PopMLvis: a tool for analysis and visualization of population structure using genotype data from genome-wide association studies.

One of the aims of population genetics is to identify genetic differences/similarities among individuals of multiple ancestries. Many approaches including principal component analysis, clustering, and maximum likelihood techniques can be used to assign individuals to a given ancestry based on their genetic makeup. Although there are several tools that implement such algorithms, there is a lack of interactive visual platforms to run a variety of algorithms in one place. Therefore, we developed PopMLvis, a platform that offers an interactive environment to visualize genetic similarity data using several algorithms, and generate figures that can be easily integrated into scientific articles.

Genetic Susceptibility to Arrhythmia Phenotypes in a Middle Eastern Cohort of 14,259 Whole-Genome Sequenced Individuals.

Background: The current study explores the genetic underpinnings of cardiac arrhythmia phenotypes within Middle Eastern populations, which are under-represented in genomic medicine research. Methods: Whole-genome sequencing data from 14,259 individuals from the Qatar Biobank were used and contained 47.8% of Arab ancestry, 18.4% of South Asian ancestry, and 4.6% of African ancestry. The frequency of rare functional variants within a set of 410 candidate genes for cardiac arrhythmias was assessed. Polygenic risk score (PRS) performance for atrial fibrillation (AF) prediction was evaluated. Results: This study identified 1196 rare functional variants, including 162 previously linked to arrhythmia phenotypes, with varying frequencies across Arab, South Asian, and African ancestries. Of these, 137 variants met the pathogenic or likely pathogenic (P/LP) criteria according to ACMG guidelines. Of these, 91 were in ACMG actionable genes and were present in 1030 individuals (~7%). Ten P/LP variants showed significant associations with atrial fibrillation p < 2.4 × 10-10. Five out of ten existing PRSs were significantly associated with AF (e.g., PGS000727, p = 0.03, OR = 1.43 [1.03, 1.97]). Conclusions: Our study is the largest to study the genetic predisposition to arrhythmia phenotypes in the Middle East using whole-genome sequence data. It underscores the importance of including diverse populations in genomic investigations to elucidate the genetic landscape of cardiac arrhythmias and mitigate health disparities in genomic medicine.

Correlations between Resting Electrocardiogram Findings and Disease Profiles: Insights from the Qatar Biobank Cohort.

BACKGROUND: Resting electrocardiogram (ECG) is a valuable non-invasive diagnostic tool used in clinical medicine to assess the electrical activity of the heart while the patient is resting. Abnormalities in ECG may be associated with clinical biomarkers and can predict early stages of diseases. In this study, we evaluated the association between ECG traits, clinical biomarkers, and diseases and developed risk scores to predict the risk of developing coronary artery disease (CAD) in the Qatar Biobank. METHODS: This study used 12-lead ECG data from 13,827 participants. The ECG traits used for association analysis were RR, PR, QRS, QTc, PW, and JT. Association analysis using regression models was conducted between ECG variables and serum electrolytes, sugars, lipids, blood pressure (BP), blood and inflammatory biomarkers, and diseases (e.g., type 2 diabetes, CAD, and stroke). ECG-based and clinical risk scores were developed, and their performance was assessed to predict CAD. Classical regression and machine-learning models were used for risk score development. RESULTS: Significant associations were observed with ECG traits. RR showed the largest number of associations: e.g., positive associations with bicarbonate, chloride, HDL-C, and monocytes, and negative associations with glucose, insulin, neutrophil, calcium, and risk of T2D. QRS was positively associated with phosphorus, bicarbonate, and risk of CAD. Elevated QTc was observed in CAD patients, whereas decreased QTc was correlated with decreased levels of calcium and potassium. Risk scores developed using regression models were outperformed by machine-learning models. The area under the receiver operating curve reached 0.84 using a machine-learning model that contains ECG traits, sugars, lipids, serum electrolytes, and cardiovascular disease risk factors. The odds ratio for the top decile of CAD risk score compared to the remaining deciles was 13.99. CONCLUSIONS: ECG abnormalities were associated with serum electrolytes, sugars, lipids, and blood and inflammatory biomarkers. These abnormalities were also observed in T2D and CAD patients. Risk scores showed great predictive performance in predicting CAD.

Representing variability and transmural differences in a model of human heart failure.

During heart failure (HF) at the cellular level, the electrophysiological properties of single myocytes get remodeled, which can trigger the occurrence of ventricular arrhythmias that could be manifested in many forms such as early afterdepolarizations (EADs) and alternans (ALTs). In this paper, based on experimentally observed human HF data, specific ionic and exchanger current strengths are modified from a recently developed human ventricular cell model: the O'Hara-Virág-Varró-Rudy (OVVR) model. A new transmural HF-OVVR model is developed that incorporates HF changes and variability of the observed remodeling. This new heterogeneous HF-OVVR model is able to replicate many of the failing action potential (AP) properties and the dynamics of both [Ca(2+)]i and [Na(+)]i in accordance with experimental data. Moreover, it is able to generate EADs for different cell types and exhibits ALTs at modest pacing rate for transmural cell types. We have assessed the HF-OVVR model through the examination of the AP duration and the major ionic currents' rate dependence in single myocytes. The evaluation of the model comes from utilizing the steady-state (S-S) and S1-S2 restitution curves and from probing the accommodation of the HF-OVVR model to an abrupt change in cycle length. In addition, we have investigated the effect of chosen currents on the AP properties, such as blocking the slow sodium current to shorten the AP duration and suppress the EADs, and have found good agreement with experimental observations. This study should help elucidate arrhythmogenic mechanisms at the cellular level and predict unseen properties under HF conditions. In addition, this AP cell model might be useful for modeling and simulating HF at the tissue and organ levels.

A quantitative comparison of the behavior of human ventricular cardiac electrophysiology models in tissue.

Numerical integration of mathematical models of heart cell electrophysiology provides an important computational tool for studying cardiac arrhythmias, but the abundance of available models complicates selecting an appropriate model. We study the behavior of two recently published models of human ventricular action potentials, the Grandi-Pasqualini-Bers (GPB) and the O'Hara-Virág-Varró-Rudy (OVVR) models, and compare the results with four previously published models and with available experimental and clinical data. We find the shapes and durations of action potentials and calcium transients differ between the GPB and OVVR models, as do the magnitudes and rate-dependent properties of transmembrane currents and the calcium transient. Differences also occur in the steady-state and S1-S2 action potential duration and conduction velocity restitution curves, including a maximum conduction velocity for the OVVR model roughly half that of the GPB model and well below clinical values. Between single cells and tissue, both models exhibit differences in properties, including maximum upstroke velocity, action potential amplitude, and minimum diastolic interval. Compared to experimental data, action potential durations for the GPB and OVVR models agree fairly well (although OVVR epicardial action potentials are shorter), but maximum slopes of steady-state restitution curves are smaller. Although studies show alternans in normal hearts, it occurs only in the OVVR model, and only for a narrow range of cycle lengths. We find initiated spiral waves do not progress to sustained breakup for either model. The dominant spiral wave period of the GPB model falls within clinically relevant values for ventricular tachycardia (VT), but for the OVVR model, the dominant period is longer than periods associated with VT. Our results should facilitate choosing a model to match properties of interest in human cardiac tissue and to replicate arrhythmia behavior more closely. Furthermore, by indicating areas where existing models disagree, our findings suggest avenues for further experimental work.

Electrophysiological properties under heart failure conditions in a human ventricular cell: a modeling study.

Heart failure (HF) is one of the major diseases across the world. During HF the electrophysiology of the failing heart is remodeled, which renders the heart more susceptible to ventricular arrhythmias. In this study, we quantitatively analyze the effects of electrophysiological remodeling of the major currents of human ventricular myocytes on the dynamics of the failing heart. We develop a HF model using a modified version of a recently published model of the human ventricular action potential, the O'Hara-Virag-Varro-Rudy (OVVR) model. The proposed HF model incorporates recently available HF clinical data. It can reproduce most of the action potential (AP) properties of failing myocytes, including action potential duration (APD), amplitude (APA), notch (APN), plateau (APP), resting membrane potential (RMP), and maximum upstroke velocity (dV/dtmax). In addition, the model reproduces the behavior of the [Na+], concentration and [Ca(2)+]i dynamics. Moreover, the HF model exhibits alternans with a fast pacing frequency and can induce early afterdepolarizations (EADs). Additionally, blocking the late sodium current shortens the APD and suppresses EADs, in agreement with experimental findings. The dynamics of the proposed model are assessed through investigating the rate dependence of the AP and the dynamics of the major currents. The steady-state (S-S) and S1-S2 restitution curves along with accommodation to an abrupt change in cycle length were evaluated. Our study should help to elucidate the roles of alterations in electrophysiological properties during HF. Also, this HF cellular model could be used to study HF in a realistic geometry and could be embedded into a model of HF electromechanics to investigate electrical and mechanical properties simultaneously during HF.