Single nucleotide polymorphisms in an intergenic chromosome 2q region associated with tissue factor pathway inhibitor plasma levels and venous thromboembolism

Abstract

Essentials Tissue factor pathway inhibitor (TFPI) regulates the blood coagulation cascade. We replicated previously reported linkage of TFPI plasma levels to the chromosome 2q region. The putative causal locus, rs62187992, was associated with TFPI plasma levels and thrombosis. rs62187992 was marginally associated with TFPI expression in human aortic endothelial cells. Click to hear Ann Gil's presentation on new insights into thrombin activatable fibrinolysis inhibitor SUMMARY: Background Tissue factor pathway inhibitor (TFPI) regulates fibrin clot formation, and low TFPI plasma levels increase the risk of arterial thromboembolism and venous thromboembolism (VTE). TFPI plasma levels are also heritable, and a previous linkage scan implicated the chromosome 2q region, but no specific genes. Objectives To replicate the finding of the linkage region in an independent sample, and to identify the causal locus. Methods We first performed a linkage analysis of microsatellite markers and TFPI plasma levels in 251 individuals from the F5L Family Study, and replicated the finding of the linkage peak on chromosome 2q (LOD = 3.06). We next defined a follow-up region that included 112 603 single nucleotide polymorphisms (SNPs) under the linkage peak, and meta-analyzed associations between these SNPs and TFPI plasma levels across the F5L Family Study and the Marseille Thrombosis Association (MARTHA) Study, a study of 1033 unrelated VTE patients. SNPs with false discovery rate q-values of < 0.10 were tested for association with TFPI plasma levels in 892 patients with coronary artery disease in the AtheroGene Study. Results and Conclusions One SNP, rs62187992, was associated with TFPI plasma levels in all three samples (β = + 0.14 and P = 4.23 × 10^-6 combined; β = + 0.16 and P = 0.02 in the F5L Family Study; β = + 0.13 and P = 6.3 × 10^-4 in the MARTHA Study; β = + 0.17 and P = 0.03 in the AtheroGene Study), and contributed to the linkage peak in the F5L Family Study. rs62187992 was also associated with clinical VTE (odds ratio 0.90, P = 0.03) in the INVENT Consortium of > 7000 cases and their controls, and was marginally associated with TFPI expression (β = + 0.19, P = 0.08) in human aortic endothelial cells, a primary site of TFPI synthesis. The biological mechanisms underlying these associations remain to be elucidated.

Keywords: blood coagulation; genetic association studies; genetic linkage; thrombosis; tissue factor pathway inhibitor.

Fig. 1.

Study design and workflow. CAD, coronary artery disease; F5L, factor V Leiden mutation; SNP, single nucleotide polymorphism; TFPI, tissue factor pathway inhibitor; VTE, venous thromboembolism.

Fig. 2.

Genome-wide multipoint linkage of tissue factor pathway inhibitor plasma levels determined with 1079 microsatellite markers. Analyses were conducted in solar, with adjustment for age and sex. The chromosome 2q region was the highest peak genome-wide, and exceeded the threshold (LOD > 3.0) for candidate region significance.

Fig. 3.

Fine-mapping of the chromosome 2q linkage region defined by the GAIT Study and F5L Family Study linkage signals. Linkage cM positions were mapped to bp positions by use of Rutger’s sex-averaged map for the Illumina Human660W-Quad beadchip, and our region spanned chr2:165147999–231778585 in the hg19 assembly. Results (log10 [P]) before (A) and after (B) adjustment for rs62187992 were plotted for the 112 603 SNPs whose association with tissue factor pathway inhibitor (TFPI) plasma levels was meta-analyzed in the F5L Family Study and MARTHA Study samples. Single nucleotide polymorphisms (SNPs) in TFPI (± 50 kb) did not explain the linkage signal. F5L, factor V Leiden mutation; GWAS, genome-wide asociation study.