Variant Carriers Research Articles

Exploring the Relationship Between NOD2 Risk Variants and First Decompensation Events in Cirrhotic Patients With Varices.

NOD2 mutations are associated with impaired gut mucosal barrier function. According to the systemic inflammation hypothesis, bacterial translocation is central in the development of decompensation. The aim was to evaluate whether the presence of NOD2 variants is associated with the development of first decompensation. Secondary analysis of prospectively collected consecutive patients with compensated cirrhosis, who were screened between 2014 and 2018. Patients with and without NOD2 variants were compared and stratified analysis according to the presence of varices was performed. 360 patients [239 (66%) men, median age 61 (53-69) years, 70 (19%) with NOD2 variants, 90 (25%) with varices] were followed for a median of 9 (4-16) months. Similar baseline characteristics were observed across NOD2 status groups, except for beta-blocker use (45% vs. 32% amongst variant carriers vs. non-carriers, p = 0.05). During follow-up, 34 patients (12%) developed their first decompensation, with no differences according to NOD2 status [HR 1.75 (95% CI 0.84-3.67)]. On multivariate analysis, only MELD remained an independent predictor of decompensation. Amongst patients with varices (n = 90), 18 (24.4%) carried a NOD2 variants, with a higher incidence of first decompensation [HR 3.00 (95% CI 1.08-8.32)], primarily due to ascites [HR 3.32 (95% CI 1.07-10.32)]. In this subgroup, MELD [HR 1.18 (95% CI 1.06-1.32)] and NOD2 variants [HR 2.91 (95% CI 0.95-8.89)] were determined to be independent predictors of decompensation. The presence of NOD2 risk variants leads to a greater incidence of first decompensation only in compensated patients with varices.

Melanoma arising from pre-existing naevus in carriers of a germline CDKN2A pathogenic variant.

In this study we used total body photography (TBP) to determine whether melanoma emerges from a preexisting naevi or normal-appearing skin in individuals with pathogenic CDKN2a variant. In total, 60 melanoma cases occurred in 44 CDKN2a germline carriers. In addition, we observed that 78% of the 60 included melanoma cases developed from preexisting naevi, significantly higher than the 30% reported for sporadic melanoma. This high incidence may be due to the numerous atypical naevi and early bi-allelic loss of CDKN2A. Our findings underscore the importance of routine TBP in these patients for early detection of melanoma. More than previously appreciated, the surgical removal of melanocytic naevi in these high-risk patients may prevent melanoma development.

Exome sequencing in over 63,000 patients in TIMI trials uncovers pathogenic cardiomyopathy variant carriers with high risk for heart failure and cardiovascular death

Abstract Background Rare genetic variants predisposing to cardiomyopathy (CMP) confer increased risk for adverse events. The prevalence of CMP variants in contemporary cardiovascular (CV) trials and their association with prevalent heart failure (HF) and incident HF hospitalizations (HHF) is not established. Purpose We aimed to identify carriers of rare pathogenic/likely pathogenic (PLP) variants for dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC) in well-phenotyped clinical trial cohorts and to evaluate their prognostic significance. Methods Rare variants were identified from high-quality exome sequencing data from 5 large clinical trials (ENGAGE AF-TIMI 48, SAVOR-TIMI 53, PEGASUS-TIMI 54, DECLARE-TIMI 58, FOURIER (TIMI 59)). Putatively pathogenic variants for cardiomyopathy were identified using phenotype- and gene-specific curation of protein-truncating variants and high-confidence variant classifications from ClinVar. We conducted logistic regression for prevalent disease and Cox proportional hazard models for incident HHF, both adjusted by age, sex, trial, and first 10 principal components and using those without CMP variants as the reference. Sensitivity analysis by history of HF at baseline was performed for prospective outcomes. Results In 63,700 participants, we identified 866 CMP variant carriers of which 518 identified as DCM carriers (age 65±9 yrs, male 66%), 194 HCM carriers (65.5±9 yrs, male 69%), and 125 ARVC carriers (66±9 yrs, male 77%). Out of the 518 DCM variant carriers, 402 had a PLP variant in TTN. DCM variant carriers had higher odds of history of HF (Odds ratio [OR] 1.94, 1.57-2.39, p<0.0001) whereas this was not observed for HCM variant carriers (OR 1.18, 0.85-1.65, p=0.33) or ARVC variant carriers (OR 1.23, 0.80-1.90, p=0.35). Over a mean follow-up of 2.5 years, the rate of HHF was significantly higher for DCM variant carriers (Hazard ratio [HR] 1.58, 1.14-2.20, p=0.006), HCM variant carriers (HR 2.78, 1.87-4.13, p<0.001), and ARVC variant carriers (HR 1.89, 1.02-3.53, p=0.04). These associations were, if anything, stronger in patients without HF at baseline (HR 2.06, 1.30-3.25) than in patients with HF at baseline (HR 1.48, 1.12-1.95). DCM variant carriers also had a higher rate of CV death (HR 1.50, 1.05-2.12, p=0.02), which was not observed for HCM (HR 1.10, 0.57-2.11, p=0.78) or ARVC (HR 0.35, 0.09-1.41, p=0.14) variant carriers. Conclusion In 5 contemporary CV trials, CMP variant carriers have an increased rate of HHF, while DCM variant carriers also have a higher rate of CV death. These findings motivate better identification of these high-risk individuals and the incorporation of genetic testing in CV trials.

Amplicon-based long-read sequencing is useful for confirming zygosity of DSG2 variants associated with Japanese ARVC

Abstract Background Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited cardiomyopathy mainly caused by desmosomal gene variants. Previously, we reported that DSG2 variants were the most common in 153 Japanese ARVC probands (DSG2 multiple, n=62 and single, n=4; PKP2, n=28; others, n=7). Among the multiple DSG2 variant carriers, 22 probands were compound heterozygous carriers, and 25 were homozygous, which were confirmed by genetic testing for family members (Figure A). On the other hand, 88% of their family members with single DSG2 variant carriers were not diagnosed with ARVC, which meant that recessive DSG2 variants were the major cause of ARVC in Japan. However, zygosities in remaining 15 probands with multiple DSG2 variants were unknown due to the lack of genome data from their parents. Purpose This study aimed to clarify the zygosities of multiple DSG2 variants using amplicon-based long-read sequencing. Methods Genomic DNA was extracted from whole blood using standard protocols. The range containing multiple variants was amplified by long-range PCR. Sequencing libraries were prepared using ONT Ligation Sequencing Kit. Each library was loaded onto a flow cell for sequencing on ONT GridION Mk1 running MinKNOW control software. FASTQ files were aligned to hg38 using minimap2. Variants were called using Clair3 and phased using WhatsHap. Integrative Genomics Viewer (IGV) was used for visualization of the phased variants. Results We successfully phased all the multiple DSG2 variants found in the 15 proband. A typical result of amplicon-based LRS was shown in Figure B. It was IGV screen shot of reads at DSG2 containing c.874C>T (p.R292C) and c.1481A>C (p.D494A). The reads colored in red belonged to one haplotype, while the ones in blue belonged to the other. Each of the two variants was on different color reads, indicating they were compound heterozygous variants. Using LRS, we confirmed all the 15 probands had compound heterozygous variants in DSG2. Overall, the 62 probands (40.5%) with DSG2 variants were recessive variant carriers (Figure A). Conclusions Japanese ARVC was mainly caused by autosomal recessive variants in DSG2. Clarifying the zygosity of causative variants is crucial for the diagnosis in recessive diseases including Japanese ARVC. Amplicon-based LRS was helpful for phasing the multiple DSG2 variants directly without genetic testing of the parents.Figure AFigure B

Pathogenic cardiomyopathy gene variants inform prognosis in atrial fibrillation: results from exome sequencing in over 17,000 patients in TIMI trials

Abstract Background Rare genetic variants in cardiomyopathy genes are associated with risk of atrial fibrillation (AF), even in the absence of overt ventricular dysfunction. Data on clinical outcomes for rare genetic variant carriers among patients with AF remain sparse. Purpose We aimed to study the prognostic implication of rare pathogenic/likely pathogenic (PLP) variants for dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM) and arrhythmogenic right ventricular cardiomyopathy (ARVC) in patients with AF from large, well-phenotyped randomized clinical trials. Methods and results Rare variants were called using exome sequencing data in 5 large clinical trials from the TIMI study group (ENGAGE-AF, FOURIER, SAVOR, PEGASUS, DECLARE). PLP variants for cardiomyopathy were identified using phenotype- and gene-specific curation of protein-truncating variants and high-confidence variant classifications from the ClinVar database. In 17,190 patients with a history of AF, we identified 421 (2.4%) PLP variant carriers (age 67±10, 35% women) and 16,769 (97.6%) pts without PLP variants (age 70±9, 36% women). Among these individuals, we identified 265 DCM carriers (1.5%), 106 (0.6%) HCM carriers and 54 (0.3%) ARVC carriers. In this cohort, 9,275 (54%) had a history of heart failure (HF) and 2,991 (17.4%) prior ischemic stroke. Over 2.5 years median follow-up, 1,365 pts (7.9%) were hospitalized for HF, 599 (3.5%) had an ischemic stroke, and 1147 (6.7%) died of cardiovascular causes. In logistic regression analyses adjusting for age, sex, trial, and principal components of ancestry, PLP variants were significantly associated with a history of HF (OR 1.66, p<0.0001), most notably for DCM variants (OR 1.97, 1.48-2.62, p<0.0001). PLP variants were independently associated with incident HF admissions (adj HR 1.75, 1.39-2.29, p<0.0001), most notably for HCM (adj HR 2.59, 1.68-3.99, p<0.0001) and ARVC variants (adj HR 2.50, 1.34-4.66, p=0.004). The increased risk of HF admissions remained consistent in patients with (adj HR 1.49, 1.11-2.00, p=0.009) and those without (adj HR 1.88, 1.00-3.54, p=0.049) a history of HF. PLP variants were also associated with higher risk of cardiovascular death (adj HR 1.46, 1.06-2.02, p=0.02), most notably for DCM variants (adj HR 1.77, 1.21-2.58, p=0.003). In contrast, PLP variants were not associated with history of ischemic stroke at baseline (adj OR 0.99, p=0.96) nor with incident ischemic stroke (adj HR 0.95, p=0.84). Conclusion In patients with AF, rare cardiomyopathy gene variants are associated with increased risks of HF and of cardiovascular death, but not stroke. These results, collected from large well-phenotyped randomized clinical trials, demonstrate an important prognostic implication for rare genetic variants for CMP in pts with AF.

Impact of high intensity and long duration exercise in genetic arrhythmogenic left ventricular cardiomyopathy

Abstract Background Arrhythmogenic left ventricular (LV) cardiomyopathy (ALVC) is a genetic disease associating extensive LV myocardial fibrosis with or without dysfunction and no or mild right ventricle (RV) involvement, at risk of life-threatening ventricular arrhythmias (VA). While high intensity (HI) and long duration (LD) exercise has been identified as a precipitating factor of RV dysfunction and VA in arrhythmogenic RV cardiomyopathy including in asymptomatic genetic variant carriers, the impact of exercise on disease phenotype and risk is not known in ALVC. Objective To study the relationship between practicing HI and LD exercise and the risk of developing an ALVC phenotype and its severity. Methods In a monocentric retrospective observational study, patients with a pathogenic variant in common ALVC genes (DSP, FLNC, DES, PLN, RBM20, TMEM43), including asymptomatic carriers without ALVC phenotype, were interviewed about their physical practice from age 7 to the time of genetic or disease diagnosis. Intensity and weekly duration of each activity were reported. HI and LD exercise were defined as having practiced at least 1 sport with an intensity ≥ 6 METs and ≥ 2.5 hours/week respectively. We studied the association of HI and LD exercise practice with the risk of ALVC phenotype occurrence and its severity, derived from clinical, ECG and imaging data. Results 114 out of 128 eligible patients answered the questionnaire and were included (85 (74.6%) with a DSP variant, 22 FLNC (19.3%), 6 DES (5.3%), 1 RBM20 (0.9%)). 35 were probands (31%) and 79 relatives (69%) among 46 families. 31 (27%) had no ALVC phenotype at the time of genetic diagnosis. Mean age at diagnosis was 41±18. 62 (54%) patients were women. 97 (85%) had practiced at least one sport, among which 81 (83.5%) at HI and 79 (81.4%) of LD. Median lifetime exercise dose was 18.5 MET.h/week. There were no differences in HI and LD exercise practice between probands and relatives (74.3% vs 69.6%, p=0.6 and 74.3% vs 67.1%, p=0.4 respectively), as well as between patients with and patients without ALVC phenotype at the time of diagnosis (74.7% vs 61.3%, p=0.2 and 72.3% vs 61.3%, p=0.3 respectively). Phenotypic features at diagnosis did not differ between patients with and without HI and LD practice (Table 1). Multivariate analysis adjusted on age and gender showed that HI and LD exercise were not significantly associated with an increased risk of developing an ALVC phenotype (Odds Ratio [95% confidence interval] for age, gender, HI and LD exercise were 1.03 [1.01-1.06] (p=0.013), 1.41 [0.58 ; 3.47] (p=0.45), 2.15 [0.63 ; 7.27] (p=0.22) and 1.17 [0.35 ; 3.87] (p=0.79) respectively). Phenotypic features at diagnosis did not differ across observed quartiles of lifetime exercise dose (Table 2). Conclusion Practicing HI and LD exercise was not associated with an increased risk of developing an ALVC phenotype and its severity at the time of diagnosis in genetic ALVC variant carriers.

Genotype-phenotype correlations in patients with titin variants and cardiomyopathy from a Swiss cohort

Abstract Background Alterations in titin (TTN) are mostly described with dilated cardiomyopathy (DCM). Few studies identified TTN variants in arrhythmogenic cardiomyopathy (ACM), but the overlap of dilated and arrhythmogenic phenotypes in TTN variants is scarcely studied. Most pathogenic TTN variants are located on the A-band, but there is few knowledge about the phenotypic presentation of I-band and Z-disc (non-A-band) variants. Purpose The aim of this study is to characterize and investigate the outcome of patients with cardiomyopathy and pathogenic (P) or likely pathogenic (LP) TTN variants with a particular focus on the cardiomyopathy phenotype (DCM vs. ACM) at initial presentation and follow-up. Further, we studied the association of the TTN variant (A-band vs. non-A-band regions) and a unique phenotype. Methods This is a retrospective multicenter study from a Swiss cohort including 34 patients with P/LP TTN variants and cardiomyopathy. The variables of the secured anonymized database include patient characteristics, genetic, ECG, echocardiographic, and cardiac magnetic resonance (CMR) data. Ventricular arrhythmia (VA) events were divided into non-sustained ventricular tachycardia (nsVT), sustained ventricular tachycardia (sVT) and sudden cardiac arrest (SCA +/- ventricular fibrillation). Results Of 34 included patients, 68% were male. Median age at presentation was 43.5 years. 29 (85%) patients presented with DCM, 7 (21%) left dominant ACM (2020 Padua criteria) and none ARVC (2010 ARVC Task Force criteria). At median follow-up of 48.5 months, 17 (50%) patients had VA events (15 nsVT, 5 sVT and 3 SCA events). VA events significantly increased over time (p=0.008) and were not associated with gender or left ventricular ejection fraction (LVEF) <35%. Under optimal guideline-directed medical therapy (GDMT) mean LVEF and right ventricular function increased significantly (LVEF: 28.3±14.4% vs. 41.9±9.8% and right ventricular fractional area change (RV FAC): 24.7±7.5% vs. 35.8±4.8%, p<0.05). Late gadolinium enhancement (LGE) on CMR was commonest in the basal septum, but no patient had higher degree atrioventricular block (AVB) at baseline and follow-up. At last follow-up, 8 (24%) patients fulfilled ACM and 13 (38%) DCM criteria (Figure 1). Most TTN variants were located on the A-band (21, 62%), 10 (29%) on the non-A-band regions. Latter had higher rates of sVT (log-rank p=0.041) during follow-up (Figure 2). 20 (59%) had LP and 11 (32%) P variants. P variant carriers were younger at disease presentation compared to LP variant carriers. Conclusion Patients with TTN variants frequently present as DCM, whereas presentation as left dominant ACM is less common. TTN does not seem to be a classical ARVC causing gene. Despite favourable biventricular remodelling under GDMT, ventricular arrhythmic events increase during follow-up. I-band and Z-disk variants are associated with a higher risk of sVT, which may help in the risk stratification process.

Genetic and phenotypic architecture of biventricular trabeculation

Abstract Introduction Cardiac trabeculae form a network of muscular strands that line the inner surfaces of the heart, and their development involves molecular pathways that regulate structural complexity. Excessive or hypertrabeculation occurs as part of normal variation in apparently healthy individuals, as an adaptation to altered loading conditions, and is observed in patients with cardiomyopathies (CMs) and heart failure (HF). Purpose In adults, trabeculation is not a prognostic factor independent of the underlying myocardial disease but may play a role in the natural history of ventricular remodelling. We sought to (i) understand the genetic and non-genetic determinants of trabeculation, (ii) understand its role in the causality of disease, and (iii) evaluate trabeculation as a biomarker for diagnosis and stratification. Methods We report genes with a burden of rare variants and novel common variant associations across the allele frequency spectrum for biventricular trabecular morphology in 47,803 participants of the UK Biobank using fractal dimension analysis of cardiac imaging (Figure 1). We assessed environmental modifiers of trabecular morphology, correlation with cardiac traits, phenome-wide association studies, and the relationship with the progression of CMs and HF. Results We identified a burden of trabeculation-associated rare variants in genes that regulate myocardial contractility and cardiac development and GWAS identified novel loci near genes implicated in CMs, conduction traits, and signalling pathways that define the early development of trabeculation. For example, we identified 56 genes with a burden of rare variants and 68 novel loci from GWAS (e.g., CASQ2, CACNA1C, MYBPC3, MYH7, NKX2-5, NOTCH1, TBX20) for the left ventricle. The strongest imaging relationships with trabeculation were with measures of volume and strain. Modifiers of trabeculation included African ancestry, alcohol intake, and physical activity. Carriers of CM-associated pathogenic variants had increased trabeculation. Of participants with CM reported after imaging, 25% had hypertrabeculation on imaging and hypertrabeculation was a risk factor for a subsequent diagnosis of HF (HR=1.3), mitral valve disorders (HR=1.4), bundle branch block (HR=1.2). Comparisons of biventricular trabeculation showed similarities in trabeculation across the ventricles in CM. Reduced right ventricular trabeculation and end-diastolic volume associated with Type-2 diabetes. Conclusions These data provide new insights into the mechanisms that regulate structural complexity in the heart. Changes in trabeculation may occur early in the pathogenesis of heart disease, can be modified by genes regulating pathways outside the sarcomere, and causality depends on the underlying cardiomyopathic substrate. Trabeculation progresses with cardiovascular disease, is a useful marker of remodelling, and identifies novel genetic modifiers of ventricular complexity.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

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

Early-onset atrial fibrillation is a risk marker for cardiomyopathy: genetic insights from the UK Biobank

Abstract Introduction Atrial fibrillation (AF) is a common cardiac arrhythmia associated with an increased risk of stroke, heart failure and premature death. Genetic associations between AF and rare variants have been identified in several cardiomyopathy-associated genes, and previous studies have shown a high prevalence of deleterious variants among individuals with early onset of AF. Consequently, genetic testing has been suggested in patients with AF onset before 45 years of age. Purpose This study aimed to explore the prevalence and distribution of deleterious genetic variants in cardiomyopathy genes according to age at AF diagnosis. Methods The UK Biobank is a large population-based biobank, comprised of clinical and genetic information on more than 500,000 individuals, enrolled between 2006 and 2010. We analyzed whole-exome sequencing data among unrelated individuals of European ancestry. The cohort was stratified by age at AF onset (AF onset <45 years, AF onset between 45-54 years, AF onset between 55-64 years, AF onset >=65 years, and individuals with no AF diagnosis). We evaluated the presence of rare (minor allele frequency <0.1%) genetic variants in core cardiomyopathy genes, according to guidelines by the American College of Medical Genomics and focused on variants predicted to lead to loss of function. Individuals with a diagnosis of cardiomyopathy prior to AF were excluded. Results Among 374,365 unrelated individuals of European ancestry, 29,119 were diagnosed with AF. Of these, 685 had onset of AF<45 years (2.35%), 2465 had onset between 45-54 years (8.46%), 7778 had onset between 55-64 years (26.71%), and 18191 had onset at or above 65 years of age (62.48%). A total of 884 were carriers of rare loss-of-function variants in cardiomyopathy genes. Among carriers, the majority of variants were in key genes for dilated cardiomyopathy (TTN), hypertrophic cardiomyopathy (MYBPC3), and arrhythmogenic right ventricular cardiomyopathy (PKP2). We observed an inverse dose-response-like relationship between prevalence of the rare genetic variants and age at AF diagnosis. The highest prevalence of carriers was observed among individuals with onset before 45 years (4.96%). In comparison, the proportion of carriers was 3.45% in individuals with AF onset between 45-54 years, 2.96% in individuals with AF onset between 55-64 years, 2.75% in individuals with onset at or after 65 years, and 2.05% among individuals without AF diagnosis. Conclusions Using whole exome sequencing, we identified a high proportion of carriers of deleterious variants in actionable genes of cardiomyopathies among individuals with early onset of AF. We observed an inverse dose-response-like relationship between age of AF diagnosis and prevalence of deleterious genetic variants. Our findings support that very early onset of AF, before 45 years of age, is a potential risk marker for cardiomyopathy and support that genetic screening may be relevant in this patient group.

Metabolomic profiling of the entire UK Biobank enables interpretation of familial hypercholesterolemia mutations and prediction of severe cardiovascular outcomes

Abstract Background Familial hypercholesterolemia (FH) is an inherited disorder resulting in high levels of LDL-C from birth. Premeature coronary heart disease occurs in half of affected men by age 50 years(1). While many genetic variants that cause FH are well understood, there are also many variants in FH genes that are of uncertain clinical significance. Furthermore, the variability in residual cardiovascular risk of FH carriers after statin treatment is not fully understood. We here investigate whether metabolomic and genomic data from the 500,000 person UK Biobank cohort can aid in interpretation of candidate pathogenic variants for FH, and characterise future risk of severe cardiac events in the carriers of such variants. Methods We have quantified 249 metabolomic parameters in 490,830 blood samples from UK Biobank cohort. Among 186,483 participants with exome sequence data we identified 896 who carried known pathogenic FH variants and 405 who carried variants of unknown significance in an established FH gene. We fitted a logistic predictive model to identify pathogenic mutations using LDL levels, statin use and 17 principal components of the metabolomic parameters. We further tested whether metabolomic and genomic scores for predicting future risk of myocardial infarction (MI), that were trained in the general population (i.e. individuals without FH), could predict risk in FH carriers. Results A model including all metabolites had a higher accuracy at identifying known pathogenic FH variants (36/56 at FDR < 0.05), compared to LDL and statin use alone (30/56). Our model also identified 8 FH variants marked as uncertain significance in ClinVar with significant (FDR < 0.05) evidence of predicted pathogenicity. We found that our metabolomic risk score predicted 10-year risk of MI among FH carriers (HR=1.96 per SD, p = 0.0011). This was indeed stronger than the effect in the general population (HR = 1.64 per SD, p = 2.5e-168). A combined metabolomic and polygenic risk score had an even larger effect at predicting MI in FH carriers (HR = 3.06 per SD, p = 2.0e-6), and this score was significantly better at predicting MI in FH carriers than in non-carriers (HR = 3.06 vs 1.88 per SD, interaction p = 0.042). Conclusion Familial hypercholesterolemia is an important source of risk for early cardiovascular disease. Population-scale metabolomics can help distinguish pathogenic from benign variants that have not yet been characterised. Metabolomic and genomic scores can also identify individuals at most elevated risk, and provide even more information to FH individuals than in the general population.

Prevalence and implications of cardiomyopathy-associated genetic variants in early-onset atrial fibrillation

Abstract Background Atrial fibrillation (AF) is a common and morbid arrhythmia. Despite a substantial heritable component, genetics does not currently play a role in personalized medicine for AF. Rare genetic variants in genes associated with inherited cardiomyopathies (CMP) are enriched in AF patients. However, prior studies on rare variants in AF mainly relied on hospital-based populations, and knowledge on clinical outcomes remains limited. Purpose We aimed to evaluate the potential diagnostic yield and prognostic implication of pathogenic or likely pathogenic (PLP) genetic variants for CMP in persons with AF, using large population-based cohorts. Methods This study utilized sequencing data and electronic health records (EHR) from the All of Us Researh Program (AllofUs) and UK Biobank (UKB). Using ClinVar, we curated a set of PLP variants in 36 CMP-associated genes and assessed the carrier prevalence overall, in participants with AF, and in participants with early-onset AF (below 65, 55 and 45 years). Next, we used Cox proportional hazards models to evaluate the association between variant carrier status and incident risk of heart failure or CMP, after AF diagnosis. In all time-to-event analyses, individuals with prevalent heart failure or CMP at AF diagnosis were excluded and models were adjusted for age, sex, and principal components of ancestry. Sensitivity analyses were performed requiring a minimum period from AF to HF or CMP, of 1, 3 and 6 months. Results After excluding related individuals, we identified 32,281 (8.19%) and 9,666 (6.06%) AF cases in UKB and AllofUs, respectively. Compared to the overall populations (UKB: 1.15%; AllofUs: 1.36%), PLP variants for CMP were about ~5 times more prevalent in AF with onset before 45 (UKB: 4.98%; AllofUs: 5.26%), ~3 times more prevalent in AF with onset before 55 (UKB: 3.41%; AllofUs: 4.34%) and ~2 times more prevalent in all AF patients (UKB: 2.03%; AllofUs: 2.67%). In turn, AF patients carrying PLP variants had increased risk of developing heart failure or CMP, after AF diagnosis (AllofUs HR 1.81, 1.44-2.29, p<1e10-6, UKB:HR=1.39 1.08-1.78, p<0.01), which remained present when requiring a minimum of 6 months after AF diagnosis (AllofUs:HR 1.70, 1.29-2.25, p<0.001; UKB:HR=1.59, 1.21-2.07, p<0.001). Effect sizes were greater when limiting analysis to AF patients with onset before 65 (cases=1021, HR 1.91, 1.35-2.68, p<0.0001) and before 55 years (cases=384, HR 2.53, 1.55-4.1, p <0.001) in AllofUs. UK Biobank did not reflect this increase (cases<65=513, HR<65=1.27, 0.63-2.39, p<65>0.05). Considering only HF events in AllofUs, the effect remained present (HR 1.70, 1.32-2.19, p<0.0001). Conclusion The yield of CMP-associated PLP variants is substantial among persons with early-onset AF, even when considering a 55 year cutoff. AF patients with PLP variants have an increased risk of future heart failure or CMP. Our results further support the clinical relevance of genetic testing in early-onset AF.Prevalence of CMP variants in AF by age

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.

Expanded carrier screening for 216 diseases in a cohort of 3 097 healthy Chinese individuals of childbearing age

Objective: To determine the carrier frequency and hot-spot variants of a custom-designed expanded carrier screening (ECS) panel with 216 diseases (216-ECS panel) within a Chinese population of childbearing age. Methods: Whole-exome sequencing data from a cohort of 3 097 unrelated healthy individuals (including 1 424 couples) from Peking Union Medical College Hospital between January 2013 and December 2023 were analyzed. Totally 220 genes which inherited in a recessive manner of 216-ECS panel were included in the analysis. The analysis included variant carrier rate, gene carrier rate, cumulative carrier rate, at-risk couple rates, and variant spectrum. Results: (1) Pathogenic variants were identified in 1 472 (47.53%, 1 472/3 097) individuals, with an average of 0.65 pathogenic variants per individual. The rate of at-risk couples was 3.93% (56/1 424). (2) A total of 180 genes were identified, with 16 genes exhibiting a gene carrier rate of ≥1% and 33 genes having a rate of ≥0.5%, most of which were associated with inherited metabolic diseases. Noteworthy genes with higher gene carrier rates and high-frequency variants included GJB2: c.235del, PAH: c.728G>A, ATP7B: c.2333G>T, SLC26A4: c.919-2A>G, GALC: c.1901T>C, POLG: c.2890C>T, SLC22A5: c.1472C>G, USH2A: c.2802T>G, SLC25A13: c.852_855del, GAA: c.761C>T and c.752C>T. Conclusion: This study offers a focused analysis of carrier frequencies and hot-spot variants of 216 diseases of the ECS panel constructed by our laboratory among the Chinese population, laying a foundation for the development of ECS programs tailored to the Chinese population.

Germline DNA damage repair variants and prognosis of patients with high-risk or metastatic prostate cancer.

Deleterious germline variants in certain DNA repair genes are risk factors for developing aggressive prostate cancer. The objective was to quantify their prognostic impact after prostate cancer diagnosis. Men with prostate cancer, predominantly of European ancestry, were included from four cohorts with long-term follow-up. Pathogenic or likely pathogenic germline variants in 26 DNA repair genes were assessed in relation to metastasis-free survival in high-risk, localized prostate cancer and to overall survival in metastatic castration-sensitive prostate cancer (mCSPC) and metastatic castration-resistant prostate cancer (mCRPC). Among 3,525 patients initially diagnosed with non-metastatic prostate cancer, 2,594 had high-risk localized prostate cancer, 429 mCSPC, and 502 mCRPC at inclusion. BRCA2 variant carriers did not have worse metastasis-free survival in high-risk localized prostate cancer (hazard ratio [HR] 1.01, 95% confidence interval [CI] 0.69, 1.46) or overall survival in mCSPC (HR 0.46, 95% CI 0.14, 1.45) or mCRPC (HR 0.60, 95% CI 0.31, 1.17) compared to non-carriers of DNA repair variants. Among 868 additional patients with de novo metastatic (M1) prostate cancer, BRCA2 variant carriers tended to have worse overall survival (HR 1.59, 95% CI 1.01, 2.51). BRCA2 prognostic associations were not explained by radiation, PARP inhibitor, or platinum therapy. Results for other genes were limited in precision because variants were less common. Among patients with high-risk or metastatic prostate cancer who were initially diagnosed with and treated for non-metastatic tumors, germline DNA repair variants in BRCA2 do not confer a substantially worse prognosis.

Targeted gene sequencing and hearing follow-up in 7501 newborns reveals an improved strategy for newborn hearing screening.

Hearing loss is a common congenital condition. Concurrent newborn hearing and limited genetic screening has been implemented in China for the last decade. However, the role of gene sequencing screening has not been evaluated. In this study, we enrolled 7501 newborns (52.7% male, 47.3% female) in our Newborn Screening with Targeted Sequencing (NESTS) program, and 90 common deafness genes were sequenced for them. Hearing status assessments were conducted via telephone from February 2021 to August 2022, for children aged 3 to 48 months. Of the universal newborn hearing screening, 126 (1.7%) newborns did not pass. Targeted sequencing identified 150 genetically positive newborns (2.0%), with 25 exhibiting dual-positive results in both screening. Following diagnostic audiometry revealed 18 hearing loss newborns and half of them had abnormal results in both screening. The positive predictive value for universal newborn hearing screening alone was merely 14.3% (18/126). However, when combined with targeted sequencing, this rate increased to 36.0% (9/25). Furthermore, limited genetic screening identified 316 carriers of hot-spot variants, but none exhibited biallelic variants. All 15 hot-spot carriers who failed physical screening demonstrated normal hearing during follow-up. In this cohort study of 7501 Newborns, Combining targeted sequencing with universal newborn hearing screening demonstrated technical feasibility and clinical utility of identifying individuals with hearing loss, especially when coupled with genetic counseling and closed-loop management. It is suggested to use this integrated method as an improved strategy instead of the current limited genetic screening program in some regions of China.

Gene-Specific Effects on Brain Volume and Cognition of TMEM106B in Frontotemporal Lobar Degeneration.

TMEM106B has been proposed as a modifier of disease risk in FTLD-TDP, particularly in GRN pathogenic variant carriers. Furthermore, TMEM106B has been investigated as a disease modifier in the context of healthy aging and across multiple neurodegenerative diseases. The objective of this study was to evaluate and compare the effect of TMEM106B on gray matter volume and cognition in each of the common genetic FTD groups and in patients with sporadic FTD. Participants were enrolled through the ARTFL/LEFFTDS Longitudinal Frontotemporal Lobar Degeneration (ALLFTD) study, which includes symptomatic and presymptomatic individuals with a pathogenic variant in C9orf72, GRN, MAPT, VCP, TBK1, TARDBP, symptomatic nonpathogenic variant carriers, and noncarrier family controls. All participants were genotyped for the TMEM106B rs1990622 SNP. Cross-sectionally, linear mixed-effects models were fitted to assess an association between TMEM106B and genetic group interaction with each outcome measure (gray matter volume and UDS3-EF for cognition), adjusting for education, age, sex, and CDR+NACC-FTLD sum of boxes. Subsequently, associations between TMEM106B and each outcome measure were investigated within the genetic group. For longitudinal modeling, linear mixed-effects models with time by TMEM106B predictor interactions were fitted. The minor allele of TMEM106B rs1990622, linked to a decreased risk of FTD, associated with greater gray matter volume in GRN pathogenic variant carriers under the recessive dosage model (N = 82, beta = 3.25, 95% CI [0.37-6.19], p = 0.034). This was most pronounced in the thalamus in the left hemisphere (beta = 0.03, 95% CI [0.01-0.06], p = 0.006), with a retained association when considering presymptomatic GRN pathogenic variant carriers only (N = 42, beta = 0.03, 95% CI [0.01-0.05], p = 0.003). The minor allele of TMEM106B rs1990622 also associated with greater cognitive scores among all C9orf72 pathogenic variant carriers (N = 229, beta = 0.36, 95% CI [0.05-0.066], p = 0.021) and in presymptomatic C9orf72 pathogenic variant carriers (N = 106, beta = 0.33, 95% CI [0.03-0.63], p = 0.036), under the recessive dosage model. We identified associations of TMEM106B with gray matter volume and cognition in the presence of GRN and C9orf72 pathogenic variants. The association of TMEM106B with outcomes of interest in presymptomatic GRN and C9orf72 pathogenic variant carriers could additionally reflect TMEM106B's effect on divergent pathophysiologic changes before the appearance of clinical symptoms.

Nephrocalcinosis, distal renal tubular acidosis and skeletal abnormality in two siblings with ROGDI-related Kohlschütter-Tönz syndrome.

Kohlschütter-Tönz (KTS) is a rare autosomal recessive, genetically heterogeneous disorder characterized by a triad of early-onset seizures, global developmental delay or regression, and amelogenesis imperfecta of both temporary and permanent teeth. To date, 66 cases have been reported in the literature, of which 44 with genetic confirmation. Here we report the observation of sibling pairs in a family from a small village in India who presented with nephrocalcinosis, distal renal tubular acidosis, and skeletal abnormality. Nephrocalcinosis has only been reported once before in an individual affected with KTS. Trio exome sequencing revealed a novel, homozygous, likely pathogenic variant, c.646-2_649del, in exon 9 of the ROGDI gene (NM_024589.3) in the first child. Sanger sequencing confirmed homozygosity in both children. Both parents are heterozygous carriers of the same variant. Further research needs to be done to identify the exact mechanism by which ROGDI-encoded protein deficiency leads to nephrocalcinosis and distal renal tubular acidosis.

Frequency and Longitudinal Course of Behavioral and Neuropsychiatric Symptoms in Participants With Genetic Frontotemporal Dementia.

Behavioral and neuropsychiatric symptoms are frequent in patients with genetic frontotemporal dementia (FTD). We aimed to describe behavioral and neuropsychiatric phenotypes in genetic FTD, quantify their temporal association, and investigate their regional association with brain atrophy. We analyzed data of pathogenic variant carriers in the chromosome 9 open reading frame 72 (c9orf72), progranulin (GRN), or microtubule-associated protein tau (MAPT) gene from the Genetic Frontotemporal dementia Initiative cohort study that enrolls both symptomatic pathogenic variant carriers and first-degree relatives of known carriers. Principal component analysis was performed to identify behavioral and neuropsychiatric clusters that were compared with respect to frequency and severity between groups. Associations between neuropsychiatric clusters and MRI-assessed atrophy were determined using voxel-based morphometry. We applied linear mixed effects and generalized linear mixed effects models to assess the longitudinal course of symptoms. A total of 522 participants were included: 221 c9orf72 (138 presymptomatic), 213 GRN (157 presymptomatic), and 88 MAPT (62 presymptomatic) pathogenic variant carriers. Principal component analysis revealed 5 phenotypic clusters (67.6% of variance), labeled diverse behavioral, affective, psychotic, euphoric/hypersexual, and tactile hallucinations phenotype. In participants presenting behavioral or neuropsychiatric symptoms, affective symptoms were most frequent across groups (83.6%-88.1%), followed by diverse behavioral symptoms (68.4%-77.9%). In c9orf72 and GRN pathogenic variant carriers, psychotic symptoms (32.0% and 19.4%, respectively) were more frequent than euphoric/hypersexual symptoms (28.7% and 14.2%, respectively), which was the other way around in MAPT pathogenic variant carriers (28.6% and 23.8%). Although diverse behavioral symptoms were associated with gray and white matter frontotemporal atrophy, only a small atrophy cluster in the right thalamus was associated with psychotic symptoms. Euphoric/hypersexual symptoms were associated with atrophy in mesial temporal lobes, basal forebrain structures, and the striatum (p < 0.05). Estimated time to symptom onset, genetic group, education, and sex influenced behavioral and neuropsychiatric symptoms (p < 0.05). Particularly, in c9orf72 pathogenic variant carriers, psychotic symptoms may be starting decades before recognition of onset of illness. We identified multiple clusters of behavioral and neuropsychiatric symptoms in participants with genetic FTD that relate to distinct cerebral atrophy patterns. Their severity depends on time, affected gene, sex, and education. These clinical-genetic associations can guide diagnostic evaluations and the design of clinical trials for new disease-modifying and preventive treatments.