Preventing Alzheimer's disease (AD) requires early-warning biomarkers. We developed a Regional Vulnerability Index (RVI) that quantifies individual brain similarity to AD patients' expected brain deficit patterns. We calculated regional effect sizes to establish brain deficit patterns in amyloid-positive AD cases compared to amyloid-negative healthy controls. RVI-AD was calculated as a linear index of individual similarity to this established brain pattern in AD. We demonstrated RVI-AD elevation associated with risk factors in 335 participants (mean age: 49 ± 13 years) in the Amish Connectome Project, followed by an independent sample consisting of 26,010 participants (mean age: 64 ± 7 years) from the UK Biobank. Genetic and cardiovascular risks were evaluated using APOE-e4 genotype and Framingham Cardiovascular Risk Scores (FCVRS), respectively. Additionally, we assessed the risk of converting from MCI to dementia in N = 1932 participants (mean age: ~74) from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Healthy participants with the APOE-e4 allele had significantly elevated RVI-AD indices (p = 0.03 and 2·10-5, for ACP and UKBB samples respectively). FCVRS significantly contributed to higher RVI-AD in an interaction with APOE-e4-specific manner (p = 2·10-4 and 7·10-6 for ACP and UKBB samples respectively). In ADNI cohort, RVI-AD significantly predicted conversion from MCI to dementia in the next decade, particularly in the first three years (AUC = 70-74%, OR = 2.16, 95% CI = 1.8-2.6, p < 10-16). In healthy individuals, the RVI-AD detected the insidious impact of APOE-ε4 and cardiovascular risks in otherwise normally aging cohorts. Elevated RVI-AD also predicted conversion to dementia within ten years in the older, high-risk cohort. Further development of this brain-pattern similarity-based approach may yield a noninvasive, clinically accessible biomarker to aid early detection of the subtle to more imminent effects of AD risks.

Rare variants in SETD1A, encoding a histone H3K4 methyltransferase, are among the strongest genetic risk factors for schizophrenia. Exome sequencing (n=3,736) revealed a population-enriched SETD1A missense variant (P596L) in the Lancaster Old Order Amish founder population, presenting a unique opportunity to elucidate variant-specific, multi-scale mechanisms. Psychiatric and cognitive phenotyping revealed nearly two-fold increased risk for bipolar disorder, accompanied by allele dose-dependent cognitive deficits in adulthood. Induced pluripotent stem cells (iPSCs) from homozygous carriers exhibited signatures of SETD1A hypofunction, including reduced proliferation and heightened susceptibility to replication stress and DNA double-strand breaks. During forebrain-directed differentiation, homozygous mutant cells displayed premature activation of neurodevelopmental transcriptional programs but impaired neural rosette formation, reduced neurite complexity, and early progenitor senescence. Multi-omic profiling revealed dysregulation of gene modules converging on replication stress pathways and neuronal regulatory networks enriched for autism and psychiatric risk genes. Pharmacologic inhibition of the H3K4 demethylase KDM5 partially rescued replication stress and neurite deficits, supporting an epigenetic mechanism and suggesting therapeutic tractability. Together, these findings link a population-enriched missense variant to disrupted chromatin regulation, genome stability, and neurodevelopmental timing, bridging human genetic risk with cellular pathophysiology.

BACKGROUND: Genome-wide association studies have identified several hundred susceptibility single nucleotide variants for coronary artery disease (CAD). Despite single nucleotide variant-based genome-wide association studies improving our understanding of the genetics of CAD, the contribution of structural variants (SVs) to the risk of CAD remains largely unclear. METHOD AND RESULTS: We leveraged SVs detected from high-coverage whole genome sequencing data in a diverse group of participants from the National Heart Lung and Blood Institute's Trans-Omics for Precision Medicine program. Single variant tests were performed on 58 706 SVs in a study sample of 11 556 CAD cases and 42 907 controls. Additionally, aggregate tests using sliding windows were performed to examine rare SVs. One genome-wide significant association was identified for a common biallelic intergenic duplication on chromosome 6q21 (P=1.54E-09, odds ratio=1.34). The sliding window-based aggregate tests found 1 region on chromosome 17q25.3, overlapping USP36, to be significantly associated with coronary artery disease (P=1.03E-10). USP36 is highly expressed in arterial and adipose tissues while broadly affecting several cardiometabolic traits. CONCLUSIONS: Our results suggest that SVs, both common and rare, may influence the risk of coronary artery disease.

Obesity is a major public health crisis associated with high mortality rates. Previous genome-wide association studies (GWAS) investigating body mass index (BMI) have largely relied on imputed data from European individuals. This study leveraged whole-genome sequencing (WGS) data from 88,873 participants from the Trans-Omics for Precision Medicine (TOPMed) Program, of which 51% were of non-European population groups. We discovered 18 BMI-associated signals (P < 5 × 10-9). Notably, we identified and replicated a novel low frequency single nucleotide polymorphism (SNP) in MTMR3 that was common in individuals of African descent. Using a diverse study population, we further identified two novel secondary signals in known BMI loci and pinpointed two likely causal variants in the POC5 and DMD loci. Our work demonstrates the benefits of combining WGS and diverse cohorts in expanding current catalog of variants and genes confer risk for obesity, bringing us one step closer to personalized medicine.

Whole genome sequencing (WGS) studies have identified hundreds of millions of rare variants (RVs) and have enabled RV association tests (RVATs) of these variants with complex traits and diseases. Analysis of non-coding variants is challenged by the considerable variability in regulatory function which candidate Cis-Regulatory Elements (cCREs) exhibit across cell types. We propose cellSTAAR, which integrates WGS data with single-cell ATAC-seq data to capture variability in chromatin accessibility across cell types via the construction of cell-type-specific functional annotations and variant sets. To reflect the uncertainty in cCRE-gene linking, cellSTAAR also links cCREs to their target genes using an omnibus framework which aggregates results from a variety of popular linking approaches. We applied cellSTAAR on Freeze 8 (N = 60,000) of the NHLBI Trans-Omics for Precision Medicine (TOPMed) consortium data to four lipids phenotypes: LDL cholesterol, a binary variable corresponding to high LDL cholesterol, HDL cholesterol, and triglycerides. We also provide replication results for all four phenotypes using UK Biobank (N = 190,000). Evidence from simulation studies and our real data analysis demonstrates that cellSTAAR boosts power and improves interpretation of RVATs of cCREs. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, ,

Schizophrenia spectrum disorder (SSD) is a chronic neuropsychiatric illness accompanied by significant brain structural and functional abnormalities and higher rate of cardio- and cerebrovascular comorbidities. We hypothesized that genetic and environmental risk factors that led to SSD act throughout the body and demonstrated the association between lower integrity of peripheral vascular endothelium and white matter (WM) microstructure. Microvascular endothelial function was evaluated using brachial artery post-occlusive reactive hyperemia (PORH), in which endothelial responses are measured under reduced blood flow and after blood flow is restored. White matter microstructure was assessed by multi-shell diffusion tensor imaging in n = 48 healthy controls (HCs) and n = 46 SSD. Patients showed significantly lower PORH (F1,90 = 5.31, P = .02) effect and lower whole-brain fractional anisotropy (FA) values by diffusion imaging (F1,84 = 7.46, P = .008) with a group × post-occlusion time interaction effect (F3,90 = 4.58, P = .02). The PORH and whole-brain FA were significantly correlated in the full sample (r = 0.28, P = .01) and in SSD (r = 0.4, P = .008) separately, but not HC (r = 0.18, P = .28). This study demonstrated, for the first time, significantly lower integrity of vascular endothelium in participants with SSD and showed that it is associated with WM microstructural abnormalities. Together, these findings support the need for a more holistic, body-brain approach to study the pathophysiology of SSD.

BACKGROUND:The American Heart Association introduced Life's Essential 8 (LE8) to promote cardiovascular health and longevity. However, its impact on brain ageing and interactions with genetic risk factors of dementia, such as APOE4, remains unclear. This study investigates the relationship between LE8 and white matter brain ageing and evaluates the moderating effects of the APOE4 allele. METHODS:This cross-sectional study utilized data from the UK Biobank, including genetic, neuroimaging, and health-related data from touchscreen questionnaires, physical examinations, and biological samples. Participants were non-pregnant whites with LE8 variables, diffusion tensor imaging (DTI) data, and APOE4 genetic information available, excluding those with extreme white matter hyperintensities. Regional fractional anisotropy measures from DTI data were used to predict white matter brain age via random forest regression. The white matter brain age gap (BAG) was calculated by subtracting chronological age from predicted brain age. FINDINGS:The analysis included 18,817 participants (9430 women and 9387 men; mean age 55.45 years [SD: 7.46]). Higher LE8 scores were associated with a lower white matter BAG, indicating delayed brain ageing. The effect was more pronounced in non-APOE4 carriers (124 days younger per 10-point increase, 95% CI: 102-146 days; p < 0.001) compared to APOE4 carriers (84 days younger per 10-point increase, 95% CI: 47-120 days; p < 0.001). Potential interaction between APOE4 and LE8 on brain ageing was observed for some age and sex groups but with only borderline significance, further investigation in larger and more targeted studies is needed to validate the finding. INTERPRETATION:Adherence to LE8 is associated with delayed brain ageing, with genetic factors such as APOE4 potentially moderating this effect in specific age and sex groups. The overall benefit from a healthier lifestyle in individuals' brain ageing across genetic, sex, and age groups underscore the importance and broad applicability of behavioural lifestyle interventions in promoting brain health. FUNDING:US National Institute of Health, University of Maryland, Montgomery County of Maryland.

Circulating lipid concentrations are clinically associated with cardiometabolic diseases. The phenotypic variance explained by identified genetic variants remains limited, highlighting the importance of searching for additional factors beyond genetic sequence variants. DNA methylation has been linked to lipid concentrations in previous studies, although most of the studies harbored moderate sample sizes and exhibited underrepresentation of non-European ancestry populations. In addition, knowledge of nongenetic factors on lipid profiles is extremely limited. In the Population Architecture Using Genomics and Epidemiology (PAGE) Study, we performed methylome-wide association analysis on 9,561 participants from diverse race and ethnicity backgrounds for HDL-c, LDL-c, TC, and TG levels, and also tested interactions between smoking or alcohol intake and methylation in their association with lipid levels. We identified novel CpG sites at 16 loci (P < 1.18E-7) with successful replication on 3,215 participants. One additional novel locus was identified in the self-reported White participants (P = 4.66E-8). Although no additional CpG sites were identified in the genome-wide interaction analysis, 13 reported CpG sites showed significant heterogeneous association across smoking or alcohol intake strata. By mapping novel and reported CpG sites to genes, we identified enriched pathways directly linked to lipid metabolism as well as ones spanning various biological functions. These findings provide new insights into the regulation of lipid concentrations.

BACKGROUND:Lean body mass is a crucial physiological component of body composition. Although lean body mass has a high heritability, studies evaluating the genetic determinants of lean mass (LM) have to date been limited largely to genome-wide association studies (GWAS) and common variants. Using whole genome sequencing (WGS)-based studies, we aimed to discover novel genetic variants associated with LM in population-based cohorts with multiple ancestries. RESULTS:We describe the largest WGS-based meta-analysis of lean body mass to date, encompassing 10,729 WGS samples from six TOPMed cohorts and the Louisiana Osteoporosis Study (LOS) cohort, measured with dual-energy X-ray absorptiometry. We identify seven genome-wide loci significantly associated with LM not reported by previous GWAS. We partially replicate these associations in UK Biobank samples. In rare variant analysis, we discover one novel protein-coding gene, DMAC1, associated with both whole-body LM and appendicular LM in females, and a long non-coding RNA gene linked to appendicular LM in males. Both genes exhibit notably high expression levels in skeletal muscle tissue. We investigate the functional roles of two novel lean-mass-related genes, EMP2 and SSUH2, in animal models. EMP2 deficiency in Drosophila leads to significantly reduced mobility without altering muscle tissue or body fat morphology, whereas an SSUH2 gene mutation in zebrafish stimulates muscle fiber growth. CONCLUSIONS:Our comprehensive analysis, encompassing a large-scale WGS meta-analysis and functional investigations, reveals novel genomic loci and genes associated with lean mass traits, shedding new insights into pathways influencing muscle metabolism and muscle mass regulation.

Previous work has shown a role of CCL2, a key chemokine governing monocyte trafficking, in atherosclerosis. However, it remains unknown whether targeting CCR2, the cognate receptor of CCL2, provides protection against human atherosclerotic cardiovascular disease. Computationally predicted damaging or loss-of-function (REVEL > 0.5) variants within CCR2 were detected in whole-exome-sequencing data from 454,775 UK Biobank participants and tested for association with cardiovascular endpoints in gene-burden tests. Given the key role of CCR2 in monocyte mobilization, variants associated with lower monocyte count were prioritized for experimental validation. The response to CCL2 of human cells transfected with these variants was tested in migration and cAMP assays. Validated damaging variants were tested for association with cardiovascular endpoints, atherosclerosis burden, and vascular risk factors. Significant associations were replicated in six independent datasets (n = 1,062,595). Carriers of 45 predicted damaging or loss-of-function CCR2 variants (n = 787 individuals) were at lower risk of myocardial infarction and coronary artery disease. One of these variants (M249K, n = 585, 0.15

BACKGROUND: Stroke incidence is decreasing in older ages but increasing in young adults. These divergent trends are at least partially attributable not only to diverging trends in stroke risk factors but may also be due to differences in the impact of stroke risk factors at different ages. To address this latter possibility, we used Mendelian randomization to assess differences in the association of stroke risk factors between early-onset ischemic stroke ([EOS]; onset 18–59 years) and late-onset ischemic stroke ([LOS]; onset ≥60 years). METHODS: We identified genetic variants from the GWAS Catalog for use as instrumental variables to proxy conventional stroke risk factors and then estimated the effects of these variants on risk factors in younger and older individuals in the UK Biobank. We then used these estimates to estimate the causal effects of stroke risk factors on EOS (n=6728 cases) and LOS (n=9272) cases from SiGN (Stroke Genetic Network) and the EOSC (Early-Onset Stroke Consortium). Lastly, we compared odds ratios between EOS and LOS, stratified by TOAST (Trial of ORG 10172 in Acute Stroke Treatment) subtypes, to determine if differences between estimates could be attributed to differences in stroke subtype distributions. RESULTS: EOS was associated with higher levels of body mass index, blood pressure, type 2 diabetes, and lower levels of HDL (high-density lipoprotein) cholesterol (all P ≤0.002), whereas LOS was associated with higher levels of systolic blood pressure ( P =0.0001). The causal effect of body mass index on stroke was significantly stronger for EOS than for LOS (odds ratio, 1.26 versus 1.03; P =0.008). After the subtype-stratified analysis, the difference in causal effect sizes between EOS and LOS for body mass index diminished and was no longer significant. CONCLUSIONS: These results support a causal relationship between body mass index, blood pressure, type 2 diabetes, and HDL cholesterol levels with EOS and blood pressure levels in LOS. Interventions that target these traits may reduce stroke risk.

BACKGROUND:Most polygenic risk scores (PRS) have been developed in European populations, frequently leading to limited transferability across diverse ancestry populations. This study aimed to develop and evaluate PRS for blood pressure (BP) traits in continental African populations and investigate how African genetic diversity influences PRS performance. METHODS:We generated PRS for systolic BP, diastolic BP, pulse pressure, and hypertension. We used a pan-African cohort as the target population and compared single-ancestry and multi-ancestry PRS methods. We compared the performance of African ancestry-derived PRS against multi-ancestry PRS on the entire data set and within South, East, and West African subpopulations. RESULTS:Multi-ancestry PRS demonstrated significantly higher predictive accuracy compared with single-ancestry PRS models. PRS predictive accuracy varied across different African regions, with the highest performance observed in East Africa. In the combined population, the difference in mean BP values between the first multi-ancestry PRS quartile and the top quartile was 6.53 (95% CI, 5.3-7.74), 3.81 (95% CI, 3.9-4.52), and 3.59 (95% CI, 2.4-4.32) mm Hg for systolic BP, diastolic BP, and pulse pressure, respectively. Individuals in the highest PRS risk quartile had odds of hypertension that were 1.47 (95% CI, 1.7-1.69) times greater than those in the lowest risk quartile. CONCLUSIONS:These findings highlight the importance of integrating diverse ancestries in PRS development and accounting for subpopulation genetic variation to improve the predictive accuracy of BP PRS in African populations.

Rare genetic variation provided by whole genome sequence datasets has been relatively less explored for its contributions to human traits. Meta-analysis of sequencing data offers advantages by integrating larger sample sizes from diverse cohorts, thereby increasing the likelihood of discovering novel insights into complex traits. Furthermore, emerging methods in genome-wide rare variant association testing further improve power and interpretability. Here, we conduct the largest meta-analysis of whole genome sequencing for low-density lipoprotein cholesterol (LDL-C), a therapeutic target for coronary artery disease, analyzing data from 246 K participants and integrating 1.23B variants from the UK Biobank and the Trans-Omics for Precision Medicine (TOPMed) program. We identify numerous rare coding and non-coding gene associations related to LDL-C, with replication across 86 K participants in All of Us. Our findings are based on single-variant analyses, rare coding and non-coding variant aggregation tests, and sliding window approaches. Through this comprehensive analysis, we identify 704 novel single-variant associations, 25 novel rare coding variant aggregates, 28 novel rare non-coding variant aggregates, and one novel sliding window aggregate. This study provides a meta-analysis framework for large-scale whole genome sequence association analyses from diverse population groups, yielding novel rare non-coding variant associations.

Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits (low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides) in 61,861 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered new associations with lipid traits missed by single-trait analysis, including rare variants within an enhancer of NIPSNAP3A and an intergenic region on chromosome 1.

The genetic underpinnings of elite sprint and power performance remain largely elusive. This study aimed to identify genetic variants associated with this complex trait as well as to understand their functional implications in elite sprint and power performance. We conducted a multi-phase genome-wide association study (GWAS) in world-class sprint and power athletes of West African and East Asian ancestry and their geographically matched controls. We carried out genotype imputation, replications for the top GWAS signal rs10196189 in two European cohorts, and gene-based and tissue-specific functional network analyses. For the first time, we uncovered the G-allele of rs10196189 in the Polypeptide N-Acetylgalactosaminyltransferase 13 (GALNT13) being significantly associated with elite sprint and power performance (P = 2.13E-09 across the three ancestral groups). Moreover, we found that GALNT13 expression level was positively associated with the relative area occupied by fast-twitch muscle fibers in the vastus lateralis muscle. In addition, significant and borderline associations were observed for BOP1, HSF1, STXBP2, GRM7, MPRIP, ZFYVE28, CERS4, and ADAMTS18 in cross-ancestry or ancestry-specific contexts, predominantly expressed in the nervous and hematopoietic systems. From the elite athlete cohorts, we further identified thirty-six previously uncharacterized genes linked to host defence, leukocyte migration, and cellular responses to interferon-gamma, and four genes - UQCRFS1, PTPN6, RALY and ZMYM4 - associated with aging, neurological conditions, and blood disorders. Taken together, these results provide new biological insights into the genetic basis of elite sprint and power performance and, importantly, offer valuable clues to the molecular mechanisms underlying elite athletic performance, health and disease.

The Amish of Lancaster County, PA has been the focus of genetic studies for many years due to its demographic history and unique genetic makeup that includes a historical bottleneck event and subsequent genetic drift, resulting in a marked decrease in genetic diversity and increased frequency of some variants that have substantially shaped the health of the community. To characterize the coding variation in the Amish genome, we sequenced the exomes of 7221 adult community members, and in this report, we contrast genetic diversity between the Amish and Europeans from the UK Biobank. Exome sequences of 7221 Amish contained only 14% as many variants as the same number of UKB participants. This reduced genetic diversity has substantial clinical implications. We identified pathogenic (P) and likely pathogenic (LP) variants from ClinVar and a population-specific genetic screening panel and found that most of the variants present in the Amish were highly enriched, resulting in 5.2% of Amish individuals being homozygous for a recessive P/LP variant and 25.6% being heterozygous for at least one dominant P/LP variant. In 43.6% of the 2141 Amish spouse-pairs in our sample, at least one spouse was heterozygous for a P/LP dominant variant, and 24.3% of couples were autosomal recessive disease carrier couples, meaning that each of their children was at ~25% risk of inheriting two copies of that variant. Gene discovery efforts in other founder communities will likely uncover distinct P (and beneficial) variants impacting the health of these communities, with implications for all of human health.

Objective: To evaluate whether genetic overlap exists between infection and adult ischemic stroke (IS). Background: Infection has long been recognized as a risk factor for stroke, but the underlying mechanism remains unknown and little work has been done to investigate the genetic underpinnings of this relationship. Design/Methods: We analyzed associations between adult IS and a polygenic risk score (PRS) for childhood ear infections using 6,728 cases from the Early Onset Stroke Consortium and 9,272 cases from the Stroke Genetics Network, for a combined sample size of 16,000 cases and 33,774 controls. This infection type was selected because it showed the greatest number of genome-wide significant associations out of the 32 common infections examined in a previously published GWAS. We then investigated whether this PRS was more strongly associated with cases who had a recent infection. Using data from the Early Onset Stroke study, we compared the association of the PRS between 33 cases with a history of infection in the 2 weeks preceding IS and 357 cases without a preceding infection. Results: PRS for childhood ear infections was significantly associated with IS (odds ratio 1.028, P=0.0055). PRS for childhood ear infections showed a stronger association with IS in cases who had a preceding infection (odds ratio 1.482, P=0.024) compared to cases without a preceding infection (odds ratio=1.027, P=0.619) (P for interaction=0.049). Conclusion: The novel finding of our study is the existence of genetic overlap between childhood ear infections and adult IS and that this genetic overlap is stronger in cases with a recent infection. This suggests that the association between the PRS for childhood infection and adult IS is mediated by an increased risk of adult infection. Our study was limited in its sample size to evaluate for IS subtypes. Continued investigation of the potential mechanisms of the infection-stroke relationship is warranted. Study Supported By: U18NS115388, R01NS100178, and R01NS105150. Disclosures: None.