Replication of a genetic risk score for venous thromboembolism in whites but not in African Americans

Genomic science of risk prediction for venous thromboembolic disease: convenient clarification or compounding complexity

Venous thromboembolism (VTE) refers to abnormal blood clots in veins occurring in 1 to 2 per 1000 individuals every year. While anticoagulant treatment can prevent VTE, it increases the risk of bleeding. This emphasizes the importance of identifying individuals with a high risk of VTE and providing prophylactic interventions to these individuals to reduce both VTE and bleeding risks. Current risk assessment of VTE is based on the combination of mainly clinical risk factors. With the identification of an increasing number of genetic variants associated with the risk of VTE, the addition of genetic findings to clinical prediction models can improve risk prediction for VTE. Especially for individuals in high-risk situations, the added value of genetic findings to clinical prediction models may have benefits such as better prophylaxis of VTE and the reduced side effects of bleeding from unnecessary treatment. Nevertheless, the question of whether these models will eventually have clinical utility remains to be proven. Here, we review the current state of knowledge on genetic risk factors for VTE, explore genetic prediction models for VTE, and discuss their clinical implications and challenges.

Antithrombin, Protein C, and Protein S: Genome and Transcriptome-Wide Association Studies Identify 7 Novel Loci Regulating Plasma Levels

BACKGROUND

Antithrombin, PC (protein C), and PS (protein S) are circulating natural anticoagulant proteins that regulate hemostasis and of which partial deficiencies are causes of venous thromboembolism. Previous genetic association studies involving antithrombin, PC, and PS were limited by modest sample sizes or by being restricted to candidate genes. In the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, we meta-analyzed across ancestries the results from 10 genome-wide association studies of plasma levels of antithrombin, PC, PS free, and PS total.

METHODS

Study participants were of European and African ancestries, and genotype data were imputed to TOPMed, a dense multiancestry reference panel. Each of the 10 studies conducted a genome-wide association studies for each phenotype and summary results were meta-analyzed, stratified by ancestry. Analysis of antithrombin included 25 243 European ancestry and 2688 African ancestry participants, PC analysis included 16 597 European ancestry and 2688 African ancestry participants, PSF and PST analysis included 4113 and 6409 European ancestry participants. We also conducted transcriptome-wide association analyses and multiphenotype analysis to discover additional associations. Novel genome-wide association studies and transcriptome-wide association analyses findings were validated by in vitro functional experiments. Mendelian randomization was performed to assess the causal relationship between these proteins and cardiovascular outcomes.

RESULTS

Genome-wide association studies meta-analyses identified 4 newly associated loci: 3 with antithrombin levels (GCKR, BAZ1B, and HP-TXNL4B) and 1 with PS levels (ORM1-ORM2). transcriptome-wide association analyses identified 3 newly associated genes: 1 with antithrombin level (FCGRT), 1 with PC (GOLM2), and 1 with PS (MYL7). In addition, we replicated 7 independent loci reported in previous studies. Functional experiments provided evidence for the involvement of GCKR, SNX17, and HP genes in antithrombin regulation.

CONCLUSIONS

The use of larger sample sizes, diverse populations, and a denser imputation reference panel allowed the detection of 7 novel genomic loci associated with plasma antithrombin, PC, and PS levels.

Epidemiology and prevention of venous thromboembolism

Venous thromboembolism, that consists of the interrelated conditions deep-vein thrombosis and pulmonary embolism, is an under-appreciated vascular disease. In Western regions, approximately 1 in 12 individuals will be diagnosed with venous thromboembolism in their lifetime. Rates of venous thromboembolism are lower in Asia, but data from other regions are sparse. Numerous risk factors for venous thromboembolism have been identified, which can be classified as acute or subacute triggers (provoking factors that increase the risk of venous thromboembolism) and basal or acquired risk factors (which can be modifiable or static). Approximately 20% of individuals who have a venous thromboembolism event die within 1 year (although often from the provoking condition), and complications are common among survivors. Fortunately, opportunities exist for primordial prevention (prevention of the development of underlying risk factors), primary prevention (management of risk factors among individuals at high risk of the condition) and secondary prevention (prevention of recurrent events) of venous thromboembolism. In this Review, we describe the epidemiology of venous thromboembolism, including the incidence, risk factors, outcomes and opportunities for prevention. Meaningful health disparities exist in both the incidence and outcomes of venous thromboembolism. We also discuss these disparities as well as opportunities to reduce them.

Prediction of venous thromboembolism incidence in the general adult population using two published genetic risk scores

INTRODUCTION

Most strategies for prevention of venous thromboembolism focus on preventing recurrent events. Yet, primary prevention might be possible through approaches targeting the whole population or high-risk patients. To inform possible prevention strategies, population-based information on the ability of genetic risk scores to identify risk of incident venous thromboembolism is needed.

MATERIALS AND METHODS

We used proportional hazards regression to relate two published genetic risk scores (273-variants versus 5-variants) with venous thromboembolism incidence in the Atherosclerosis Risk in Communities Study (ARIC) cohort (n = 11,292), aged 45-64 at baseline, drawn from 4 US communities.

RESULTS

Over a median of 28 years, ARIC identified 788 incident venous thromboembolism events. Incidence rates rose more than two-fold across quartiles of the 273-variant genetic risk score: 1.7, 2.7, 3.4 and 4.0 per 1,000 person-years. For White participants, age, sex, and ancestry-adjusted hazard ratios (95% confidence intervals) across quartiles were strong [1 (reference), 1.30 (0.99,1.70), 1.85 (1.43,2.40), and 2.58 (2.04,3.28)] but weaker for Black participants [1, 1.05 (0.63,1.75), 1.37 (0.84,2.22), and 1.32 (0.80,2.20)]. The 5-variant genetic risk score showed a less steep gradient, with hazard ratios in Whites of 1, 1.17 (0.89,1.54), 1.48 (1.14,1.92), and 2.18 (1.71,2.79). Models including the 273-variant genetic risk score plus lifestyle and clinical factors had a c-statistic of 0.67.

CONCLUSIONS

In the general population, middle-aged adults in the highest quartile of either genetic risk score studied have approximately two-fold higher risk of an incident venous thromboembolism compared with the lowest quartile. The genetic risk scores show a weaker association with venous thromboembolism for Black people.

Exploring Opportunities for Primary Prevention of Unprovoked Venous Thromboembolism: Ready for Prime Time?

Venous thromboembolism (VTE) is an important vascular disease and public health problem. Prevention of VTE has focused mainly on using thromboprophylaxis to avoid provoked VTE or recurrent VTE, with little attention paid to the possibility of preventing the one third to one half of VTEs that are unprovoked. We review growing research suggesting that unhealthy lifestyle risk factors may cause a considerable proportion of unprovoked VTE. Using epidemiologic data to calculate population attributable risks, we estimate that in the United States obesity may contribute to 30% of VTEs, physical inactivity to 4%, current smoking to 3%, and Western dietary pattern to 11%. We also review possibilities for VTE primary prevention either through a high-risk individual approach or a population-wide approach. Interventions for outpatients at high VTE risk but without VTE provoking factors have not been fully tested; yet, improving patient awareness of risk and symptoms, lifestyle counseling, and possibly statins or direct oral anticoagulants may prove useful in primary prevention of unprovoked VTE. A population approach to prevention would bolster awareness of VTE and aim to shift lifestyle risk factors downward in the whole population using education, environmental changes, and policy. Assuming the epidemiological associations are accurate, causal, and independent of each other, a reduction of obesity, physical inactivity, current smoking, and Western diet by 25% in the general population might reduce the incidence of unprovoked VTE by 12%. We urge further research and consideration that primary prevention of unprovoked VTE may be a worthwhile public health aim.

Lifestyle Moderates Genetic Risk of Venous Thromboembolism: The ARIC Study

OBJECTIVE

Venous thromboembolism (VTE) is a common disease that has a genetic basis. Lifestyle factors contribute to risk, but it is unknown whether healthy lifestyle can mitigate the genetic risk. We studied whether greater adherence to the American Heart Association's cardiovascular health metric, Life's Simple 7 (LS7), is associated with lower incidence of VTE in individuals across categories of a genetic risk score (GRS) for VTE. Approach AND RESULTS: We followed 9026 White participants from the ARIC (Atherosclerosis Risk in Communities) Study, a prospective cohort enrolled in 1987 to 1989 until 2015. We tested the joint associations with VTE of a validated VTE GRS comprising 5 well-known gene variants and baseline LS7 categories. There were 466 incident VTE events over 22.8 years. Participants with an optimal LS7 score had a lower incidence of VTE (3.9%) than those with inadequate LS7 (5.7%). Compared with the high GRS and inadequate LS7 group (hazard ratio=1), those with high GRS and optimal LS7 indeed had a reduced hazard ratio of VTE: 0.65 (95% CI, 0.48-0.89). The group with low GRS and optimal LS7 had the lowest hazard ratio of VTE (0.39 [95% CI, 0.25-0.61]). Of the LS7 components, in all GRS groups, the factor most strongly protective for VTE was normal weight.

CONCLUSIONS

Among people at low or high genetic risk for VTE, healthier lifestyle factors, particularly normal weight, were associated with a lower incidence of VTE. Further studies should determine the impact of lifestyle changes among patients at high genetic risk of VTE, such as in thrombophilic families.

Resting heart rate and incidence of venous thromboembolism

BACKGROUND/OBJECTIVES

Higher resting heart rate is a risk factor for arterial cardiovascular diseases. We assessed whether higher heart rate is a risk factor for venous thromboembolism (VTE).

METHODS

In a prospective epidemiologic cohort, the Atherosclerosis Risk in Communities (ARIC) Study, we associated resting heart rate by electrocardiogram with physician-validated incident hospitalized VTE through 2015. We also examined whether lower heart rate variability (HRV), a marker of cardiac autonomic imbalance, might be a risk factor for VTE.

RESULTS

Resting heart rate at Visit 1 (1987-1989), when participants were 45 to 64 years old (mean, 54 years), was not associated with incidence of VTE (n = 882 cases). However, heart rate at Visit 4 (1996-1998; mean age, 63 years) was associated positively with VTE (n = 557 cases). The adjusted hazard ratios (95% confidence intervals) of VTE across Visit 4 heart rate categories of <60, 60 to 69, 70 to 79, and ≥80 bpm were 1 (reference), 1.22 (1.01-1.49), 1.39 (1.09-1.78), and 1.44 (1.01-2.06), respectively, and when evaluated continuously 1.11 (1.02-1.21) per 10 bpm greater heart rate. For the most part, HRV indices were not associated with VTE or associations were explained by inverse correlations of HRV indices with heart rate.

CONCLUSION

We found a significant positive and independent association of resting heart rate at ARIC Visit 4 with incidence of VTE. The reason why high heart rate is a risk marker for VTE warrants further exploration.

Genetic Basis of Obesity and Type 2 Diabetes in Africans: Impact on Precision Medicine

PURPOSE OF REVIEW

Recent advances in genomics provide opportunities for novel understanding of the biology of human traits with the goal of improving human health. Here, we review recent obesity and type 2 diabetes (T2D)-related genomic studies in African populations and discuss the implications of limited genomics studies on health disparity and precision medicine.

RECENT FINDINGS

Genome-wide association studies in Africans have yielded genetic discovery that would otherwise not be possible; these include identification of novel loci associated with obesity (SEMA-4D, PRKCA, WARS2), metabolic syndrome (CA-10, CTNNA3), and T2D (AGMO, ZRANB3). ZRANB3 was recently demonstrated to influence beta cell mass and insulin response. Despite these promising results, genomic studies in African populations are still limited and thus genomics tools and approaches such as polygenic risk scores and precision medicine are likely to have limited utility in Africans with the unacceptable possibility of exacerbating prevailing health disparities. African populations provide unique opportunities for increasing our understanding of the genetic basis of cardiometabolic disorders. We highlight the need for more coordinated and sustained efforts to increase the representation of Africans in genomic studies both as participants and scientists.

Identifying mutation-driven changes in gene functionality that lead to venous thromboembolism

Venous thromboembolism (VTE) is a common hematological disorder. VTE affects millions of people around the world each year and can be fatal. Earlier studies have revealed the possible VTE genetic risk factors in Europeans. The 2018 Critical Assessment of Genome Interpretation (CAGI) challenge had asked participants to distinguish between 66 VTE and 37 non-VTE African American (AA) individuals based on their exome sequencing data. We used variants from AA VTE association studies and VTE genes from DisGeNET database to evaluate VTE risk via four different approaches; two of these methods were most successful at the task. Our best performing method represented each exome as a vector of predicted functional effect scores of variants within the known genes. These exome vectors were then clustered with k-means. This approach achieved 70.8% precision and 69.7% recall in identifying VTE patients. Our second-best ranked method had collapsed the variant effect scores into gene-level function changes, using the same vector clustering approach for patient/control identification. These results show predictability of VTE risk in AA population and highlight the importance of variant-driven gene functional changes in judging disease status. Of course, more in-depth understanding of AA VTE pathogenicity is still needed for more precise predictions.

Reasons for Differences in the Incidence of Venous Thromboembolism in Black Versus White Americans

INTRODUCTION

Venous thromboembolism incidence rates are 30%-100% higher in US blacks than whites. We examined the degree to which differences in the frequencies of socioeconomic, lifestyle, medical risk factors, and genetic variants explain the excess venous thromboembolism risk in blacks and whether some risk factors are more strongly associated with venous thromboembolism in blacks compared with whites.

METHODS

We measured venous thromboembolism risk factors in black and white participants of the Atherosclerosis Risk in Communities study in 1987-1989 and followed them prospectively through 2015 for venous thromboembolism incidence.

RESULTS

Over a mean of 22 years, we identified 332 venous thromboembolisms in blacks and 578 in whites, yielding 65% higher crude incidence rates per 1000 person-years in blacks. The age and sex-adjusted hazard ratio (95% confidence interval) of venous thromboembolism for blacks compared with whites was 2.04 (1.76, 2.37) for follow-up >10 years and was attenuated to 1.14 (0.89, 1.46) when adjusted for baseline confounders or mediators of the race association, which tended to be more common in blacks. For example, adjustment for just baseline weight, family income, and concentration of plasma factor VIII reduced the regression coefficient for race by 75%. There were no significant (P <0.05) 2-way multiplicative interactions of race with any risk factor, except with a 5-single nucleotide polymorphism (5-SNP) genetic risk score (a weaker venous thromboembolism risk factor in blacks) and with hospitalization for heart failure (a stronger venous thromboembolism risk factor in blacks).

CONCLUSION

The higher incidence rate of venous thromboembolism in blacks than whites was mostly explained by blacks having higher frequencies of venous thromboembolism risk factors.

A prospective study of migraine history and venous thromboembolism in older adults

BACKGROUND

Limited evidence suggests that migraine might be a risk factor for venous thromboembolism (VTE). We conducted an epidemiologic study to assess whether migraine history is associated prospectively with VTE or cross sectionally with hemostatic risk markers for VTE.

METHODS

In a population-based US cohort, 11 985 participants free of VTE reported headache symptoms in 1993-1995. We classified participants as having either migraines with or without aura, severe nonmigraine headaches, or no severe headaches. We followed them through 2015 for incident VTE verified by medical records.

RESULTS

Participants' mean age at baseline was 60 years (SD: 6). Eleven percent were classified as having a migraine history (932 without aura and 396 with aura). Over a mean of 18 years and 211 913 person-years at risk, 688 participants developed VTE. Participants with a migraine history had no greater risk of VTE compared with those free of severe headache (adjusted hazard ratio [HR]: 1.06, 95% confidence interval [CI]: 0.82-1.36). Those with migraine history with aura had an HR of 1.25 (95% CI: 0.85-1.85). Self-reported physician diagnosis of migraine carried an HR of 1.22 (0.96-1.55). At baseline, those with a history of migraine, furthermore, did not have a higher frequency of elevated hemostatic risk factors or a higher genetic risk score for VTE.

CONCLUSION

This study does not support the hypothesis that migraine history is an important risk factor for VTE in older adults.

Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Genetics play a key role in venous thromboembolism (VTE) risk, however established risk factors in European populations do not translate to individuals of African descent because of the differences in allele frequencies between populations. As part of the fifth iteration of the Critical Assessment of Genome Interpretation, participants were asked to predict VTE status in exome data from African American subjects. Participants were provided with 103 unlabeled exomes from patients treated with warfarin for non-VTE causes or VTE and asked to predict which disease each subject had been treated for. Given the lack of training data, many participants opted to use unsupervised machine learning methods, clustering the exomes by variation in genes known to be associated with VTE. The best performing method using only VTE related genes achieved an area under the ROC curve of 0.65. Here, we discuss the range of methods used in the prediction of VTE from sequence data and explore some of the difficulties of conducting a challenge with known confounders. In addition, we show that an existing genetic risk score for VTE that was developed in European subjects works well in African Americans.

Plasma Concentrations of High Molecular Weight Kininogen and Prekallikrein and Venous Thromboembolism Incidence in the General Population

The kallikrein/kinin system, an intravascular biochemical pathway that includes several proteins involved in the contact activation system of coagulation, renin-angiotensin activation and inflammation, may or may not play a role in venous thromboembolism (VTE) occurrence. Within a large prospective population-based study in the United States, we conducted a nested case-cohort study to test the hypothesis that higher plasma levels of high molecular weight kininogen (HK) or prekallikrein are associated with greater VTE incidence. We related baseline enzyme-linked immunosorbent assay measures of HK and prekallikrein in 1993 to 1995 to incidence VTE of the lower extremity (n = 612) through 2015 (mean follow-up = 18 years). We found no evidence that plasma HK or prekallikrein was associated positively with incident VTE. HK, in fact, was associated inversely and significantly with VTE in most proportional hazards regression models. For example, the hazard ratio of VTE per standard deviation higher HK concentration was 0.88 (95% confidence interval = 0.81, 0.97), after adjustment for several VTE risk factors. Our findings suggest that plasma levels of these factors do not determine the risk of VTE in the general population.

Whole-exome sequencing in evaluation of patients with venous thromboembolism

Genetics play a significant role in venous thromboembolism (VTE), yet current clinical laboratory-based testing identifies a known heritable thrombophilia (factor V Leiden, prothrombin gene mutation G20210A, or a deficiency of protein C, protein S, or antithrombin) in only a minority of VTE patients. We hypothesized that a substantial number of VTE patients could have lesser-known thrombophilia mutations. To test this hypothesis, we performed whole-exome sequencing (WES) in 64 patients with VTE, focusing our analysis on a novel 55-gene extended thrombophilia panel that we compiled. Our extended thrombophilia panel identified a probable disease-causing genetic variant or variant of unknown significance in 39 of 64 study patients (60.9%), compared with 6 of 237 control patients without VTE (2.5%) (P < .0001). Clinical laboratory-based thrombophilia testing identified a heritable thrombophilia in only 14 of 54 study patients (25.9%). The majority of WES variants were either associated with thrombosis based on prior reports in the literature or predicted to affect protein structure based on protein modeling performed as part of this study. Variants were found in major thrombophilia genes, various SERPIN genes, and highly conserved areas of other genes with established or potential roles in coagulation or fibrinolysis. Ten patients (15.6%) had >1 variant. Sanger sequencing performed in family members of 4 study patients with and without VTE showed generally concordant results with thrombotic history. WES and extended thrombophilia testing are promising tools for improving our understanding of VTE pathogenesis and identifying inherited thrombophilias.

Thrombosis Related ABO, F5, MTHFR, and FGG Gene Polymorphisms in Morbidly Obese Patients

Objective. Obesity is a well-known risk factor for thrombotic complications. The aim of the present study was to determine the frequency of thrombosis related ABO, F5, MTHFR, and FGG gene polymorphisms in morbidly obese patients and compare them with the group of nonobese individuals. Methods. Gene polymorphisms were analyzed in 320 morbidly obese patients (BMI > 40 kg/m²) and 303 control individuals (BMI < 30 kg/m²) of European descent. ABO C>T (rs505922), F5 C>G (rs6427196), MTHFR C>T (rs1801133), and FGG C>T (rs6536024) SNPs were genotyped by RT-PCR. Results. We observed a tendency for MTHFR rs1801133 TT genotype to be linked with morbid obesity when compared to CC genotype; however, the difference did not reach the significant P value (OR 1.84, 95% CI 0.83–4.05, P = 0.129). Overall, the genotypes and alleles of rs505922, rs6427196, rs1801133, and rs6536024 SNPs had similar distribution between morbidly obese and nonobese control individuals. Distribution of height and weight means among individuals carrying different rs505922, rs6427196, rs1801133, and rs6536024 genotypes did not differ significantly. Conclusions. Gene polymorphisms ABO C>T (rs505922), F5 C>G (rs6427196), MTHFR C>T (rs1801133), and FGG C>T (rs6536024) were not associated with height, weight, or morbid obesity among European subjects.

Environmental and Genetic Risk Factors Associated with Venous Thromboembolism

Venous thromboembolism (VTE) includes deep vein thrombosis and pulmonary embolism, and a combination of environmental and genetic risk factors contributes to VTE risk. Within environmental risk factors, some are provoking (e.g., cancer, surgery, trauma or fracture, immobilization, pregnancy and the postpartum period, long-distance travel, hospitalization, catheterization, and acute infection) and others are nonprovoking (e.g., age, sex, race/ethnicity, body mass index and obesity, oral contraceptive or hormone therapy use, corticosteroid use, statin use, diet, physical activity, sedentary time, and air pollution). Additionally, VTE has a strong genetic basis, with approximately 50 to 60% of the variance in VTE incidence attributed to genetic effects. Some genetic susceptibility variants that contribute to risk have been identified in candidate genes, mostly related to the clotting system and responsible for inherited hypercoagulable states (e.g., factor V Leiden, prothrombin, fibrinogen gamma, or blood group non-O). Other susceptibility single-nucleotide polymorphisms have been identified from genome-wide association studies, such as the two new loci in TSPAN15 (rs78707713) and SCL44A2 (rs2288904) genes. Risk factors are not always associated with VTE in isolation; however, and an understanding of how environmental and genetic factors interact may provide insight into the pathophysiology of VTE, possibly identifying opportunities for targeted prevention and treatment.