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Background: Venous thromboembolism (VTE) is a life-threatening vascular event with environmental and genetic determinants. Recent VTE genome-wide association studies (GWAS) meta-analyses involved nearly 30 000 VTE cases and identified up to 40 genetic loci associated with VTE risk, including loci not previously suspected to play a role in hemostasis. The aim of our research was to expand discovery of new genetic loci associated with VTE by using cross-ancestry genomic resources. Methods: We present new cross-ancestry meta-analyzed GWAS results involving up to 81 669 VTE cases from 30 studies, with replication of novel loci in independent populations and loci characterization through in silico genomic interrogations. Results: In our genetic discovery effort that included 55 330 participants with VTE (47 822 European, 6320 African, and 1188 Hispanic ancestry), we identified 48 novel associations, of which 34 were replicated after correction for multiple testing. In our combined discovery-replication analysis (81 669 VTE participants) and ancestry-stratified meta-analyses (European, African, and Hispanic), we identified another 44 novel associations, which are new candidate VTE-associated loci requiring replication. In total, across all GWAS meta-analyses, we identified 135 independent genomic loci significantly associated with VTE risk. A genetic risk score of the significantly associated loci in Europeans identified a 6-fold increase in risk for those in the top 1% of scores compared with those with average scores. We also identified 31 novel transcript associations in transcriptome-wide association studies and 8 novel candidate genes with protein quantitative-trait locus Mendelian randomization analyses. In silico interrogations of hemostasis and hematology traits and a large phenome-wide association analysis of the 135 GWAS loci provided insights to biological pathways contributing to VTE, with some loci contributing to VTE through well-characterized coagulation pathways and others providing new data on the role of hematology traits, particularly platelet function. Many of the replicated loci are outside of known or currently hypothesized pathways to thrombosis. Conclusions: Our cross-ancestry GWAS meta-analyses identified new loci associated with VTE. These findings highlight new pathways to thrombosis and provide novel molecules that may be useful in the development of improved antithrombosis treatments.

Background: Rare sequence variation in genes underlying cardiac repolarization and common polygenic variation influence QT interval duration. However, current clinical genetic testing of individuals with unexplained QT prolongation is restricted to examination of monogenic rare variants. The recent emergence of large-scale biorepositories with sequence data enables examination of the joint contribution of rare and common variations to the QT interval in the population. Methods: We performed a genome-wide association study of the QTc in 84 630 UK Biobank participants and created a polygenic risk score (PRS). Among 26 976 participants with whole-genome sequencing and ECG data in the TOPMed (Trans-Omics for Precision Medicine) program, we identified 160 carriers of putative pathogenic rare variants in 10 genes known to be associated with the QT interval. We examined QTc associations with the PRS and with rare variants in TOPMed. Results: Fifty-four independent loci were identified by genome-wide association study in the UK Biobank. Twenty-one loci were novel, of which 12 were replicated in TOPMed. The PRS composed of 1 110 494 common variants was significantly associated with the QTc in TOPMed (ΔQTc /decile of PRS =1.4 ms [95% CI, 1.3 to 1.5]; P =1.1×10 -196 ). Carriers of putative pathogenic rare variants had longer QTc than noncarriers (ΔQTc=10.9 ms [95% CI, 7.4 to 14.4]). Of individuals with QTc>480 ms, 23.7% carried either a monogenic rare variant or had a PRS in the top decile (3.4% monogenic, 21% top decile of PRS). Conclusions: QTc duration in the population is influenced by both rare variants in genes underlying cardiac repolarization and polygenic risk, with a sizeable contribution from polygenic risk. Comprehensive assessment of the genetic determinants of QTc prolongation includes incorporation of both polygenic and monogenic risk.

Background: Plasma proteins are critical mediators of cardiovascular processes and are the targets of many drugs. Previous efforts to characterize the genetic architecture of the plasma proteome have been limited by a focus on individuals of European descent and leveraged genotyping arrays and imputation. Here we describe whole genome sequence analysis of the plasma proteome in individuals with greater African ancestry, increasing our power to identify novel genetic determinants. Methods: Proteomic profiling of 1301 proteins was performed in 1852 Black adults from the Jackson Heart Study using aptamer-based proteomics (SomaScan). Whole genome sequencing association analysis was ascertained for all variants with minor allele count ≥5. Results were validated using an alternative, antibody-based, proteomic platform (Olink) as well as replicated in the Multi-Ethnic Study of Atherosclerosis and the HERITAGE Family Study (Health, Risk Factors, Exercise Training and Genetics). Results: We identify 569 genetic associations between 479 proteins and 438 unique genetic regions at a Bonferroni-adjusted significance level of 3.8×10 -11 . These associations include 114 novel locus-protein relationships and an additional 217 novel sentinel variant-protein relationships. Novel cardiovascular findings include new protein associations at the APOE gene locus including ZAP70 (sentinel single nucleotide polymorphism [SNP] rs7412-T, β=0.61±0.05, P =3.27×10 -30 ) and MMP-3 (β=-0.60±0.05, P =1.67×10 -32 ), as well as a completely novel pleiotropic locus at the HPX gene, associated with 9 proteins. Further, the associations suggest new mechanisms of genetically mediated cardiovascular disease linked to African ancestry; we identify a novel association between variants linked to APOL1-associated chronic kidney and heart disease and the protein CKAP2 (rs73885319-G, β=0.34±0.04, P =1.34×10 -17 ) as well as an association between ATTR amyloidosis and RBP4 levels in community-dwelling individuals without heart failure. Conclusions: Taken together, these results provide evidence for the functional importance of variants in non-European populations, and suggest new biological mechanisms for ancestry-specific determinants of lipids, coagulation, and myocardial function.

Introduction: Clonal hematopoiesis of indeterminate potential (CHIP) is an aging-related accumulation of somatic mutations in hematopoietic stem cells, leading to clonal expansion. CHIP presence has been implicated in elevated risks for coronary heart disease (CHD) and death, but its association with incident type 2 diabetes (T2D) is unknown. Hypothesis: We hypothesized that CHIP is associated with elevated risk of incident T2D. Methods: CHIP was derived from whole genome sequencing of blood DNA in NHLBI Trans-omics for Precision Medicine (TOPMed) cohorts. We analyzed 17,637 participants without prior T2D, cardiovascular disease, or cancer at blood draw, with prospective follow-up for incident T2D. We evaluated baseline prevalence of CHIP vs. no CHIP with incident T2D risk using Cox regression. We also investigated CHIP variants previously related to CHD: DNMT3A , TET2 , ASXL1 , JAK2 , and TP53 . We estimated multivariable-adjusted hazard ratios and 95% confidence intervals (HR [CI]) adjusted for age, sex, body mass index, smoking, alcohol, and education. We combined cohort estimates via fixed effects meta-analysis. Results: On average, participants were age 63.4 years (SD=11.5) and 76% female. Prevalence of CHIP was 6.0% (1,055) at baseline. There were 2,467 incident T2D cases over mean=9.8 years follow-up. Compared to those without a mutation, having CHIP was associated with a 23% higher T2D risk, both overall (combined HR=1.23; 95% CI=1.04, 1.45), and among those with CHD-related CHIP mutations (87% of total CHIP): HR=1.23 (1.03, 1.46). Although those with CHIP mutations of TET2 (HR=1.48; 1.05, 2.08) and ASXL1 (HR=1.76; 1.03, 2.99) had larger elevations in T2D risk, and DNMT3A was suggestive of increased T2D risk (HR=1.15; 0.93, 1.43), statistical power was limited for JAK2 and TP53 mutation analyses. Conclusions: CHIP was associated with higher incidence of T2D. CHIP mutations located on loci previously implicated in aging and CHD were also related to T2D, suggesting shared pathology of atherosclerosis and T2D.

Background: Despite considerable advances in obesity genetics, much remains to be learned regarding the pathway from genes to obesity development. Prior studies have shown that that 40-70% of the variation in body mass index (BMI), a measure of obesity, is due to heritable factors, yet BMI-identified genetic variants only account for a limited portion of the heritability. Research suggests epigenetic variation, which reflects both genetic and environmental influence, may account for some of the missing heritability. However, such studies have largely been conducted in primarily European ancestry populations, despite the disproportionate burden of obesity in African Americans (AAs). Methods: To identify CpG sites associated with BMI in AAs, we conducted an epigenome-wide association study (EWAS) using participants from the Jackson Heart Study (JHS, n=1604) and a subset of AA participants from the Multi-Ethnic Study of Atherosclerosis (MESA, n=179) using the Illumina HumanMethylationEPIC array (~850K CpG sites). Analyses were stratified by study and sex and meta-analyzed using an inverse-variance weighted approach. EWAS was performed using a linear regression model with methylation M-values (n=573,388 CpGs) as the outcome and continuous BMI as the predictor. Covariates in the linear models included age, centered-mean-age-squared, smoking status (never/past/current), 10 genetic ancestry principal components, and Houseman-estimated blood cell proportions. Results: The meta-analysis resulted in 204 CpGs that reached epigenome-wide significance (p < 8.72 x 10 -8 ) after multiple-testing correction, and these include both previously identified and novel BMI-associated sites. 48 of the 204 have been previously reported in EWAS of obesity phenotypes, 11 of which were in studies of AAs. 156 of the methylation sites significantly associated with BMI in this study are novel, and potentially AA-specific. Differentially methylated region (DMR) analysis showed significant association of these CpGs in the promoters of genes previously associated with obesity traits, such as SOCS3, ABCG1, and TGFB1 , although TGFB1 had not previously been associated in AAs. In addition, the DMR analysis revealed novel obesity-associated CpGs in genes, including JAK3, which has previously been shown to have differential gene expression in association with BMI in MESA. Conclusion: We identified novel, potentially AA-specific, methylation sites associated with BMI in the largest African-ancestry EWAS conducted thus far, supporting that continued analysis in diverse populations is crucial for increased understanding of obesity.

Introduction: Even though various risk estimators are widely used to predict atherosclerosis from subclinical levels to hard CHD, there is a remarkable proportion of low-risk individuals with inordinately high coronary artery calcification (CAC) or with hard CHD events. Rare pathogenic variants ( Hypothesis: There are rare pathogenic variants in the atherosclerosis gene panel in low-ASCVD-risk individuals with high CAC scores or hard CHD events than low-risk individuals with a CAC score of zero or no events. Methods: The MESA whole-genome sequencing data (2000-02) was evaluated to capture variants in 224 atherosclerosis-related genes. Coding variants with a frequency of th percentile of age, sex, and race-adjusted reference scores. Associated control groups were age-, sex-, and race-matched participants with no CHD events or zero CAC score. Results: A total of 159 cases with high CAC and 1256 matched controls were evaluated within the low-risk group. In the case group, there were three rare, likely pathogenic variants ( LDLR c.681C>G, p.D227E and c.2026G>A, p.G676S; and AHI1 c.2168G>A, p.R723Q ) . None of these variants were observed in the control group. A total of 86 cases had a hard CHD event, among whom two had rare, likely pathogenic variants ( KCNQ1 c.517G>A, p.A173T and LDLR c.1201C>G, p.L401V). None of the 1546 controls had these variants. The LDLR c.1201C>G variant is currently a variant of uncertain significance that would be likely pathogenic with the assumption of genotype-phenotype specificity [pathogenicity supporting criterion 4]. Conclusions: We observed five likely pathogenic variants in atherosclerosis-related genes in low-risk individuals for ASCVD who had high CAC scores or hard CHD events. Rare variants with large effect sizes may unravel the missed risk prediction of a common trait like atherosclerosis.

Background: The relative prevalence and clinical importance of monogenic mutations related to familial hypercholesterolemia and of high polygenic score (cumulative impact of many common variants) pathways for early-onset myocardial infarction remain uncertain. Whole-genome sequencing enables simultaneous ascertainment of both monogenic mutations and polygenic score for each individual. Methods: We performed deep-coverage whole-genome sequencing of 2081 patients from 4 racial subgroups hospitalized in the United States with early-onset myocardial infarction (age ≤55 years) recruited with a 2:1 female-to-male enrollment design. We compared these genomes with those of 3761 population-based control subjects. We first identified individuals with a rare, monogenic mutation related to familial hypercholesterolemia. Second, we calculated a recently developed polygenic score of 6.6 million common DNA variants to quantify the cumulative susceptibility conferred by common variants. We defined high polygenic score as the top 5% of the control distribution because this cutoff has previously been shown to confer similar risk to that of familial hypercholesterolemia mutations. Results: The mean age of the 2081 patients presenting with early-onset myocardial infarction was 48 years, and 66% were female. A familial hypercholesterolemia mutation was present in 36 of these patients (1.7%) and was associated with a 3.8-fold (95% CI, 2.1-6.8; P3-fold increased odds of early-onset myocardial infarction. However, high polygenic score has a 10-fold higher prevalence among patients presents with early-onset myocardial infarction. Clinical Trial Registration: URL: https://www.clinicaltrials.gov. Unique identifier: NCT00597922. ©2019, National Institutes of Health (no. TR001100), American Heart Association (no. 17SDG33680041), National Human Genome Research Institute (no. 5UM1HG008895)

Hispanic populations in the US have increased risk of obesity, elevated circulating triglycerides, nonalcoholic fatty liver disease, and diabetes. Our previous studies suggest that ancestry-related differences in the frequency of variants in the fatty acid desaturase ( FADS) gene cluster in the context of the modern Western diet can lead to inadequate circulating and tissues levels of n-3 long-chain (LC-; ≥ 20 carbons) polyunsaturated fatty acids (PUFA); these deficiencies in turn have the capacity to increase metabolic disease risk. Specifically, we and others have demonstrated Amerindian (AI)-Ancestry populations have high frequencies of FADS gene variants that may lead to less efficient n-3 LC-PUFA biosynthesis. To test this hypothesis, concentrations of fatty acids, including LC-PUFAs in plasma phospholipids were analyzed in 1,102 Hispanic American participants from Multi-Ethnic Study of Atherosclerosis (MESA) cohort, which represent six Hispanic subgroups based on self-reported region of origin: Central America, South America, Mexico, Cuba, Dominican Republic, and Puerto Rico. These data revealed a striking inverse relationship between genome-wide AI-ancestry and levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Additional analyses revealed that the genotype at FADS SNP rs174537, for which the frequency of the T allele increases with AI-ancestry, could primarily explain the associations. There also was a strong association between the number of T alleles (additive model) at rs174537 and circulating triglycerides (18.5 mg/dL per T allele; P =2.0 x 10 -5 ) as well as an important marker of vascular inflammation sICAM-1 (β=12.7 ng/mL, P =0.02). We also genotyped the FADS SNP, rs174537, in a separate adult Arizona Hispanic cohort (Arizona Insulin Resistance [AIR] registry) and compared the FADS genotypic frequencies with other racial/ethnic groups. Importantly, the TT genotype associated with limited LC-PUFA biosynthesis ranges from FADS gene*dietary PUFA interactions give rise to n-3 LC-PUFA deficiencies and may enhance metabolic and inflammatory diseases in a large proportion of individuals in AI-Ancestry Hispanic populations.

The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care.

Markers of inflammation reflect metabolic dysfunction and may predict incident cardiovascular events. GlycA is a new NMR-derived plasma marker of inflammation. Our goal was to undertake first characterization of the genetic variants associated with fasting GlycA, to elucidate the pathways from genes to inflammation. We completed a GWAS in the Caucasian-ancestry population of The Multi-Ethnic Study of Atherosclerosis (MESA; N=2,520; 48% male, mean age 62.7 y). We specified linear regressions models with GlycA as the outcome, and ~2.5 million single nucleotide polymorphisms (SNPs) directly genotyped or imputed from HapMap as the predictors in separate models; all models additionally controlled for age, gender, alcohol intake (g/day), smoking status (yes / no) and 4 principal components of population structure. In MESA, 5 SNPs reached genome-wide levels of significance (P-8 ; Table 1). Forty six SNPs reached a ‘discovery threshold’ of P-5 in MESA, but only one (rs217181; minor allele frequency = .18) replicated in the Genetics of Lipid Lowering Drug Network (GOLDN; N=817; 48% male, mean age=48.8 years) after an FDR multiple testing correction. Rs217181 is located in the intron of TXNL4B , thioredoxin-like 4B, and in close proximity to HP , Haptoglobin , and HPR, Haptoglobin-related Protein . Rs217181 has been validated as associating with levels of haptoglobin protein. Haptoglobin is released by the liver and reduces hemoglobin’s oxidative activity. Our data suggests that rs217181 is involved in inflammation status, and may be a risk factor for adverse cardiovascular events. We would encourage replication of these findings in other cohorts, and are undertaking examination of this association in non-Caucasian individuals.

Several loci have been discovered and replicated for urine albumin-creatinine ratio (ACR), a measure of kidney function, in European populations; however, other ethnic populations such as African-Americans have been less studied for this trait. We examined the association of genetic variants on the Metabochip with natural log transformed ACR (ln(ACR)) in 4,629 African-Americans from the Population Architecture using Genomics and Epidemiology (PAGE) Study which includes participants from the Atherosclerosis Risk in Communities (ARIC), Cardiovascular Health Study (CHS), Coronary Artery Risk Development in Young Adults (CARDIA), and Epidemiologic Architecture for Genes Linked to the Environment (EAGLE-BioVU) studies. We then replicated our findings in 1,533 African-American participants from the Multi-Ethnic Study of Atherosclerosis (MESA). Linear regression models were used to examine associations, assuming additive effects of the SNPs. Within each study, models were adjusted for age, field center (where applicable), and principal components of ancestry, and stratified by sex. Fixed effects inverse variance weighted meta-analysis was used to combine results from contributing studies. Array-wide statistical significance was concluded for SNP associations of p-value less than 2.8 x 10-7. Mean ln(ACR) ranged from 1.4 to 2.9 mg/g, average age ranged from 44 to 77 years, and percent female participants ranged from 59-65% in the contributing studies. Four SNPs were significantly associated array-wide with ACR in the discovery sample: rs17399841 in GRHL2 (β=-0.67, MAF=0.01, p=2.7x10-9), rs153914 near SPATA9/RHOBTB3 (β=-0.59, MAF=0.01, p=1.0x10-7), rs17439845 in LEF1 (β=-0.49, MAF=0.02, p=1.3x10-7), and rs11836243 near ZNF641/ANP32D (β=0.23, MAF=0.12, p=1.8x10-7). Of these four loci, only the association of rs17439845 with ACR replicated in MESA (β=-0.36, p=0.038), with a combined discovery-replication beta of -0.46 and p value of 1.8x10-8. Combined discovery-replication for rs17399841, rs153914, and rs11836243 no longer achieved array-wide significance (p-values 9.84x10-7, 1.98x10-5, and 1.32x10-4, respectively). LEF1 is a mediator in the Wnt signaling pathway, and has been previously implicated in systemic lupus erythematosus and osteoporosis, as well as previously associated with waist circumference, echocardiographic traits, bone mineral density, and blood count traits. Continuing studies in diverse populations are warranted to identify a set of loci important in contributing to the variation in ACR.

Introduction: D-dimer, a marker of blood coagulation and fibrinolysis, is a widely-used biomarker of venous thromboembolism. While the coagulation factors V, III, II and fibrinogen alpha chain genes contain known genetic determinants of D-dimer, other determinants are not well characterized, especially in populations other than European Americans (EAs); no data have been reported for Asian American populations. Hypothesis: Large-scale candidate gene association analysis will identify D-dimer related gene variants in EA, African-American (AA), Chinese, and Hispanic populations. Methods: Four cohorts, comprised of 6,848 EA, 2,192 AAs, 670 Chinese, and 1,286 Hispanics from Cleveland Family Study, Cardiovascular Health Study, Framingham Heart Study, and Multi-Ethnic Study of Atherosclerosis in the Candidate Gene Association Resource (CARe) consortium, were included. The inverse normal transformed residual of D-dimer was used in genetic analysis. About 50,000 SNPs located in 2,100 inflammation and atherosclerosis-related genes were genotyped using the custom ITMAT-Broad-CARe (IBC) chip and analyzed by linear regression adjusted for age, sex, study site, and principal components to account for potential population stratification in each cohort and race group. Significance was set at p Results: Twelve SNPs in the coagulation factor V gene and 3 SNPs in the fibrinogen alpha chain genes exceeded the significant p-value threshold in EA. The top SNPs in these two regions were rs6025 (p-value=7.41x10-16) and rs13109457 (p-value=7.52x10-7), respectively. The signals for the remaining significant SNPs in these two regions were no longer statistically significant after adjusting for the known functional SNPs in each region (rs6025 and rs6050, respectively). The top signal at the coagulation factor V gene was replicated in Hispanics but not other race groups. Neither AA nor the other race groups replicated the signals for fibrinogen alpha chain gene. No additional variants in AA, Chinese, or Hispanics showed significant associations with D-dimer, but several SNPs in neuregulin 1 and Bruton agammaglobulinemia tyrosine kinase for AA and vanin 1 for Chinese were suggestively associated with D-dimer levels (p-value Conclusion: Our study replicated previously reported associations of D-dimer with coagulation factor V and fibrinogen alpha chain variants in EAs and identified coagulation factor V variation in Hispanics. Additional studies are required to confirm the suggestive findings in AAs, Chinese, and Hispanic populations.

Background— Many different genetic and clinical factors have been identified as causes or contributors to atherosclerosis. We present a model of preclinical atherosclerosis based on genetic and clinical data that predicts the presence of coronary artery calcification in healthy Americans of European descent 45 to 84 years of age in the Multi-Ethnic Study of Atherosclerosis (MESA). Methods and Results— We assessed 712 individuals for the presence or absence of coronary artery calcification and assessed their genotypes for 2882 single-nucleotide polymorphisms. With the use of these single-nucleotide polymorphisms and relevant clinical data, a Bayesian network that predicts the presence of coronary calcification was constructed. The model contained 13 single-nucleotide polymorphisms (from genes AGTR1, ALOX15, INSR, PRKAB1, IL1R2, ESR2, KCNK1, FBLN5, PPARA, VEGFA, PON1, TDRD6, PLA2G7, and 1 ancestry informative marker) and 5 clinical variables (sex, age, weight, smoking, and diabetes mellitus) and achieved 85% predictive accuracy, as measured by area under the receiver operating characteristic curve. This is a significant ( P Conclusions— We present an investigation of joint genetic and clinical factors associated with atherosclerosis that shows predictive results for both cases, as well as enhanced performance for their combination.