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

Essentials•Deep vein thrombosis (DVT) has a large unknown genetic component.•We sequenced coding areas of 734 hemostasis‐related genes in 899 DVT patients and 599 controls.•Variants in F5, FGA‐FGG, CYP4V2‐KLKB1‐F11, and ABO were associated with DVT risk.•Associations in KLKB1 and F5 suggest a more complex genetic architecture than previously thought.Summary: BackgroundAlthough several genetic risk factors for deep vein thrombosis (DVT) are known, almost all related to hemostasis, a large genetic component remains unexplained.ObjectivesTo identify novel genetic determinants by using targeted DNA sequencing.Patients/MethodsWe 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).ResultsSixty‐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 1.10–1.69). 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).ConclusionsWe 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. Essentials•Deep vein thrombosis (DVT) has a large unknown genetic component.•We sequenced coding areas of 734 hemostasis‐related genes in 899 DVT patients and 599 controls.•Variants in F5, FGA‐FGG, CYP4V2‐KLKB1‐F11, and ABO were associated with DVT risk.•Associations in KLKB1 and F5 suggest a more complex genetic architecture than previously thought. •Deep vein thrombosis (DVT) has a large unknown genetic component.•We sequenced coding areas of 734 hemostasis‐related genes in 899 DVT patients and 599 controls.•Variants in F5, FGA‐FGG, CYP4V2‐KLKB1‐F11, and ABO were associated with DVT risk.•Associations in KLKB1 and F5 suggest a more complex genetic architecture than previously thought. Although several genetic risk factors for deep vein thrombosis (DVT) are known, almost all related to hemostasis, a large genetic component remains unexplained. To identify novel genetic determinants by using targeted DNA sequencing. 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). 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 1.10–1.69). 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). 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.