Targeted sequencing to identify novel genetic risk factors for deep vein thrombosis: a study of 734 genes

BACKGROUND: Although several genetic risk factors for deep vein thrombosis (DVT) are known, almost all related to hemostasis, a large genetic component remains unexplained. OBJECTIVES: To identify novel genetic determinants by using targeted DNA sequencing. PATIENTS/METHODS: We included 899 DVT patients and 599 controls from three case–control studies (DVT-Milan, Multiple Environmental and Genetic Assessment of risk factors for venous thrombosis [MEGA], and the Thrombophilia, Hypercoagulability and Environmental Risks in Venous Thromboembolism [THE-VTE] study) for sequencing of the coding regions of 734 genes involved in hemostasis or related pathways. We performed single-variant association tests for common variants (minor allele frequency [MAF] ≥ 1%) and gene-based tests for rare variants (MAF ≤ 1%), accounting for multiple testing by use of the false discovery rate (FDR). RESULTS: Sixty-two of 3617 common variants were associated with DVT risk (FDR < 0.10). Most of these mapped to F5, ABO, FGA-FGG, and CYP4V2–KLKB1–F11. The lead variant at F5 was rs6672595 (odds ratio [OR] 1.58, 95% confidence interval [CI] 1.29–1.92), in moderate linkage with the known variant rs4524. Reciprocal conditional analyses suggested that intronic variation might drive this association. We also observed a secondary association at the F11 region: missense KLKB1 variant rs3733402 remained associated conditional on known variants rs2039614 and rs2289252 (OR 1.36, 95% CI 1.101.69). Two novel variant associations were observed, in CBS and MASP1, but these were not replicated in the meta-analysis data from the International Network against Thrombosis (INVENT) consortium. There was no support for a burden of rare variants contributing to DVT risk (FDR > 0.2). CONCLUSIONS: We confirmed associations between DVT and common variants in F5, ABO, FGA–FGG, and CYP4V2–KLKB1–F11, and observed secondary signals in F5 and CYP4V2–KLKB1–F11 that warrant replication and fine-mapping in larger studies.