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Pshenichnikova O, Selivanova D, Shchemeleva E, Abramova T, Zozulya N, Surin V. Molecular Genetic Analysis of Russian Patients with Coagulation Factor FVII Deficiency. Genes (Basel) 2023; 14:1767. [PMID: 37761907 PMCID: PMC10531009 DOI: 10.3390/genes14091767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Coagulation factor VII (proconvertin) is one of the proteins starting the blood coagulation cascade. Plasma FVII concentration is regulated by different factors. A low level of FVII could also be a result of FVII deficiency (MIM# 227500), the rare autosomal recessive inherited disease caused by pathogenic variants in the F7 gene. The aim of this study was to describe a mutation spectrum of the F7 gene and genotype-phenotype relationship in patients with FVII deficiency in Russia for the first time. We studied the primary structure of the F7 gene of 54 unrelated patients with FVII deficiency by direct Sanger sequencing. Pathogenic variants in the F7 gene were detected in 37 (68.5%) of them. We identified 24 different mutations located mostly in the serine protease domain. Five pathogenic variants had never been reported before. A major mutation in the Russian population was c.1391delC (p. Pro464Hisfs*32), linked with rs36209567 and rs6046 functional polymorphisms, that is widely distributed in East Europe. As in other countries, the F7 genotypes poorly correlated with the severity of clinical manifestations but were quite well associated with FVII levels. Minor alleles of functional polymorphisms rs510335, rs5742910, rs561241, rs36209567, and rs6046 could also participate in the F7 genotype and influence FVII levels.
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Affiliation(s)
- Olesya Pshenichnikova
- Laboratory of Genetic Engineering of National Medical Research Center for Hematology, Novy Zykovski lane 4a, 125167 Moscow, Russia
| | - Daria Selivanova
- Laboratory of Genetic Engineering of National Medical Research Center for Hematology, Novy Zykovski lane 4a, 125167 Moscow, Russia
| | - Ekaterina Shchemeleva
- Laboratory of Genetic Engineering of National Medical Research Center for Hematology, Novy Zykovski lane 4a, 125167 Moscow, Russia
| | - Tatiana Abramova
- Laboratory of Genetic Engineering of National Medical Research Center for Hematology, Novy Zykovski lane 4a, 125167 Moscow, Russia
| | - Nadezhda Zozulya
- Coagulopathies Department of National Medical Research Center for Hematology, Novy Zykovski lane 4a, 125167 Moscow, Russia
| | - Vadim Surin
- Laboratory of Genetic Engineering of National Medical Research Center for Hematology, Novy Zykovski lane 4a, 125167 Moscow, Russia
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Pruthi RK. Testing strategies used in the diagnosis of rare inherited bleeding disorders. Expert Rev Hematol 2023:1-15. [PMID: 37144355 DOI: 10.1080/17474086.2023.2211257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
INTRODUCTION Rare Bleeding Disorders have a low population prevalence and may not be recognized by most clinicians. In addition, knowledge gaps of the indicated laboratory tests and their availability add to the potential for delayed diagnosis or misdiagnosis. The lack of widely available commercial, regulatory body approved esoteric tests limit them to reference laboratories, thus limiting easy access for patients. AREAS COVERED A literature search of Pubmed, Medline, Embase and review of international society guidelines was performed. Additional references from published articles were reviewed. A patient-centered approach to recognition and evaluation of RBD is discussed. EXPERT OPINION Recognition of RBD relies on obtaining a detailed patient personal and family hemostatic history. Inquiry into a history of involvement of other organ systems is important and if present should lead to suspicion of an inherited platelet disorder or a variant of Ehlers Danlos Syndrome. Multiple factors contribute to the complexity of development of efficient algorithms for diagnostic testing. Limitations in diagnostic sensitivity and specificity of screening tests, diagnostic tests, and esoteric tests further compound the complexity of establishing a diagnosis. Educational efforts focusing on clinician awareness of RBDs and available testing options are vital for optimal management of such patients.
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Affiliation(s)
- Rajiv K Pruthi
- Mayo Comprehensive Hemophilia Center, Division of Hematology, Department of Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
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Resolving Differential Diagnostic Problems in von Willebrand Disease, in Fibrinogen Disorders, in Prekallikrein Deficiency and in Hereditary Hemorrhagic Telangiectasia by Next-Generation Sequencing. Life (Basel) 2021; 11:life11030202. [PMID: 33807613 PMCID: PMC7999415 DOI: 10.3390/life11030202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/19/2022] Open
Abstract
Diagnosis of rare bleeding disorders is challenging and there are several differential diagnostics issues. Next-generation sequencing (NGS) is a useful tool to overcome these problems. The aim of this study was to demonstrate the usefulness of molecular genetic investigations by summarizing the diagnostic work on cases with certain bleeding disorders. Here we report only those, in whom NGS was indicated due to uncertainty of diagnosis or if genetic confirmation of initial diagnosis was required. Based on clinical and/or laboratory suspicion of von Willebrand disease (vWD, n = 63), hypo-or dysfibrinogenemia (n = 27), hereditary hemorrhagic telangiectasia (HHT, n = 10) and unexplained activated partial thromboplastin time (APTT) prolongation (n = 1), NGS using Illumina platform was performed. Gene panel covered 14 genes (ACVRL1, ENG, MADH4, GDF2, RASA1, F5, F8, FGA, FGB, FGG, KLKB1, ADAMTS13, GP1BA and VWF) selected on the basis of laboratory results. We identified forty-seven mutations, n = 29 (6 novel) in vWD, n = 4 mutations leading to hemophilia A, n = 10 (2 novel) in fibrinogen disorders, n = 2 novel mutations in HHT phenotype and two mutations (1 novel) leading to prekallikrein deficiency. By reporting well-characterized cases using standardized, advanced laboratory methods we add new pieces of data to the continuously developing “bleeding disorders databases”, which are excellent supports for clinical patient management.
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Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders. Blood 2020; 134:2082-2091. [PMID: 31064749 DOI: 10.1182/blood.2018891192] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/22/2019] [Indexed: 12/17/2022] Open
Abstract
A targeted high-throughput sequencing (HTS) panel test for clinical diagnostics requires careful consideration of the inclusion of appropriate diagnostic-grade genes, the ability to detect multiple types of genomic variation with high levels of analytic sensitivity and reproducibility, and variant interpretation by a multidisciplinary team (MDT) in the context of the clinical phenotype. We have sequenced 2396 index patients using the ThromboGenomics HTS panel test of diagnostic-grade genes known to harbor variants associated with rare bleeding, thrombotic, or platelet disorders (BTPDs). The molecular diagnostic rate was determined by the clinical phenotype, with an overall rate of 49.2% for all thrombotic, coagulation, platelet count, and function disorder patients and a rate of 3.2% for patients with unexplained bleeding disorders characterized by normal hemostasis test results. The MDT classified 745 unique variants, including copy number variants (CNVs) and intronic variants, as pathogenic, likely pathogenic, or variants of uncertain significance. Half of these variants (50.9%) are novel and 41 unique variants were identified in 7 genes recently found to be implicated in BTPDs. Inspection of canonical hemostasis pathways identified 29 patients with evidence of oligogenic inheritance. A molecular diagnosis has been reported for 894 index patients providing evidence that introducing an HTS genetic test is a valuable addition to laboratory diagnostics in patients with a high likelihood of having an inherited BTPD.
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Ferraresi P, Balestra D, Guittard C, Buthiau D, Pan-Petesh B, Maestri I, Farah R, Pinotti M, Giansily-Blaizot M. Next-generation sequencing and recombinant expression characterized aberrant splicing mechanisms and provided correction strategies in factor VII deficiency. Haematologica 2019; 105:829-837. [PMID: 31273093 PMCID: PMC7049351 DOI: 10.3324/haematol.2019.217539] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/02/2019] [Indexed: 01/22/2023] Open
Abstract
Despite the exhaustive screening of F7 gene exons and exon-intron boundaries and promoter region, a significant proportion of mutated alleles remains unidentified in patients with coagulation factor VII deficiency. Here, we applied next-generation sequencing to 13 FVII-deficient patients displaying genotype-phenotype discrepancies upon conventional sequencing, and identified six rare intronic variants. Computational analysis predicted splicing effects for three of them, which would strengthen (c.571+78G>A; c.806-329G>A) or create (c.572-392C>G) intronic 5′ splice sites (5′ss). In F7 minigene assays, the c.806-329G>A was ineffective while the c.571+78G>A change led to usage of the +79 cryptic 5′ss with only trace levels of correct transcripts (3% of wild-type), in accordance with factor VII activity levels in homozygotes (1-3% of normal). The c.572-392C>G change led to pseudo-exonization and frame-shift, but also substantial levels of correct transcripts (approx. 70%). However, this variant was associated with the common F7 polymorphic haplotype, predicted to further decrease factor VII levels; this provided some kind of explanation for the 10% factor VII levels in the homozygous patient. Intriguingly, the effect of the c.571+78G>A and c.572-392C>G changes, and particularly of the former (the most severe and well-represented in our cohort), was counteracted by antisense U7snRNA variants targeting the intronic 5′ss, thus demonstrating their pathogenic role. In conclusion, the combination of next-generation sequencing of the entire F7 gene with the minigene expression studies elucidated the molecular bases of factor VII deficiency in 10 of 13 patients, thus improving diagnosis and genetic counseling. It also provided a potential therapeutic approach based on antisense molecules that has been successfully exploited in other disorders.
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Affiliation(s)
- Paolo Ferraresi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Caroline Guittard
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
| | - Delphine Buthiau
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
| | | | - Iva Maestri
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Roula Farah
- Department of Pediatrics, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Muriel Giansily-Blaizot
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
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Lin CC, Wu CH, Chen LY, Tsai MC, Elsarawy AM, Huang KT. Coagulation factor VII gene polymorphisms are not associated with the occurrence or the survival of hepatocellular carcinoma: a report of 37 cases. Cancer Biol Med 2018; 15:275-281. [PMID: 30197794 PMCID: PMC6121054 DOI: 10.20892/j.issn.2095-3941.2017.0144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Objective : Coagulation factor VII (FVII) triggers the extrinsic pathway of blood coagulation. In our previous study, we showed that FVII plays an important role in tumorigenesis of hepatocellular carcinoma (HCC). However, the role of FVII polymorphism in HCC is still unknown. The present study aimed to investigate the relationship between HCC carcinogenesis and single nucleotide polymorphism of FVII. Methods : Thirty-seven HCC patients and 30 healthy donors were recruited in this study. Four common FVII gene polymorphisms - a decanucleotide insertion at position -323 (-323ins10-bp), a G to T substitution at position -401 (-401G/T), a G to A substitution at position -402 (-402G/A), and a T to C substitution at position -122 (-122T/C) - were analyzed by sequencing or commercialized assays using genomic DNA isolated from blood samples. Clinicopathological parameters between control and HCC subjects were compared according to the specific genotypes. Results : The most common nucleotide variation was -402G/A. However, no statistically significant difference was observed between healthy controls and HCC subjects for all four polymorphisms in terms of genotype distribution and allele frequencies, indicating that these polymorphisms may not affect HCC tumorigenesis. Furthermore, no association was found between -402G/A polymorphisms and tumor stage, recurrence, and overall survival. Conclusions : Our results indicate that FVII polymorphisms may not be a key factor that clinically impact tumorigenesis and outcomes of HCC, although further investigations should be conducted to confirm our findings.
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Affiliation(s)
- Chih-Che Lin
- Liver Transplantation Center, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China
| | - Chun-Hsien Wu
- Liver Transplantation Center, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China.,Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China
| | - Li-Yu Chen
- Liver Transplantation Center, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China.,Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China
| | - Ming-Chao Tsai
- Division of Hepato-Gastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China
| | - Ahmed M Elsarawy
- Liver Transplantation Center, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China
| | - Kuang-Tzu Huang
- Liver Transplantation Center, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China.,Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan, China
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7
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Olson NC, Raffield LM, Lange LA, Lange EM, Longstreth WT, Chauhan G, Debette S, Seshadri S, Reiner AP, Tracy RP. Associations of activated coagulation factor VII and factor VIIa-antithrombin levels with genome-wide polymorphisms and cardiovascular disease risk. J Thromb Haemost 2018; 16:19-30. [PMID: 29112333 PMCID: PMC5760305 DOI: 10.1111/jth.13899] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Indexed: 11/26/2022]
Abstract
ESSENTIALS Essentials A fraction of coagulation factor VII circulates in blood as an activated protease (FVIIa). We evaluated FVIIa and FVIIa-antithrombin (FVIIa-AT) levels in the Cardiovascular Health Study. Polymorphisms in the F7 and PROCR loci were associated with FVIIa and FVIIa-AT levels. FVIIa may be an ischemic stroke risk factor in older adults and FVIIa-AT may assess mortality risk. SUMMARY Background A fraction of coagulation factor (F) VII circulates as an active protease (FVIIa). FVIIa also circulates as an inactivated complex with antithrombin (FVIIa-AT). Objective Evaluate associations of FVIIa and FVIIa-AT with genome-wide single nucleotide polymorphisms (SNPs) and incident coronary heart disease, ischemic stroke and mortality. Patients/Methods We measured FVIIa and FVIIa-AT in 3486 Cardiovascular Health Study (CHS) participants. We performed a genome-wide association scan for FVIIa and FVIIa-AT in European-Americans (n = 2410) and examined associations of FVII phenotypes with incident cardiovascular disease. Results In European-Americans, the most significant SNP for FVIIa and FVIIa-AT was rs1755685 in the F7 promoter region on chromosome 13 (FVIIa, β = -25.9 mU mL-1 per minor allele; FVIIa-AT, β = -26.6 pm per minor allele). Phenotypes were also associated with rs867186 located in PROCR on chromosome 20 (FVIIa, β = 7.8 mU mL-1 per minor allele; FVIIa-AT, β = 9.9 per minor allele). Adjusted for risk factors, a one standard deviation higher FVIIa was associated with increased risk of ischemic stroke (hazard ratio [HR], 1.12; 95% confidence interval [CI], 1.01, 1.23). Higher FVIIa-AT was associated with mortality from all causes (HR, 1.08; 95% CI, 1.03, 1.12). Among European-American CHS participants the rs1755685 minor allele was associated with lower ischemic stroke (HR, 0.69; 95% CI, 0.54, 0.88), but this association was not replicated in a larger multi-cohort analysis. Conclusions The results support the importance of the F7 and PROCR loci in variation in circulating FVIIa and FVIIa-AT. The findings suggest FVIIa is a risk factor for ischemic stroke in older adults, whereas higher FVIIa-AT may reflect mortality risk.
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Affiliation(s)
- N C Olson
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
- Cardiovascular Research Institute of Vermont, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
| | - L M Raffield
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - L A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - E M Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - W T Longstreth
- Department of Neurology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - G Chauhan
- INSERM U1219 Neuroepidemiology, Bordeaux, France
- University of Bordeaux, Bordeaux, France
- Centre for Brain Research, Indian Institute of Science, Bangalore, India
| | - S Debette
- INSERM U1219 Neuroepidemiology, Bordeaux, France
- University of Bordeaux, Bordeaux, France
- Department of Neurology, Bordeaux University Hospital, Bordeaux, France
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA
| | - S Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA, USA
| | - A P Reiner
- Department of Neurology, Bordeaux University Hospital, Bordeaux, France
| | - R P Tracy
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
- Cardiovascular Research Institute of Vermont, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, USA
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Quintavalle G, Riccardi F, Rivolta GF, Martorana D, Di Perna C, Percesepe A, Tagliaferri A. F7 gene variants modulate protein levels in a large cohort of patients with factor VII deficiency. Results from a genotype-phenotype study. Thromb Haemost 2017; 117:1455-1464. [PMID: 28447100 DOI: 10.1160/th17-02-0085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/10/2017] [Indexed: 12/14/2022]
Abstract
Congenital factor VII (FVII) deficiency is a rare bleeding disorder caused by mutations in F7 gene with autosomal recessive inheritance. A clinical heterogeneity with poor correlation with FVII:C levels has been described. It was the objective of this study to identify genetic defects and to evaluate their relationships with phenotype in a large cohort of patients with FVII:C<50 %. One hundred twenty-three probands were genotyped for F7 mutations and three polymorphic variants and classified according to recently published clinical scores. Forty out of 123 patients (33 %) were symptomatic (43 bleedings). A severe bleeding tendency was observed only in patients with FVII:C<0.10 %. Epistaxis (11 %) and menorrhagia (32 % of females in fertile age) were the most frequent bleedings. Molecular analysis detected 48 mutations, 20 not reported in the F7 international databases. Most mutations (62 %) were missense, large deletions were 6.2 %. Compound heterozygotes/homozygotes for mutations presented lower FVII:C levels compared to the other classes (Chi2=43.709, p<0,001). The polymorphisms distribution was significantly different among the three F7 genotypic groups (Chi2=72.289, p<0,001). The presence of truncating mutations was associated with lowest FVII:C levels (Chi2=21.351, p=0.002). This study confirms the clinical and molecular variability of the disease and the type of symptoms. It shows a good correlation between the type of F7 mutation and/or polymorphisms and FVII:C levels, without a direct link between FVII:C and bleeding tendency. The results suggest that large deletions are underestimated and that they represent a common mechanism of F7 gene inactivation which should always be investigated in the diagnostic testing for FVII deficiency.
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Affiliation(s)
- Gabriele Quintavalle
- Gabriele Quintavalle, Regional Reference Centre for inherited bleeding disorders, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy, Tel.: +39 0521 703971, Fax: +39 0521 704332, E-mail:
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Synergistic effect of factor VII gene polymorphisms causing mild factor VII deficiency in a case of severe factor X deficiency. Blood Coagul Fibrinolysis 2017; 28:105-106. [PMID: 26919454 DOI: 10.1097/mbc.0000000000000544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Abstract
BACKGROUND Identifying variants that regulate gene expression and delineating their genetic architecture is a critical next step in our endeavors to better understand the genetic etiology of complex diseases. The appropriate genomic tools are in place, and preliminary analytic strategies have been developed. METHODS Here we used Genetic Analysis Workshop (GAW) 19 data to investigate the genetic complexity of expression quantitative trait loci (eQTL), chromosomal regions likely to harbor regulatory elements responsible for gene expression. For this investigation, we analyzed the lymphocyte expression profiles of 653 individuals in 20 pedigrees who were also genotyped by single nucleotide polymorphism (SNP) arrays, followed by sequencing and imputation. We used these data to examine the degree of allelic heterogeneity, a contributor to genetic complexity at eQTL, by sequentially conditioning on the most significantly associated SNPs. RESULT SOLAR (Sequential Oligogenic Linkage Analysis Routines)-MGA (measured genotype approach) and FaST-LMM (Factored Spectrally Transformed Linear Mixed Model) software allowed us to analyze pedigree data. The power and Type 1 error rates for single SNP association testing and multiple SNP sequential association testing were consistent for these programs. Sequential conditioning of the real expression data revealed substantial levels of allelic heterogeneity at the 2 eQTL examined, illustrating this feature of genetic complexity. CONCLUSIONS eQTL exhibit substantial genetic complexity among and within pedigrees.
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Affiliation(s)
- Rita M. Cantor
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Dr, South, Los Angeles, CA 90024-7088 USA
| | - Calvin Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Dr, South, Los Angeles, CA 90024-7088 USA
| | - Kimberly Siegmund
- Department of Preventive Medicine, Keck School of Medicine of USC, SSB 202WHealth Sciences Campus, Los Angeles, CA 90089-9234 USA
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Schreiner C, Suter S, Watzka M, Hertfelder HJ, Schreiner F, Oldenburg J, Bartmann P, Heep A. Genetic variants of the vitamin K dependent coagulation system and intraventricular hemorrhage in preterm infants. BMC Pediatr 2014; 14:219. [PMID: 25179312 PMCID: PMC4236669 DOI: 10.1186/1471-2431-14-219] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 08/19/2014] [Indexed: 01/10/2023] Open
Abstract
Background Pathogenesis of intraventricular hemorrhage (IVH) in premature infants is multifactorial. Little is known about the impact of genetic variants in the vitamin K-dependent coagulation system on the development of IVH. Methods Polymorphisms in the genes encoding vitamin K epoxide reductase complex 1 (VKORC1 -1639G>A) and coagulation factor 7 (F7 -323Ins10) were examined prospectively in 90 preterm infants <32 weeks gestational age with respect to coagulation profile and IVH risk. Results F7-323Ins10 was associated with lower factor VII levels, but not with individual IVH risk. In VKORC1-wildtype infants, logistic regression analysis revealed a higher IVH risk compared to carriers of the -1639A allele. Levels of the vitamin K-dependent coagulation parameters assessed in the first hour after birth did not differ between VKORC1-wildtype infants and those carrying -1639A alleles. Conclusions Our data support the assumption that genetic variants in the vitamin K-dependent coagulation system influence the coagulation profile and the IVH risk in preterm infants. Further studies focussing on short-term changes in vitamin K-kinetics and the coagulation profile during the first days of life are required to further understand a possible link between development of IVH and genetic variants affecting the vitamin K-metabolism.
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Affiliation(s)
| | | | | | | | | | | | | | - Axel Heep
- School of Clinical Sciences, University of Bristol, Neonatal Intensive Care Unit, Southmead Road, Bristol BS10 NB5, UK.
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Giansily-Blaizot M, Lopez E, Viart V, Chafa O, Tapon-Bretaudière J, Claustres M, Taulan M. Lethal factor VII deficiency due to novel mutations in the F7 promoter: functional analysis reveals disruption of HNF4 binding site. Thromb Haemost 2012; 108:277-83. [PMID: 22628013 DOI: 10.1160/th11-09-0638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 05/02/2012] [Indexed: 12/15/2022]
Abstract
Hereditary factor VII (FVII) deficiency is a rare autosomal recessive disorder. Deleterious mutations that prevent the synthesis of any amount of functional FVII have been associated with life-threatening haemorrhage in neonates. Here we report two infants, of Maghrebian origin, who suffered a fatal spontaneous cerebral haemorrhage. Investigation of the molecular basis for their severe FVII deficiency revealed novel mutations in a homozygous state within the F7 gene promoter: a single nucleotide substitution (c.-65G>C) and a 2bp deletion (c.-60_-59delTT). To determine whether these promoter variants were responsible for the FVII deficiency, computer-assisted sequence analyses were performed. The data predicted a disrupted binding of both HNF4 and COUP-TF transcription factors with each variant. Concordantly, experimental results revealed an altered HNF4-induced transactivation in the promoter mutated variants. The execution of functional tests is critical to ensuring a complete understanding of the effect of any promoter mutant on FVII deficiency. Only then can an accurate molecular diagnosis be made and further genetic counselling and prenatal diagnosis be offered.
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Affiliation(s)
- Muriel Giansily-Blaizot
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, 641 Avenue du Doyen Gaston Giraud, 34095 Montpellier Cedex 5, France.
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13
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Taylor KC, Lange LA, Zabaneh D, Lange E, Keating BJ, Tang W, Smith NL, Delaney JA, Kumari M, Hingorani A, North KE, Kivimaki M, Tracy RP, O'Donnell CJ, Folsom AR, Green D, Humphries SE, Reiner AP. A gene-centric association scan for Coagulation Factor VII levels in European and African Americans: the Candidate Gene Association Resource (CARe) Consortium. Hum Mol Genet 2011; 20:3525-34. [PMID: 21676895 DOI: 10.1093/hmg/ddr264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Polymorphisms in several distinct genomic regions, including the F7 gene, were recently associated with factor VII (FVII) levels in European Americans (EAs). The genetic determinants of FVII in African Americans (AAs) are unknown. We used a 50,000 single nucleotide polymorphism (SNP) gene-centric array having dense coverage of over 2,000 candidate genes for cardiovascular disease (CVD) pathways in a community-based sample of 16,324 EA and 3898 AA participants from the Candidate Gene Association Resource (CARe) consortium. Our aim was the discovery of new genomic loci and more detailed characterization of existing loci associated with FVII levels. In EAs, we identified three new loci associated with FVII, of which APOA5 on chromosome 11q23 and HNF4A on chromosome 20q12-13 were replicated in a sample of 4289 participants from the Whitehall II study. We confirmed four previously reported FVII-associated loci (GCKR, MS4A6A, F7 and PROCR) in CARe EA samples. In AAs, the F7 and PROCR regions were significantly associated with FVII. Several of the FVII-associated regions are known to be associated with lipids and other cardiovascular-related traits. At the F7 locus, there was evidence of at least five independently associated SNPs in EAs and three independent signals in AAs. Though the variance in FVII explained by the existing loci is substantial (20% in EA and 10% in AA), larger sample sizes and investigation of lower frequency variants may be required to identify additional FVII-associated loci in EAs and AAs and further clarify the relationship between FVII and other CVD risk factors.
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Affiliation(s)
- Kira C Taylor
- Department of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, Chapel Hill, NC 27514, USA.
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Corral J, Antón AI, Quiroga T, González-Conejero R, Pereira J, Roldán V, Vicente V, Mezzano D. Influence of the F12 -4 C>T polymorphism on hemostatic tests. Blood Coagul Fibrinolysis 2011; 21:632-9. [PMID: 20814302 DOI: 10.1097/mbc.0b013e32833a9048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The common F12 -4 C>T polymorphism significantly regulates plasma levels of FXII, the first element of the intrinsic pathway of coagulation. Due to the robust effects that this pathway has on blood coagulation in vitro, the objective of our study was to evaluate the influence of this polymorphism on different hemostatic tests. We studied 46 hemostatic parameters in 566 participants: 280 patients with mucocutaneous bleeding and 286 controls. The F12 -4T allele, associated with reduced levels of FXII (P < 0.001), also significantly delayed the activated partial thromboplastin time (aPTT) expressed as aPTTr (ratio sample plasma/normal pooled plasma). Thus, both patients and controls carrying the T allele had higher aPTTr than C/C homozygous individuals (P < 0.001). Interestingly, 92% of healthy controls who had prolonged aPTTr carried the F12 -4T allele. Moreover, individuals with the F12 -4T allele also had less thrombin generation (assessed by endogenous thrombin potential, thrombin peak and time to achieve the peak of thrombin) using a test with low tissue factor concentration and explicit contact phase activation. Finally, both patients and controls carrying the F12 -4T allele also displayed significantly lower FIXc and FVIIc levels than C/C individuals (P < 0.01). For all associations except for FVIIc, a gene-dosage effect was observed, and homozygous TT individuals had the farthest values. Our study reveals a significant effect of the F12 -4 C>T polymorphism on hemostatic tests widely used in routine clinical practice.
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Affiliation(s)
- Javier Corral
- Servicio de Hematología y Oncología Médica HU Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, Murcia, Spain.
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Brunel H, Gallardo-Chacón JJ, Buil A, Vallverdú M, Soria JM, Caminal P, Perera A. MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis. ACTA ACUST UNITED AC 2010; 26:1811-8. [PMID: 20562420 DOI: 10.1093/bioinformatics/btq273] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Finding association between genetic variants and phenotypes related to disease has become an important vehicle for the study of complex disorders. In this context, multi-loci genetic association might unravel additional information when compared with single loci search. The main goal of this work is to propose a non-linear methodology based on information theory for finding combinatorial association between multi-SNPs and a given phenotype. RESULTS The proposed methodology, called MISS (mutual information statistical significance), has been integrated jointly with a feature selection algorithm and has been tested on a synthetic dataset with a controlled phenotype and in the particular case of the F7 gene. The MISS methodology has been contrasted with a multiple linear regression (MLR) method used for genetic association in both, a population-based study and a sib-pairs analysis and with the maximum entropy conditional probability modelling (MECPM) method, which searches for predictive multi-locus interactions. Several sets of SNPs within the F7 gene region have been found to show a significant correlation with the FVII levels in blood. The proposed multi-site approach unveils combinations of SNPs that explain more significant information of the phenotype than their individual polymorphisms. MISS is able to find more correlations between SNPs and the phenotype than MLR and MECPM. Most of the marked SNPs appear in the literature as functional variants with real effect on the protein FVII levels in blood. AVAILABILITY The code is available at http://sisbio.recerca.upc.edu/R/MISS_0.2.tar.gz
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Affiliation(s)
- Helena Brunel
- Institut de Bioenginyeria de Catalunya, Departament d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, Pau Gargallo 5, 08028 Barcelona, Spain.
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Athanasiadis G, Esteban E, Gayà -Vidal M, Dugoujon JM, Moschonas N, Chaabani H, Bissar-Tadmouri N, Harich N, Stoneking M, Moral P. Different Evolutionary Histories of the Coagulation Factor VII Gene in Human Populations? Ann Hum Genet 2010; 74:34-45. [DOI: 10.1111/j.1469-1809.2009.00557.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Combined cis-regulator elements as important mechanism affecting FXII plasma levels. Thromb Res 2009; 125:e55-60. [PMID: 19786295 DOI: 10.1016/j.thromres.2009.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 08/04/2009] [Accepted: 08/18/2009] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Factor XII (FXII) deficiency is a recessive Mendelian trait due to mutations in the F12 gene. There is no bleeding associated with FXII deficiency, but FXII deficiency has been reported to be associated with risk of thrombosis in some studies. MATERIAL AND METHODS We examined the functional effect of two naturally-occurring mutations in two Spanish FXII deficient families: a C/G substitution at position -8, and a C/T substitution at position -13. Both mutations were located on a putative HNF4 binding site of F12 gene promoter. We also analyzed the F12 C46T polymorphism (rs1801020), associated with a decrease in the FXII levels, which also segregated in both families. A fragment containing each one of both -8 and -13 mutations, was cloned 5' of a reporter gene. We compared the in vitro expression of these constructs to the wild type expression. RESULTS Our analyses confirm that the -8C/G and the -13C/T mutations decreased expression levels, demonstrating that both mutations are involved in the observed FXII deficiency. In addition, electrophoretic shift analyses suggest that they alter the union of nuclear proteins to the promoter. Coinheritance of these mutations with the C46T polymorphism, result in a significant genotype-phenotype correlation. CONCLUSIONS We have identified two naturally-occurring mutations in the F12 promoter that drastically reduce FXII levels. Knowing rare genetic alterations in the F12 gene, together with the C46T common variant, may yield further understanding about the genetic architecture of FXII levels, which may have a role in the risk of thrombosis.
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Abstract
Human quantitative trait locus (QTL) linkage mapping, although based on classical statistical genetic methods that have been around for many years, has been employed for genome-wide screening for only the last 10-15 years. In this time, there have been many success stories, ranging from QTLs that have been replicated in independent studies to those for which one or more genes underlying the linkage peak have been identified to a few with specific functional variants that have been confirmed in in vitro laboratory assays. Despite these successes, there is a general perception that linkage approaches do not work for complex traits, possibly because many human QTL linkage studies have been limited in sample size and have not employed the family configurations that maximize the power to detect linkage. We predict that human QTL linkage studies will continue to be productive for the next several years, particularly in combination with RNA expression level traits that are showing evidence of regulatory QTLs of large effect sizes and in combination with high-density genome-wide SNP panels. These SNP panels are being used to identify QTLs previously localized by linkage and linkage results are being used to place informative priors on genome-wide association studies.
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Perera A, Buil A, Di Bernardo MC, Sabater-Lleal M, Pattini L, Souto JC, Fontcuberta J, Vallverdu M, Soria JM, Caminal P. Clustering of individuals given SNPs similarity based on normalized mutual information: F7 SNPs in the GAIT sample. ACTA ACUST UNITED AC 2008; 2007:123-6. [PMID: 18001904 DOI: 10.1109/iembs.2007.4352238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This paper proposes the clustering of individuals given their genotype using a normalized Mutual Information dissimilarity distance. This method is applied to a Single Nucleotyde Polymorphism set belonging to F7 gene, uncovering the intrinsic genetic variability on one Spanish population. This genetic variability corresponds to results published using a complete different approach in population genetics literature. Identified groups are shown to express significant differences in the level of FVII concentration.
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Affiliation(s)
- Alexandre Perera
- Centre de Recerca en Enginyeria Biomedica, Dept. d'Eng. Sistemes i Automatica Industrial, Universitat Politecnica de Catalunya, Pau Gargallo, 5, 08028 Barcelona, Spain.
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Abstract
Model-free linkage methods are based on identifying regions of the genome in which patterns of allele sharing among family members correspond to patterns of phenotype correlation among family members. Two general classes of model-free linkage methods are discussed in this chapter, relative pair methods designed primarily for analysis of discrete traits and variance component methods designed primarily for analysis of quantitative traits. These methods have been used to identify numerous genes influencing complex human phenotypes and remain viable approaches to gene localization in the twenty-first century.
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Affiliation(s)
- Laura Almasy
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245, USA
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