Molecular genetic testing of polymorphisms associated with venous thrombosis: A review of molecular technologies

Diagnostic Molecular Pathology

Volumn 14, Issue 4, 2005, Pages 193-202

  Xu, Bo ^a   Tubbs, Raymond R ^a   Kottke Marchant, Kandice ^a  

^a LERNER RESEARCH INSTITUTE   (United States)

Author keywords

Molecular genetic testing; Risk factor; Single nucleotide polymorphism; Venous thrombosis

Indexed keywords

ACCURACY; COST EFFECTIVENESS ANALYSIS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; HUMAN; MOLECULAR GENETICS; MUTATIONAL ANALYSIS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RELIABILITY; REVIEW; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; THROMBOPHILIA; VEIN THROMBOSIS;

DNA MUTATIONAL ANALYSIS; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; POLYMORPHISM, GENETIC; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RISK FACTORS; VENOUS THROMBOSIS;

EID: 28444465849     PISSN: 10529551     EISSN: None     Source Type: Journal    
DOI: 10.1097/01.pas.0000177796.73583.ml     Document Type: Review

References (101)

1. Dahlback B, Carlsson M, Svensson PJ. Familial thrombophilia due to a previously unrecognized mechanism characterized by poor anticoagulant response to activated protein C: Prediction of a cofactor to activated protein C. Proc Natl Acad Sci USA. 1993;90:1004-1008.
2. Bertina RM, Koeleman BP, Koster T, et al. Mutation in blood coagulation factor V associated with resistance to activated protein C. Nature. 1994; 369:64-67.
3. Svensson PJ, Dahlback B. Resistance to activated protein C as a basis for venous thrombosis. N Engl J Med. 1994;330:517-522.
4. Bertina RM. Factor V Leiden and other coagulation factor mutations affecting thrombotic risk. Clin Chem. 1997;43:1678-1683.
5. Hoerl HD, Tabares A, Kottke-Marchant K. The diagnosis and clinical manifestations of activated protein C resistance: A case report and review of the literature. Vasc Med. 1996;1:275-280.
6. Rees DC, Cox M, Clegg JB. World distribution of factor V Leiden. Lancet. 1995;346:1133-1134.
7. Rees DC. The population genetics of factor V Leiden (Arg506Gln). Br J Haematol. 1996;95:579-586.
8. Rosendaal FR, Koster T, Vandenbroucke JP, et al. High risk of thrombosis in patients homozygous for factor V Leiden (activated protein C resistance). Blood. 1995;85:1504-1508.
9. Bertina RM, Reitsma PH, Rosendaal FR, et al. Resistance to activated protein C and factor V Leiden as risk factors for venous thrombosis. Thromb Haemost. 1995;74:449-453.
10. Martinelli I, Mannucci PM, De Stefano V, et al. Different risks of thrombosis in four coagulation defects associated with inherited thrombophilia: A study of 150 families. Blood. 1998;92:2353-2358.
11. Franco RF, Reitsma PH. Genetic risk factors of venous thrombosis. Hum Genet. 2001;109:369-384.
12. Bernardi F, Faioni EM, Castoldi E, et al. A factor V genetic component differing from factor V R506Q contributes to the activated protein C resistance phenotype. Blood. 1997;90:1552-1557.
13. Hoekema L, Castoldi E, Tans G, et al. Functional properties of factor V and factor Va encoded by the R2-gene. Thromb Haemost. 2001;85:75-81.
14. Luddington R, Jackson A, Pannerselvam S, et al. The factor V R2 allele: Risk of venous thromboembolism, factor V levels and resistance to activated protein C. Thromb Haemost. 2000;83:204-208.
15. Castaman G, Faioni EM, Tosetto A, et al. The factor V HR2 haplotype and the risk of venous thrombosis: A meta-analysis. Haematologica. 2003;88:1182-1189.
16. Poort SR, Rosendaal FR, Reitsma PH, et al. A common genetic variation in the 3′-untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increase in venous thrombosis. Blood. 1996;88:3698-3703.
17. Kottke-Marchant K. Genetic polymorphisms associated with venous and arterial thrombosis: An overview. Arch Pathol Lab Med. 2002;126:295-304.
18. Arruda VR, von Zuben PM, Chiaparini LC, et al. The mutation Ala677→Val in the methylene tetrahydrofolate reductase gene: A risk factor for arterial disease and venous thrombosis. Thromb Haemost. 1997;77:818-821.
19. Margaglione M, D'Andrea G, d'Addedda M, et al. The methylenetetrahydrofolate reductase TT677 genotype is associated with venous thrombosis independently of the coexistence of the FV Leiden and the prothrombin A20210 mutation. Thromb Haemost. 1998;79:907-911.
20. Gemmati D, Serino ML, Trivellato C, et al. C677T substitution in the methylenetetrahydrofolate reductase gene as a risk factor for venous thrombosis and arterial disease in selected patients. Haematologica. 1999;84:824-828.
21. Frosst P, Blom HJ, Milos R, et al. A candidate genetic risk factor for vascular disease: A common mutation in methylenetetrahydrofolate reductase. Nat Genet. 1995;10:111-113.
22. Weisberg I, Tran P, Christensen B, et al. A second genetic polymorphism in methylenetetrahydrofolate reductase (MTHFR) associated with decreased enzyme activity. Mol Genet Metab. 1998;64:169-172.
23. Hanson NQ, Aras O, Yang F, et al. C677T and A1298C polymorphisms of the methylenetetrahydrofolate reductase gene: Incidence and effect of combined genotypes on plasma fasting and post-methionine load homocysteine in vascular disease. Clin Chem. 2001;47:661-666.
24. Haviv YS, Shpichinetsky V, Goldschmidt N, et al. The common mutations C677T and A1298C in the human methylenetetrahydrofolate reductase gene are associated with hyperhomocysteinemia and cardiovascular disease in hemodialysis patients. Nephron. 2002;92: 120-126.
25. Lievers KJ, Boers GH, Verhoef P, et al. A second common variant in the methylenetetrahydrofolate reductase (MTHFR) gene and its relationship to MTHFR enzyme activity, homocysteine, and cardiovascular disease risk. J Mol Med. 2001;79:522-528.
26. Hessner MJ, Luhm RA, Pearson SL, et al. Prevalence of prothrombin G20210A, factor V G1691A (Leiden), and methylenetetrahydrofolate reductase (MTHFR) C677T in seven different populations determined by multiplex allele-specific PCR. Thromb Haemost. 1999;81:733-738.
27. Cortese C, Motti C. MTHFR gene polymorphism, homocysteine and cardiovascular disease. Public Health Nutr. 2001;4:493-497.
28. Franco RF, Araujo AG, Guerreiro JF, et al. Analysis of the 677 C→T mutation of the methylenetetrahydrofolate reductase gene in different ethnic groups. Thromb Haemost. 1998;79:119-121.
29. McAndrew PE, Brandt JT, Pearl DK, et al. The incidence of the gene for thermolabile methylene tetrahydrofolate reductase in African Americans. Thromb Res. 1996;83:195-198.
30. Rintelen C, Mannhalter C, Lechner K, et al. No evidence for an increased risk of venous thrombosis in patients with factor V Leiden by the homozygous 677 C to T mutation in the methylenetetrahydrofolate-reductase gene. Blood Coagul Fibrinolysis. 1999;10:101-105.
31. den Heijer M. Hyperhomocysteinaemia as a risk factor for venous thrombosis: An update of the current evidence. Clin Chem Lab Med. 2003;41:1404-1407.
32. Domagala TB, Adamek L, Nizankowska E, et al. Mutations C677T and A1298C of the 5,10-methylenetetrahydrofolate reductase gene and fasting plasma homocysteine levels are not associated with the increased risk of venous thromboembolic disease. Blood Coagul Fibrinolysis. 2002;13: 423-431.
33. Nizankowska-Mogilnicka E, Adamek L, Grzanka P, et al. Genetic polymorphisms associated with acute pulmonary embolism and deep venous thrombosis. Eur Respir J. 2003;21:25-30.
34. Dawson SJ, Wiman B, Hamsten A, et al. The two allele sequences of a common polymorphism in the promoter of the plasminogen activator inhibitor-1 (PAI-1) gene respond differently to interleukin-1 in HepG2 cells. J Biol Chem. 1993;268:10739-10745.
35. Ye S, Green FR, Scarabin PY, et al. The 4G/5G genetic polymorphism in the promoter of the plasminogen activator inhibitor-1 (PAI-1) gene is associated with differences in plasma PAI-1 activity but not with risk of myocardial infarction in the ECTIM study. Etude CasTemoins de I'nfarctus du Mycocarde. Thromb Haemost. 1995;74:837-841.
36. Kohler HP, Grant PJ. Plasminogen-activator inhibitor type 1 and coronary artery disease. N Engl J Med. 2000;342:1792-1801.
37. Margaglione M, Grandone E, Vecchione G, et al. Plasminogen activator inhibitor-1 (PAI-1) antigen plasma levels in subjects attending a metabolic ward: relation to polymorphisms of PAI-1 and angiontensin converting enzyme (ACE) genes. Arterioscler Thromb Vasc Biol. 1997; 17:2082-2087.
38. Eriksson P, Kallin B, van't Hooft FM, et al. Allele-specific increase in basal transcription of the plasminogen-activator inhibitor 1 gene is associated with myocardial infarction. Proc Natl Acad Sci USA. 1995;92: 1851-1855.
39. Burzotta F, Di Castelnuovo A, Amore C, et al. 4G/5G promoter PAI-1 gene polymorphism is associated with plasmatic PAI-1 activity in Italians: A model of gene-environment interaction. Thromb Haemost. 1998;79:354-358.
40. Aucella F, Margaglione M, Vigilante M, et al. PAI-1 4G/5G and ACE I/D gene polymorphisms and the occurrence of myocardial infarction in patients on intermittent dialysis. Nephrol Dial Transplant. 2003;18: 1142-1146.
41. Barcellona D, Fenu L, Cauli C, et al. Allele 4G of gene PAI-1 associated with prothrombin mutation G20210A increases the risk for venous thrombosis. Thromb Haemost. 2003;90:1061-1064.
42. Folsom AR, Cushman M, Heckbert SR, et al. Prospective study of fibrinolytic markers and venous thromboembolism. J Clin Epidemiol. 2003;56:598-603.
43. Segui R, Estelles A, Mira Y, et al. PAI-1 promoter 4G/5G genotype as an additional risk factor for venous thrombosis in subjects with genetic thrombophilic defects. Br J Haematol. 2000;111:122-128.
44. Sartori MT, Wiman B, Vettore S, et al. 4G/5G polymorphism of PAI-1 gene promoter and fibrinolytic capacity in patients with deep vein thrombosis. Thromb Haemost. 1998;80:956-960.
45. Stegnar M, Uhrin P, Peternel P, et al. The 4G/5G sequence polymorphism in the promoter of plasminogen activator inhibitor-1 (PAI-1) gene: Relationship to plasma PAI-1 level in venous thromboembolism. Thromb Haemost. 1998;79:975-979.
46. Akar N, Yilmaz E, Akar E, et al. Effect of plasminogen activator inhibitor-1 4G/5G polymorphism in Turkish deep vein thrombotic patients with and without FV1691 G-A. Thromb Res. 2000;97:227-230.
47. Coleman W, Tsongalis GJ, eds. Molecular Diagnostics: For the Clinical Laboratorian. Totowa, NJ: Humana Press; 1996.
48. Almawi WY, Ameen G, Tamim H, et al. Factor V G1691 A, prothrombin G20210A, and methylenetetrahydrofolate reductase [MTHFR] C677T gene polymorphism in angiographically documented coronary artery disease. J Thromb Thrombolysis. 2004;17:199-205.
49. Baris I, Koksal V, Etlik O. Multiplex PCR-RFLP assay for detection of factor V Leiden and prothrombin G20210A. Genet Test. 2004;8:381-383.
50. Linfert DR, Rezuke WN, Tsongalis GJ. Rapid multiplex analysis for the factor V Leiden and prothrombin G 20210A mutations associated with hereditary thrombophilia. Conn Med. 1998;62:519-525.
51. Blasczyk R, Ritter M, Thiede C, et al. Simple and rapid detection of factor V Leiden by allele-specific PCR amplification. Thromb Haemost. 1996;75:757-759.
52. Bladbjerg EM, Andersen-Ranberg K, de Maat MP, et al. Longevity is independent of common variations in genes associated with cardiovascular risk. Thromb Haemost. 1999;82:1100-1105.
53. Patnaik M, Dlott JS, Fontaine RN, et al. Detection of genomic polymorphisms associated with venous thrombosis using the invader biplex assay. J Mol Diagn. 2004;6:137-144.
54. Sell SM, Lugemwa PR. Development of a highly accurate, rapid PCR-RFLP genotyping assay for the methylenetetrahydrofolate reductase gene. Genet Test. 1999;3:287-289.
55. Gasparini P, Bonizzato A, Dognini M, et al. Restriction site generating-polymerase chain reaction (RG-PCR) for the probeless detection of hidden genetic variation: Application to the study of some common cystic fibrosis mutations. Mol Cell Probes. 1992;6:1-7.
56. van der Steege G, Grootscholten PM, van der Vlies P, et al. PCR-based DNA test to confirm clinical diagnosis of autosomal recessive spinal muscular atrophy. Lancet. 1995;345:985-986.
57. Warshawsky I, Hren C, Sercia L, et al. Detection of a novel point mutation of the prothrombin gene at position 20209. Diagn Mol Pathol. 2002;11:152-156.
58. von Ahsen N, Schutz E, Armstrong VW, et al. Rapid detection of prothrombotic mutations of prothrombin (G20210A), factor V (G1691A), and methylenetetrahydrofolate reductase (C677T) by real-time fluorescence PCR with the LightCycler. Clin Chem. 1999;45:694-696.
59. Nauck M, Marz W, Wieland H. Evaluation of the Roche diagnostics LightCycler-Factor V Leiden Mutation Detection Kit and the LightCycler- Prothrombin Mutation Detection Kit. Clin Biochem. 2000;33: 213-216.
60. Schrijver I, Lay MJ, Zehnder JL. Diagnostic single nucleotide polymorphism analysis of factor V Leiden and prothrombin 20210G > A. A comparison of the Nanogen Eelectronic Microarray with restriction enzyme digestion and the Roche LightCycler. Am J Clin Pathol. 2003;119:490-496.
61. Cooper PC, Cooper SM, Smith JM, et al. Evaluation of the Roche LightCycler: a simple and rapid method for direct detection of factor V Leiden and prothrombin G20210A genotypes from blood samples without the need for DNA extraction. Blood Coagul Fibrinolysis. 2003;14: 499-503.
62. Ayyildiz O, Kalkanli S, Batun S, et al. Prothrombin G20210A gene mutation with LightCycler polymerase chain reaction in venous thrombosis and healthy population in the southeast of Turkey. Heart Vessels. 2004;19:164-166.
63. Lay MJ, Wittwer CT. Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clin Chem. 1997;43:2262-2267.
64. Aslanidis C, Nauck M, Schmitz G. High-speed prothrombin G→A 20210 and methylenetetrahydrofolate reductase C→T 677 mutation detection using real-time fluorescence PCR and melting curves. Biotechniques. 1999;27:234-236, 238.
65. Bernard PS, Ajioka RS, Kushner JP, et al. Homogeneous multiplex genotyping of hemochromatosis mutations with fluorescent hybridization probes. Am J Pathol. 1998;153:1055-1061.
66. von Ahsen N, Oellerich M, Schutz E. A method for homogeneous color-compensated genotyping of factor V (G1691A) and methylenetetrahydrofolate reductase (C677T) mutations using real-time multiplex fluorescence PCR. Clin Biochem. 2000;33:535-539.
67. Erali M, Schmidt B, Lyon E, et al. Evaluation of electronic microarrays for genotyping factor V, factor II, and MTHFR. Clin Chem. 2003;49: 732-739.
68. Schroell-Metzger B, Dicato M, Bosseler M, et al. Comparison of standard PCR and the LightCycler technique to determine the thrombophilic mutations: An efficiency and cost study. Clin Chem Lab Med. 2003;41: 482-485.
69. Keslar K, Murugesan G, Kottke-Marchant K, et al. High-throughput clinical genotyping: Simultanous analysis of multiple SNPs using the LightTyper. J Mol Diagn. 2004;6:411.
70. Wylenzek M, Geisen C, Stapenhorst L, et al. A novel point mutation in the 3′ region of the prothrombin gene at position 20221 in a Lebanese/Syrian family. Thromb Haemost. 2001;85:943-944.
71. Gilles PN, Wu DJ, Foster CB, et al. Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat Biotechnol. 1999;17:365-370.
72. Radtkey R, Feng L, Muralhidar M, et al. Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip. Nucleic Acids Res. 2000;28:E17.
73. Forster AH, Krihak M, Swanson PD, et al. A laminated, flex structure for electronic transport and hybridization of DNA. Biosens Bioelectron. 2001;16:187-194.
74. Moutereau S, Narwa R, Matheron C, et al. An improved electronic microarray-based diagnostic assay for identification of MEFV mutations. Hum Mutat. 2004;23:621-628.
75. Evans JG, Lee-Tataseo C. Determination of the factor V Leiden single-nucleotide polymorphism in a commercial clinical laboratory by use of NanoChip microelectronic array technology. Clin Chem. 2002;48:1406-1411.
76. Xu B, Koenigsberger C, Pettay J, et al. Clinical validation of genetic polymorphisms associated with venous thromboembolism by the GeneOhm ePlex electrochemical array. J Mol Diagn. 2004;6:411.
77. Renshaw MA, Ellingsen D, Costner B, et al. Fluorescent multiplex polymerase chain reaction analysis of four genes associated with inpaired fibrinolysis and myocardial infarction. Blood Coagul Fibrinolysis. 2001; 12:245-251.
78. Benson JM, Ellingsen D, Renshaw MA, et al. Multiplex analysis of mutations in four genes using fluorescence scanning technology. Thromb Res. 1999;96:57-64.
79. Makridakis NM, Reichardt JK. Multiplex automated primer extension analysis: Simultaneous genotyping of several polymorphisms. Biotechniques. 2001;31:1374-1380.
80. Bjorheim J, Abrahamsen TW, Kristensen AT, et al. Approach to analysis of single nucleotide polymorphisms by automated constant denaturant capillary electrophoresis. Mutat Res. 2003;526:75-83.
81. Schmalzing D, Belenky A, Novotny MA, et al. Microchip electrophoresis: a method for high-speed SNP detection. Nucleic Acids Res. 2000; 28:E43.
82. Benson JM, Ellingsen D, El-Jamil M, et al. Factor V Leiden and factor V R2 allele: High-throughput analysis and association with venous thromboembolism. Thromb Haemost. 2001;86:1188-1192.
83. Happich D, Madiener K, Schwaab R, et al. Application of the TaqMan-PCR for genotyping of the prothrombin 020210A mutation and of the thermolabile methylenetetrahydrofolate reductase mutation. Thromb Haemost. 2000;84:144-145.
84. Inamoto N, Katsuya T, Kokubo Y, et al. Association of methylenetetrahydrofolate reductase gene polymorphism with carotid atherosclerosis depending on smoking status in a Japanese general population. Stroke. 2003;34:1628-1633.
85. Robien K, Ulrich CM, Bigler J, et al. Methylenetetrahydrofolate reductase genotype affects risk of relapse after hematopoietic cell transplantation for chronic myelogenous leukemia. Clin Cancer Res. 2004; 10:7592-7598.
86. Happich D, Schwaab R, Hanfland P, et al. Allelic discrimination of factor V Leiden using a 5′ nuclease assay. Thromb Haemost. 1999;82:1294-1296.
87. Behrens M, Lange R. A highly reproducible and economically competitive SNP analysis of several well characterized human mutations. Clin Lab. 2004;50:305-316.
88. Louis M, Dekairelle AF, Gala JL. Rapid combined genotyping of factor V, prothrombin and methylenetetrahydrofolate reductase single nucleotide polymorphisms using minor groove binding DNA oligonucleotides (MGB probes) and real-time polymerase chain reaction. Clin Chem Lab Med. 2004;42:1364-1369.
89. Chen DC, Saarela J, Nuotio I, et al. Comparison of GenFlex Tag array and Pyrosequencing in SNP genotyping. J Mol Diagn. 2003;5:243-249.
90. Ramon D, Braden M, Adams S, et al. Pyrosequencing trade mark: A one-step method for high resolution HLA typing. J Transl Med. 2003;1:9.
91. Ahmadian A, Gharizadeh B, Gustafsson AC, et al. Single-nucleotide polymorphism analysis by Pyrosequencing. Anal Biochem. 2000;280: 103-110.
92. Alderborn A, Kristofferson A, Hammerling U. Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res. 2000;10:1249-1258.
93. Zhang Z, Liu W, Jia X, et al. Use of pyrosequencing to detect clinically relevant polymorphisms of genes in basal cell carcinoma. Clin Chim Acta. 2004;342:137-143.
94. Lyamichev V, Neri B. Invader assay for SNP genotyping. Methods Mol Biol. 2003;212:229-240.
95. Kwiatkowski RW, Lyamichev V, de Arruda M, et al. Clinical, genetic, and pharmacogenetic applications of the Invader assay. Mol Diagn. 1999;4:353-364.
96. Hessner MJ, Budish MA, Friedman KD. Genotyping of factor V G1691A (Leiden) without the use of PCR by invasive cleavage of oligonucleotide probes. Clin Chem. 2000;46:1051-1056.
97. Hessner MJ, Friedman KD, Voelkerding KV, et al. Multisite study for genotyping of the factor II (prothrombin) G20210A mutation by the invader assay. Clin Chem. 2001;47:2048-2050.
98. Moser MJ, Marshall DJ, Grenier JK, et al. Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system. Clin Chem. 2003;49:407-414.
99. Ryan D, Nuccie B, Arvan D. Non-PCR-dependent detection of the factor V Leiden mutation from genomic DNA using a homogeneous invader microtiter plate assay. Mol Diagn. 1999;4:135-144.
100. Ledford M, Friedman KD, Hessner MJ, et al. A multi-site study for detection of the factor V (Leiden) mutation from genomic DNA using a homogeneous invader microtiter plate fluorescence resonance energy transfer (FRET) assay. J Mol Diagn. 2000;2:97-104.
101. Huber S, McMaster KJ, Voelkerding KV Analytical evaluation of primer engineered multiplex polymerase chain reaction-restriction fragment length polymorphism for detection of factor V Leiden and prothrombin G20210A. J Mol Diagn. 2000;2:153-157.