Common Variants Research Articles

Straw return can increase maize yield by regulating soil bacteria and improving soil properties in arid and semi-arid areas

Straw return has been found to benefit soil fertility and crop yield, however, by which it affects microbial communities to mediate soil factors driving crop yields under maize continuous cropping systems in dryland areas is still unclear. To fill this gap, a 6-year field experiment was established with five straw return amounts (T0, T1, T2, T3, and T4, representing 0, 3,000, 6,000, 9,000, and 12,000kgha-1 of straw, respectively), and investigated the effects of on soil properties, enzymes, bacterial community composition and diversity, and crop yields. Our analysis showed that soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) contents significantly increased by 1-8%, 5-25%, and 2-9% under straw return treatments, respectively, compared to the T0, and soil catalase, urease, and alkaline phosphatase activities increased by at least 34.00%. Additionally, crop yield significantly increased by 4.23-12.00% under T1-T4 treatments, and showed highly significant relationships with SOC, TN, and TP. Importantly, we found straw return significantly altered the community of bacteria involved in the carbon and nitrogen cycle, and their abundance of strong responses depending on the amounts of straw return. For example, straw input increased the abundance of Proteobacteria (+2.64–5.57%), Acidobacteria (+3.82–13.83%), and Bacteroidetes (+15.37–30.49%). Similarly, the amount of straw application increased the bacterial diversity indexes (Shannon, 2.65–10.93%; Chao1, 13.47–18.50%), and had significant positive correlations with SOC, TN, and TP contents. Structural equation models (SEM) revealed that straw return management practice had positive and indirect effects on crop yields by influencing soil properties or the bacteria community. In conclusion, our findings revealed common associations and variations of bacterial community diversity with soil factors and crop yields at different straw return rates, and these findings provide insights and options for the development of better straw return strategies and sustainable agriculture in semi-arid regions.

Polygenic risk score for drug-induced long QT syndrome: independent validation in a real-world patient cohort.

Drug-induced long QT syndrome (diLQTS) is an adverse reaction from over 150 FDA-approved medications, posing the risk of triggering torsades de pointes and sudden death. While common genetic variants may modestly impact QT interval individually, their collective effect can significantly amplify risk of diLQTS. Consequently, this study aimed to validate a polygenic risk score (PRS) for diLQTS previously proposed by Strauss et al. A retrospective cohort study was conducted utilizing patients from the Michigan Genomics Initiative prescribed 27 high-risk QT-prolonging drugs and an ECG during the prescription. The primary outcome was marked prolongation of the QTc interval (either >60 ms change from baseline or >500 ms absolute value) during treatment with a high-risk QT-prolonging drug. The primary outcome occurred in 12.0% of n = 6070 self-reported White, 12.4% of 558 African American, and 8.2% of 110 Asian patients. The PRS significantly associated with diLQTS in White patients [adjusted odds ratio = 1.44 (95% CI: 1.09-1.89); P = 0.009]. However the study lacked sufficient statistical power to confirm the PRS as a risk factor in African Americans [adjusted odds ratio = 2.18 (95% CI: 0.98-5.49); P = 0.073] and Asians [adjusted odds ratio = 3.21 (95% CI: 0.69-16.87); P = 0.139] due to smaller sample sizes in these groups. The previously published PRS for diLQTS was validated in a large, real-world cohort, demonstrating its potential as a tool for identifying high-risk patients. Incorporating this PRS into routine clinical practice could enable proactive measures to prevent life-threatening diLQTS.

Predicting progression from coronary artery disease to heart failure in community cohorts

Abstract Background Approximately 10% of people develop heart failure (HF) within 5 years after an acute coronary event. Once ischaemic damage has occurred, the heart undergoes remodeling, which can lead to subclinical dysfunction and HF. However, remodeling varies considerably between patients and is difficult to predict. Purpose To assess whether adding genetic information to clinical factors improves the accuracy of predicting incident non-fatal/fatal HF within 5 years in people with coronary artery disease (CAD). Methods In the UK Biobank (UKB) [1], we developed a clinical risk model (predictors age, sex, ethnicity, body mass index, social deprivation, smoking, personal medical history, time since most recent CAD admission, lipids, HbA1C, creatinine, medications). Separately, we performed a genome-wide association meta-analysis of 13,360 (6,315 + 7,045) cases and 58,126 (37,245 + 20,881) non-cases from the UKB and deCODE [2] cohorts, relating common genetic variants to non-fatal/fatal HF or cardiomyopathy in people with CAD. For the current analysis of the UKB cohort, we derived a polygenic risk score using summary statistics from deCODE alone. We then compared risk estimates and assessed reclassification of 5-year risk using the clinical risk model with and without polygenic risk score, in UKB. Risk groups were <5%, 5-9.9%, 10-14.9%, ≥15%. Results Among people with CAD in the 5 years prior to assessment in UKB (n=8,880, mean age 61y, 27% women) or deCODE (n=10,113, mean age 66y, 34% women), 377 (4%) and 915 (9%) developed non-fatal/fatal HF over 5 years follow-up, respectively. In the UKB cohort, median 5-year risk with the clinical model was 3.2% (IQR 2-5.4%, C-statistic 0.72, 95% CI 0.70–0.74, Table 1) and plots of predicted versus observed risk showed very good calibration across deciles. The polygenic risk score was predictive of non-fatal/fatal HF in the UKB (hazard ratio 1.03, 95% CI 1.00 to 1.05 per standard deviation) with significance decreasing after adjusting for the prognostic index of the clinical risk model (hazard ratio 1.02, 95% CI 0.99 to 1.05 per standard deviation). Median 5-year risk by the clinical+polygenic model was 3.0% (IQR 1.9-5.0%). Net reclassification with the addition of the polygenic score improved accuracy of risk prediction for 3.6% of non-cases but deteriorated accuracy of risk prediction for 6% of cases. Overall net reclassification was deterioration of -0.025. Conclusion Our data suggest that common genetic variants may be associated with progression from CAD to HF, but that adding genetic data did not improve the accuracy of predicting progression from CAD to HF beyond established clinical predictors in the UKB cohort. Confirmation of these findings in deCODE and other large cohorts is warranted.

Role of common variants and new genes associated with arrhythmogenic cardiomyopathy

Abstract Introduction Arrhythmogenic Cardiomyopathy (ACM) is an inherited cardiac disease, predominantly affecting males, characterized by fibro-fatty myocardial replacement mainly in the right ventricle. It leads to 5% sudden cardiac death in affected young adults (<25 yo) without an implantable cardioverter defibrillator. Early diagnosis is crucial for appropriate clinical management to reduce mortality and prevent disease progression. Rare variants in desmosomal genes (PKP2,DSC2,DSG2,DSP and JUP) are found in 50% of cases. However, challenges persist since we observe a low penetrance in relatives (28-58%) and a high variability in expressivity and severity annihilating any preventive strategy. Objective We aim to decipher the genetic architecture of ACM by investigating the role of common variants in disease susceptibility/severity and to idendify new genes associated to ACM. Method A Genome Wide Association Study (GWAS) was performed on 1079 ACM index patients and 7305 controls, followed by conditional analysis. New candidate genes were knocked out (KO) in Zebrafish and/or hiPSC using CRISPR/Cas9. Impedance and external field potential measurements were performed on hiPSC derived cardiomyocytes (CM-hiPSC). Results The GWAS identified 5 significant loci (Figure 1, P<5.10-8), including 2 desmosomal genes (PKP2 a n d DSG2) and 3 new candidates (KLF12, CTNNA3, and ARL17B/WNT3). Conditional analysis revealed 3 additional loci with suggestive p-values (P<1.10-6), highlighting 3 new susceptible loci. Among them, we uncovered key non-coding regulatory regions near desmosomal genes (DSC2 and DSG2). Initial findings in PKP2-KO zebrafish present hearts with structural defects, while CM-hiPS KLF12-KO(-/-) exhibited altered interbeat interval and relaxation time compared to isogenic controls. Conclusion Our findings reveal ACM's complex genetic architecture, implicating common variants in disease susceptibility. A polygenic risk score will be implemented to improve patient risk stratification. Three novel loci/genes for ACM as well as specific regulatory regions of desmosomal genes have been highlighted. Their functional studies in isogenic hiPSC and Zebrafish models will offer new insights in ACM underlying molecular mechanism and potential therapeutic targets.

Identification of genetic variants by using a whole exome sequencing approach in Taiwanese patients with Brugada Syndrome

Abstract Background Brugada Syndrome (BrS) is a life-threatening arrhythmia disease primarily affecting young men. Many genetic studies have been conducted mainly in Caucasian BrS patients to identify potential genetic drivers. SCN5A mutations are less common in Asian BrS patients (around 10%) compared to Caucasian patients (20-30%). This means the pathogenic process of more than 70% of BrS patients remains unclear. With the advancement in NGS technologies, we can conduct genome-wide screening of DNA variants in BrS patients efficiently. Purpose Since less than 30% of the BrS patients have known genetic drivers for the disease, we aimed to identify more DNA variants in BrS patients by using the whole exome sequencing (WES) approach. Furthermore, we evaluated the landscape of DNA variants in the two groups of BrS patients according to whether they have SCN5A mutations or not. Methods A total of 201 BrS patients were recruited for the WES experiments. After obtaining the raw sequencing data, we performed the quality check procedures using the multiQC and Trimmomatic softwares (Figure 1). For reads passing the quality check, the BWA algorithm was used for the alignment. Next, the samtools, bamtools, and Picard methods were used to remove duplicates and perform the sorting. Subsequently, those sorted sequencing files were used to call the DNA variants by using the GATK approach and annotate them using the ANNOVAR method. The 201 BrS patients were classified into two different groups based on their mutation status of SCN5A, presentation of sudden cardiac death (SCD), and SCD along with syncope. The gene-based algorithm, SKAT, was used to analyze the summarized effects of DNA variants located in a single gene. For each DNA variant, Fisher's exact test was used to compare the allele frequency in the BrS patients under their groupings. Results The WES approach in the 201 BrS patients revealed a total of 205,454 variants, which were further categorized into two groups, common variants (51,867) and rare variants (153,587), based on their allele frequencies (5%). The SKAT algorithm was performed in the 30 genes that have been previously reported to be associated with BrS. No significant differences were observed in any gene in BrS patients for the common variants. Intriguingly, KCNJ8, SCN1B, ZFPM2, MAPRE2, and KCNE5 showed significant differences in allele frequencies between the SCN5A+ and SCN5A- patients (Figure 2). Fisher's exact test further revealed that three DNA variants (chr19:35524980, chr12:21926440, chr6:126210346) were significantly enriched in SCN5A+ patients. The 5 DNA variants located in ZFPM2 showed a linkage disequilibrium block and were enriched in SCN5A+ patients. Conclusions The WES approach in BrS patients revealed DNA variants that were reported in previous studies. Several DNA variants were significantly enriched in SCN5A+ patients, suggesting that the genome-wide mutation landscape was different in SCN5A+ and SCN5A- BrS patients.Figure 1Figure 2

Investigating the role of WT1 in Brugada syndrome pathophysiology

Abstract Background Brugada syndrome (BrS) is a heritable arrhythmic disorder presumably caused by conduction slowing in the right ventricular (RV) outflow tract (RVOT). A recent genome-wide association study found an association between common variants on chromosome 11 near WT1, tagged by the SNP rs72905083, and BrS susceptibility. Purpose To study whether WT1 affects cardiac conduction and could therefore represents the underlying association of the chr11 locus with BrS susceptibility. Methods We conducted in silico analyses of omics datasets to identify the likely causal gene at the chr11 BrS locus. Next, we conducted electrophysiological studies in heterozygous young adult (4 months old) Wt1-deficient (Wt1+/-) mice and wild-type littermates to explore the effect of Wt1 on cardiac conduction. To study the potential role of Wt1 in the setting of reduced conduction reserve, we compared aged Scn5a haploinsufficient mice (Scn5a+/-;Wt1+/+, 17 months) with littermates haploinsufficient for both Wt1 and Scn5a (Scn5a+/-;Wt1+/-). Optical mapping was performed in Langendorff-perfused hearts, where conduction was further challenged by acute ajmaline administration or by pacing at the effective refractory period (ERP). Transcriptomic analyses were conducted in Wt1+/- and wild-type mice by RNAseq of PCM1-sorted cardiomyocytes. Results Analysis of omics datasets uncovered WT1 as the likely causal gene since WT1 was the closest gene to, and in fact overlapped, the BrS-associated region; promoter capture Hi-C data in human tissue showed chromatin contact between the promoter of WT1 and the associated region; and H3K27ac ChIP-seq signals (i.e. enhancer activity) of putative cardiac enhancers located within the associated region were correlated with WT1 transcript abundance across multiple tissues (Z-score = 4.32, p=1.57e-05). No differences were observed in ECG parameters or optically mapped epicardial conduction between Wt1+/- mice and wild-type littermates. However, comparison of aged Scn5a+/-;Wt1+/- and Scn5a+/-; Wt1+/+ hearts, in the setting of acute ajmaline challenge or pacing at the ERP, showed faster conduction in RV/RVOT in the presence of Wt1 haploinsufficiency (genotype effect: p=0.057 and p=0.041 for RV and RVOT epicardial conduction, respectively, during ajmaline challenge; p=0.034 for RV epicardial conduction during pacing at ERP). RNAseq of RV/RVOT cardiomyocytes revealed higher Scn5a expression in Wt1+/- vs wild-type (p=0.006). Conclusion We identified WT1 as the gene that most likely underlies the effect of the chr11 BrS susceptibility locus. Functional data revealed protective effects of reduced Wt1 expression in the setting of reduced conduction reserve. Transcriptomic data suggest that this occurs through a transcriptional effect on Scn5a expression.

A review on efficacy of polygenic risk score information on behavioral change and clinical outcomes

Abstract Background Polygenic Risk Score (PRS) represents a promising advancement in personalized medicine, enabling the inherited risk assessment for disease outcomes based on the effect of various common genetic variants. The utilization of PRS information to promote the adoption of healthier behaviors has witnessed an increase interest in recent years, but its full potential still needs to be fully addressed. Methods This systematic review aims to assess the efficacy of disclosing PRS information on individuals’ engagement in risk-reducing interventions. CENTRAL database has been searched up to December 2023 to identify randomized controlled trials (RCTs) comparing the disclosure of PRS results, with scenarios where other or no information is provided. We performed a preliminary meta-analysis on the mean difference of clinical and psychological outcomes between the two arms. Results Out of 4419 results, we included 12 studies. Trials focused on primary (83%), secondary (8%) and tertiary (8%) preventive interventions. As for the possible diseases predicted by the PRS, cardiovascular diseases (33%) were the most common (n = 4), along with cancers (33%), diabetes (25%) and metabolic disease (8%). PRS result disclosure was compared to standard care (n = 7), no information provided (n = 4), and family risk (n = 1). By pooling data from four comparable studies, we report a reduction in the mean difference for LDL cholesterol in the intervention group of -6.39mg/dL (95%CI -10.09, -2.70, I²=0%, p < 0.001). No significant changes were observed for systolic and diastolic blood pressure, and weight, in 3 studies and 4 analyzed studies, respectively. An increase in anxiety levels was observed towards the PRS group in 4 studies (SMD 0.24, 95%CI 0.02, 0.46, I² = 66%, p = 0.03). Conclusions Preliminary analysis show small or no effects of PRS disclosure on intermediate health or psychological outcomes. Larger trials assessing the potentiality of PRS disclosure are still needed. Key messages • From the analysis of twelve preventive trials on the efficacy of PRS on behavior change, we report a positive effect on LDL cholesterol reduction. • Larger well conducted trials are needed to integrate PRS-based information into future preventive strategies.

Potential use of pharmacogenetics in cardiology: genome-wide association studies of amiodarone-induced thyroid disorders

Abstract Background Amiodarone is a commonly prescribed antiarrhythmic drug used to manage supraventricular and ventricular arrhythmias. The use of amiodarone is associated with a broad range of adverse effects, including amiodarone-induced hypothyroidism (AIH) or amiodarone-induced thyrotoxicosis (AIT) (1). Both conditions are linked with increased mortality and have no known reliable risk predictors (2). Purpose We investigated the genetic underpinnings of amiodarone-induced thyroid disorders, and the clinical validity and utility of screening for genetic variants. Methods We conducted the first genome-wide association studies (GWAS) of AIH and AIT using data from three large biobanks. We compared the AUCs for SNPs identified through the above GWAS with polygenic risk scores for both hypo- and hyperthyroidism. Finally, we tested the clinical validity and utility of screening for risk variants. Results We found two risk loci for AIH. The lead variant at the first locus, rs1443438, was intronic to FOXE1 (OR 0.39, MAF = 35%, P = 1.59 × 10-42). The other lead variant, rs2209796, was located 93 kb upstream to FOXA2 (OR 0.56, MAF = 29%, P = 2.64 × 10-15: Figure 1). For AIT, we found one risk locus. The lead variant, rs2268803, was intronic to CAPZB (OR 1.81, MAF = 42%, P = 2.43 × 10-8: Figure 1). Next, we added GWAS SNPs or polygenic risk scores to risk prediction models consisting of age, sex and 4 principal components (PCs), and compared AUC estimates between risk models. Using GWAS SNPs, we found that the AIT variant increased the AUC with 6% (95%CI 1.1 – 10.3, AUC: 0.72) and 9% (95%CI 6.2 – 11.2, AUC: 0.75) for AIH, compared to the benchmark model. Both GWAS SNP models were superior to polygenic risk scores in terms of AUC (P for difference <0.05). The positive and negative predictive value (PPV and NPV) for the AIT-variant was 14.6% and 95.7%, respectively. For the AIH-variants combined, we found a PPV of 17% and a NPV of 95%. Conclusions Common genetic variants are associated with both amiodarone-induced hypo- and hyperthyroidism and are at this point, superior to polygenic risk scores in predicting amiodarone-induced thyroid disorders. These findings add to the potentials of pharmacogenetics in cardiology. Figure 1. Double Manhattan plot of amiodarone induced thyroid disorders. The Y-axis is the negative log10 of the P-value for each single nucleotide polymorphism. The X-axis is the chromosome, with positions on each chromosome ranging from lower to higher (left to right). The dotted line marks the threshold for genome-wide significance. Amiodoarone-induced hypothyroidism at the top, and amiodarone-induced thyrotoxicosis at the bottom.Figure 1

Identification of genetic variants associated with exercise-induced atrial fibrillation in high-performing racehorses

Abstract Background Atrial fibrillation (AF) is the most common cardiac arrhythmia in athletes. Despite a lower burden of classical cardiovascular risk factors, the prevalence of AF in athletes is comparable to that in the general population of similar age (~13%, mean age 65.5), suggesting that exercise-induced AF may have different underlying mechanisms. The prevalence of AF in thoroughbred (TB) and standardbred (STB) racehorses is also relatively high (~5%), suggesting exercise as an independent risk factor. Due to selective breeding and complete control of pedigrees, racehorses are well-suited for genetic studies. Common and rare genetic variation explain a substantial part of AF variance, but no study has identified genetic variants associated with exercise-induced AF in any species. Objective In this project, we aimed to use the racehorse as a model to identify genetic variants associated with exercise-induced AF, and in a future study, possibly replicate the results in human athletes. Here we present preliminary results from the genome-wide association study (GWAS) of AF in racehorses. Methods We collected blood or hair samples from 181 STB and TB racehorses in which 71 had paroxysmal or persistent AF verified by ECG. We extracted DNA and performed whole-genome genotyping using a commercial equine genotyping platform (670k markers). We phased and imputed un-genotyped markers and increased the sample size of the control group, using publicly available equine data from similar breeds from the European Nucleotide Archive. We conducted a GWAS of 7.85 million markers in 71 cases and 296 controls using PLINK2 with covariates adjusted for population stratification, batch and sex. Results We identified one significant locus downstream of the protocadherin gene PCDH18 associated with AF in racehorses. The same locus has been associated with the ECG-trait P-wave terminal force in humans. Changes in P-wave terminal force is associated with increased atrial size, delayed interatrial conduction, left ventricular fibrosis and left atrial function, and considered a good predictor of AF occurrence. Several non-significant but interesting signals were also identified including the genes SLC6A15 (amino acid transport), MYBPH (myosin binding), MYF6 and MYOG (myoblast differentiation). Conclusion In these preliminary results, we have identified a new genetic locus associated with AF in racehorses. In addition, we have identified several candidate genes for further studies to elucidate the genetic background of exercise-induced AF. We aim to replicate our findings in a population of human athletes. Our results may aid the development of risk prediction tools for exercise-induced AF and new drugs for tailored treatment of AF in general.

Genome-wide association analysis reveals insights into the molecular etiology of dilated cardiomyopathy

Abstract Introduction Dilated cardiomyopathy (DCM) is a primary heart muscle disease characterized by ventricular dilatation and impaired contractility. While considered a Mendelian disorder, recent evidence highlights the important role of common genetic variation. Better characterization of the genetic architecture will provide opportunities for improved diagnosis, risk stratification and biological understanding. Methods We performed a GWAS meta-analysis of 14,256 DCM cases and 1,185,671 controls of European ancestry from 16 studies (GWASDCM). To improve discovery power, we performed multi-trait analysis of GWAS (GWASMTAG) with three genetically correlated and clinically relevant cardiac imaging traits in 36,203 individuals. To identify effector genes at loci, we used a two-step approach: 1) the nearest gene and top 3 genes prioritized by PoPS or V2G were selected as candidates; and 2) totality of evidence including 5 additional methods (coding variant, co-localization with expression, TWAS, ABC-model, and known Mendelian cardiomyopathy genes) was summarized in a single score. We performed rare variant burden analysis (MAF<0.1%) for predicted truncating variants (PTV) in established DCM-causing genes to highlight DCM genetic architecture, and in prioritized GWAS genes, against DCM and quantitative CMR traits in UK Biobank (UKB) and 100,000 Genomes Project (GeL), implemented by REGENIE. A polygenic score (PGS) generated using a Bayesian framework (PRS-CS) was assessed for association with the same outcomes in UKB participants, including among PTV carriers in established DCM-causing genes. Results We identified 80 independent loci, of which 65 were novel (62 loci in GWASDCM, and 54 loci in GWASMTAG) (Figure 1A). High-confidence genes were prioritized at 62 loci, including in genes with established roles in Mendelian cardiomyopathies (TTN, BAG3, FLNC, MYBPC3, FHOD3, ALPK3), and were enriched in key biological processes (Figure 1B). We characterized DCM genetic architecture across the allelic spectrum (Figure 2A). Rare variant burden analysis highlighted novel associations with DCM and quantitative traits for PTVs in NEDD4L and MAP3K7 in UKB that were replicated in GeL (Figure 2B). PGS was associated with DCM and quantitative CMR traits (OR per PGS SD 1.8, P<1x10-16) (Figure 2C). Individuals in the top centile had 4-fold increased risk of having DCM compared with median risk. PGS stratified penetrance of rare variants in 1,546 carriers of pathogenic variants (top quintile 7.3%, bottom quintile 1.7%, P 0.005). Conclusion We have performed the largest DCM GWAS, resulting in 80 significant loci (65 novel), and prioritized genes using a systematic approach. We identify novel DCM-causing genes (NEDD4L and MAP3K7) and generate a PGS that associates with DCM and modulates penetrance in carriers of Mendelian disease-causing rare variants.Figure 1Figure 2

Can variants of genes associated with familial heart block predict conduction disease in the general population? A UK Biobank study.

Abstract Background Progressive familial heart block is a genetic disease that can present with worsening cardiac conduction disease (CCD) and risk of life-threatening bradycardia. The prevalence, penetrance, and expressivity of known rare pathogenic/likely pathogenic variants (P/LP) in the general population is unclear. In addition, the role of common genetic variation in this phenotypic expression is unknown. Understanding this is essential for patient management in clinic. Purpose 1). To investigate the prevalence of variants linked with early-onset CCD and phenotypic expression in a large biobank. 2). To investigate whether a PR interval polygenic risk score (PRS) improves risk prediction. Methods Early-onset conduction disease P/LP or variants of uncertain significance (VUS) were identified from ClinVar, genetic testing reports at a teaching hospital (6 variants), and the literature, mapping to 22 genes. From the full UK Biobank prospective cohort, 469,511 participants passed genetic quality control and were assigned to P/LP, VUS, or genotype negative (G-) groups, using whole exome sequencing analysed with bcftools. A PR-PRS was constructed using weights from a published meta-analysis excluding UKB data. The primary outcome was CCD (atrioventricular (AV) block, bundle branch block, pacemaker or ICD implantation) and secondary outcomes were high-grade AV block or pacemaker insertion, compared with lifetime risk Cox proportional hazards controlled for sex and age as a timescale. Results 55% of participants were female, 95% had European ancestry, and average age at censor was 71 years. There were 25 P/LP carriers, and 8,862 with a VUS, in 6 genes (MYH7, SCN5A, TNNI3K, TRPM4, TTN, and LMNA). Major demographic factors were the same between groups. CCD was significantly more prevalent in P/LP individuals (28% vs 5.8% in VUS vs 5.5% in G-; p<0.001) with a hazard ratio of HR 6.47 [95% CI=3.09-13.6] vs G-. This was driven by AV block and pacemaker implantation (HR 23.2 [95% CI=8.69-61.8] and 13.4 [95% CI=6.01-29.8], respectively). Results were similar in an unrelated subset and controlling for ischaemic heart disease and heart failure. The 7 P/LP individuals with conduction disease were mostly linked to a single LMNA variant (4 out of 6 carriers with penetrant disease). In the full cohort, the PR-PRS was predictive of CCD (HR=1.07 [95% CI=1.06-1.08]), AV block (HR=1.09 [95% CI=1.06-1.13]), and pacemaker implantation (HR=1.04 [95% CI=1.02-1.06]). When combined with P/LP status, both PR-PRS (HR=1.07 [95% CI=1.06-1.08]) and P/LP (HR=6.42 [95% CI=3.06-13.5]) were independent predictors of CCD. Conclusion(s) Rare variant carrier status predicts a 6.5-fold increased lifetime risk of CCD, a 23-fold increased risk of AV block and 13-fold risk for pacemaker requirement. However, phenotypic expression for some variants is highly variable. A PR-PRS captures risk independent of P/LP variants and warrants further investigation with updated PRS construction methods.

Utility of polygenic risk score for prediction of dilated cardiomyopathy and modulation of severity of LV dysfunction among cases

Abstract Background Dilated cardiomyopathy (DCM) is a predominant cause of heart failure and a leading indication for cardiac transplantation. While rare genetic variants are established as causative factors in familial forms of the disease, recent genome-wide association studies (GWAS) have also underscored the significant contribution of common genetic variation to DCM. Polygenic scores (PGS) constructed from GWAS have demonstrated promise in risk stratification for a range of common diseases and may similarly have value for risk prediction in DCM. However, data regarding the clinical utility of PGS in DCM remains sparse. Purpose We aimed to evaluate the utility of PGS for prediction of DCM and its association with left ventricular ejection fraction (LVEF) and family history. We further aimed to assess the contribution of PGS in DCM patients with established causative rare variants (genotype-positive) and those without (genotype-negative). Methods We used a previously-constructed PGS, which was developed from a GWAS meta-analysis (8387 DCM cases and 939161 controls) and multi-trait analysis (MTAG) with cardiac MRI traits. In the present analysis, we calculated PGS for a newly assembled cohort of 978 DCM cases from a major university medical centre and 7207 controls from a national register. To evaluate the clinical utility of PGS, we built logistic regression models and assessed the association between PGS and DCM status. Subsequently, we performed subgroup analyses, including: i) individuals of European ancestry, ii) non-European ancestry, iii) males, iv) females, v) genotype-positive participants(n=193), and vi) genotype-negative participants (n=294). We then used linear and logistic regression models, respectively, to assess the associations of PGS with LVEF and documented family history of DCM. Results PGS demonstrated a significant enrichment among DCM cases compared to controls (OR per SD 1.93, P = 9.47E-68). This association persisted with consistent effect estimates - ranging from OR 1.5 to 2.2 - across all examined subgroups and demonstrated sufficient statistical significance (all P<1.58E-06) (Figure 1). Genotype-negative cases had a significantly higher PGS compared to genotype-positive individuals (P = 0.0015), although PGS was significantly enriched in both groups as compared to controls. Furthermore, among DCM cases, higher PGS was significantly associated with lower LVEF at first presentation (P=0.03, beta=-0.5% per SD) (Figure 2). There was no significant association found between PGS and family history. Conclusions PGS is strongly associated with risk of DCM, and may modulate the severity of LV dysfunction among DCM cases. Polygenic burden contributes to DCM risk in both genotype-positive and negative cases, although the contribution is stronger in patients without known causative rare variants. Overall, our results suggest a potential clinical applicability for PGS in DCM risk stratification.Figure 1.Association of PGS with DCMFigure 2.Association of PGS with LVEF

Association between genetic predisposition of AF and the risk of ischemic stroke and thromboembolism

Abstract Background Ischemic stroke and thromboembolism are the major complications of atrial fibrillation (AF), however, its association with genetic background of AF remains unclear. To investigate the association between genetic predisposition of AF underlying common variants and the risk of ischemic stroke and thromboembolism. Methods We included unrelated individuals with non-valvular AF from UK biobank. The polygenic risk scores of AF (PRSAF) was calculated for each individual using the effect weight from a previous study which has been validated in both European and mixed-ancestry population[1, 2]. The SNPs from the original score were lifted over to GRCh38 and 6514708 of 6730541 were available in the UK biobank genotype data. The clinical data was defined by ICD-10 code. The primary endpoint is ischemic stroke or thromboembolism resulting in hospitalization after first AF diagnosis. Results A total of 28810 unrelated patients were included in the study. Among them, 4064 had PRSAF over 90th percentile of the general population, and were considered having high genetic risk. The rest 18746 with per SD increase in PRSAF lower than 90th percentile of the general population were considered having lower genetic risk. Generally, age and sex adjusted model demonstrated that per standard deviation change in PRSAF is associated with 9% increase in the risk of stroke or thromboembolism (HR=1.09, 95%CI: 1.03-1.14), and patients with high genetic risk was associated with 15% increase in the risk of stroke or thromboembolism (HR=1.15, 95%CI: 1.02-1.31).The result remained stable when further adjusted for clinical risk factors (1.09, 95%CI: 1.04-1.15 per SD increase in PRSAF) and competing risk of death (1.10, 95%CI: 1.05-1.16 per SD increase in PRSAF). There was no interaction between CHA2DS2-VASc score risk stratification and the per SD increase in PRSAF (P interaction = 0.751, Figure 1A). However, the association between per SD increase in PRSAF and the event tended to be affected by age at AF onset (HR = 1.02 95%CI: 0.94, 1.11 for early onset AF; HR = 1.12 95%CI: 1.05, 1.19 for non-early onset AF, P for interaction = 0.062, Figure 1B). Multi-variate COX regression including PRSAF, components of CHA2DS2-VASc score, and other AF risk factors revealed that history of stroke/thromboembolism, age over 65 years, hypertension, diabetes and high AF genetic risk were significantly associated with the outcome (Figure 1C). To evaluate the importance of these risk factors, average population attributable fraction for 10-year risk of stroke/thromboembolism in the study population was calculated, indicating that genetic risk of AF is responsible for 3.26% (0.89%-5.63%) of the events (Figure 1D). Conclusion Genetic predisposition of AF underlying common variants is associated with ischemic stroke and thromboembolism independent of clinical risk factors. But its role in different AF populations, like early onset AF, remains further investigation.Figure 1

Rare genetic variants in LDLR, APOB, and PCSK9 are associated with aortic stenosis

Abstract Background Aortic stenosis (AS) is the most common cardiac valvular disease in the developed world. Although AS is associated with substantial morbidity and mortality, current treatment options are limited to invasive procedures and reserved for severe symptomatic disease. Genetic studies have linked common variants near lipid genes to AS and cohort studies have linked diagnoses of familial hypercholesterolemia to AS. In contrast, randomized controlled trials have shown no benefit of lipid-lowering therapy in AS. Purpose We aimed to assess the impact on AS conferred by lifelong decreased or increased LDL levels, by studying rare genetic variation in three important lipid handling genes (LDLR, APOB, PCSK9) from a genome-first perspective. Methods We utilized sequencing data and electronic health records from the UK Biobank (UKB) and the All of Us Research Program (AllofUs). We used LOFTEE to identify carriers of truncating variants in LDLR (LDLRtv), APOB (APOBtv) and PCSK9 (PCSK9tv); we used AlphaMissense to identify predicted-damaging missense variants (LDLR-AM, APOB-AM, PCSK9-AM). Linear regression analyses were used to assess the impact of the variant groupings on LDL levels in the UK Biobank, adjusting for sex, age, age^2, and principal components of ancestry. We then conducted Firth’s logistic regression analyses in UK Biobank and AllofUs modelling AS as outcome and variant status as predictor, adjusting for the same covariates; we used an inverse-variance-weighted meta-analysis to combine results. Results We identified 421,058 unrelated participants (N=5,322 AS cases) in the UK Biobank, and 232,170 unrelated participants (N=1,087 AS cases) in AllofUs. Across both cohorts, we identified 198 LDLRtv carriers, 1095 LDLR-AM carriers, 662 APOBtv carriers, 1422 APOB-AM carriers, 712 PCSK9tv carriers and 794 PCSK9-AM carriers. In the UK Biobank LDL values were substantially elevated in LDLRtv (P=1.9x10-48) and LDLR-AM carriers (P=7.5e-200), while LDL levels were substantially decreased in APOBtv (P<1x10-200), APOB-AM (P=6.3x10-19), PCSK9tv (P=1.2x10-114) and PCSK9-AM carriers (P=9.9x10-73; Figure 1). Across UK Biobank and AllofUs, the risk of being diagnosed with AS was strongly increased in LDLRtv (odds ratio [OR]=9.2 [4.32–19.50], P=8e-9) and LDLR-AM carriers (OR=2.76 [1.75–4.35], P=1e-5; Figure 2). Directionally consistent with these effects, we observed a trend towards decreased AS risk among carriers of either APOBtv or PCSK9tv (OR=0.57, [0.30–1.08], P=0.08) and a significantly reduced risk among carriers of APOB-AM or PCSK9-AM (OR=0.46, [0.26-0.82], P=0.009). Conclusion Rare genetic variants that confer lifelong increased LDL levels are associated with substantially increased risk of AS, and vice versa. Our results support a causal role of LDL in AS pathogenesis. In the context of trials demonstrating no benefit in AS, our findings suggest that lipid-lowering may need to be initiated earlier to affect AS development.LDL levels in UK BiobankAS risk in UK Biobank and AllofUs

A cross‐sectional study on quality of life in adult indolent systemic mastocytosis and its association with cutaneous involvement

AbstractBackgroundSystemic mastocytosis (SM) is characterized by abnormal mast cell accumulation in various tissues, including the skin, and encompasses several clinical variants, ranging from less aggressive to more severe forms. ISM, the most common variant, often presents with cutaneous manifestations, causing significant impairment in QoL due to mediator‐release symptoms and stigma associated with typical cutaneous lesions.ObjectivesThe study aimed to assess QoL impairment in ISM patients and its correlation with demographic and clinical data.MethodsA cohort of 52 adult ISM patients was evaluated using the Dermatology Life Quality Index (DLQI) and the mastocytosis QoL questionnaire (MC‐QoL). Questionnaire scores were then analyzed in relation to the clinical and demographic characteristics of the patients.ResultsOver half of the patients experienced mild or higher levels of impairment in QoL, with female patients showing greater impairment than males. Patients with recent symptom onset reported higher MC‐QoL scores, possibly due to psychological factors and lack of disease knowledge. Cutaneous symptoms significantly impacted QoL, and the visibility of lesions affected DLQI scores more than MC‐QoL scores. A moderately strong correlation was observed between DLQI and MC‐QoL scores, particularly in the Skin and Social Life domains. The study highlights gender differences in QoL impairment, suggesting the need for further investigation into potential social or cultural factors.ConclusionsWhile the study provides valuable insights into QoL impairment in ISM patients, its monocentric nature and small sample size are notable limitations. Further research is warranted to better understand the impact of SM on patients' well‐being and to identify effective strategies for managing symptoms and improving overall QoL in this population.

A burden of rare copy number variants in obsessive-compulsive disorder.

Current genetic research on obsessive-compulsive disorder (OCD) supports contributions to risk specifically from common single nucleotide variants (SNVs), along with rare coding SNVs and small insertion-deletions (indels). The contribution to OCD risk from rare copy number variants (CNVs), however, has not been formally assessed at a similar scale. Here we describe an analysis of rare CNVs called from genotype array data in 2248 deeply phenotyped OCD cases and 3608 unaffected controls from Sweden and Norway. Cases carry an elevated burden of CNVs ≥30 kb in size (OR = 1.12, P = 1.77 × 10-3). The excess rate of these CNVs in cases versus controls was around 0.07 (95% CI 0.02-0.11, P = 2.58 × 10-3). This signal was largely driven by CNVs overlapping protein-coding regions (OR = 1.19, P = 3.08 × 10-4), particularly deletions impacting loss-of-function intolerant genes (pLI >0.995, OR = 4.12, P = 2.54 × 10-5). We did not identify any specific locus where CNV burden was associated with OCD case status at genome-wide significance, but we noted non-random recurrence of CNV deletions in cases (permutation P = 2.60 × 10-3). In cases where sufficient clinical data were available (n = 1612) we found that carriers of neurodevelopmental duplications were more likely to have comorbid autism (P < 0.001), and that carriers of deletions overlapping neurodevelopmental genes had lower treatment response (P = 0.02). The results demonstrate a contribution of rare CNVs to OCD risk, and suggest that studies of rare coding variation in OCD would have increased power to identify risk genes if this class of variation were incorporated into formal tests.

Hybridization has localized effect on genetic variation in closely related pine species

BackgroundHybridization is a known phenomenon in nature but its genetic impact on populations of parental species remains less understood. We investigated the evolutionary consequences of the interspecific gene flow in several contact zones of closely related pine species. Using a set of genetic markers from both nuclear and organellar genomes, we analyzed four hybrid zones (384 individuals) and a large panel of reference allopatric populations of parental taxa (2104 individuals from 96 stands).ResultsWe observed reduced genetic diversity in maternally transmitted mitochondrial genomes of pure pine species and hybrids from contact zones compared to reference allopatric populations. The distribution of mtDNA haplotypes followed geographic rather than species boundaries. Additionally, no new haplotypes emerged in the contact zones, instead these zones contained the most common local variants. However, species diverged significantly at nuclear genomes and populations in contact zones exhibited similar or higher genetic diversity compared to the reference stands. There were no signs of admixture in any allopatric population, while clear admixture was evident in the contact zones, indicating that hybridization has a geographically localized effect on the genetic variation of the analyzed pine species.ConclusionsOur results suggest that hybrid zones act as sinks rather than melting pots of genetic diversity. Hybridization influences sympatric populations but is confined to contact zones. The spectrum of parental species ancestry in hybrids reflects the old evolutionary history of the sympatric populations. These findings also imply that introgression may play a crucial role in the adaptation of hybrids to specific environments.

Adult-Onset EIF2B-Pathies: A Clinical, Imaging and Genetic Profiling with Literature Review.

Vanishing white matter syndrome is one of the leukoencephalopathies caused by recessive mutations in gene EIF2B1-5. Adult-onset EIF2B-pathies (clinical onset after age 16 years) have been reported to be less common. Description of the clinical, imaging and genetic profile of adult-onset EIF2B-pathies and comparison of Indian cohort with Asian and European cohorts. Report of two cases of adult-onset EIF2B-pathies and a comprehensive review of genetically confirmed adult-onset EIF2B-pathies since 2001 from Indian, Asian and European cohorts. Two patients were females, with median age at presentation of 25.5 years (24-27 years) and onset at 19 years (18-20 years). The median duration of symptoms was 6.5 years (6-7 years). Both had cerebellar ataxia, spasticity, cognitive impairment and bladder involvement. Brain magnetic resonance imaging (MRI) showed leukoencephalopathy with rarefaction in both patients and corpus callosum involvement in one patient. Genetics showed homozygous missense variant in the EIF2B3 gene in both patients. The Indian cohort of seven patients had similar clinical and radiological features and common variants in EIF2B3 (n = 4). The Asian cohort had 24 cases, and the European cohort had 61 cases with similar clinical features, radiological features and common variants in EIF2B5. Adult-onset EIF2B-pathies have a distinct clinical profile of female predominance with cerebellar ataxia, spasticity and cognitive decline as the commonest triad of clinical manifestations and leukoencephalopathy with rarefaction on brain MRI. Variants in EIF2B5 were common in the Asian and European cohorts and EIF2B3 in the Indian cohort.

OSSN in South India: Clinical presentation, treatment outcomes, and histopathologic correlations.

This study aimed to analyze the clinical presentation, treatment outcomes, and histopathology features of ocular surface squamous neoplasia (OSSN) in a South Indian population and correlate the area of lesions to the histopathological grade/severity of carcinoma in situ (CIN) and squamous cell carcinoma (SqCC) invasive and noninvasive tumors. The study was a retrospective cross-sectional study. The study reviewed electronic medical records (EMRs) of 99 eyes of 99 South Indian patients who underwent en bloc excision and biopsy for tumors in the corneal and conjunctival epithelium with suspicion of OSSN over 1 year from January 2019 to December 2019. Postoperatively, patients were treated with three cycles of topical 0.04% mitomycin C eye drops. Sixty-three had requisite EMR data with a follow-up period of 1 year. Patients had equal gender distribution with an age range of 28-83 years. The most common clinical variant was leukoplakic lesion, and the area of the lesion was the only predicting factor for SqCC and CIN. Bigger (T2) lesions should be strongly suspected for OSSN and promptly excised. Histopathologic analysis should be performed, and post-op topical mitomycin C or interferon alpha 2b is administered to avoid recurrence. In this study, by correlating the area of the lesion, we introduce a new variable that may aid in clinical prognostication alongside the AJCC classification.

Genetic Prediction Modeling in Large Cohort Studies via Boosting Targeted Loss Functions.

Polygenic risk scores (PRS) aim to predict a trait from genetic information, relying on common genetic variants with low to medium effect sizes. As genotype data are high-dimensional in nature, it is crucial to develop methods that can be applied to large-scale data (large and large ). Many PRS tools aggregate univariate summary statistics from genome-wide association studies into a single score. Recent advancements allow simultaneous modeling of variant effects from individual-level genotype data. In this context, we introduced snpboost, an algorithm that applies statistical boosting on individual-level genotype data to estimate PRS via multivariable regression models. By processing variants iteratively in batches, snpboost can deal with large-scale cohort data. Having solved the technical obstacles due to data dimensionality, the methodological scope can now be broadened-focusing on key objectives for the clinical application of PRS. Similar to most methods in this context, snpboost has, so far, been restricted to quantitative and binary traits. Now, we incorporate more advanced alternatives-targeted to the particular aim and outcome. Adapting the loss function extends the snpboost framework to further data situations such as time-to-event and count data. Furthermore, alternative loss functions for continuous outcomes allow us to focus not only on the mean of the conditional distribution but also on other aspects that may be more helpful in the risk stratification of individual patients and can quantify prediction uncertainty, for example, median or quantile regression. This work enhances PRS fitting across multiple model classes previously unfeasible for this data type.