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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.

Background Prospective studies have suggested higher factor VIII (FVIII) levels are an independent risk factor for coronary heart disease (CHD) and stroke. However, limited information, including on genetic and epigenetic contributors to FVIII variation, is available specifically among African Americans (AAs), who have higher FVIII levels than Europeans. Objectives We measured FVIII levels in ~3400 AAs from the community-based Jackson Heart Study and assessed genetic, epigenetic, and epidemiological correlates of FVIII, as well as incident cardiovascular disease (CVD) associations. Methods We assessed cross-sectional associations of FVIII with CVD risk factors as well as incident CHD, stroke, heart failure, and mortality associations. We additionally assessed associations with TOPMed whole genome sequencing data and an epigenome-wide methylation array. Results Our results confirmed associations between FVIII and risk of incident CHD events and total mortality in AAs; mortality associations were largely independent of traditional risk factors. We also demonstrate an association of FVIII with incident heart failure, independent of B-type natriuretic peptide. Two genomic regions were strongly associated with FVIII (ABO and VWF). The index variant at VWF is specific to individuals of African descent and is distinct from the previously reported European VWF association signal. Epigenome-wide association analysis showed significant FVIII associations with several CpG sites in the ABO region. However, after adjusting for ABO genetic variants, ABO CpG sites were not significant. Conclusions Larger sample sizes of AAs will be required to discover additional genetic and epigenetic contributors to FVIII phenotypic variation, which may have consequences for CVD health disparities.

Platelets are critical in inflammation, wound healing, and thrombosis. Platelet count (PLT) and mean platelet volume (MPV) are heritable, frequently assessed measures for which hundreds of genetic associations have been identified, predominantly in European populations. However, causal variants are unknown at most loci, and additional genetic determinants in diverse ancestral populations remain to be discovered. We performed a multi-ancestry whole genome sequencing analysis for PLT in three Phase 1 TOPMed cohorts, the European American Framingham Heart (FHS, n=2259) and Old Order Amish (OOA, n=1095) studies and the African American Jackson Heart Study (JHS, n=3523). MPV was additionally analyzed in JHS and FHS. Heritability in JHS and FHS was 45-73%. Single variant and aggregate burden and sequence kernel association (SKAT) tests [5 and 50 kilobase (kb) sliding windows] were performed using a mixed model approach in GENESIS, with aggregate tests for variants with a minor allele frequency (MAF) < 1% only. Inverse normalized residuals were adjusted for sex, age, study, and an empirical genetic relationship matrix, allowing for heterogeneous variance by study. For PLT, several associations had the same index SNP ( ARHGEF3 , TPM4 ) or were in moderate LD ( TAOK1 , r 2 =0.46) with a previously reported signal; two associations were not in LD (r 2 -8 , MAF=16%), an intergenic variant upstream of telomerase reverse transcriptase ( TERT ), is common only in African ancestry populations (~36%, 1% in Europeans) and was significant only in JHS (p=4.7 x 10 -9 , p=0.91 FHS, absent OOA). This variant and an LD proxy (rs10052815) overlap a GATA1 binding site in erythroblasts, the sister lineage of platelet producing megakaryocytes. An intronic TERT variant (rs2736100) 17 kb away (r 2 =0.025, D’=0.418 in included TOPMed cohorts) has been associated with PLT in Europeans, as well as with red blood cell traits, telomere length, pulmonary fibrosis, and multiple cancer subtypes. The second locus (rs73437176, p=1.5 x 10 -8 , MAF=12%), an intronic variant in progestin and adipoQ receptor family member V ( PAQR5 ), is also more frequent in African ancestry populations (~25%, 4% in Europeans) and significant only in JHS (p=2.5 x 10 -8 , FHS p=0.47, OOA p=0.12); the nearest previously identified signal is ~4 Mb away and not in significant LD (D’DNM3 , ARHGEF3 , CCDC71L , JMJD1C , RHOF , TAOK1 , TPM4 ), with either the same lead variant as previously reported or a variant in close LD (r 2 >0.75). Aggregated sliding window tests did not identify any additional signals. These results show suggestive evidence for association with PLT for two novel variants common only in African ancestry populations, but larger sample sizes of diverse ancestry will be necessary for replication and further discovery of novel loci.