Compared with array-based, imputation-based, and exome-focused analyses, whole genome sequencing (WGS) data provides better coverage of the genome and better representation of non-European variants.

To better understand the genetics underlying plasma levels of fibrinogen we utilized data from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium and the NHLBI’s Trans-Omics for Precision Medicine (TOPMed) program. TOPMed phenotypes were centrally harmonized across up to 12 studies of European, African, Asian, or Hispanic ancestry then association analyses were conducted using Freeze 6 deep WGS data (N=32,575). Inverse normalized and rescaled residuals adjusting for age, sex, study, TOPMed phase, study-specific parameters, self-reported ancestry, 11 ancestry informative principal components, and a kinship matrix. Analyses were conducted on the Analysis Commons using the SMMAT function implemented in GENESIS and included all variants with a minor allele count ≥40. Each CHARGE cohort undertook the same analyses using genotypic dosages imputed to the TOPMed backbone (N=75,882). Inverse-variance weighted meta-analysis was undertaken using GWAMA for a final sample size of 108,454.

16 regions were significantly associated with plasma levels of fibrinogen. Most were in loci previously associated with these phenotypes, and the majority were common variants in high linkage disequilibrium with previously reported variants. The most significant association for fibrinogen was a rare missense mutation (rs148685782, p=5.85x10-161, MAF=0.003, FGG) located within the fibrinogen structural genes region.

WGS data provides better resolution of existing and potential detection of novel gene regions. Additional data is anticipated from several more CHARGE cohorts, therefore update results from >150,000 samples will be presented.

Background: Coagulation factor VIII (FVIII) and its carrier protein von Willebrand factor (vWF) are implicated in increasing the risk of thrombotic events.

Aims: We aimed to combine whole genome sequencing data from NHLBI’s TOPMed program with TOPMed-based imputation of genotypes in the CHARGE consortium to identify genetic associations with plasma levels of FVIII and vWF.

Methods: We included 9 TOPMed studies with European, African, Asian, and Hispanic ancestry participants. Association analyses in TOPMed were conducted across all individuals adjusting for age, sex, ancestry, principal components, and a kinship matrix. Using TOPMed as a reference panel, we imputed genotypes in 12 CHARGE studies. Association analyses in CHARGE were conducted separately within each study and stratified by ancestry group. Our primary analysis consisted of a meta-analysis of TOPMed and CHARGE (N=35,006 for FVIII and N=35,362 for vWF).

Results: We identified associations (P< 5E-9) with variants at 11 known loci for FVIII and 12 for vWF, of which 10 overlapped. Additionally, 4 new loci were associated with FVIII (F12, KNG1, ASGR1, and CD36). F12 and KNG1 encode kininogen 1 and factor XII, which are both involved in the contact activation pathway that FVIII also participates in. Variants at F12 and KNG1 were not associated with vWF (P>0.05). At the ASGR1 locus, top variant rs62061426 is associated with ASGR1 expression in liver. ASGR1 encodes a protein that degrades glycoproteins like FVIII and vWF. Consistent with this, the ASGR1-decreasing allele is associated with increased levels of FVIII. The driving variant in CD36, rs3211938, is a loss-of-function variant that causes CD36 deficiency and is associated with other hematological phenotypes. The loss-of-function allele was only found among the African ancestry participants (frequency = 11.6%). Top variants at ASGR1 and CD36 were suggestively associated with vWF (P<0.05).

Conclusions: Four new loci were identified for FVIII, including 2 loci that were independent of vWF.