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Lunghi B, Ziliotto N, Balestra D, Rossi L, Della Valle P, Pignatelli P, Pinotti M, D’Angelo A, Marchetti G, Bernardi F. Whole-Exome Sequencing in a Family with an Unexplained Tendency for Venous Thromboembolism: Multicomponent Prediction of Low-Frequency Variant Deleteriousness and of Individual Protein Interaction. Int J Mol Sci 2023; 24:13809. [PMID: 37762110 PMCID: PMC10530467 DOI: 10.3390/ijms241813809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Whole-exome sequencing (WES) in families with an unexplained tendency for venous thromboembolism (VTE) may favor detection of low-frequency variants in genes with known contribution to hemostasis or associated with VTE-related phenotypes. WES analysis in six family members, three of whom affected by documented VTE, filtered for MAF < 0.04 in 192 candidate genes, revealed 22 heterozygous (16 missense and six synonymous) variants in patients. Functional prediction by multi-component bioinformatics tools, implemented by a database/literature search, including ClinVar annotation and QTL analysis, prioritized 12 missense variants, three of which (CRP Leu61Pro, F2 Asn514Lys and NQO1 Arg139Trp) were present in all patients, and the frequent functional variants FGB Arg478Lys and IL1A Ala114Ser. Combinations of prioritized variants in each patient were used to infer functional protein interactions. Different interaction patterns, supported by high-quality evidence, included eight proteins intertwined in the "acute phase" (CRP, F2, SERPINA1 and IL1A) and/or in the "fibrinogen complex" (CRP, F2, PLAT, THBS1, VWF and FGB) significantly enriched terms. In a wide group of candidate genes, this approach highlighted six low-frequency variants (CRP Leu61Pro, F2 Asn514Lys, SERPINA1 Arg63Cys, THBS1 Asp901Glu, VWF Arg1399His and PLAT Arg164Trp), five of which were top ranked for predicted deleteriousness, which in different combinations may contribute to disease susceptibility in members of this family.
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Affiliation(s)
- Barbara Lunghi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| | - Nicole Ziliotto
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy;
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| | - Lucrezia Rossi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| | - Patrizia Della Valle
- Unit of Coagulation Service and Thrombosis Research, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (P.D.V.); (A.D.)
| | - Pasquale Pignatelli
- Department of Clinical Internal, Anesthesiological, and Cardiovascular Sciences, Sapienza University of Rome, 00185 Rome, Italy;
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
| | - Armando D’Angelo
- Unit of Coagulation Service and Thrombosis Research, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (P.D.V.); (A.D.)
| | - Giovanna Marchetti
- Department of Neuroscience and Rehabilitation, University of Ferrara, 44121 Ferrara, Italy;
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (B.L.); (D.B.); (L.R.); (M.P.)
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Tavares V, Pinto R, Assis J, Pereira D, Medeiros R. Venous thromboembolism GWAS reported genetic makeup and the hallmarks of cancer: Linkage to ovarian tumour behaviour. Biochim Biophys Acta Rev Cancer 2020; 1873:188331. [DOI: 10.1016/j.bbcan.2019.188331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022]
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Mulder R, Lisman T, Meijers JCM, Huntington JA, Mulder AB, Meijer K. Linkage analysis combined with whole-exome sequencing identifies a novel prothrombin ( F2) gene mutation in a Dutch Caucasian family with unexplained thrombosis. Haematologica 2019; 105:e370-e372. [PMID: 31582550 DOI: 10.3324/haematol.2019.232504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- René Mulder
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ton Lisman
- Surgical Research Laboratory and Section of Hepatobiliary Surgery and Liver Transplantation, Department of Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Joost C M Meijers
- Department of Molecular and Cellular Hemostasis, Sanquin Research, Amsterdam and Amsterdam UMC, University of Amsterdam, Department of Experimental Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - James A Huntington
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - André B Mulder
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Karina Meijer
- Department of Hematology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Genetic Determinants of Thrombin Generation and Their Relation to Venous Thrombosis: Results from the GAIT-2 Project. PLoS One 2016; 11:e0146922. [PMID: 26784699 PMCID: PMC4718515 DOI: 10.1371/journal.pone.0146922] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/23/2015] [Indexed: 02/07/2023] Open
Abstract
Background Venous thromboembolism (VTE) is a common disease where known genetic risk factors explain only a small portion of the genetic variance. Then, the analysis of intermediate phenotypes, such as thrombin generation assay, can be used to identify novel genetic risk factors that contribute to VTE. Objectives To investigate the genetic basis of distinct quantitative phenotypes of thrombin generation and its relationship to the risk of VTE. Patients/Methods Lag time, thrombin peak and endogenous thrombin potential (ETP) were measured in the families of the Genetic Analysis of Idiopathic Thrombophilia 2 (GAIT-2) Project. This sample consisted of 935 individuals in 35 extended families selected through a proband with idiopathic thrombophilia. We performed also genome wide association studies (GWAS) with thrombin generation phenotypes. Results The results showed that 67% of the variation in the risk of VTE is attributable to genetic factors. The heritabilities of lag time, thrombin peak and ETP were 49%, 54% and 52%, respectively. More importantly, we demonstrated also the existence of positive genetic correlations between thrombin peak or ETP and the risk of VTE. Moreover, the major genetic determinant of thrombin generation was the F2 gene. However, other suggestive signals were observed. Conclusions The thrombin generation phenotypes are strongly genetically determined. The thrombin peak and ETP are significantly genetically correlated with the risk of VTE. In addition, F2 was identified as a major determinant of thrombin generation. We reported suggestive signals that might increase our knowledge to explain the variability of this important phenotype. Validation and functional studies are required to confirm GWAS results.
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Zapponi KCS, Mazetto BM, Bittar LF, Barnabé A, Santiago-Bassora FD, De Paula EV, Orsi FA, Franco-Penteado CF, Conran N, Annichino-Bizzacchi JM. Increased adhesive properties of neutrophils and inflammatory markers in venous thromboembolism patients with residual vein occlusion and high D-dimer levels. Thromb Res 2014; 133:736-42. [PMID: 24560897 DOI: 10.1016/j.thromres.2014.01.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 12/12/2013] [Accepted: 01/28/2014] [Indexed: 01/20/2023]
Abstract
BACKGROUND Venous thromboembolism (VTE) develops via a multicellular process on the endothelial surface. Although widely recognized, the relationship between inflammation and thrombosis, this relationship has been mostly explored in clinical studies by measuring circulating levels of inflammatory cytokines. However, the role of inflammatory cells, such as neutrophils, in the pathogenesis of VTE is not clear in humans. AIMS To evaluate the adhesive properties of neutrophils, erythrocytes and platelets in VTE patients and to correlate findings with inflammatory and hypercoagulability marker levels. METHODS Study group consisted of twenty-nine VTE patients and controls matched according to age, gender and ethnic background. Adhesive properties of neutrophils, erythrocytes and platelets were determined using a static adhesion assay. Neutrophil adhesion molecules expressions were evaluated by flow cytometry. Inflammatory and hypercoagulability marker levels were evaluated by standard methods. Residual vein occlusion (RVO) was evaluated by Doppler ultrasound. RESULTS No significant difference could be observed in platelet and erythrocyte adhesion between VTE patients and controls. Interestingly, VTE patients with high levels of D-dimer and RVO, demonstrated a significant increase in neutrophil adhesion, compared to controls and remaining patients. Inflammatory markers (IL-6, IL-8, TNF-α) were also significantly elevated in this subgroup, compared to other VTE patients. Adhesive properties of neutrophils correlated with IL-6 and D-dimer levels. Neutrophils adhesion molecules (CD11a, CD11b and CD18) were not altered in any of the groups. CONCLUSION These findings not only support the hypothesis of an association between inflammation and hypercoagulability, but more importantly, highlight the role of neutrophils in this process.
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Affiliation(s)
- Kiara C S Zapponi
- Hematology and Hemotherapy Center, University of Campinas - UNICAMP, São Paulo, Brazil.
| | - Bruna M Mazetto
- Hematology and Hemotherapy Center, University of Campinas - UNICAMP, São Paulo, Brazil
| | - Luis F Bittar
- Hematology and Hemotherapy Center, University of Campinas - UNICAMP, São Paulo, Brazil
| | - Aline Barnabé
- Hematology and Hemotherapy Center, University of Campinas - UNICAMP, São Paulo, Brazil
| | | | - Erich V De Paula
- Department of Clinical Pathology, University of Campinas - UNICAMP, São Paulo, Brazil
| | - Fernanda A Orsi
- Hematology and Hemotherapy Center, University of Campinas - UNICAMP, São Paulo, Brazil
| | | | - Nicola Conran
- Hematology and Hemotherapy Center, University of Campinas - UNICAMP, São Paulo, Brazil
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Lotta LA, Tuana G, Yu J, Martinelli I, Wang M, Yu F, Passamonti SM, Pappalardo E, Valsecchi C, Scherer SE, Hale W, Muzny DM, Randi G, Rosendaal FR, Gibbs RA, Peyvandi F. Next-generation sequencing study finds an excess of rare, coding single-nucleotide variants of ADAMTS13 in patients with deep vein thrombosis. J Thromb Haemost 2013; 11:1228-39. [PMID: 23648131 DOI: 10.1111/jth.12291] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 04/30/2013] [Indexed: 01/08/2023]
Abstract
BACKGROUND The considerable genetic predisposition to deep vein thrombosis (DVT) is only partially accounted for by known genetic risk variants. Rare single-nucleotide variants (SNVs) of the coding areas of hemostatic genes may explain part of this missing heritability. The ADAMTS13 and VWF genes encode two interconnected proteins with fundamental hemostatic functions, the disruption of which may result in thrombosis. OBJECTIVES To study the distribution and burden of rare coding SNVs of ADAMTS13 and VWF found by sequencing in cases and controls of DVT. PATIENTS/METHODS The protein-coding areas of 186 hemostatic/proinflammatory genes were sequenced by next-generation technology in 94 thrombophilia-negative patients with DVT and 98 controls. Gene-specific information on ADAMTS13 and VWF was used to study the association between DVT and rare coding SNVs of the two genes. RESULTS More than 70 billion base pairs of raw sequence data were produced to sequence the 700-kb target area with a median redundancy of × 45 in 192 individuals. Most of the 4366 SNVs identified were rare and non-synonymous, indicating pathogenetic potential. Rare (frequency of < 1%) and low-frequency (< 5%) coding SNVs of ADAMTS13 were associated with DVT (prevalence 17% vs. 4%; odds ratio [OR] 4.8 and 95% confidence interval [CI] 1.6-15.0 for rare coding; prevalence 36% vs. 23%, OR 1.9 and 95% CI 1.0-3.5 for low-frequency coding). Patients with rare coding SNVs of ADAMTS13 had lower plasma levels of ADAMTS-13 activity than patients without them. SNVs of VWF were not associated with DVT. CONCLUSIONS We found an excess of rare coding SNVs of the ADAMTS13 gene in patients with DVT.
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Affiliation(s)
- L A Lotta
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Università degli Studi di Milano and Fondazione Luigi Villa, Via Pace 9, Milan, Italy.
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Greliche N, Germain M, Lambert JC, Cohen W, Bertrand M, Dupuis AM, Letenneur L, Lathrop M, Amouyel P, Morange PE, Trégouët DA. A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis. BMC MEDICAL GENETICS 2013; 14:36. [PMID: 23509962 PMCID: PMC3607886 DOI: 10.1186/1471-2350-14-36] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 03/13/2013] [Indexed: 12/31/2022]
Abstract
BACKGROUND Venous Thrombosis (VT) is a common multifactorial disease with an estimated heritability between 35% and 60%. Known genetic polymorphisms identified so far only explain ~5% of the genetic variance of the disease. This study was aimed to investigate whether pair-wise interactions between common single nucleotide polymorphisms (SNPs) could exist and modulate the risk of VT. METHODS A genome-wide SNP x SNP interaction analysis on VT risk was conducted in a French case-control study and the most significant findings were tested for replication in a second independent French case-control sample. The results obtained in the two studies totaling 1,953 cases and 2,338 healthy subjects were combined into a meta-analysis. RESULTS The smallest observed p-value for interaction was p = 6.00 10(-11) but it did not pass the Bonferroni significance threshold of 1.69 10(-12) correcting for the number of investigated interactions that was 2.96 10(10). Among the 37 suggestive pair-wise interactions with p-value less than 10(-8), one was further shown to involve two SNPs, rs9804128 (IGFS21 locus) and rs4784379 (IRX3 locus) that demonstrated significant interactive effects (p = 4.83 10(-5)) on the variability of plasma Factor VIII levels, a quantitative biomarker of VT risk, in a sample of 1,091 VT patients. CONCLUSION This study, the first genome-wide SNP interaction analysis conducted so far on VT risk, suggests that common SNPs are unlikely exerting strong interactive effects on the risk of disease.
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Affiliation(s)
- Nicolas Greliche
- INSERM, UMR_S 937; Institute of Cardiometabolism And Nutrition (ICAN), Université Pierre et Marie Curie Paris 6, Paris F-75013, France
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Lotta LA, Wang M, Yu J, Martinelli I, Yu F, Passamonti SM, Consonni D, Pappalardo E, Menegatti M, Scherer SE, Lewis LL, Akbar H, Wu Y, Bainbridge MN, Muzny DM, Mannucci PM, Gibbs RA, Peyvandi F. Identification of genetic risk variants for deep vein thrombosis by multiplexed next-generation sequencing of 186 hemostatic/pro-inflammatory genes. BMC Med Genomics 2012; 5:7. [PMID: 22353194 PMCID: PMC3305575 DOI: 10.1186/1755-8794-5-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 02/21/2012] [Indexed: 01/31/2023] Open
Abstract
Background 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. Results 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). Conclusions 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.
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Affiliation(s)
- Luca A Lotta
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, U.O.S. Dipartimentale per la Diagnosi e la Terapia delle Coagulopatie, Fondazione IRCCS Cà Granda - Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
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Oudot-Mellakh T, Cohen W, Germain M, Saut N, Kallel C, Zelenika D, Lathrop M, Trégouët DA, Morange PE. Genome wide association study for plasma levels of natural anticoagulant inhibitors and protein C anticoagulant pathway: the MARTHA project. Br J Haematol 2012; 157:230-9. [DOI: 10.1111/j.1365-2141.2011.09025.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
From the first genome wide association studies (GWAS) conducted on age-related macular degeneration back in 2005 until now, hundreds of studies have applied this strategy to identify novel genetic loci associated with hundreds of human diseases and related quantitative risk factors. While the GWAS revolution has just started to shift towards the next generation sequencing's burst, it is important to illustrate how the genetics research in venous thrombosis has benefit from the GWAS paradigm.
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Morange PE, Bezemer I, Saut N, Bare L, Burgos G, Brocheton J, Durand H, Biron-Andreani C, Schved JF, Pernod G, Galan P, Drouet L, Zelenika D, Germain M, Nicaud V, Heath S, Ninio E, Delluc A, Münzel T, Zeller T, Brand-Herrmann SM, Alessi MC, Tiret L, Lathrop M, Cambien F, Blankenberg S, Emmerich J, Trégouët DA, Rosendaal FR. A follow-up study of a genome-wide association scan identifies a susceptibility locus for venous thrombosis on chromosome 6p24.1. Am J Hum Genet 2010; 86:592-5. [PMID: 20226436 DOI: 10.1016/j.ajhg.2010.02.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 02/08/2010] [Accepted: 02/11/2010] [Indexed: 12/21/2022] Open
Abstract
To identify genetic susceptibility factors conferring increased risk of venous thrombosis (VT), we conducted a multistage study, following results of a previously published GWAS that failed to detect loci for developing VT. Using a collection of 5862 cases with VT and 7112 healthy controls, we identified the HIVEP1 locus on chromosome 6p24.1 as a susceptibility locus for VT. Indeed, the HIVEP1 rs169713C allele was associated with an increased risk for VT, with an odds ratio of 1.20 (95% confidence interval 1.13-1.27, p = 2.86 x 10(-9)). HIVEP1 codes for a protein that participates in the transcriptional regulation of inflammatory target genes by binding specific DNA sequences in their promoter and enhancer regions. The current results provide the identification of a locus involved in VT susceptibility that lies outside the traditional coagulation/fibrinolysis pathway.
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C4BPB/C4BPA is a new susceptibility locus for venous thrombosis with unknown protein S-independent mechanism: results from genome-wide association and gene expression analyses followed by case-control studies. Blood 2010; 115:4644-50. [PMID: 20212171 DOI: 10.1182/blood-2010-01-263038] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Through its binding with protein S (PS), a key element of the coagulation/fibrinolysis cascade, the C4b-binding protein (C4BP) has been hypothesized to be involved in the susceptibility to venous thrombosis (VT). To identify genetic factors that may influence the plasma levels of the 3 C4BP existing isoforms, alpha(7)beta(1), alpha(6)beta(1), and alpha(7)beta(0), we conducted a genome-wide association study by analyzing 283 437 single nucleotide polymorphisms (SNPs) in the Genetic Analysis of Idiopathic Thrombophilia (GAIT) study composed of 352 persons. Three SNPs at the C4BPB/C4BPA locus were found genome-wide significantly associated with alpha(7)beta(0) levels. One of these SNPs was further found to explain approximately 11% of the variability of mRNA C4BPA expression in the Gutenberg Heart Study composed of 1490 persons, with no effect on C4BPB mRNA expression. The allele associated with increased alpha(7)beta(0) plasma levels and increased C4BPA expression was further found associated with increased risk of VT (odds ratio [OR] = 1.24 [1.03-1.53]) in 2 independent case-control studies (MARseille THrombosis Association study [MARTHA] and FActeurs de RIsque et de récidives de la maladie thromboembolique VEineuse [FARIVE]) gathering 1706 cases and 1379 controls. This SNP was not associated with free PS or total PS. In conclusion, we observed strong evidence that the C4BPB/C4BPA locus is a new susceptibility locus for VT through a PS-independent mechanism that remains to be elucidated.
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