A Large-Scale Genome-Wide Study of Gene-Sleep Duration Interactions for Blood Pressure in 811,405 Individuals from Diverse Populations

Although both short and long sleep duration are associated with elevated hypertension risk, our understanding of their interplay with biological pathways governing blood pressure remains limited. To address this, we carried out genome-wide cross-population gene-by-short-sleep and long-sleep duration interaction analyses for three blood pressure traits (systolic, diastolic, and pulse pressure) in 811,405 individuals from diverse population groups. We discover 22 novel gene-sleep duration interaction loci for blood pressure, mapped to genes involved in neurological, thyroidal, bone metabolism, and hematopoietic pathways. Non-overlap between short sleep (12) and long sleep (10) interactions underscores the plausibility of distinct influences of both sleep duration extremes in cardiovascular health. With several of our loci reflecting specificity towards population background or sex, our discovery sheds light on the importance of embracing granularity when addressing heterogeneity entangled in gene-environment interactions, and in therapeutic design approaches for blood pressure management.

[Prevalence of frailty and related factors in middle-aged and elderly people in island and mountainous areas of Taizhou, Zhejiang Province]

Objective: To compare the prevalence of frailty and related factors in middle-aged and elderly people aged ≥45 years in island and mountainous areas of Taizhou, Zhejiang Province. Methods: Based on cross-sectional design, stratified cluster sampling and quota sampling methods were adopted. One administrative district was randomly selected from each of six coastal and three inland administrative districts in Taizhou during July to August, representing two different geographical terrains. In the island area (Jiaojiang District), all residents aged ≥45 years were included by cluster sampling. In the mountainous area (Xianju County), participants were selected through quota sampling, with same gender and age distributions. Data about their demographic characteristics, lifestyle and health-related factors were collected through questionnaire surveys and laboratory examinations. The prevalence of frailty was assessed using the Fried frailty phenotype scale. Hierarchical analysis and multivariate logistic regression analysis were used to compare the influencing factors of frailty. Results: A total of 1 011 local residents were studied, in whom island and mountainous residents accounted for 48.1% (486/1 011) and 51.9% (525/1 011) respectively; men and women accounted for 45.9% (464/1 011) and 54.1% (547/1 011) respectively. Middle-aged (45-49 years), younger elderly (60-74 years), and older elderly (≥75 years) residents accounted for 38.6% (390/1 011), 44.6% (451/1 011), and 16.8% (170/1 011) respectively. The overall prevalence rate of frailty was 3.6% (36/1 011), the prevalence rate was 3.7% (17/464) in men and 3.5% (19/547) in women. The prevalence rates in age groups 45-59,60-74 years and ≥75 years were 0.3% (1/390), 2.2% (10/451), and 14.7% (25/170), respectively. The prevalence rates of frailty and pre-frailty in island area were 6.0% (29/486) and 39.1% (190/486), respectively, which was higher than those in mountainous area (1.3%, 7/525) and (30.9%, 162/525). After adjusting for potential confounding factors, the risk for frailty in island residents was significantly higher than that in mountainous residents (aOR=1.55,95%CI: 1.07-2.25,P=0.019). In island area, older age (60-74 years:aOR=2.52,95%CI: 1.56-4.13; ≥75 years:aOR=11.65,95%CI:5.38-26.70), being women (aOR=1.94,95%CI: 1.20-3.17), suffering from depression (aOR=1.09,95%CI:1.02-1.17) were associated with frailty symptoms. In mountainous area, older age was also associated with an increased risk of frailty symptoms, but the OR value was lower than those in island area (60-74 years: aOR=1.74,95%CI:1.04-2.94;≥75 years: aOR=4.78,95%CI:2.45-9.50). Polydrug use (aOR=2.08,95%CI: 1.14-3.80) and suffering from depression (aOR=1.10,95%CI: 1.02-1.18) had significant positive association with frailty symptoms. Higher education level had significant negative association with frailty symptoms (junior high school: aOR=0.40,95%CI: 0.21-0.75; senior high school and technical secondary school: aOR=0.29,95%CI: 0.15-0.53; college or above:aOR=0.22,95%CI: 0.11-0.42). Conclusions: The prevalence of frailty in middle-aged and elderly community residents was significantly higher in island area than in mountainous area in Taizhou. The frailty-related factors varied with area. The elderly people (≥75 years) and women in island area had higher risk for frailty. Older age and suffering from depression were the independent risk factors for frailty. It is necessary to pay attention to the health risk factors and special environment in island area, and take comprehensive intervention measures to delay the process of debilitation and improve the quality of life of middle-aged and elderly people.

The functional impact of rare variation across the regulatory cascade

Each human genome has tens of thousands of rare genetic variants; however, identifying impactful rare variants remains a major challenge. We demonstrate how use of personal multi-omics can enable identification of impactful rare variants by using the Multi-Ethnic Study of Atherosclerosis, which included several hundred individuals, with whole-genome sequencing, transcriptomes, methylomes, and proteomes collected across two time points, 10 years apart. We evaluated each multi-omics phenotype's ability to separately and jointly inform functional rare variation. By combining expression and protein data, we observed rare stop variants 62 times and rare frameshift variants 216 times as frequently as controls, compared to 13-27 times as frequently for expression or protein effects alone. We extended a Bayesian hierarchical model, "Watershed," to prioritize specific rare variants underlying multi-omics signals across the regulatory cascade. With this approach, we identified rare variants that exhibited large effect sizes on multiple complex traits including height, schizophrenia, and Alzheimer's disease.

[Analysis on death causes of HIV/AIDS patients in Taizhou, Zhejiang Province, 1998-2022]

Objective: To understand the incidence and causes of HIV/AIDS death patients in Taizhou from 1998 to 2022. Methods: The data were collected from the AIDS Integrated Prevention and Control Information System of China Information System for Diseases Control and Prevention and Taizhou Chronic Disease Information Management System. By the end of 2022, a total of 5 126 HIV/AIDS patients living in Taizhou for a long time were included, SAS 9.4 was used for Kruskal-Wallis test, χ2 test and trend analysis. Results: From 1998 to 2022, a total of 796 HIV/AIDS patients died, with a fatality rate of 15.53% (796/5 126), in whom 52.26% (416/796) died within one year after confirmation. The proportion of HIV/AIDS patients who died within one year decreased (trend χ2=5.60, P<0.001). For the constituent of death causes, there were 140 (17.59%) deaths of AIDS, 237 (29.77%) deaths of malignant tumors, 99 (12.44%) deaths of cardiovascular disease, 58 (7.29%) deaths caused by injuries, 160 (20.10%) deaths due to other causes, and 102 (12.81%) deaths due to unknown causes. The constituent ratio of deaths of malignant tumor, cardiovascular disease and other causes increased over time (trend χ2=1.92, P=0.028; trend χ2=2.81, P=0.003; trend χ2=2.07, P=0.020). There were differences in the distribution of death causes in HIV/AIDS cases in terms of age, occupation, marital status, ethnic group, educational level and mode of transmission (all P<0.05). The average age of the death cases due to cardiovascular disease was higher than other death cases, the cases who died from AIDS had shorter survival time and the lower initial CD4+T cells after confirmation compared with all other death cases, and the time interval from confirmation to treatment in HIV/AIDS patients with unknown death causes was longer than those of all other death cases (all P<0.05). Conclusions: The constituent ratio of non-AIDS related deaths in HIV/AIDS patients in Taizhou was relatively high and showed an upward trend during 1998-2022. It is necessary to further strengthen the early screening, prevention and treatment of chronic non infectious diseases.

Genetic insights into resting heart rate and its role in cardiovascular disease

Resting heart rate is associated with cardiovascular diseases and mortality in observational and Mendelian randomization studies. The aims of this study are to extend the number of resting heart rate associated genetic variants and to obtain further insights in resting heart rate biology and its clinical consequences. A genome-wide meta-analysis of 100 studies in up to 835,465 individuals reveals 493 independent genetic variants in 352 loci, including 68 genetic variants outside previously identified resting heart rate associated loci. We prioritize 670 genes and in silico annotations point to their enrichment in cardiomyocytes and provide insights in their ECG signature. Two-sample Mendelian randomization analyses indicate that higher genetically predicted resting heart rate increases risk of dilated cardiomyopathy, but decreases risk of developing atrial fibrillation, ischemic stroke, and cardio-embolic stroke. We do not find evidence for a linear or non-linear genetic association between resting heart rate and all-cause mortality in contrast to our previous Mendelian randomization study. Systematic alteration of key differences between the current and previous Mendelian randomization study indicates that the most likely cause of the discrepancy between these studies arises from false positive findings in previous one-sample MR analyses caused by weak-instrument bias at lower P-value thresholds. The results extend our understanding of resting heart rate biology and give additional insights in its role in cardiovascular disease development.

Evaluating the use of blood pressure polygenic risk scores across race/ethnic background groups

We assess performance and limitations of polygenic risk scores (PRSs) for multiple blood pressure (BP) phenotypes in diverse population groups. We compare "clumping-and-thresholding" (PRSice2) and LD-based (LDPred2) methods to construct PRSs from each of multiple GWAS, as well as multi-PRS approaches that sum PRSs with and without weights, including PRS-CSx. We use datasets from the MGB Biobank, TOPMed study, UK biobank, and from All of Us to train, assess, and validate PRSs in groups defined by self-reported race/ethnic background (Asian, Black, Hispanic/Latino, and White). For both SBP and DBP, the PRS-CSx based PRS, constructed as a weighted sum of PRSs developed from multiple independent GWAS, perform best across all race/ethnic backgrounds. Stratified analysis in All of Us shows that PRSs are better predictive of BP in females compared to males, individuals without obesity, and middle-aged (40-60 years) compared to older and younger individuals.

Octahedral Distortion and Displacement-Type Ferroelectricity with Switchable Photovoltaic Effect in a 3d^{3}-Electron Perovskite System

Because of the half-filled t_{2g}-electron configuration, the BO_{6} octahedral distortion in a 3d^{3} perovskite system is usually very limited. In this Letter, a perovskitelike oxide Hg_{0.75}Pb_{0.25}MnO_{3} (HPMO) with a 3d^{3} Mn^{4+} state was synthesized by using high pressure and high temperature methods. This compound exhibits an unusually large octahedral distortion enhanced by approximately 2 orders of magnitude compared with that observed in other 3d^{3} perovskite systems like RCr^{3+}O_{3} (R=rare earth). Essentially different from centrosymmetric HgMnO_{3} and PbMnO_{3}, the A-site doped HPMO presents a polar crystal structure with the space group Ama2 and a substantial spontaneous electric polarization (26.5  μC/cm^{2} in theory) arising from the off-center displacements of A- and B-site ions. More interestingly, a prominent net photocurrent and switchable photovoltaic effect with a sustainable photoresponse were observed in the current polycrystalline HPMO. This Letter provides an exceptional d^{3} material system which shows unusually large octahedral distortion and displacement-type ferroelectricity violating the "d^{0}-ness" rule.

Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease

The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.

Association of a Multiancestry Genome-Wide Blood Pressure Polygenic Risk Score With Adverse Cardiovascular Events

BACKGROUND

Traditional cardiovascular risk factors and the underlying genetic risk of elevated blood pressure (BP) determine an individual's composite risk of developing adverse cardiovascular events. We sought to evaluate the relative contributions of the traditional cardiovascular risk factors to the development of adverse cardiovascular events in the context of varying BP genetic risk profiles.

METHODS

Genome-wide polygenic risk score (PRS) was computed using multiancestry genome-wide association estimates among US adults who underwent whole-genome sequencing in the Trans-Omics for Precision program. Individuals were stratified into high, intermediate, and low genetic risk groups (>80th, 20-80th, and <20th centiles of systolic BP [SBP] PRS). Based on the ACC/AHA Pooled Cohort Equations, participants were stratified into low and high (10 year-atherosclerotic cardiovascular disease [CVD] risk: <10% or ≥10%) cardiovascular risk factor profile groups. The primary study outcome was incident cardiovascular event (composite of incident heart failure, incident stroke, and incident coronary heart disease).

RESULTS

Among 21 897 US adults (median age: 56 years; 56.0% women; 35.8% non-White race/ethnicity), 1 SD increase in the SBP PRS, computed using 1.08 million variants, was associated with SBP (β: 4.39 [95% CI, 4.13-4.65]) and hypertension (odds ratio, 1.50 [95% CI, 1.46-1.55]), respectively. This association was robustly seen across racial/ethnic groups. Each SD increase in SBP PRS was associated with a higher risk of the incident CVD (multivariable-adjusted hazards ratio, 1.07 [95% CI, 1.04-1.10]) after controlling for ACC/AHA Pooled Cohort Equations risk scores. Among individuals with a high SBP PRS, low atherosclerotic CVD risk was associated with a 58% lower hazard for incident CVD (multivariable-adjusted hazards ratio, 0.42 [95% CI, 0.36-0.50]) compared to those with high atherosclerotic CVD risk. A similar pattern was noted in intermediate and low genetic risk groups.

CONCLUSIONS

In a multiancestry cohort of >21 000 US adults, genome-wide SBP PRS was associated with BP traits and adverse cardiovascular events. Adequate control of modifiable cardiovascular risk factors may reduce the predisposition to adverse cardiovascular events among those with a high SBP PRS.

[Neurocognitive impairment and characteristics of neurocognitive performance among people with HIV on antiretroviral treatment]

Objective: Using two measuring tools to examine the prevalence and correlates of neurocognitive impairment (NCI) as well as characteristics of neurocognitive performance among people with HIV (PWH) on antiretroviral treatment (ART). Methods: A total of 2 250 treated PWH from the Comparative HIV and Aging Research in Taizhou (CHART) were recruited in Taizhou, Zhejiang province. The Chinese version of the Mini-mental State Examination (MMSE) and the International HIV Dementia Scale (IHDS) were used to evaluate their neurocognitive performance. Cluster analysis was conducted on the seven cognitive domains in the scale. Results: Among 2 250 treated PWH, 48.0% (1 080/2 250) were aged 45 to 89, 79.2% (1 782/2 250) were male, and 37.8% (852/2 250) had primary school education or below. The prevalence of neurocognitive impairment judged by MMSE and IHDS among HIV-infected people was 14.3% (321/2 250) and 31.8% (716/2 250), respectively. Aged 60 to 89 (aOR=2.63, 95%CI:1.52-4.56), depressive symptoms (aOR=5.58, 95%CI:4.20-7.40) and treatment with EFV (aOR=2.86, 95%CI:1.89-4.34) were main risk factors of NCI diagnosed by MMSE. Male (aOR=0.71, 95%CI:0.51-1.00), overweight (aOR=0.63, 95%CI:0.44-0.89), and high education level (aOR=0.11, 95%CI:0.05-0.25) were protective factors of NCI diagnosed by MMSE. Aged 60 to 89 (aOR=3.10, 95%CI:2.09-4.59), depressive symptoms (aOR=1.78, 95%CI:1.44-2.20) and treatment with EFV (aOR=1.79, 95%CI:1.41-2.29) were risk factors of NCI diagnosed by IHDS. Male (aOR=0.75, 95%CI:0.58-0.97), underweight (aOR=0.67, 95%CI:0.47-0.96), baseline CD4⁺ T lymphocyte (CD4) counts ≥350 cells/μl (aOR=0.69, 95%CI:0.53-0.91) and high education level (aOR=0.23, 95%CI:0.14-0.39) were protective factors of NCI diagnosed by IHDS. The neurocognitive performance of HIV-infected people can be divided into four main types. Among four types, age, gender, education level, alcohol drinking, depressive symptoms, waist-to-hip ratio, hypertension, diabetes, baseline CD4 counts and treatment with EFV were different statistically (all P<0.05). Conclusions: There are four main types of neurocognitive performance in treated PWH. The prevalence of NCI is high among this population, underscoring the need for tailored prevention and intervention.

Genome-wide analyses identify SCN5A as a susceptibility locus for premature atrial contraction frequency

Premature atrial contractions (PACs) are frequently observed on electrocardiograms and are associated with increased risks of atrial fibrillation (AF), stroke, and mortality. In this study, we aimed to identify genetic susceptibility loci for PAC frequency. We performed a genome-wide association study meta-analysis with PAC frequency obtained from ambulatory cardiac monitoring in 4,831 individuals of European ancestry. We identified a genome-wide significant locus at the SCN5A gene. The lead variant, rs7373862, located in an intron of SCN5A, was associated with an increase of 0.12 [95% CI 0.08–0.16] standard deviations of the normalized PAC frequency per risk allele. Among genetic variants previously associated with AF, there was a significant enrichment in concordance of effect for PAC frequency (n = 73/106, p = 5.1 × 10⁻⁵). However, several AF risk loci, including PITX2, were not associated with PAC frequency. These findings suggest the existence of both shared and distinct genetic mechanisms for PAC frequency and AF.

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Variants in SCN5A are associated with premature atrial contractions (PAC) frequency

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Other atrial fibrillation (AF) risk variants are also associated with PAC frequency

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Both shared and distinct genetic mechanisms exist for PAC frequency and AF

Association of polygenic risk scores with incident atherosclerotic cardiovascular disease events among individuals with coronary artery calcium score of zero: The multi-ethnic study of atherosclerosis

BACKGROUND

Polygenic risk scores (PRS) are associated with atherosclerotic cardiovascular disease (ASCVD) events. We studied incident ASCVD among individuals with absent coronary artery calcium (CAC = 0), to investigate the association of PRS with incident ASCVD among such individuals.

METHODS

Data was used from Multi-Ethnic Study of Atherosclerosis (MESA), a prospective cohort study of participants free of clinical CVD at baseline. PRS were developed based on a literature-derived list of single-nucleotide polymorphisms (SNPs) weighted by effect size. The coronary heart disease (CHD) PRS contained 180 SNPs, and the stroke PRS had 32 SNPs. These SNPs were combined to compute an ASCVD PRS. The PRS were calculated among 3132 participants with CAC = 0. Multivariable-adjusted Cox proportional hazards models evaluated the association between each PRS (top 20% vs bottom 50%) and ASCVD.

RESULTS

The study population included 3132 individuals with CAC = 0 [mean (SD) age 58 (9) years; 63% female, 33% White, 31% Black, 12% Chinese-American, 24% Hispanic]. Over a median follow-up of 16 years, there were 108 incident CHD events and 93 stroke events. ASCVD event rates were generally <7.5 per 1000-person years for all ASCVD events regardless of PRS risk stratum. The ASCVD PRS was significantly associated with incident ASCVD: (HR; 95% CI) (1.63; 1.11, 2.39). The CHD PRS was not associated with any ASCVD outcome, whereas the stroke PRS was significantly associated with ASCVD (1.84; 1.27, 2.68), CHD (1.79; 1.05, 3.06), and stroke (1.96; 1.19, 3.23). The stroke PRS results were significant among women and non-Whites.

CONCLUSIONS

Among individuals with CAC = 0, the ASCVD PRS was associated with incident ASCVD events. This appears to be driven by genetic variants related to stroke but not CHD, and particularly among women and non-Whites. ASCVD event rates remained below the threshold recommended for consideration for initiation of statin therapy even in the high PRS groups.

Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways

The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry analyses (>250,000 individuals) we identify 177, 156 and 121 independent loci for QT, JT and QRS, respectively, including a male-specific X-chromosome locus. Using gene-based rare-variant methods, we identify associations with Mendelian disease genes. Enrichments are observed in established pathways for QT and JT, and previously unreported genes indicated in insulin-receptor signalling and cardiac energy metabolism. In contrast for QRS, connective tissue components and processes for cell growth and extracellular matrix interactions are significantly enriched. We demonstrate polygenic risk score associations with atrial fibrillation, conduction disease and sudden cardiac death. Prioritization of druggable genes highlight potential therapeutic targets for arrhythmia. Together, these results substantially advance our understanding of the genetic architecture of ventricular depolarization and repolarization.

Endophenotype effect sizes support variant pathogenicity in monogenic disease susceptibility genes

Accurate and efficient classification of variant pathogenicity is critical for research and clinical care. Using data from three large studies, we demonstrate that population-based associations between rare variants and quantitative endophenotypes for three monogenic diseases (low-density-lipoprotein cholesterol for familial hypercholesterolemia, electrocardiographic QTc interval for long QT syndrome, and glycosylated hemoglobin for maturity-onset diabetes of the young) provide evidence for variant pathogenicity. Effect sizes are associated with pathogenic ClinVar assertions (P < 0.001 for each trait) and discriminate pathogenic from non-pathogenic variants (area under the curve 0.82-0.84 across endophenotypes). An effect size threshold of ≥ 0.5 times the endophenotype standard deviation nominates up to 35% of rare variants of uncertain significance or not in ClinVar in disease susceptibility genes with pathogenic potential. We propose that variant associations with quantitative endophenotypes for monogenic diseases can provide evidence supporting pathogenicity.

Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

Polygenic risk scores (PRS) are commonly used to quantify the inherited susceptibility for a trait, yet they fail to account for non-linear and interaction effects between single nucleotide polymorphisms (SNPs). We address this via a machine learning approach, validated in nine complex phenotypes in a multi-ancestry population. We use an ensemble method of SNP selection followed by gradient boosted trees (XGBoost) to allow for non-linearities and interaction effects. We compare our results to the standard, linear PRS model developed using PRSice, LDpred2, and lassosum2. Combining a PRS as a feature in an XGBoost model results in a relative increase in the percentage variance explained compared to the standard linear PRS model by 22% for height, 27% for HDL cholesterol, 43% for body mass index, 50% for sleep duration, 58% for systolic blood pressure, 64% for total cholesterol, 66% for triglycerides, 77% for LDL cholesterol, and 100% for diastolic blood pressure. Multi-ancestry trained models perform similarly to specific racial/ethnic group trained models and are consistently superior to the standard linear PRS models. This work demonstrates an effective method to account for non-linearities and interaction effects in genetics-based prediction models.

Combining a standard polygenic risk score (PRS) as a feature in a machine learning model increases the percentage variance explained for those traits, helping to account for non-linearities or interaction effects in genetics-based prediction models.

A multi-ethnic polygenic risk score is associated with hypertension prevalence and progression throughout adulthood

In a multi-stage analysis of 52,436 individuals aged 17-90 across diverse cohorts and biobanks, we train, test, and evaluate a polygenic risk score (PRS) for hypertension risk and progression. The PRS is trained using genome-wide association studies (GWAS) for systolic, diastolic blood pressure, and hypertension, respectively. For each trait, PRS is selected by optimizing the coefficient of variation (CV) across estimated effect sizes from multiple potential PRS using the same GWAS, after which the 3 trait-specific PRSs are combined via an unweighted sum called "PRSsum", forming the HTN-PRS. The HTN-PRS is associated with both prevalent and incident hypertension at 4-6 years of follow up. This association is further confirmed in age-stratified analysis. In an independent biobank of 40,201 individuals, the HTN-PRS is confirmed to be predictive of increased risk for coronary artery disease, ischemic stroke, type 2 diabetes, and chronic kidney disease.

A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation

Nonalcoholic fatty liver disease (NAFLD) is a growing cause of chronic liver disease. Using a proxy NAFLD definition of chronic elevation of alanine aminotransferase (cALT) levels without other liver diseases, we performed a multiancestry genome-wide association study (GWAS) in the Million Veteran Program (MVP) including 90,408 cALT cases and 128,187 controls. Seventy-seven loci exceeded genome-wide significance, including 25 without prior NAFLD or alanine aminotransferase associations, with one additional locus identified in European American-only and two in African American-only analyses (P < 5 × 10-8). External replication in histology-defined NAFLD cohorts (7,397 cases and 56,785 controls) or radiologic imaging cohorts (n = 44,289) replicated 17 single-nucleotide polymorphisms (SNPs) (P < 6.5 × 10-4), of which 9 were new (TRIB1, PPARG, MTTP, SERPINA1, FTO, IL1RN, COBLL1, APOH and IFI30). Pleiotropy analysis showed that 61 of 77 multiancestry and all 17 replicated SNPs were jointly associated with metabolic and/or inflammatory traits, revealing a complex model of genetic architecture. Our approach integrating cALT, histology and imaging reveals new insights into genetic liability to NAFLD.

Monogenic and Polygenic Contributions to QTc Prolongation in the Population

BACKGROUND

Rare sequence variation in genes underlying cardiac repolarization and common polygenic variation influence QT interval duration. However, current clinical genetic testing of individuals with unexplained QT prolongation is restricted to examination of monogenic rare variants. The recent emergence of large-scale biorepositories with sequence data enables examination of the joint contribution of rare and common variations to the QT interval in the population.

METHODS

We performed a genome-wide association study of the QTc in 84 630 UK Biobank participants and created a polygenic risk score (PRS). Among 26 976 participants with whole-genome sequencing and ECG data in the TOPMed (Trans-Omics for Precision Medicine) program, we identified 160 carriers of putative pathogenic rare variants in 10 genes known to be associated with the QT interval. We examined QTc associations with the PRS and with rare variants in TOPMed.

RESULTS

Fifty-four independent loci were identified by genome-wide association study in the UK Biobank. Twenty-one loci were novel, of which 12 were replicated in TOPMed. The PRS composed of 1 110 494 common variants was significantly associated with the QTc in TOPMed (ΔQTc/decile of PRS=1.4 ms [95% CI, 1.3 to 1.5]; P=1.1×10-196). Carriers of putative pathogenic rare variants had longer QTc than noncarriers (ΔQTc=10.9 ms [95% CI, 7.4 to 14.4]). Of individuals with QTc>480 ms, 23.7% carried either a monogenic rare variant or had a PRS in the top decile (3.4% monogenic, 21% top decile of PRS).

CONCLUSIONS

QTc duration in the population is influenced by both rare variants in genes underlying cardiac repolarization and polygenic risk, with a sizeable contribution from polygenic risk. Comprehensive assessment of the genetic determinants of QTc prolongation includes incorporation of both polygenic and monogenic risk.

Glucose-6-phosphate dehydrogenase deficiency presenting with rhabdomyolysis in a patient with coronavirus disease 2019 pneumonia: a case report

Background

Glucose-6-phosphate dehydrogenase deficiency is a rarely recognized predisposing factor for rhabdomyolysis. Rhabdomyolysis with coronavirus disease 2019 has been increasingly seen during the pandemic. We report the uncommon occurrence of coronavirus disease 2019 pneumonia, severe rhabdomyolysis, and acute renal failure in the setting of glucose-6-phosphate dehydrogenase deficiency.

Case presentation

A 19-year-old African American male presented with myalgias, diaphoresis, and dark urine. Testing for severe acute respiratory syndrome coronavirus 2 was positive. He had severe rhabdomyolysis with creatine kinase levels up to 346,695 U/L. He was oliguric and eventually required hemodialysis. Progressive hypoxemia, methemoglobinemia, and hemolytic anemia occurred following one dose of rasburicase for hyperuricemia. Glucose-6-phosphate dehydrogenase deficiency was diagnosed. Full recovery followed a single volume exchange transfusion and simple packed red blood cell transfusions.

Conclusions

Glucose-6-phosphate dehydrogenase deficiency may predispose individuals to rhabdomyolysis due to severe acute respiratory syndrome coronavirus 2, presumably due to altered host responses to viral oxidative stress. Early screening for glucose-6-phosphate dehydrogenase deficiency can be useful for management of patients with rhabdomyolysis.

[Correlation between HIV infection, club drug use and anal canal human papillomavirus infection in men who have sex with men in Taizhou]

Objective: To explore the correlation between club drug use and anal canal human papillomavirus (HPV) infection in HIV-negative and HIV-positive men who have sex with men (MSM) in Taizhou. Methods: A cross-sectional survey was conducted in Taizhou. HIV-negative MSM were recruited by convenient sampling in voluntary counseling and testing clinics of Taizhou prefectural CDC from August 2016 to October 2017, and HIV-positive MSM were recruited through the routine follow-up and management by Taizhou prefectural CDC from August 2016 to June 2019. A face-to-face questionnaire interview was conducted to collect the information about the socio-demographic characteristics, sexual orientation, sexual behavior, club drug use and other information of the participants. Anal canal swabs were collected for HPV genotyping. The correlation between club drug use and the prevalence of HPV infection were evaluated with χ² test and logistic regression analysis. Results: A total of 69 HIV-negative and 345 HIV-infected MSM were included. The prevalence of any type of anal canal HPV infection in HIV-negative MSM (27.5%, 19/69) was lower than that in HIV-positive MSM (66.4%, 229/345) (χ²=36.114,P<0.001). The prevalence of self-reported club drug use in HIV-negative MSM was higher (17.4%, 12/69) than that in HIV-positive MSM (7.0%, 24/345) (χ²=7.886, P=0.005). For HIV-negative MSM, the prevalence of club drug use was higher in MSM who had homosexual group sex (P=0.036); the prevalence of HPV infection was 50.0% (6/12) in club drug users and 22.8% (13/57) in non-club drug users (χ²=3.674, P=0.055). For HIV-positive MSM, the prevalence of HPV infection was 70.8% (17/24) in club drug users and 66.0% (212/321) in non-club drug users (χ²=0.230, P=0.632). Multivariable logistic regression model showed that HPV infection in MSM was positively correlated with HIV infection (OR=5.42, 95%CI: 2.92-10.06), and the association between HPV infection and club drug use (OR=1.66, 95%CI: 0.75-3.71) was not significant. Conclusions: HIV infection was positively correlated with anal canal HPV infection in MSM in Taizhou. Club drug use was positively correlated with high-risk sexual behaviors, while its association with HPV infection needs further study.

Identification of Functional Genetic Determinants of Cardiac Troponin T and I in a Multiethnic Population and Causal Associations With Atrial Fibrillation

BACKGROUND

Elevated cardiac troponin levels in blood are associated with increased risk of cardiovascular diseases and mortality. Cardiac troponin levels are heritable, but their genetic architecture remains elusive.

METHODS

We conducted a transethnic genome-wide association analysis on high-sensitivity cTnT (cardiac troponin T; hs-cTnT) and high-sensitivity cTnI (cardiac troponin I; hs-cTnI) levels in 24 617 and 14 336 participants free of coronary heart disease and heart failure from 6 population-based cohorts, followed by a series of bioinformatic analyses to decipher the genetic architecture of hs-cTnT and hs-cTnI.

RESULTS

We identified 4 genome-wide significant loci for hs-cTnT including a novel locus rs3737882 in PPFIA4 and 3 previously reported loci at NCOA2, TRAM1, and BCL2. One known locus at VCL was replicated for hs-cTnI. One copy of C allele for rs3737882 was associated with a 6% increase in hs-cTnT levels (minor allele frequency, 0.18; P=2.80×10-9). We observed pleiotropic loci located at BAG3 and ANO5. The proportions of variances explained by single-nucleotide polymorphisms were 10.15% and 7.74% for hs-cTnT and hs-cTnI, respectively. Single-nucleotide polymorphisms were colocalized with BCL2 expression in heart tissues and hs-cTnT and with ANO5 expression in artery, heart tissues, and whole blood and both troponins. Mendelian randomization analyses showed that genetically increased hs-cTnT and hs-cTnI levels were associated with higher odds of atrial fibrillation (odds ratio, 1.38 [95% CI, 1.25-1.54] for hs-cTnT and 1.21 [95% CI, 1.06-1.37] for hs-cTnI).

CONCLUSIONS

We identified a novel genetic locus associated with hs-cTnT in a multiethnic population and found that genetically regulated troponin levels were associated with atrial fibrillation.

[Machine learning and its epidemiological applications]

As an important branch of artificial intelligence, machine learning is widely used in various fields. Machine learning has similarity to classical statistical methods, but can solve many problems which are difficult for traditional statistics, so it is one of the important tools in epidemiological research. This paper introduced 9 common algorithms of machine learning and summarized their characteristics and applications in epidemiological research. Readers could choose appropriate machine learning method according to the research purpose for the better application of machine learning in epidemiological research.

Rare Coding Variants Associated With Electrocardiographic Intervals Identify Monogenic Arrhythmia Susceptibility Genes: A Multi-Ancestry Analysis

BACKGROUND

Alterations in electrocardiographic (ECG) intervals are well-known markers for arrhythmia and sudden cardiac death (SCD) risk. While the genetics of arrhythmia syndromes have been studied, relations between electrocardiographic intervals and rare genetic variation at a population level are poorly understood.

METHODS

Using a discovery sample of 29 000 individuals with whole-genome sequencing from Trans-Omics in Precision Medicine and replication in nearly 100 000 with whole-exome sequencing from the UK Biobank and MyCode, we examined associations between low-frequency and rare coding variants with 5 routinely measured electrocardiographic traits (RR, P-wave, PR, and QRS intervals and corrected QT interval).

RESULTS

We found that rare variants associated with population-based electrocardiographic intervals identify established monogenic SCD genes (KCNQ1, KCNH2, and SCN5A), a controversial monogenic SCD gene (KCNE1), and novel genes (PAM and MFGE8) involved in cardiac conduction. Loss-of-function and pathogenic SCN5A variants, carried by 0.1% of individuals, were associated with a nearly 6-fold increased odds of the first-degree atrioventricular block (P=8.4×10^-5). Similar variants in KCNQ1 and KCNH2 (0.2% of individuals) were associated with a 23-fold increased odds of marked corrected QT interval prolongation (P=4×10^-25), a marker of SCD risk. Incomplete penetrance of such deleterious variation was common as over 70% of carriers had normal electrocardiographic intervals.

CONCLUSIONS

Our findings indicate that large-scale high-depth sequence data and electrocardiographic analysis identifies monogenic arrhythmia susceptibility genes and rare variants with large effects. Known pathogenic variation in conventional arrhythmia and SCD genes exhibited incomplete penetrance and accounted for only a small fraction of marked electrocardiographic interval prolongation.

[HIV-1 drug resistance and subtypes in newly reported HIV/AIDS patients before antiretroviral therapy in Taizhou city, 2016-2018]

Objective: To explore the HIV-1 drug resistance and subtypes in newly reported HIV/AIDS patients before antiretroviral therapy (ART) in Taizhou city. Methods: A cross-sectional study of HIV-1 drug resistance was conducted among newly reported HIV/AIDS patients before ART in Taizhou from January 2016 to December 2018. HIV-1 pol gene sequences were obtained by RT-PCR. The sequences were submitted to the Stanford University drug resistance database. The drug resistance mutation and the sensitivity of HIV-1 strains to antiretroviral drugs were determined according to WHO Guidelines on HIV drug resistance surveillance of 2014. Results: A total of 806 HIV-1 pol gene sequences were obtained successfully. The overall HIV-1 drug resistance rate was 2.9% (23/806), 1.9% for non-nucleoside reverse transcriptase inhibitors (NNRTIs), 0.6% for nucleoside reverse transcriptase inhibitors (NRTIs), and 0.0% for protease inhibitors (PIs), respectively. From 2016 to 2018, the HIV-1 drug resistance rate was 1.6%, 1.8%, and 4.8%, respectively. The resistance mutations of NNRTIs and NRTIs were mainly K103 N (0.7%) and M184I/V (0.5%). HIV-1 subtypes were mostly CRF01_AE (42.7%,344/806),CRF07_BC (28.9%,233/806) and CRF08_BC (11.2%,90/806).HIV-1 subtypes among homosexually transmitted infections were mostly CRF01_AE (53.3%, 136/255) and CRF07_BC (32.2%, 82/255), and HIV-1 subtypes among heterosexually transmitted infections were mainly CRF01_AE (37.7%, 203/539), CRF07_BC (27.5%, 148/539) and CRF08_BC (16.1%, 87/539). Conclusion: HIV-1 drug resistance rate among newly reported HIV/AIDS patients before ART remained low in Taizhou during 2016 to 2018, an increasing trend seemed to be notifiable and warrants continuous surveillance of HIV-1 drug resistance.

[Prevalence and correlates of plasma cytomegalovirus viremia among newly reported HIV/AIDS patients in Taizhou city, 2017-2018]

Objective: To study the prevalence and correlates of plasma cytomegalovirus (CMV) viremia among newly reported antiretroviral therapy (ART)-naive HIV/AIDS patients in Taizhou during 2017-2018. Methods: CMV DNA was measured in plasma specimens of newly reported ART-naive HIV/AIDS patients by quantitative PCR. Both univariable and multivariable logistic regression analyses were carried out to evaluate CMV viremia correlations among the individuals. Results: Of 612 HIV/AIDS patients, 480 (78.4%) were male, 125 (20.4%) were over 60 years old, 177 (28.9%) were infected via homosexual transmission, and 430 (70.3%) via heterosexual transmission. The prevalence of CMV viremia among HIV/AIDS patients was 13.4% (82/612). Multivariable logistic regression analysis showed that the risk of CMV viremia in CD₄⁺ lymphocyte cells counts (CD₄⁺) ≤200 cells/μl group was higher than CD₄ counts >500 cells/μl (OR=5.10, 95%CI:1.74-14.96, P=0.003); The median CMV DNA level (log₁₀) of 82 viremic patients was 1.57 (P₂₅,P₇₅:1.04,2.13); Viremic patients with CD₄ counts ≤200 cells/μl had the highest CMV viral load (P<0.01). Conclusions: Among ART-naive HIV/AIDS patients, the prevalence of CMV viremia was significantly associated with immunodeficiency status. Further research is needed to evaluate the association between CMV viremia and the course of HIV infection.

[Influencing factors of antiretroviral therapy and its association with immunological effect among HIV/AIDS patients in Taizhou city, 2006-2019]

Objective: To analyze influencing factors of instant antiretroviral therapy (ART) and explore associution between strategies of ART and immunological effects among HIV/AIDS patients in Taizhou city during 2006-2019. Methods: A retrospective cohort study was conducted on HIV/AIDS patients under ART, and a logistic regression model was used to analyze factors of instant ART. The student t-test and chi-square test were used to compare immunological effect of different ART strategies while the Kaplan-Meier method was used to generate a survival curve. Results: A total of 2 971 HIV/AIDS patients were enrolled with 1 786 cases (60.1%) having instant ART strategy. The proportion of instant ART were 77.8% (1 170/1 504) during 2016 to 2019. The treatment success rate of the instant ART group (87.4%, 1 561/1 786) were higher than the delayed ART group (84.4%, 1 000/1 185). The results of multivariate logistic regression model indicated that male (aOR=1.28, 95%CI: 1.03-1.59), married (aOR=1.71, 95%CI: 1.33-2.19) and baseline CD(4)(+)T lymphocyte cells (CD(4)) counts ≤200 cells/μl (aOR=1.60, 95%CI: 1.27-2.02) were factors positively related to instant ART while 31-40 years old (aOR=0.63, 95%CI: 0.48-0.84), infected through heterosexual transmission(aOR=0.60, 95%CI: 0.49-0.74) and diagnosed before 2015 (aOR=0.20, 95%CI: 0.17-0.23) were inversely related to instant ART. The increase of the CD(4)/CD(8) ratio was greater, and the cumulative ART success rate was higher each year in the instant ART group than in the delayed ART group (P<0.05). Conclusions: The instant ART strategy has been well implemented in Taizhou city during 2006-2019, and the immunological effect was better in instant ART group. The proportion of instant ART were more than 60.0% among HIV/AIDS patients. Instant ART strategy needs to be strengthened for those who are 31-40 years old, women, unmarried, and infected through heterosexual transmission in an attempt to further increase treatment level and improve treatment effect.

[Risk analysis of immunological failure of antiretroviral therapy in HIV/AIDS patients in Taizhou prefecture, 2006-2019]

Objective: To analyze the immunological failure of antiretroviral therapy (ART), its association with baseline anemia and related factors in HIV/AIDS patients in Taizhou prefecture, during 2006-2019. Methods: A retrospective cohort study was conducted among HIV/AIDS patients under ART. Cox regression model was used to analyze predictors of immunological failure and logistic regression model was used to analyze factors of baseline anemia. Results: A total of 2 904 HIV/AIDS patients were enrolled with a median time of 28 (P(25)-P(75):12-53) months follow-up of ART, in which 177 cases (6.1%) were identified as immunological failure with a failure rate of 2.17 per 100 person-years. The cumulative incidence rates of immunological failure in the first, third, fifth, and tenth years were 5.49%, 6.94%, 7.30% and 8.82%, respectively. Results of multivariate logistic regression analysis showed that for the risk of baseline anemia, ≥66 years old group had 4.17 times higher risk than 18-25 years old group (95%CI: 1.68-10.33), males had 0.67 times higher risk than females (95%CI: 0.50-0.89), and CD(4)(+)T cell counts (CD(4))<200 cells/μl group had 4.35 times higher risk than CD(4)≥350 cells/μl group (95%CI: 2.81-6.72), baseline white blood cells<4.0×10(9) cells/L group had 1.73 times higher risk than 4.0×10(9) cells/L-9.9×10(9) cells/L group (95%CI: 1.31-2.29), baseline platelet counts <100×10(9) cells/L and >300×10(9) cells/L groups had 2.02 times and 4.45 times higher risk than 100×10(9) cells/L-299×10(9) cells/L group (95%CI: 1.36-3.01, 95%CI: 3.05-6.50), respectively. WHO classified stage Ⅲ/Ⅳ group had 2.15 times higher risk than WHO classified stageⅠ/Ⅱ group (95%CI: 1.61-2.87), while heterosexual transmission group had 2.03 times higher risk than homosexual transmission group (95%CI: 1.42-2.92). Results of multivariate cox proportional risk regression showed that for the risk of immunological failure, baseline anemia group had 1.77 times higher risk than no anemia group (95%CI: 1.20-2.60), WHO classified stage Ⅲ/Ⅳ group had 1.66 times higher risk than WHO classified stage Ⅰ/Ⅱ group (95%CI: 1.10-2.48), and withdrawal of follow up and death groups had 3.18 times and 4.61 times higher risks than treatment group (95%CI: 1.96-5.19, 95%CI: 2.98-7.13), respectively. Conclusions: The immunological effect of ART among HIV/AIDS patients in Taizhou prefecture was affected by multiple factors, including anemia, clinical stage and follow-up status. Enhancing surveillance of baseline anemia and timely correction of anemia in elder group can help improve treatment outcome of HIV/AIDS patients.

Role of active cycle of breathing technique for patients with chronic obstructive pulmonary disease: A pragmatic, randomized clinical trial

BACKGROUND

While active cycle of breathing technique for chronic obstructive pulmonary disease patients with more sputum can improve clinic outcomes, less is known about sputum viscosity and sputum production of the intervention.

OBJECTIVE

The purpose of our study was to explore the effect of active cycle of breathing technique on sputum viscosity and production among patients with chronic obstructive pulmonary disease.

DESIGN

This was a two-arms, parallel, randomized clinical trial.

SETTING

Study enrollment, randomization and implementation were conducted in the department of respiratory medicine inpatient at the Medical Center in Changchun, China.

PARTICIPANTS

Hospitalized patients due to chronic obstructive pulmonary disease who met additional eligibility criteria were randomized to active cycle of breathing technique (n = 50) or usual care group (n = 50).

METHODS

Patients in the intervention group received a week-long intervention from an experienced physical therapist. Patients in the usual care group received usual care as well as information and advice in the light of their health plan from respiratory medicine. The primary outcome was the changes on sputum viscosity and production.

RESULTS

Among one hundred patients who were randomized (mean [SD] age, 54.89 [12.06] years; females, 58%), ninety-six participants completed the study. No significant differences were found between two groups on the changes of sputum viscosity (t = 0.277, P = 0.782). And there were insignificant differences between groups in the average amount of sputum among 1 h (Z=-1.848, P = 0.065) and significant differences in the average amount of sputum among 24 h (Z=-2.236, P = 0.025). From admission to one week recovery, the changes in ratio of forced expiratory volume in 1 s to forced vital capacity (Z=-4.511, P<0.0001) and arterial oxygen saturation (Z=-2.997, P = 0.003) were better in active cycle breathing technique group. Total Chronic Obstructive Pulmonary Disease Assessment Test scale were similar among two groups (Z=-1.818, P = 0.069). No adverse events occurred during the study.

CONCLUSION

For patients with chronic obstructive pulmonary disease, active cycle of breathing technique can significantly result in sputum production and respiratory function, especially those of Global Initiative for Chronic Obstructive Lung Disease classification level 3, but did not result in the short-term improvement of sputum viscosity, quality of life and cost effectiveness. Registration number: ChiCTR2000033068.

Genetic Determinants of Electrocardiographic P-Wave Duration and Relation to Atrial Fibrillation

BACKGROUND

The P-wave duration (PWD) is an electrocardiographic measurement that represents cardiac conduction in the atria. Shortened or prolonged PWD is associated with atrial fibrillation (AF). We used exome-chip data to examine the associations between common and rare variants with PWD.

METHODS

Fifteen studies comprising 64 440 individuals (56 943 European, 5681 African, 1186 Hispanic, 630 Asian) and ≈230 000 variants were used to examine associations with maximum PWD across the 12-lead ECG. Meta-analyses summarized association results for common variants; gene-based burden and sequence kernel association tests examined low-frequency variant-PWD associations. Additionally, we examined the associations between PWD loci and AF using previous AF genome-wide association studies.

RESULTS

We identified 21 common and low-frequency genetic loci (14 novel) associated with maximum PWD, including several AF loci (TTN, CAND2, SCN10A, PITX2, CAV1, SYNPO2L, SOX5, TBX5, MYH6, RPL3L). The top variants at known sarcomere genes (TTN, MYH6) were associated with longer PWD and increased AF risk. However, top variants at other loci (eg, PITX2 and SCN10A) were associated with longer PWD but lower AF risk.

CONCLUSIONS

Our results highlight multiple novel genetic loci associated with PWD, and underscore the shared mechanisms of atrial conduction and AF. Prolonged PWD may be an endophenotype for several different genetic mechanisms of AF.

Mitochondrial DNA copy number and incident atrial fibrillation

BACKGROUND

Mechanistic studies suggest that mitochondria DNA (mtDNA) dysfunction may be associated with increased risk of atrial fibrillation (AF). The association between mtDNA copy number (mtDNA-CN) and incident AF in the general population, however, remains unknown.

METHODS

We conducted prospective analyses of 19,709 participants from the Atherosclerosis Risk in Communities Study (ARIC), the Multi-Ethnic Study of Atherosclerosis (MESA), and the Cardiovascular Health Study (CHS). mtDNA-CN from the peripheral blood was calculated from probe intensities on the Affymetrix Genome-Wide Human single nucleotide polymorphisms (SNP) Array 6.0 in ARIC and MESA and from multiplexed real-time quantitative polymerase chain reaction (qPCR) in CHS. Incident AF cases were identified through electrocardiograms, review of hospital discharge codes, Medicare claims, and death certificates.

RESULTS

The median follow-up time was 21.4 years in ARIC, 12.9 years in MESA, and 11.0 years in CHS, during which 4021 participants developed incident atrial fibrillation (1761 in ARIC, 790 in MESA, and 1470 in CHS). In fully adjusted models, participants with the lowest quintile of mitochondria DNA copy number had an overall 13% increased risk (95% CI 1 to 27%) of incident atrial fibrillation compared to those with the highest quintile. Dose-response spline analysis also showed an inverse association between mitochondria DNA copy number and hazard for atrial fibrillation for all three cohorts. These associations were consistent across subgroups.

CONCLUSIONS

Mitochondria DNA copy number was inversely associated with the risk of AF independent of traditional cardiovascular risk factors. These findings implicate mitochondria DNA copy number as a novel risk factor for atrial fibrillation. Further research is warranted to understand the underlying mechanisms and to evaluate the role of mitochondria DNA copy number in the management of atrial fibrillation risk.

Multi-Ethnic Genome-Wide Association Study of Decomposed Cardioelectric Phenotypes Illustrates Strategies to Identify and Characterize Evidence of Shared Genetic Effects for Complex Traits

BACKGROUND

We examined how expanding electrocardiographic trait genome-wide association studies to include ancestrally diverse populations, prioritize more precise phenotypic measures, and evaluate evidence for shared genetic effects enabled the detection and characterization of loci.

METHODS

We decomposed 10 seconds, 12-lead electrocardiograms from 34 668 multi-ethnic participants (15% Black; 30% Hispanic/Latino) into 6 contiguous, physiologically distinct (P wave, PR segment, QRS interval, ST segment, T wave, and TP segment) and 2 composite, conventional (PR interval and QT interval) interval scale traits and conducted multivariable-adjusted, trait-specific univariate genome-wide association studies using 1000-G imputed single-nucleotide polymorphisms. Evidence of shared genetic effects was evaluated by aggregating meta-analyzed univariate results across the 6 continuous electrocardiographic traits using the combined phenotype adaptive sum of powered scores test.

RESULTS

We identified 6 novels (CD36, PITX2, EMB, ZNF592, YPEL2, and BC043580) and 87 known loci (adaptive sum of powered score test P<5×10-9). Lead single-nucleotide polymorphism rs3211938 at CD36 was common in Blacks (minor allele frequency=10%), near monomorphic in European Americans, and had effects on the QT interval and TP segment that ranked among the largest reported to date for common variants. The other 5 novel loci were observed when evaluating the contiguous but not the composite electrocardiographic traits. Combined phenotype testing did not identify novel electrocardiographic loci unapparent using traditional univariate approaches, although this approach did assist with the characterization of known loci.

CONCLUSIONS

Despite including one-third as many participants as published electrocardiographic trait genome-wide association studies, our study identified 6 novel loci, emphasizing the importance of ancestral diversity and phenotype resolution in this era of ever-growing genome-wide association studies.

A structural variation reference for medical and population genetics

Structural variants (SVs) rearrange large segments of DNA¹ and can have profound consequences in evolution and human disease^2,3. As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD)⁴ have become integral in the interpretation of single-nucleotide variants (SNVs)⁵. However, there are no reference maps of SVs from high-coverage genome sequencing comparable to those for SNVs. Here we present a reference of sequence-resolved SVs constructed from 14,891 genomes across diverse global populations (54% non-European) in gnomAD. We discovered a rich and complex landscape of 433,371 SVs, from which we estimate that SVs are responsible for 25–29% of all rare protein-truncating events per genome. We found strong correlations between natural selection against damaging SNVs and rare SVs that disrupt or duplicate protein-coding sequence, which suggests that genes that are highly intolerant to loss-of-function are also sensitive to increased dosage⁶. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than all noncoding effects. Finally, we identified very large (over one megabase), rare SVs in 3.9% of samples, and estimate that 0.13% of individuals may carry an SV that meets the existing criteria for clinically important incidental findings⁷. This SV resource is freely distributed via the gnomAD browser⁸ and will have broad utility in population genetics, disease-association studies, and diagnostic screening.

A large empirical assessment of sequence-resolved structural variants from 14,891 genomes across diverse global populations in the Genome Aggregation Database (gnomAD) provides a reference map for disease-association studies, population genetics, and diagnostic screening.

Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction

The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N = 293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease.

Assessment of the Relationship Between Genetic Determinants of Thyroid Function and Atrial Fibrillation: A Mendelian Randomization Study

Importance

Increased free thyroxine (FT4) and decreased thyrotropin are associated with increased risk of atrial fibrillation (AF) in observational studies, but direct involvement is unclear.

Objective

To evaluate the potential direct involvement of thyroid traits on AF.

Design, Setting, and Participants

Study-level mendelian randomization (MR) included 11 studies, and summary-level MR included 55 114 AF cases and 482 295 referents, all of European ancestry.

Exposures

Genomewide significant variants were used as instruments for standardized FT4 and thyrotropin levels within the reference range, standardized triiodothyronine (FT3):FT4 ratio, hypothyroidism, standardized thyroid peroxidase antibody levels, and hyperthyroidism. Mendelian randomization used genetic risk scores in study-level analysis or individual single-nucleotide polymorphisms in 2-sample MR for the summary-level data.

Main Outcomes and Measures

Prevalent and incident AF.

Results

The study-level analysis included 7679 individuals with AF and 49 233 referents (mean age [standard error], 62 [3] years; 15 859 men [29.7%]). In study-level random-effects meta-analysis, the pooled hazard ratio of FT4 levels (nanograms per deciliter) for incident AF was 1.55 (95% CI, 1.09-2.20; P = .02; I2 = 76%) and the pooled odds ratio (OR) for prevalent AF was 2.80 (95% CI, 1.41-5.54; P = .003; I2 = 64%) in multivariable-adjusted analyses. The FT4 genetic risk score was associated with an increase in FT4 by 0.082 SD (standard error, 0.007; P < .001) but not with incident AF (risk ratio, 0.84; 95% CI, 0.62-1.14; P = .27) or prevalent AF (OR, 1.32; 95% CI, 0.64-2.73; P = .46). Similarly, in summary-level inverse-variance weighted random-effects MR, gene-based FT4 within the reference range was not associated with AF (OR, 1.01; 95% CI, 0.89-1.14; P = .88). However, gene-based increased FT3:FT4 ratio, increased thyrotropin within the reference range, and hypothyroidism were associated with AF with inverse-variance weighted random-effects OR of 1.33 (95% CI, 1.08-1.63; P = .006), 0.88 (95% CI, 0.84-0.92; P < .001), and 0.94 (95% CI, 0.90-0.99; P = .009), respectively, and robust to tests of horizontal pleiotropy. However, the subset of hypothyroidism single-nucleotide polymorphisms involved in autoimmunity and thyroid peroxidase antibodies levels were not associated with AF. Gene-based hyperthyroidism was associated with AF with MR-Egger OR of 1.31 (95% CI, 1.05-1.63; P = .02) with evidence of horizontal pleiotropy (P = .045).

Conclusions and Relevance

Genetically increased FT3:FT4 ratio and hyperthyroidism, but not FT4 within the reference range, were associated with increased AF, and increased thyrotropin within the reference range and hypothyroidism were associated with decreased AF, supporting a pathway involving the pituitary-thyroid-cardiac axis.

The effect of orbital-lattice coupling on the electrical resistivity of YBaCuFeO5 investigated by X-ray absorption

Temperature-dependent X-ray absorption near-edge structures, X-ray linear dichroism (XLD) and extended X-ray absorption fine structure (EXAFS) spectroscopic techniques were used to investigate the valence state, preferred orbital and local atomic structure that significantly affect the electrical and magnetic properties of a single crystal of YBaCuFeO5 (YBCFO). An onset of increase of resistivity at ~180 K, followed by a rapid increase at/below 125 K, is observed. An antiferromagnetic (AFM)-like transition is close to the temperature at which the resistivity starts to increase in the ab-plane and is also observed with strong anisotropy between the ab-plane and the c-axis. The XLD spectra at the Fe L3,2-edge revealed a change in Fe 3d eg holes from the preferential [Formula: see text] orbital at high temperature (300-150 K) to the [Formula: see text] orbital at/below 125 K. The analysis of the Fe K-edge EXAFS data of YBCFO further revealed an unusual increase in the Debye-Waller factor of the nearest-neighbor Fe-O bond length at/below 125 K, suggesting phonon-softening behavior, resulting in the breaking of lattice symmetry, particularly in the ab-plane of Fe-related square pyramids. These findings demonstrate a close correlation between electrical resistivity and coupling of the preferred Fe 3d orbital with lattice distortion of a single crystal of YBCFO.

GWAS of QRS duration identifies new loci specific to Hispanic/Latino populations

Background

The electrocardiographically quantified QRS duration measures ventricular depolarization and conduction. QRS prolongation has been associated with poor heart failure prognosis and cardiovascular mortality, including sudden death. While previous genome-wide association studies (GWAS) have identified 32 QRS SNPs across 26 loci among European, African, and Asian-descent populations, the genetics of QRS among Hispanics/Latinos has not been previously explored.

Methods

We performed a GWAS of QRS duration among Hispanic/Latino ancestry populations (n = 15,124) from four studies using 1000 Genomes imputed genotype data (adjusted for age, sex, global ancestry, clinical and study-specific covariates). Study-specific results were combined using fixed-effects, inverse variance-weighted meta-analysis.

Results

We identified six loci associated with QRS (P<5x10^-8), including two novel loci: MYOCD, a nuclear protein expressed in the heart, and SYT1, an integral membrane protein. The top SNP in the MYOCD locus, intronic SNP rs16946539, was found in Hispanics/Latinos with a minor allele frequency (MAF) of 0.04, but is monomorphic in European and African descent populations. The most significant QRS duration association was with intronic SNP rs3922344 (P = 1.19x10^-24) in SCN5A/SCN10A. Three other previously identified loci, CDKN1A, VTI1A, and HAND1, also exceeded the GWAS significance threshold among Hispanics/Latinos. A total of 27 of 32 previously identified QRS duration SNPs were shown to generalize in Hispanics/Latinos.

Conclusions

Our QRS duration GWAS, the first in Hispanic/Latino populations, identified two new loci, underscoring the utility of extending large scale genomic studies to currently under-examined populations.

Effects of Calcium, Magnesium, and Potassium Concentrations on Ventricular Repolarization in Unselected Individuals

BACKGROUND

Subclinical changes on the electrocardiogram are risk factors for cardiovascular mortality. Recognition and knowledge of electrolyte associations in cardiac electrophysiology are based on only in vitro models and observations in patients with severe medical conditions.

OBJECTIVES

This study sought to investigate associations between serum electrolyte concentrations and changes in cardiac electrophysiology in the general population.

METHODS

Summary results collected from 153,014 individuals (54.4% women; mean age 55.1 ± 12.1 years) from 33 studies (of 5 ancestries) were meta-analyzed. Linear regression analyses examining associations between electrolyte concentrations (mmol/l of calcium, potassium, sodium, and magnesium), and electrocardiographic intervals (RR, QT, QRS, JT, and PR intervals) were performed. The study adjusted for potential confounders and also stratified by ancestry, sex, and use of antihypertensive drugs.

RESULTS

Lower calcium was associated with longer QT intervals (-11.5 ms; 99.75% confidence interval [CI]: -13.7 to -9.3) and JT duration, with sex-specific effects. In contrast, higher magnesium was associated with longer QT intervals (7.2 ms; 99.75% CI: 1.3 to 13.1) and JT. Lower potassium was associated with longer QT intervals (-2.8 ms; 99.75% CI: -3.5 to -2.0), JT, QRS, and PR durations, but all potassium associations were driven by use of antihypertensive drugs. No physiologically relevant associations were observed for sodium or RR intervals.

CONCLUSIONS

The study identified physiologically relevant associations between electrolytes and electrocardiographic intervals in a large-scale analysis combining cohorts from different settings. The results provide insights for further cardiac electrophysiology research and could potentially influence clinical practice, especially the association between calcium and QT duration, by which calcium levels at the bottom 2% of the population distribution led to clinically relevant QT prolongation by >5 ms.

[Prevalence of alcohol use and related factors in HIV positive and HIV negative males]

Objective: To understand the prevalence of alcohol use and related factors in HIV positive and HIV negative males. Methods: Baseline data were from the prospective cohort study of comparative HIV and aging research in Taizhou of Zhejiang province from January to December, 2017. The information about alcohol use in the last month was collected through a face-to-face questionnaire interview. Participants were categorized into non-current drinkers, light/moderate drinkers and heavy drinkers according to the US National Institute on Alcoholism and Alcohol Abuse (NIAAA) standard. Results: A total of 1 367 HIV positive males and 2 418 HIV negative males were included. Current alcohol use rate (35.2%, 481/1 367) and heavy alcohol use rate (5.0%, 24/481) were significantly lower in HIV positive males than in HIV negative males (48.0%, 1 161/2 418; 23.5%, 273/1 161), but the proportion of drinking wine and yellow rice wine were significantly higher (21.8%, 105/481; 9.1%, 44/481) in HIV positive males than in HIV negative males (13.5%, 157/1 161; 5.8%, 67/1 161). The multivariate multinomial logistic regression analysis results showed that larger waist circumference, current smoking and regular physical exercise were associated with heavy alcohol use behavior in HIV positive males, and age ≥30 years, current smoking, regular physical exercise, higher score of depressive symptoms, heterosexual transmission route and baseline CD(4)(+)T cells counts of 200-499 cells/μl were significantly associated with mild/moderate alcohol use behavior in HIV positive males. Conclusions: The alcohol use rate was significantly lower in HIV positive males than in HIV negative males in Taizhou. It is important to strengthen intervention on alcohol drinking behavior and chronic disease risk factors, such as larger waist circumference, smoking and so on.

Superconductivity in a unique type of copper oxide

The mechanism of superconductivity in cuprates remains one of the big challenges of condensed matter physics. High-T c cuprates crystallize into a layered perovskite structure featuring copper oxygen octahedral coordination. Due to the Jahn Teller effect in combination with the strong static Coulomb interaction, the octahedra in high-T c cuprates are elongated along the c axis, leading to a 3dx 2-y 2 orbital at the top of the band structure wherein the doped holes reside. This scenario gives rise to 2D characteristics in high-T c cuprates that favor d-wave pairing symmetry. Here, we report superconductivity in a cuprate Ba2CuO4-y , wherein the local octahedron is in a very exceptional compressed version. The Ba2CuO4-y compound was synthesized at high pressure at high temperatures and shows bulk superconductivity with critical temperature (T c ) above 70 K at ambient conditions. This superconducting transition temperature is more than 30 K higher than the T c for the isostructural counterparts based on classical La2CuO4 X-ray absorption measurements indicate the heavily doped nature of the Ba2CuO4-y superconductor. In compressed octahedron, the 3d3z 2-r 2 orbital will be lifted above the 3dx 2-y 2 orbital, leading to significant 3D nature in addition to the conventional 3dx 2-y 2 orbital. This work sheds important light on advancing our comprehensive understanding of the superconducting mechanism of high T c in cuprate materials.

Home use of a compact, 12‑lead ECG recording system for newborns

BACKGROUND

An easy-to-operate ECG recorder should be useful for newborn screening for heart conditions, by health care workers - or parents. We developed a one-piece electrode strip and a compact, 12‑lead ECG recorder for newborns.

METHOD

We enrolled 2582 newborns in a trial to assess abilities of parents to record a 12‑lead ECG on their infants (2-4 weeks-old). Newborns were randomized to recordings by parents (1290) or our staff (1292 controls). Educational backgrounds of parents varied, including 64% with no more than a high school diploma.

RESULTS

For newborns randomized to parent recorded ECGs, 94% of parents completed a 10-minute recording. However, 42.6% asked for verbal help, and 12.7% needed physical help. ECG quality was the same for recordings by parents versus staff.

CONCLUSIONS

By use of a one-piece electrode strip and a compact recorder, 87% of parents recorded diagnostic quality ECGs on their newborn infants, with minimal assistance.

miRNA-185 regulates retained fetal membranes of cattle by targeting STIM1

Retained fetal membranes (RFM) of cows is an important reproductive disturbance, and is related to miRNA-185. Stromal interaction molecule 1 (STIM1), a potential target gene of miRNA-185, could influence placenta release via regulating Ca²⁺ concentration intracellular. The aim of this study was to explore the mechanism of RFM by investigating the regulatory relationship between miRNA-185 and STIM1 in primary uterine caruncel epithelial (UCE) cells. Serum samples of healthy Holstein dairy cows (n = 20) and RFM cows (n = 12), with a similar age, parity, weight, and milk yield, were collected to detect Ca²⁺ concentration at prepartum 1-5 d and postpartum 6, 12 and 24 h. Caruncle tissues were collected from healthy (n = 6) and RFM cows (n = 6) at 12 h after calving. Quantitative polymerase chain reaction (Q-PCR) and western blotting (WB) were performed to detect the mRNA and protein levels of STIM1, respectively. UCE cells were cultured by the explant culture method, further purified, and subsequently treated with PmirGLO-STIM1-Mut + miRNA-185 mimics and mirGLO-STIM1-Mut + miRNA-185 NC. Q-PCR and WB were performed to detect mRNA and protein levels of STIM1 with treated miRNA-185 mimics. Serum levels of Ca²⁺ from RFM cows were abnormally decreased at prepartum 1 d and postpartum 6, 12 and 24 h. Expression level of STIM1 was down-regulated in the caruncle tissue of RFM cows. The luciferase activity was decresed about 30.9% by miRNA-185 mimics (p < 0.01), and the mRNA and protein levels of STIM1 were downregulated miRNA-185-mimics. It was suggesting that miRNA-185 might play an important role in RFM through regulating the expression of STIM1.

Community Partnership in Precision Medicine: Themes from a Community Engagement Conference

Background

Patient and community engagement in under-resourced communities is a key issue for precision medicine research. We report proceedings from a community-academic partnered conference in Los Angeles to promote community understanding of precision medicine and generate engagement recommendations.

Methods

Planning group review of planning, presentations, and audience discussions from facilitator notes and participant survey data from a one-day conference.

Findings

Community-academic planning broadened community participation and presentations. More than 80% of survey participants indicated they would participate in the national precision medicine initiative, and most were willing to share diverse sources of data. Discussions identified trust concerns related to historical research abuses, data privacy, potential effects of findings on health care, personal safety, research procedures, the time-frame for benefit, and confusion about different initiatives. Concerns were balanced by belief in science to improve health. Recommendations included a community partnered participatory approach with support for local community and academic teams to engage stakeholders with written/online resources and partnered workgroups addressing key concerns.

Conclusion

Conference participants expressed high willingness to participate in precision medicine studies, but discussions highlighted trust and transparency issues and suggested community partnered research with local capacity building.

IRF2BPL Is Associated with Neurological Phenotypes

Interferon regulatory factor 2 binding protein-like (IRF2BPL) encodes a member of the IRF2BP family of transcriptional regulators. Currently the biological function of this gene is obscure, and the gene has not been associated with a Mendelian disease. Here we describe seven individuals who carry damaging heterozygous variants in IRF2BPL and are affected with neurological symptoms. Five individuals who carry IRF2BPL nonsense variants resulting in a premature stop codon display severe neurodevelopmental regression, hypotonia, progressive ataxia, seizures, and a lack of coordination. Two additional individuals, both with missense variants, display global developmental delay and seizures and a relatively milder phenotype than those with nonsense alleles. The IRF2BPL bioinformatics signature based on population genomics is consistent with a gene that is intolerant to variation. We show that the fruit-fly IRF2BPL ortholog, called pits (protein interacting with Ttk69 and Sin3A), is broadly detected, including in the nervous system. Complete loss of pits is lethal early in development, whereas partial knockdown with RNA interference in neurons leads to neurodegeneration, revealing a requirement for this gene in proper neuronal function and maintenance. The identified IRF2BPL nonsense variants behave as severe loss-of-function alleles in this model organism, and ectopic expression of the missense variants leads to a range of phenotypes. Taken together, our results show that IRF2BPL and pits are required in the nervous system in humans and flies, and their loss leads to a range of neurological phenotypes in both species.

PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity

Electrocardiographic PR interval measures atrio-ventricular depolarization and conduction, and abnormal PR interval is a risk factor for atrial fibrillation and heart block. Our genome-wide association study of over 92,000 European-descent individuals identifies 44 PR interval loci (34 novel). Examination of these loci reveals known and previously not-yet-reported biological processes involved in cardiac atrial electrical activity. Genes in these loci are over-represented in cardiac disease processes including heart block and atrial fibrillation. Variants in over half of the 44 loci were associated with atrial or blood transcript expression levels, or were in high linkage disequilibrium with missense variants. Six additional loci were identified either by meta-analysis of ~105,000 African and European-descent individuals and/or by pleiotropic analyses combining PR interval with heart rate, QRS interval, and atrial fibrillation. These findings implicate developmental pathways, and identify transcription factors, ion-channel genes, and cell-junction/cell-signaling proteins in atrio-ventricular conduction, identifying potential targets for drug development.

Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6

BACKGROUND

Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying mechanisms remain unclear.

RESULTS

Here, we identify putative functional coding variation associated with changes in the QRS interval duration by combining Illumina HumanExome BeadChip genotype data from 77,898 participants of European ancestry and 7695 of African descent in our discovery cohort, followed by replication in 111,874 individuals of European ancestry from the UK Biobank and deCODE cohorts. We identify ten novel loci, seven within coding regions, including ADAMTS6, significantly associated with QRS duration in gene-based analyses. ADAMTS6 encodes a secreted metalloprotease of currently unknown function. In vitro validation analysis shows that the QRS-associated variants lead to impaired ADAMTS6 secretion and loss-of function analysis in mice demonstrates a previously unappreciated role for ADAMTS6 in connexin 43 gap junction expression, which is essential for myocardial conduction.

CONCLUSIONS

Our approach identifies novel coding and non-coding variants underlying ventricular depolarization and provides a possible mechanism for the ADAMTS6-associated conduction changes.

Multi-ethnic genome-wide association study for atrial fibrillation

Atrial fibrillation (AF) affects more than 33 million individuals worldwide1 and has a complex heritability2. We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.