Dikilitas, Ozan

ABSTRACT Pathogenic variants in AMMECR1 have been associated with a rare multisystem disorder characterized by midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (MFHIEN). To date, most reported cases involve copy number variants or presumed loss‐of‐function alterations, with only a single prior report describing a missense variant supported by functional studies. Here, we report a patient with a heterozygous de novo AMMECR1 missense variant, NM_015365.3:c.649G>A p.(Val217Met) presenting with clinical features consistent with MFHIEN, including midface hypoplasia, partial hearing impairment, nephrocalcinosis, and elliptocytosis identified on peripheral blood smear. Comparative review of the literature highlights that while previously reported missense variants in AMMECR1 demonstrated altered intranuclear protein distribution and reduced expression in functional assays, clinical evidence supporting pathogenicity of non‐truncating variants remains limited. The phenotypic overlap between our patient and prior report strengthens the association between missense variations and the MFHIEN phenotype. Our findings support the pathogenic relevance of missense variation in AMMECR1 and emphasize the importance of integrating detailed phenotyping, including hematologic evaluation, with genomic data in the diagnosis of rare multisystem disorders. Additional cases and functional studies are needed to clarify genotype–phenotype correlations and underlying disease mechanisms.

BACKGROUND: Performance and transferability of contemporary polygenic risk scores (PRS) for atherosclerotic cardiovascular disease phenotypes may vary across PRS methods, training data, and trait ascertainment. METHODS: We aimed to investigate the performance and transferability of contemporary PRS for atherosclerotic cardiovascular disease subtypes: coronary heart disease (CHD), abdominal aortic aneurysm (AAA), ischemic stroke (IS), and peripheral artery disease (PAD), using the All of Us Workbench, which consists of a large, diverse cohort with whole-genome sequence data. We also developed and evaluated a multi-trait PRS for each subtype. Performance of PRS for 4 atherosclerotic cardiovascular disease subtypes was compared across genetic similarity groups in 245 388 All of Us participants. Groups genetically similar to European, African, admixed American, and remaining groups (combined as other) were used to assess PRS for CHD, IS, AAA, PAD, and multi-trait. RESULTS: PRS for CHD and AAA performed better than IS and PAD. For CHD, CHD PGS003725 performed the best (hazard ratio per SD increase [95% CI]), across genetic ancestry groups, European, and African (1.72 [1.67–1.78], 1.23 [1.17–1.29]), with CHD PGS004696 being best for admixed American (1.91 [1.70–2.15]), and CHD PGS003356 for other (1.75 [1.58–1.95]). The best performing PRS for AAA was AAA Multi for European, other, and admixed American (1.71 [1.52–1.92], 1.59 [1.07–2.37], 1.50 [0.90–2.52]) and AAA PGS003972 for African (1.39 [1.19–1.63]). For IS, IS Multi performed best for other and European (1.49 [1.17–1.89], 1.33 [1.25–1.42]), and IS PGS000039 performed best in admixed American and African (1.17 [1.07–1.27], 1.09 [1.04–1.15]). For PAD, PAD Multi performed best for all groups (other, 1.51 [1.19–1.92]; European, 1.32 [1.24–1.41]; admixed American, 1.23 [1.05–1.45]; and African, 1.18 [1.04–1.34]). CONCLUSIONS: Multi-trait and multi-ancestry PRS performed better than individual trait and/or single ancestry PRS for each atherosclerotic cardiovascular disease phenotype across ancestrally diverse and admixed individuals, with minimal change including adjustment for conventional risk factors.

Abstract Pathogenic variants in cardiomyopathy genes confer substantial disease risk, yet clinical penetrance varies widely. The population-level prevalence, age-specific penetrance, and the extent to which polygenic susceptibility modifies disease risk across diverse ancestries remain poorly defined. This population-based cohort study leveraged genome sequencing and linked electronic health record data from the All of Us Research Program (n=414,830). This study found that P/LP variants in cardiomyopathy-associated genes were present in 0.91% of participants (95% CI, 0.88%–0.94%), with similar prevalence across ancestry groups. Compared with non-carriers, variant carriers had significantly higher odds of all-cause heart failure (ACHF, OR, 2.58; 95% CI, 2.31–2.89), non-ischemic heart failure (NIHF, OR, 2.74; 95% CI, 2.42–3.10), and non-ischemic cardiomyopathy (NICM, OR, 4.99; 95% CI, 4.44–5.63). Among carriers, by age 50 years, 24.5% (95% CI, 14.5%–33.4%) developed ACHF, 17.2% (95% CI, 8.8%–24.8%) developed NIHF, and 30.1% (95% CI, 19.5%–40.2%) developed NICM. Higher polygenic risk for heart failure was independently associated with increased risk of ACHF (OR, 1.81; 95% CI, 1.74–1.89), NIHF (OR, 1.66; 95% CI, 1.58–1.75), and NICM (OR, 1.69; 95% CI, 1.59–1.80). Among carriers with elevated polygenic risk, odds of disease were substantially higher than among non-carriers at average polygenic risk (ACHF: OR, 4.71; 95% CI, 4.17–5.32; NIHF: OR, 4.56; 95% CI, 3.99–5.22; NICM: OR, 8.51; 95% CI, 7.44–9.73). Results showed that P/LP variants in cardiomyopathy genes were relatively common in this large, ancestrally diverse cohort, and conferred increased risk of cardiomyopathy and HF, with incomplete but clinically meaningful penetrance. Polygenic risk for HF independently and additively increased disease risk across ancestries. Integrating both may improve risk stratification and enable more precise, equitable care.

Abstract Background Contemporary prevalence and penetrance of familial hypercholesterolemia (FH) and the associated coronary heart disease (CHD) risk across diverse genetic ancestries in the United States are unclear. Purpose To estimate prevalence of individuals harboring pathogenic/likely pathogenic (P/LP) variants in LDLR, APOB, and PCSK9, distribution of low-density-lipoprotein cholesterol (LDL-C) levels, and associated CHD risk for carriers in an ancestrally diverse cohort. Methods In 242,167 All of Us (AoU) participants with available whole-genome sequencing data, we obtained LDL-C measurements, statin prescriptions, and ascertained P/LP variants in FH-related genes and presence of CHD based on electronic-health record data. P/LP variants in LDLR, APOB, and PCSK9 were identified in AoU data by filtering for high-impact (frameshift, canonical splice site, indels, and stop gain) and predicted-deleterious missense variants, then selecting those classified as P/LP in ClinVar. Untreated LDL-C levels were estimated assuming a 30% reduction if there was a record of a statin prescription in the preceding 12 months and the highest value among multiple measurements for each individual were selected. Penetrance was defined as LDL-C>155 mg/dl. CHD was determined using a validated phenotyping algorithm based on diagnostic and procedural billing codes. Logistic regression models were used to obtain prevalence and penetrance estimates and odds ratios for CHD, along with associated 95% confidence intervals (95% CI). Results We identified 221 FH-related P/LP variants (LDLR=169, APOB=50, PCSK9=2) in the study cohort. Of 125,841 European (EUR), 53,367 African (AFR), 40,189 admixed American (AMR), and 22,770 other ancestry individuals, 1:218 (0.46%, 95% CI 0.42%-0.50%), 1:307 (0.33%,0.28%-0.38%), 1:350 (0.29%, 0.24%-0.34%), and 1:201 (0.50%, 0.41%-0.59%) were carriers of a P/LP variant. In 92,616 individuals with at least one LDL-C measurement, carriers of a P/LP variant had a higher distribution of LDL-C across all ancestries with similarly high penetrance (Figure 1). Harboring a P/LP variant in LDLR, APOB, and PCSK9 was associated with similarly increased odds of CHD across all the different ancestry groups (Figure 2). Conclusions Monogenic FH was prevalent, penetrant, and significantly associated with CHD similarly across diverse ancestry groups in the AoU cohort. These findings support a ‘genotype first’ approach to detection of FH to enable early intervention across diverse ancestry groups.Figure 1 Figure 2

Background: Susceptibility to cardiometabolic diseases (CDs) is shaped by genetic, socio-environmental, and lifestyle factors. We evaluated the associations of disease-specific polysocial risk scores (PSSs)— derived from social determinants of health (SDOH) and lifestyle factors—and genetic risk factors with six CDs, across self-identified race/ethnicity (SIRE) groups in the eMERGE IV cohort. Methods: The six CDs included: atrial fibrillation, coronary heart disease, chronic kidney disease, hyperlipidemia, obesity, and type 2 diabetes. Disease-specific PSSs were developed using machine-learning models based on 65 SDOH and lifestyle factors. Participants were grouped based on their SIRE as Asian, Black, Hispanic/Latino, and White. We evaluated PSS distributions across SIRE groups. Genetic risk was assessed through disease-specific polygenic risk scores (PRSs), monogenic etiologies, and family history (FamHx). High PSS and high PRS were defined as the top 5th percentile. Associations were tested using multivariable logistic regression; model performance was assessed using the C-statistic. Results: Among 20178 participants (50±15 years, 68% female, 40% non-White), the most frequently associated PSS components were physical activity, sleep, self-perceived health, and income. PSS distributions varied across SIRE groups, with Whites having the lowest and Black and Hispanic/Latinos the highest scores for most CDs (Figure 1). All PSSs were significantly associated with their respective CDs, independent of confounders (OR per 1 SD increase: 1.19–2.68; Figure 2-A). No significant interactions were observed between PSSs and PRSs or monogenic etiologies. However, significant interactions were noted between PSSs and FamHx for CKD and obesity. PSS and PRS effects on the odds of CDs were independent (Figure 2-B) and additive (Figure 2-C). Incorporating PSSs into models that included clinical and genetic risk factors improved predictive performance of risk prediction models (Figure 3). Conclusion: PSSs, reflecting socio-environmental and lifestyle disadvantage, varied significantly across SIRE groups and were associated with risk of six CDs, independent of and additive to PRS. Given the substantial variation in socio-environmental and lifestyle risks across SIRE groups, integrating these factors into risk prediction models for CDs may help address health disparities and enhance preventive efforts, especially in marginalized populations.

Background: We investigated the impact of genetic risk factors for coronary heart disease (CHD) -polygenic risk score (PRS), familial hypercholesterolemia (FH), and family history (FamHx)- on CHD risk estimates, across the age spectrum, in two diverse cohorts of US adults -eMERGE IV (eIV) and All of Us (AoU). Methods: CHD was defined as myocardial infarction, unstable angina, and coronary revascularization. Self-identified race/ethnicity (SIRE) was used as a population descriptor. We calculated a PRS for CHD (PRS CHD , PGS004698), ascertained FH as the presence of pathogenic/likely pathogenic variants in FH genes, and defined FamHx as early-onset CHD in first-degree relatives. We employed Pooled Cohort Equations (PCE) to estimate the 10y risk of CHD for adults ≥40y and modeled the association of conventional risk factors with CHD in adults <40y. AoU served as the training set, and eIV as the testing set. We analyzed the impact of PRS CHD and FamHx on CHD risk estimates by a) using multivariable logistic regression and Cox proportional hazard models, assessing discrimination and the extent of risk reclassification; and b) net benefit analysis and decision curves to assess the performance of prediction models across actionable thresholds. Results: We analyzed data for 19348 participants from eIV (age 50±15, 68% female, 41% non-White) and 239645 participants from AoU (age 55±17, 61% female, 48% non-White). Genetic risk factors were significantly associated with CHD. PRS CHD performance varied by SIRE groups, while FamHx was consistent. The effects of PRS CHD and FamHx on CHD were independent and additive (Figure 1). In adults ≥40y, incorporating PRS CHD and FamHx into PCE improved discrimination (C-statistic increased from 0.719 to 0.753; P -diff=9.1×10 -3 , Figure 2) and reclassified risk in 19% and 20% of participants at the 7.5% and 10% 10y CHD risk thresholds, respectively. Between the 7.5% and 10% 10y CHD risk thresholds, incorporating PRS CHD and FamHx into the PCE improved the net benefit of the risk prediction models across White, Black, and Hispanic/Latino groups (Figure 3). Conclusion: PRS CHD and FamHx were independently and additively associated with CHD in two large diverse cohorts in the US. Incorporating PRS CHD and FamHx into PCE improved risk discrimination, reclassified risk in a significant portion of participants, and improved net benefit of the PCE across all three major SIRE groups, motivating the addition of these factors to clinical risk calculators.

Background: Congenital long QT syndrome (LQTS) is characterized by a prolongation of the heart rate-corrected QT interval (QTc) and an increased risk of syncope, seizure and sudden cardiac arrest/death (SCA/SCD). Genome-wide association studies have identified numerous QT interval-influencing loci of small effect sizes. Herein, we sought to investigate whether a polygenic background for the QT interval contributes to the phenotypic heterogeneity in patients with genotype-positive LQTS. Methods: We used summary statistics from a recent genome-wide meta-analysis for QT interval (n = 117,532) to derive 160 different polygenic scores for QT interval (PGS QT ) using LDpred2-grid, each comprising ~1.4 million common variants with varying assumptions of the underlying genetic architecture. Next, we applied these PGS QT to predict the QTc value in a genetically unrelated, European ancestry subset of the ‘All of Us’ cohort with available electrocardiogram and genetic data (n=6,404), where the best performing PGS QT was determined based on explained variance. Next, using 225 patients with genetically confirmed LQTS who were evaluated in the Mayo Clinic Windland Smith Rice Genetic Heart Rhythm Clinic, we tested the effect of the best performing PGS QT on QTc duration and LQTS-associated cardiac events (defined as a composite of syncope, seizures, sustained ventricular arrhythmia, appropriate ICD shocks, and SCA/SCD) using Bayesian regression models. Results: Overall, the best performing PGS QT explained 11.8% of the variance in the QTc in the ‘All of Us’ cohort. Among patients with genotype-positive LQTS (n [%]; KCNQ1 125 [55.6], KCHN2 76 [33.8], SCN5A 21 [9.3], Other 3 [1.3]), those with higher PGS QT had a higher QTc (predicted mean QTc [95% uncertainty interval], 95 th percentile vs 50 th percentile for PGS QT , 478 ms [464-491] vs 459 ms [449-468]). In comparison to the median PGS, those LQTS patients with a PGS QT >95 th percentile were more than twice as likely to have experienced a LQTS-associated cardiac event (Odds ratio [95% UI], 95 th percentile vs 50 th percentile for PGS QT ; 2.16 [1.02-5.41]), ( Figure ). Conclusions: Individuals with genotype-positive LQTS who have high polygenic susceptibility for QTc prolongation are more likely to phenotypically exhibit a higher QTc value and experience potentially life-threatening LQTS-associated cardiac events. Accounting for polygenic background may refine risk stratification strategies for patients with genotype-positive LQTS

BACKGROUND: In the Myocardial Infarction Genes clinical trial (URL: https://www.clinicaltrials.gov ; Unique identifier: NCT01936675), participants at intermediate risk of coronary heart disease (CHD) were randomized to receive a Framingham risk score (Framingham risk score group, n=103) or an integrated risk score (integrated risk score group [IRS g ], n=104) that additionally included a polygenic risk score. After 6 months, IRS g participants had higher statin initiation and lower low-density lipoprotein cholesterol. We conducted a post hoc 10-year follow-up analysis to investigate whether disclosure of a polygenic risk score for CHD was associated with a reduction in major adverse cardiovascular events (MACE). METHODS: Participants were followed from randomization in October 2013 to September 2023 to ascertain MACE, testing for CHD, and changes in risk factors. The primary outcome was time to first MACE, defined as cardiovascular death, nonfatal myocardial infarction, coronary revascularization, and nonfatal stroke. Statistical analyses included Cox proportional hazards regression and linear mixed-effects models. RESULTS: We followed all participants who completed the trial, 100 in Framingham risk score group and 103 in IRS g (mean age at the end of follow-up, 68.2±5.2; 48% male). During a median follow-up of 9.5 years, 9 MACEs occurred in Framingham risk score group and 2 in IRS g (hazard ratio, 0.20 [95% CI, 0.04–0.94]; P =0.042). In Framingham risk score group, 47 (47%) underwent at least 1 diagnostic test for CHD, compared with 30 (29%) in IRS g (hazard ratio, 0.51 [95% CI, 0.32–0.81]; P =0.004). A higher proportion of IRS g participants were on statin therapy during the first 4 years postrandomization and had a greater reduction in low-density lipoprotein cholesterol for up to 3 years postrandomization. No significant differences were observed between 2 groups in other traditional cardiovascular risk factors during follow-up. CONCLUSIONS: Disclosure of an integrated risk score that included a polygenic risk score to individuals at intermediate risk for CHD was associated with lower MACE incidence after 10 years, likely due to higher statin initiation, leading to lower low-density lipoprotein cholesterol levels.

Introduction: The MI-GENES randomized clinical trial (NCT01936675) assessed the effect of disclosing a polygenic risk score (PRS) for coronary heart disease (CHD), in addition to a clinical risk based on Framingham risk score (FRS), on LDL-C levels. The trial enrolled participants from Olmsted County, Minnesota, without cardiovascular disease, at intermediate CHD risk (10-y risk: 5-20%), and not on statins. There was a significant LDL-C reduction in the integrated risk score group (IRS g ; received PRS information in addition to the FRS) compared to the FRS group (FRS g ; received their risk based on FRS), due to more frequent statin initiation. Research Question: Does disclosure of an IRS for CHD lead to a lower rate of major adverse cardiovascular events (MACE)? Methods: Participants were followed from randomization beginning in October 2013 until September 2023 to ascertain cardiovascular events, testing for CHD, and risk factor changes, by blinded review of electronic health records. The primary outcome was time from randomization to the first MACE— defined as cardiovascular death, nonfatal MI, coronary revascularization, and nonfatal stroke. Analyses were done using Cox and linear mixed-effects models. Results: We followed all 203 participants, who completed the MI-GENES trial, 100 in FRS g and 103 in IRS g (mean age at the end of follow-up 68.2±5.2 years, 48% male). During a median follow-up of 9.5 years, 9 MACE occurred in FRS g and 2 in IRS g (HR, 0.20; 95% CI, 0.04 to 0.94; P =0.042, Figure 1A). In FRS g , 47 (47%) underwent at least one test for CHD, compared to 30 (29%) in IRS g (HR, 0.51; 95% CI, 0.32 to 0.81; P =0.004, Figure 1B). IRS g participants had a longer duration of statin therapy during the first four years post-randomization (Figure 1C) and a greater reduction in LDL-C for up to 3 years post-randomization (Figure 1D). No significant differences between the two groups were observed for hemoglobin A1C, blood pressure, weight, and smoking cessation rate during follow-up. Conclusion: The disclosure of 10-year CHD risk that included a PRS to those at intermediate risk was associated with lower incidence of MACE after a decade, likely due to more frequent and prolonged statin use, leading to lower LDL-C levels.