (CHARGE-AF) score for AF and the Pooled Cohort Equations (PCE) score for ASCVD in three large datasets: Explorys Life Sciences Dataset (Explorys, n = 21,809,334), Mass General Brigham (MGB, n = 520,868), and the UK Biobank (UKBB, n = 502,521). Our results demonstrate important performance heterogeneity across subpopulations defined by age, sex, and presence of preexisting disease, with fairly consistent patterns across both scores. For example, using CHARGE-AF, discrimination declined with increasing age, with a concordance index of 0.72 [95% CI 0.72–0.73] for the youngest (45–54 years) subgroup to 0.57 [0.56–0.58] for the oldest (85–90 years) subgroup in Explorys. Even though sex is not included in CHARGE-AF, the statistical parity difference (i.e., likelihood of being classified as high risk) was considerable between males and females within the 65–74 years subgroup with a value of − 0.33 [95% CI − 0.33 to − 0.33]. We also observed weak discrimination (i.e., < 0.7) and suboptimal calibration (i.e., calibration slope outside of 0.7–1.3) in large subsets of the population; for example, all individuals aged 75 years or older in Explorys (17.4%). Our findings highlight the need to characterize and quantify the behavior of clinical risk models within specific subpopulations so they can be used appropriately to facilitate more accurate, consistent, and equitable assessment of disease risk.

Atrial fibrillation (AF) is common and increases stroke risk and mortality. Many knowledge gaps remain with respect to practice patterns and outcomes. Electronic medical records (EMRs) may serve as powerful research tools if AF status can be properly ascertained. We sought to develop an algorithm for identifying subjects with and without AF in the EMR and compare it to previous methods. Using a hospital network EMR (n = 5,737,846), we randomly selected 8,200 subjects seen at a large academic medical center in January 2014 to derive and validate 7 AF classification schemas (4 cases and 3 controls) to construct a composite AF algorithm. In an independent sample of 172,138 subjects, we compared this algorithm against published AF classification methods. In total, we performed manual adjudication of AF in 700 subjects. Three AF schemas (AF1, AF2, and AF4) achieved positive predictive value (PPV) >0.9. Two control schemas achieved PPV >0.9 (control 1 and control 3). A combination algorithm AF1, AF2, and AF4 (PPV 88%; 8.2% classified) outperformed published classification methods including >1 outpatient International Statistical Classification of Diseases, Ninth Revision code or 1 outpatient code with an electrocardiogram demonstrating AF (PPV 82%; 5.9% classified), ≥1 inpatient International Statistical Classification of Diseases, Ninth Revision code or electrocardiogram demonstrating AF (PPV 88%; 6.1% classified), or the intersection of these (PPV 84%; 7.4% classified). When applied simultaneously, the case and control algorithms classified 98.4% of the cohort with zero disagreement. In conclusion, we derived a parsimonious and portable algorithm to identify subjects with and without AF with high sensitivity. If broadly applied, this algorithm can provide optimal power for EMR-based AF research.

Undiagnosed atrial fibrillation (AF) is an important cause of stroke. Screening for AF using wrist-worn wearable devices may prevent strokes, but their cost-effectiveness is unknown. To evaluate the cost-effectiveness of contemporary AF screening strategies, particularly wrist-worn wearable devices. This economic evaluation used a microsimulation decision-analytic model and was conducted from September 8, 2020, to May 23, 2022, comprising 30 million simulated individuals with an age, sex, and comorbidity profile matching the US population aged 65 years or older. Eight AF screening strategies, with 6 using wrist-worn wearable devices (watch or band photoplethysmography, with or without watch or band electrocardiography) and 2 using traditional modalities (ie, pulse palpation and 12-lead electrocardiogram) vs no screening. The primary outcome was the incremental cost-effectiveness ratio, defined as US dollars per quality-adjusted life-year (QALY). Secondary measures included rates of stroke and major bleeding. In the base case analysis of this model, the mean (SD) age was 72.5 (7.5) years, and 50% of the individuals were women. All 6 screening strategies using wrist-worn wearable devices were estimated to be more effective than no screening (range of QALYs gained vs no screening, 226-957 per 100 000 individuals) and were associated with greater relative benefit than screening using traditional modalities (range of QALYs gained vs no screening, -116 to 93 per 100 000 individuals). Compared with no screening, screening using wrist-worn wearable devices was associated with a reduction in stroke incidence by 20 to 23 per 100 000 person-years but an increase in major bleeding by 20 to 44 per 100 000 person-years. The overall preferred strategy was wearable photoplethysmography, followed conditionally by wearable electrocardiography with patch monitor confirmation, which had an incremental cost-effectiveness ratio of $57 894 per QALY, meeting the acceptability threshold of $100 000 per QALY. The cost-effectiveness of screening was consistent across multiple scenarios, including strata of sex, screening at earlier ages (eg, ≥50 years), and with variation in the association of anticoagulation with risk of stroke in the setting of screening-detected AF. This economic evaluation of AF screening using a microsimulation decision-analytic model suggests that screening using wearable devices is cost-effective compared with either no screening or AF screening using traditional methods.

Physical activity is regarded as favorable to health but effects across the spectrum of human disease are poorly quantified. In contrast to self-reported measures, wearable accelerometers can provide more precise and reproducible activity quantification. Using wrist-worn accelerometry data from the UK Biobank prospective cohort study, we test associations between moderate-to-vigorous physical activity (MVPA) – both total MVPA minutes and whether MVPA is above a guideline-based threshold of ≥150 min/week—and incidence of 697 diseases using Cox proportional hazards models adjusted for age, sex, body mass index, smoking, Townsend Deprivation Index, educational attainment, diet quality, alcohol use, blood pressure, anti-hypertensive use. We correct for multiplicity at a false discovery rate of 1%. We perform analogous testing using self-reported MVPA. Among 96,244 adults wearing accelerometers for one week (age 62 ± 8 years), MVPA is associated with 373 (54%) tested diseases over a median 6.3 years of follow-up. Greater MVPA is overwhelmingly associated with lower disease risk (98% of associations) with hazard ratios (HRs) ranging 0.70–0.98 per 150 min increase in weekly MVPA, and associations spanning all 16 disease categories tested. Overall, associations with lower disease risk are enriched for cardiac (16%), digestive (14%), endocrine/metabolic (10%), and respiratory conditions (8%) (chi-square p  < 0.01). Similar patterns are observed using the guideline-based threshold of ≥150 MVPA min/week. Some of the strongest associations with guideline-adherent activity include lower risks of incident heart failure (HR 0.65, 95% CI 0.55–0.77), type 2 diabetes (HR 0.64, 95% CI 0.58–0.71), cholelithiasis (HR 0.61, 95% CI 0.54–0.70), and chronic bronchitis (HR 0.42, 95% CI 0.33–0.54). When assessed within 456,374 individuals providing self-reported MVPA, effect sizes for guideline-adherent activity are substantially smaller (e.g., heart failure HR 0.84, 95% CI 0.80–0.88). Greater wearable device-based physical activity is robustly associated with lower disease incidence. Future studies are warranted to identify potential mechanisms linking physical activity and disease, and assess whether optimization of measured activity can reduce disease risk.