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

ABSTRACT: 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: 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 1.10-1.69). 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). 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.

SUBMITTER: de Haan HG

PROVIDER: S-EPMC6467059 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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

de Haan H G HG van Hylckama Vlieg A A Lotta L A LA Gorski M M MM Bucciarelli P P Martinelli I I Baglin T P TP Peyvandi F F Rosendaal F R FR

Journal of thrombosis and haemostasis : JTH 20181016 12

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: Background Although several genetic risk factors for deep vein thrombosis (DVT) are known, almost all related to hemostasis, a large genet ...[more]

PMID: 30168256

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Project description:Next-generation DNA sequencing is opening new avenues for genetic association studies in common diseases that, like deep vein thrombosis (DVT), have a strong genetic predisposition still largely unexplained by currently identified risk variants. In order to develop sequencing and analytical pipelines for the application of next-generation sequencing to complex diseases, we conducted a pilot study sequencing the coding area of 186 hemostatic/proinflammatory genes in 10 Italian cases of idiopathic DVT and 12 healthy controls.A molecular-barcoding strategy was used to multiplex DNA target capture and sequencing, while retaining individual sequence information. Genomic libraries with barcode sequence-tags were pooled (in pools of 8 or 16 samples) and enriched for target DNA sequences. Sequencing was performed on ABI SOLiD-4 platforms. We produced > 12 gigabases of raw sequence data to sequence at high coverage (average: 42X) the 700-kilobase target area in 22 individuals. A total of 1876 high-quality genetic variants were identified (1778 single nucleotide substitutions and 98 insertions/deletions). Annotation on databases of genetic variation and human disease mutations revealed several novel, potentially deleterious mutations. We tested 576 common variants in a case-control association analysis, carrying the top-5 associations over to replication in up to 719 DVT cases and 719 controls. We also conducted an analysis of the burden of nonsynonymous variants in coagulation factor and anticoagulant genes. We found an excess of rare missense mutations in anticoagulant genes in DVT cases compared to controls and an association for a missense polymorphism of FGA (rs6050; p = 1.9 × 10(-5), OR 1.45; 95% CI, 1.22-1.72; after replication in > 1400 individuals).We implemented a barcode-based strategy to efficiently multiplex sequencing of hundreds of candidate genes in several individuals. In the relatively small dataset of our pilot study we were able to identify bona fide associations with DVT. Our study illustrates the potential of next-generation sequencing for the discovery of genetic variation predisposing to complex diseases.

Project description:Background: Venothromboembolism (VTE) including deep venous thrombosis (DVT) and pulmonary embolism (PE) are significant health care problems. A highly specific DVT risk stratification model requires a combination of genetic, environmental, clinical, laboratory and radiographic measurements. Genetic factors associated with DVT in post-hospitalized medical and surgical patients are incompletely understood. Aim: Using the Personalized Medicine Research Project (PMRP) population and a limited number of disease associated polymorphisms were used to determine whether these markers were associated with DVT in the post-hospitlalization period. Methods: Marshfield Clinic patients who have experienced a DVT between 1999 and 2007 enrolled in the PMRP were genotyped for 52 disease associated polymorphisms (N=1124). From these individuals we identified 451 who experienced a DVT after post-hospitalization for a medical (N=164) or surgical (N=136) procedure or both (N=151). This cohort was compared to the PMRP population that had a recorded hospitalization without a post-hospitalization DVT during the same time period (N=1662). Results: Polymorphisms in APOB (rs1042031), PLAU (rs2227564), HTR2A (rs6313) and the Vitamin D receptor haplotype (rs731236 and rs7975232) were associated with post hospitalization DVT. When the population that incurred a DVT was stratified by DVT category (post medical, post surgical or both), the PLAU polymorphism was most strongly associated with individuals experiencing a DVT post-surgically. Vitamin D receptor haplotype was significantly associated with individuals experiencing both post medical and post surgical DVTs, and polymorphisms associated with cholesterol and lipid levels were most likely to be associated with post-medical DVTs. Conclusions: This hypothesis generating study demonstrates that there are many polymorphisms that are associated with DVT that have yet to be characterized. Categorization of associated DVT polymorphisms will involve careful interrogation of both the environmental conditions as well as genetic alleles of individuals. Genes such as PLAU, HTR2A, and Vitamin D are just now being investigated for thrombogenic effects and in future may lead to a better understanding of indentifying the individuals at risk for a DVT post hospitilization.

Project description:BackgroundWe previously described the association between rare ADAMTS13 single nucleotide variants (SNVs) and deep vein thrombosis (DVT). Moreover, DVT patients with at least one rare ADAMTS13 SNV had a lower ADAMTS13 activity than non-carriers.AimsTo confirm ADAMTS13 variants association with DVT and reduced plasma ADAMTS13 activity levels in a larger population. To investigate the role of VWF and F8 variants.MethodsADAMTS13, VWF and F8 were sequenced using next-generation sequencing in 594 Italian DVT patients and 571 controls. Genetic association testing was performed using logistic regression and gene-based tests. The association between rare ADAMTS13 variants and the respective plasmatic activity, available for 365 cases and 292 controls, was determined using linear regression. All analyses were age-, sex- adjusted.ResultsWe identified 48 low-frequency/common and 272 rare variants. Nine low-frequency/common variants had a P<0.05, but a false discovery rate between 0.06 and 0.24. Of them, 7 were found in ADAMTS13 (rs28641026, rs28503257, rs685523, rs3124768, rs3118667, rs739469, rs3124767; all protective) and 2 in VWF (rs1800382 [risk], rs7962217 [protective]). Rare ADAMTS13 variants were significantly associated with DVT using the burden, variable threshold (VT) and UNIQ (P<0.05), but not with C-ALPHA, SKAT and SKAT-O tests. Rare VWF and F8 variants were not associated with DVT. Carriers of rare ADAMTS13 variants had lower ADAMTS13 activity than non-carriers (ß -6.2, 95%CI -11,-1.5). This association was stronger for DVT patients than controls (ß -7.5, 95%CI -13.5,-1.5 vs. ß -2.9, 95%CI -10.4,4.5).ConclusionsADAMTS13 and VWF low-frequency/common variants mainly showed a protective effect, although their association with DVT was not confirmed. DVT patients carrying a rare ADAMTS13 variants had slightly reduced ADAMTS13 activity levels, but a higher DVT risk. Rare VWF and FVIII variants were not associated with DVT suggesting that other mechanisms are responsible for the high VWF and FVIII levels measured in DVT patients.

Dataset Information

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

Publications

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

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