A genetic association study of circulating coagulation factor VIII and von Willebrand factor levels.

ABSTRACT: Coagulation factor VIII (FVIII) and its carrier protein von Willebrand factor (VWF) are critical to coagulation and platelet aggregation. We leveraged whole-genome sequence data from the Trans-Omics for Precision Medicine (TOPMed) program along with TOPMed-based imputation of genotypes in additional samples to identify genetic associations with circulating FVIII and VWF levels in a single-variant meta-analysis, including up to 45 289 participants. Gene-based aggregate tests were implemented in TOPMed. We identified 3 candidate causal genes and tested their functional effect on FVIII release from human liver endothelial cells (HLECs) and VWF release from human umbilical vein endothelial cells. Mendelian randomization was also performed to provide evidence for causal associations of FVIII and VWF with thrombotic outcomes. We identified associations (P < 5 × 10-9) at 7 new loci for FVIII (ST3GAL4, CLEC4M, B3GNT2, ASGR1, F12, KNG1, and TREM1/NCR2) and 1 for VWF (B3GNT2). VWF, ABO, and STAB2 were associated with FVIII and VWF in gene-based analyses. Multiphenotype analysis of FVIII and VWF identified another 3 new loci, including PDIA3. Silencing of B3GNT2 and the previously reported CD36 gene decreased release of FVIII by HLECs, whereas silencing of B3GNT2, CD36, and PDIA3 decreased release of VWF by HVECs. Mendelian randomization supports causal association of higher FVIII and VWF with increased risk of thrombotic outcomes. Seven new loci were identified for FVIII and 1 for VWF, with evidence supporting causal associations of FVIII and VWF with thrombotic outcomes. B3GNT2, CD36, and PDIA3 modulate the release of FVIII and/or VWF in vitro.

Whole genome analysis of plasma fibrinogen reveals population-differentiated genetic regulators with putative liver roles.

Genetic studies have identified numerous regions associated with plasma fibrinogen levels in Europeans, yet missing heritability and limited inclusion of non-Europeans necessitates further studies with improved power and sensitivity. Compared with array-based genotyping, whole genome sequencing (WGS) data provides better coverage of the genome and better representation of non-European variants. To better understand the genetic landscape regulating plasma fibrinogen levels, we meta-analyzed WGS data from the NHLBI's Trans-Omics for Precision Medicine (TOPMed) program (n=32,572), with array-based genotype data from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium (n=131,340) imputed to the TOPMed or Haplotype Reference Consortium panel. We identified 18 loci that have not been identified in prior genetic studies of fibrinogen. Of these, four are driven by common variants of small effect with reported MAF at least 10% higher in African populations. Three ( SERPINA1, ZFP36L2 , and TLR10) signals contain predicted deleterious missense variants. Two loci, SOCS3 and HPN , each harbor two conditionally distinct, non-coding variants. The gene region encoding the protein chain subunits ( FGG;FGB;FGA ), contains 7 distinct signals, including one novel signal driven by rs28577061, a variant common (MAF=0.180) in African reference panels but extremely rare (MAF=0.008) in Europeans. Through phenome-wide association studies in the VA Million Veteran Program, we found associations between fibrinogen polygenic risk scores and thrombotic and inflammatory disease phenotypes, including an association with gout. Our findings demonstrate the utility of WGS to augment genetic discovery in diverse populations and offer new insights for putative mechanisms of fibrinogen regulation. Key Points: Largest and most diverse genetic study of plasma fibrinogen identifies 54 regions (18 novel), housing 69 conditionally distinct variants (20 novel).Sufficient power achieved to identify signal driven by African population variant.Links to (1) liver enzyme, blood cell and lipid genetic signals, (2) liver regulatory elements, and (3) thrombotic and inflammatory disease.

Gene Expression and Splicing QTL Analysis of Blood Cells in African American Participants from the Jackson Heart Study.

Most gene expression and alternative splicing quantitative trait loci (eQTL/sQTL) studies have been biased toward European ancestry individuals. Here, we performed eQTL and sQTL analysis using TOPMed whole genome sequencing-derived genotype data and RNA sequencing data from stored peripheral blood mononuclear cells in 1,012 African American participants from the Jackson Heart Study (JHS). At a false discovery rate (FDR) of 5%, we identified 4,798,604 significant eQTL-gene pairs, covering 16,538 unique genes; and 5,921,368 sQTL-gene-cluster pairs, covering 9,605 unique genes. About 31% of detected eQTL and sQTL variants with a minor allele frequency (MAF) > 1% in JHS were rare (MAF < 0.1%), and therefore unlikely to be detected, in European ancestry individuals. We also generated 17,630 eQTL credible sets and 24,525 sQTL credible sets for genes (gene-clusters) with lead QTL p < 5e-8. Finally, we created an open database, which is freely available online, allowing fast query and bulk download of our QTL results.

Whole genome sequence analysis of platelet traits in the NHLBI Trans-Omics for Precision Medicine (TOPMed) initiative.

Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing (WGS) from NHLBI's Trans-Omics for Precision Medicine initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet-related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several genome-wide association study identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of WGS in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits.

Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program.

Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.

Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program.

Whole-genome sequencing (WGS), a powerful tool for detecting novel coding and non-coding disease-causing variants, has largely been applied to clinical diagnosis of inherited disorders. Here we leveraged WGS data in up to 62,653 ethnically diverse participants from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and assessed statistical association of variants with seven red blood cell (RBC) quantitative traits. We discovered 14 single variant-RBC trait associations at 12 genomic loci, which have not been reported previously. Several of the RBC trait-variant associations (RPN1, ELL2, MIDN, HBB, HBA1, PIEZO1, and G6PD) were replicated in independent GWAS datasets imputed to the TOPMed reference panel. Most of these discovered variants are rare/low frequency, and several are observed disproportionately among non-European Ancestry (African, Hispanic/Latino, or East Asian) populations. We identified a 3 bp indel p.Lys2169del (g.88717175_88717177TCT[4]) (common only in the Ashkenazi Jewish population) of PIEZO1, a gene responsible for the Mendelian red cell disorder hereditary xerocytosis (MIM: 194380), associated with higher mean corpuscular hemoglobin concentration (MCHC). In stepwise conditional analysis and in gene-based rare variant aggregated association analysis, we identified several of the variants in HBB, HBA1, TMPRSS6, and G6PD that represent the carrier state for known coding, promoter, or splice site loss-of-function variants that cause inherited RBC disorders. Finally, we applied base and nuclease editing to demonstrate that the sentinel variant rs112097551 (nearest gene RPN1) acts through a cis-regulatory element that exerts long-range control of the gene RUVBL1 which is essential for hematopoiesis. Together, these results demonstrate the utility of WGS in ethnically diverse population-based samples and gene editing for expanding knowledge of the genetic architecture of quantitative hematologic traits and suggest a continuum between complex trait and Mendelian red cell disorders.

Preferences for Return of Genetic Results Among Participants in the Jackson Heart Study and Framingham Heart Study.

BACKGROUND: Surveys suggest that most research participants desire access to secondary (incidental) genomic findings. However, few studies clarify whether preferences vary by the nature of the finding. METHODS: We surveyed members of the JHS (Jackson Heart Study, n=960), the FHS (Framingham Heart Study; n=955), and African American members of the FHS Omni cohort (n=160) who had consented to genomic studies. Each factorial survey included 3 vignettes, randomly selected from a set of 64, that described a secondary genomic result. Vignettes varied systematically by 5 factors identified by expert panels as salient: phenotype severity, actionability (preventability), reproductive significance, and relative and absolute risk of the phenotype. Respondents indicated whether they would want to receive the result. Data were analyzed separately by cohort using generalized linear mixed models. RESULTS: Response rates ranged from 67% to 73%. Across vignettes, 88% to 92% of respondents would definitely or probably want to learn the result. In multivariate analyses among JHS respondents, desire for results was associated with positive attitudes towards genetic testing, lower education, higher subjective numeracy, and younger age, but not with any of the 5 factors. Among FHS respondents, desire for results was associated with higher absolute risk, preventability, reproductive risk, and positive attitudes towards genetic testing. Among FHS Omni respondents, desire for results was associated with positive attitudes towards genetic testing and younger age. CONCLUSIONS: Most genetic research participants desire return of secondary genetic results. Several factors identified by expert panels as salient are associated with preferences among FHS, but not JHS or FHS Omni, participants.

Attitudes Toward Genetics and Genetic Testing Among Participants in the Jackson and Framingham Heart Studies.

Genetic analysis has become integral to many large cohort studies. However, little is known about longitudinal cohort study participants' attitudes toward genetics and genetic testing. We analyzed data from a survey of participants in the Jackson Heart Study (n = 960), Framingham Heart Study (n = 955), and Framingham Heart Study-Omni Cohort (n = 160). Based on a three-question attitude scale, most participants had positive attitudes toward genetic testing (median score = 4.3-5/5). Participants were also asked to select words to describe their attitudes toward genetics. More respondents endorsed the positive words "hopeful" (60%-70%), "optimistic" (44%-64%), "enthusiastic" (35%-43%), or "excited" (28%-30%) than the negative words "cautious" (35%-38%), "concerned" (25%-55%), "worried" (6%-13%), "pessimistic" (2%-5%), or "horrified" (1%-5%). Characteristics associated with favorable attitudes were greater genetics knowledge, higher subjective numeracy, experience with genetic testing, less frequent religious attendance, and not being employed. These findings demonstrate variation in attitudes even among participants in long-standing cohort studies, indicating a need for ongoing participant engagement and education.

PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes.

UNLABELLED: PRIMUS is a pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data. However, when genetic data for individuals within a pedigree are missing, often multiple pedigrees can be reconstructed that fit the data. We report a major expansion of PRIMUS that uses mitochondrial (mtDNA) and non-recombining Y chromosome (NRY) haplotypes to eliminate many pedigree structures that are inconsistent with the genetic data. We demonstrate that discordances in mtDNA and NRY haplotypes substantially reduce the number of potential pedigrees, and often lead to the identification of the correct pedigree. AVAILABILITY AND IMPLEMENTATION: We have implemented PRIMUS updates in PERL and it is available at primus.gs.washington.edu.

The socioeconomic gradient of diabetes prevalence, awareness, treatment, and control among African Americans in the Jackson Heart Study.

PURPOSE: Little research has focused on the social patterning of diabetes among African Americans. We examined the relationship between socioeconomic status (SES) and the prevalence, awareness, treatment, and control of diabetes among African Americans. METHODS: Education, income and occupation were examined among 4,303 participants (2,726 women and 1,577 men). Poisson regression estimated relative probabilities (RP) of diabetes outcomes by SES. RESULTS: The prevalence of diabetes was 19.6% in women and 15.9% in men. Diabetes awareness, treatment, and control were 90.0%, 86.8%, and 39.2% in women, respectively, and 88.2%, 84.4%, and 35.9% in men, respectively. In adjusted models, low-income men and women had greater probabilities of diabetes than high-income men and women (RP, 1.94; 95% confidence interval [CI], 1.28-2.92; and RP, 1.35; 95% CI, 1.04-1.74, respectively). Lack of awareness was associated with low education and low occupation in women (RP, 2.28; 95%CI 1.01-5.18; and RP, 2.62; 95% CI, 1.08-6.33, respectively) but not in men. Lack of treatment was associated with low education in women. Diabetes control was not patterned by SES. CONCLUSIONS: Diabetes prevalence is patterned by SES, and awareness and treatment are patterned by SES in women but not men. Efforts to prevent diabetes in African Americans need to address the factors that place those of low SES at higher risk.

Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium.

While genome-wide association studies (GWAS) have primarily examined populations of European ancestry, more recent studies often involve additional populations, including admixed populations such as African Americans and Latinos. In admixed populations, linkage disequilibrium (LD) exists both at a fine scale in ancestral populations and at a coarse scale (admixture-LD) due to chromosomal segments of distinct ancestry. Disease association statistics in admixed populations have previously considered SNP association (LD mapping) or admixture association (mapping by admixture-LD), but not both. Here, we introduce a new statistical framework for combining SNP and admixture association in case-control studies, as well as methods for local ancestry-aware imputation. We illustrate the gain in statistical power achieved by these methods by analyzing data of 6,209 unrelated African Americans from the CARe project genotyped on the Affymetrix 6.0 chip, in conjunction with both simulated and real phenotypes, as well as by analyzing the FGFR2 locus using breast cancer GWAS data from 5,761 African-American women. We show that, at typed SNPs, our method yields an 8% increase in statistical power for finding disease risk loci compared to the power achieved by standard methods in case-control studies. At imputed SNPs, we observe an 11% increase in statistical power for mapping disease loci when our local ancestry-aware imputation framework and the new scoring statistic are jointly employed. Finally, we show that our method increases statistical power in regions harboring the causal SNP in the case when the causal SNP is untyped and cannot be imputed. Our methods and our publicly available software are broadly applicable to GWAS in admixed populations.

Pericardial adipose tissue, atherosclerosis, and cardiovascular disease risk factors: the Jackson heart study.

OBJECTIVE: Pericardial adipose tissue (PAT), a regional fat depot that surrounds the heart, is associated with an unfavorable cardiometabolic risk factor profile. The associations among PAT, cardiometabolic risk factors, and coronary artery calcification (CAC) and abdominal aortic artery calcification (AAC) in African American populations have not been explored. RESEARCH DESIGN AND METHODS: A total of 1,414 African Americans (35% men; mean +/- SD age 58 +/- 11 years) drawn from the Jackson Heart Study (JHS) underwent multidetector computed tomography assessment of abdominal visceral adipose tissue (VAT) and PAT between 2007 and 2009. Cardiometabolic risk factors, CAC, and AAC were examined in relation to increments of PAT and VAT. RESULTS: PAT was significantly correlated with BMI, waist circumference, and VAT (r = 0.35, 0.46, and 0.69; all P < 0.0001). PAT (per 1-SD increase) was associated with elevated levels of systolic blood pressure (P < 0.04), fasting glucose, triglycerides, and C-reactive protein and lower levels of HDL (all P values<0.0001). PAT was also associated with metabolic syndrome (odds ratio [OR] 1.89; P < 0.0001), hypertension (1.48; P < 0.0006), and diabetes (1.40; P < 0.04); all associations were diminished after further adjustment for VAT (most P > 0.05). However, the association of PAT with CAC but not with AAC remained significant (OR 1.34 [95% CI 1.10-1.64]; P < 0.004) after multivariable and VAT adjustment. CONCLUSIONS: PAT is significantly correlated with most cardiometabolic risk factors and CAC in the JHS cohort. The results suggest that PAT is an important VAT depot that may exert a local effect on the coronary vasculature.

Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy antigen receptor for chemokines gene.

Persistently low white blood cell count (WBC) and neutrophil count is a well-described phenomenon in persons of African ancestry, whose etiology remains unknown. We recently used admixture mapping to identify an approximately 1-megabase region on chromosome 1, where ancestry status (African or European) almost entirely accounted for the difference in WBC between African Americans and European Americans. To identify the specific genetic change responsible for this association, we analyzed genotype and phenotype data from 6,005 African Americans from the Jackson Heart Study (JHS), the Health, Aging and Body Composition (Health ABC) Study, and the Atherosclerosis Risk in Communities (ARIC) Study. We demonstrate that the causal variant must be at least 91% different in frequency between West Africans and European Americans. An excellent candidate is the Duffy Null polymorphism (SNP rs2814778 at chromosome 1q23.2), which is the only polymorphism in the region known to be so differentiated in frequency and is already known to protect against Plasmodium vivax malaria. We confirm that rs2814778 is predictive of WBC and neutrophil count in African Americans above beyond the previously described admixture association (P = 3.8 x 10(-5)), establishing a novel phenotype for this genetic variant.

Study design for genetic analysis in the Jackson Heart Study.

OBJECTIVE: This paper describes the preparation of genetic materials and the recruitment and initial characterization of a nested Family Study within the Jackson Heart Study (JHS) METHODS: Genomic DNA was prepared from all consenting JHS participants. In addition, family members of a subset of JHS participants were recruited to the JHS Family Study to allow heritability and linkage analyses and family-based association studies. Family Study participants completed the same questionnaires, measures, and procedures as all other JHS participants and provided blood samples for lymphocyte cryopreservation and transformation. RESULTS: DNA samples were obtained from 4726 JHS participants, including 1499 members of 291 families. In the family cohort, estimated heritabilities of body mass index, selected lipid levels, and blood pressure are highly significant, supporting the validity of the sample. DISCUSSION: The JHS data and genetic materials (DNA and cryopreserved cells) offer valuable opportunities to identify susceptibility alleles for common complex diseases by positional and candidate gene approaches.

Bacillus subtilis is a potential degrader of pyrene and benzo[a]pyrene.

Polycyclic Aromatic Hydrocarbons (PAHs) are a group of compounds that pose many health threats to human and animal life. They occur in nature as a result of incomplete combustion of organic matter, as well as from many anthropogenic sources including cigarette smoke and automobile exhaust. PAHs have been reported to cause liver damage, red blood cell damage and a variety of cancers. Because of this, methods to reduce the amount of PAHs in the environment are continuously being sought. The purpose of this study was to find soil bacteria capable of degrading high molecular weight PAHs, such as pyrene (Pyr) and benzo[a]pyrene (BaP), which contain more than three benzene rings and so persist in the environment. Bacillus subtilis, identified by fatty acid methyl ester (FAME) analysis, was isolated from PAH contaminated soil. Because it grew in the presence of 33 microg/ml each of pyrene, 1-AP and 1-HP, its biodegradation capabilities were assessed. It was found that after a four-day incubation period at 30 degrees C in 20 microg/ml pyrene or benzo[a]pyrene, B. subtilis was able to transform approximately 40% and 50% pyrene and benzo[a]pyrene, respectively. This is the first report implicating B. subtilis in PAH degradation. Whether or not the intermediates resulting from the transformation are more toxic than their parent compounds, and whether B. subtilis is capable of mineralizing pyrene or benzo[a]pyrene to carbon dioxide and water, remains to be evaluated.