Copy number variation and warfarin dosing: Evaluation of CYP2C9, VKORC1, CYP4F2, GGCX and CALU

Pharmacogenomics

Volumn 13, Issue 3, 2012, Pages 297-307

  Scott, Stuart A ^a   Patel, Manishkumar ^a   Martis, Suparna ^a   Lubitz, Steven A ^b   Van Der Zee, Sarina ^a   Yoo, Chang ^c   Edelmann, Lisa ^a   Halperin, Jonathan L ^a   Desnick, Robert J ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c ELMHURST HOSPITAL CENTER   (United States)

Author keywords

CALU; CNV; copy number variation; CYP2C9; CYP4F2; GGCX; pharmacogenetics; VKORC1; warfarin

Indexed keywords

DNA; WARFARIN;

ADULT; AFRICAN AMERICAN; AGED; ARTICLE; ASIAN; CALU GENE; CAUCASIAN; COHORT ANALYSIS; CONTROLLED STUDY; COPY NUMBER VARIATION; CYP2C9 GENE; CYP4F2 GENE; DEEP VEIN THROMBOSIS; DNA DETERMINATION; ETHNIC DIFFERENCE; EXON; FEMALE; GENE; GENE DELETION; GENE DUPLICATION; GENE INSERTION; GENETIC POLYMORPHISM; GGCX GENE; HEART ATRIUM FIBRILLATION; HISPANIC; HUMAN; INTERNATIONAL NORMALIZED RATIO; LUNG EMBOLISM; MAJOR CLINICAL STUDY; MALE; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; PATIENT COMPLIANCE; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; VKORC1 GENE;

AGED; ANTICOAGULANTS; ARYL HYDROCARBON HYDROXYLASES; CALCIUM-BINDING PROTEINS; CARBON-CARBON LIGASES; COHORT STUDIES; CYTOCHROME P-450 ENZYME SYSTEM; DNA COPY NUMBER VARIATIONS; DOSE-RESPONSE RELATIONSHIP, DRUG; ETHNIC GROUPS; EXONS; FEMALE; GENE DELETION; GENE DUPLICATION; HUMANS; INDEL MUTATION; MALE; MIXED FUNCTION OXYGENASES; WARFARIN;

EID: 84856740545     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/pgs.11.156     Document Type: Article

References (66)

1. Hirsh J. Oral anticoagulant drugs. N. Engl. J. Med. 324(26), 1865-1875 (1991).
2. Cavallari LH, Limdi NA. Warfarin pharmacogenomics. Curr. Opin. Mol. Ther. 11(3), 243-251 (2009).
3. Kurnik D, Loebstein R, Halkin H, Gak E, Almog S. 10 years of oral anticoagulant pharmacogenomics: what difference will it make? A critical appraisal. Pharmacogenomics 10(12), 1955-1965 (2009).
4. Wadelius M, Pirmohamed M. Pharmacogenetics of warfarin: current status and future challenges. Pharmacogenomics J. 7(2), 99-111 (2007). (Pubitemid 46567142)
5. Limdi NA, Veenstra DL. Warfarin pharmacogenetics. Pharmacotherapy 28(9), 1084-1097 (2008).
6. Schelleman H, Limdi NA, Kimmel SE. Ethnic differences in warfarin maintenance dose requirement and its relationship with genetics. Pharmacogenomics 9(9), 1331-1346 (2008).
7. Sconce EA, Khan TI, Wynne HA et al. The impact of CYP2C9 and VKORC1 genetic polymorphism and patient characteristics upon warfarin dose requirements: proposal for a new dosing regimen. Blood 106(7), 2329-2333 (2005). (Pubitemid 41510803)
8. Gage BF, Eby C, Johnson JA et al. Use of pharmacogenetic and clinical factors to predict the therapeutic dose of warfarin. Clin. Pharmacol. Ther. 84(3), 326-331 (2008).
9. Perini JA, Struchiner CJ, Silva-Assuncao E et al. Pharmacogenetics of warfarin: development of a dosing algorithm for Brazilian patients. Clin. Pharmacol. Ther. 84(6), 722-728 (2008).
10. Wu AH, Wang P, Smith A et al. Dosing algorithm for warfarin using CYP2C9 and VKORC1 genotyping from a multi-ethnic population: comparison with other equations. Pharmacogenomics 9(2), 169-178 (2008). (Pubitemid 351566941)
11. Klein TE, Altman RB, Eriksson N et al. Estimation of the warfarin dose with clinical and pharmacogenetic data. N. Engl. J. Med. 360(8), 753-764 (2009).
12. Lenzini P, Wadelius M, Kimmel S et al. Integration of genetic, clinical, and INR data to refine warfarin dosing. Clin. Pharmacol. Ther. 87(5), 572-578 (2010).
13. Lubitz SA, Scott SA, Rothlauf EB et al. Comparative performance of gene-based warfarin dosing algorithms in a multiethnic population. J. Thromb. Haemost. 8(5), 1018-1026 (2010).
14. Roper N, Storer B, Bona R, Fang M. Validation and comparison of pharmacogenetics-based warfarin dosing algorithms for application of pharmacogenetic testing. J. Mol. Diagn. 12(3), 283-291 (2010).
15. Shin J, Cao D. Comparison of warfarin pharmacogenetic dosing algorithms in a racially diverse large cohort. Pharmacogenomics 12(1), 125-134 (2010).
16. Finkelman BS, Gage BF, Johnson JA, Brensinger CM, Kimmel SE. Genetic warfarin dosing: tables versus algorithms. J. Am. Coll. Cardiol. 57(5), 612-618 (2011).
17. Hirsh J, Dalen J, Anderson DR et al. Oral anticoagulants: mechanism of action, clinical effectiveness, and optimal therapeutic range. Chest 119(Suppl. 1), 8S-21S (2001). (Pubitemid 32154192)
18. Caldwell MD, Awad T, Johnson JA et al. CYP4F2 genetic variant alters required warfarin dose. Blood 111(8), 4106-4112 (2008).
19. Cooper GM, Johnson JA, Langaee TY et al. A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose. Blood 112(4), 1022-1027 (2008).
20. Takeuchi F, Mcginnis R, Bourgeois S et al. A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose. PLoS Genet. 5(3), e1000433 (2009).
21. Cha PC, Mushiroda T, Takahashi A et al. Genome-wide association study identifies genetic determinants of warfarin responsiveness for Japanese. Hum. Mol. Genet. 19(23), 4735-4744 (2010).
22. Scott SA, Jaremko M, Lubitz SA, Kornreich R, Halperin JL, Desnick RJ. CYP2C9*8 is prevalent among African-Americans: implications for pharmacogenetic dosing. Pharmacogenomics 10(8), 1243-1255 (2009).
23. Cavallari LH, Langaee TY, Momary KM et al. Genetic and clinical predictors of warfarin dose requirements in African Americans. Clin. Pharmacol. Ther. 87(4), 459-464 (2010).
24. Sagreiya H, Berube C, Wen A et al. Extending and evaluating a warfarin dosing algorithm that includes CYP4F2 and pooled rare variants of CYP2C9. Pharmacogenet. Genomics 20(7), 407-413 (2010).
25. Perera MA, Gamazon E, Cavallari LH et al. The missing association: sequencing-based discovery of NOVEL SNPs in VKORC1 and CYP2C9 that affect warfarin dose in African-Americans. Clin. Pharmacol. Ther. 89(3), 408-415 (2011).
26. Wadelius M, Chen LY, Downes K et al. Common VKORC1 and GGCX polymorphisms associated with warfarin dose. Pharmacogenomics J. 5(4), 262-270 (2005). (Pubitemid 41131718)
27. Rieder MJ, Reiner AP, Rettie AE. Gamma-glutamyl carboxylase (GGCX) tagSNPs have limited utility for predicting warfarin maintenance dose. J. Thromb. Haemost. 5(11), 2227-2234 (2007). (Pubitemid 47617875)
28. King CR, Deych E, Milligan P et al. Gamma-glutamyl carboxylase and its influence on warfarin dose. Thromb. Haemost. 104(4), 750-754 (2010).
29. Voora D, Koboldt DC, King CR et al. A polymorphism in the VKORC1 regulator calumenin predicts higher warfarin dose requirements in African-Americans. Clin. Pharmacol. Ther. 87(4), 445-451 (2010).
30. Shahin MH, Khalifa SI, Gong Y et al. Genetic and nongenetic factors associated with warfarin dose requirements in Egyptian patients. Pharmacogenet. Genomics 21(3), 130-135 (2011).
31. Iafrate AJ, Feuk L, Rivera MN et al. Detection of large-scale variation in the human genome. Nat. Genet 36(9), 949-951 (2004). (Pubitemid 39167488)
32. Sharp AJ, Locke DP, McGrath SD et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77(1), 78-88 (2005). (Pubitemid 40848038)
33. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet 38(1), 75-81 (2006). (Pubitemid 43011885)
34. Redon R, Ishikawa S, Fitch KR et al. Global variation in copy number in the human genome. Nature 444(7118), 444-454 (2006). (Pubitemid 44809057)
35. Weiss LA. Autism genetics: emerging data from genome-wide copy-number and single nucleotide polymorphism scans. Expert Rev. Mol. Diagn. 9(8), 795-803 (2009).
36. Chen X, Li X, Wang P et al. Novel association strategy with copy number variation for identifying new risk loci of human diseases. PLoS ONE 5(8), e12185 (2010).
37. Conrad DF, Pinto D, Redon R et al. Origins and functional impact of copy number variation in the human genome. Nature 464(7289), 704-712 (2010).
38. Lee C, Scherer SW. The clinical context of copy number variation in the human genome. Expert Rev. Mol. Med. 12, e8 (2010).
39. Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437-455 (2010).
40. Sudmant PH, Kitzman JO, Antonacci F et al. Diversity of human copy number variation and multicopy genes. Science 330(6004), 641-646 (2010).
41. Mills RE, Walter K, Stewart C et al. Mapping copy number variation by population-scale genome sequencing. Nature 470(7332), 59-65 (2011).
42. Gaedigk A, Blum M, Gaedigk R, Eichelbaum M, Meyer UA. Deletion of the entire cytochrome P450 CYP2D6 gene as a cause of impaired drug metabolism in poor metabolizers of the debrisoquine/sparteine polymorphism. Am. J. Hum. Genet. 48(5), 943-950 (1991). (Pubitemid 21891638)
43. Meijerman I, Sanderson LM, Smits PH, Beijnen JH, Schellens JH. Pharmacogenetic screening of the gene deletion and duplications of CYP2D6. Drug Metab. Rev. 39(1), 45-60 (2007).
44. Rose-Zerilli MJ, Barton SJ, Henderson AJ, Shaheen SO, Holloway JW. Copy-number variation genotyping of GSTT1 and GSTM1 gene deletions by real-time PCR. Clin. Chem. 55(9), 1680-1685 (2009).
45. Huang RS, Chen P, Wisel S et al. Population-specific GSTM1 copy number variation. Hum. Mol. Genet. 18(2), 366-372 (2009).
46. Hebbring SJ, Adjei AA, Baer JL et al. Human SULT1A1 gene: copy number differences and functional implications. Hum. Mol. Genet. 16(5), 463-470 (2007). (Pubitemid 46522610)
47. Hebbring SJ, Moyer AM, Weinshilboum RM. Sulfotransferase gene copy number variation: pharmacogenetics and function. Cytogenet. Genome Res. 123(1-4), 205-210 (2008).
48. Yang TL, Chen XD, Guo Y et al. Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. Am. J. Hum. Genet. 83(6), 663-674 (2008).
49. Scott SA, Khasawneh R, Peter I, Kornreich R, Desnick RJ. Combined CYP2C9, VKORC1 and CYP4F2 frequencies among racial and ethnic groups. Pharmacogenomics 11(6), 781-791 (2010).
50. Scott SA, Edelmann L, Kornreich R, Desnick RJ. Warfarin pharmacogenetics: CYP2C9 and VKORC1 genotypes predict different sensitivity and resistance frequencies in the Ashkenazi and Sephardi Jewish populations. Am. J. Hum. Genet. 82(2), 495-500 (2008).
51. Scott SA, Edelmann L, Liu L, Luo M, Desnick RJ, Kornreich R. Experience with carrier screening and prenatal diagnosis for 16 Ashkenazi Jewish genetic diseases. Hum. Mutat. 31(11), 1240-1250 (2010).
52. Limdi NA, Wadelius M, Cavallari L et al. Warfarin pharmacogenetics: a single VKORC1 polymorphism is predictive of dose across 3 racial groups. Blood 115(18), 3827-3834 (2010).
53. Aithal GP, Day CP, Kesteven PJ, Daly AK. Association of polymorphisms in the cytochrome P450 CYP2C9 with warfarin dose requirement and risk of bleeding complications. Lancet 353(9154), 717-719 (1999). (Pubitemid 29103806)
54. Higashi MK, Veenstra DL, Kondo LM et al. Association between CYP2C9 genetic variants and anticoagulation-related outcomes during warfarin therapy. JAMA 287(13), 1690-1698 (2002). (Pubitemid 34289221)
55. Rieder MJ, Reiner AP, Gage BF et al. Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N. Engl. J. Med. 352(22), 2285-2293 (2005). (Pubitemid 40740552)
56. Mills RE, Luttig CT, Larkins CE et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16(9), 1182-1190 (2006). (Pubitemid 44320405)
57. Mills RE, Pittard WS, Mullaney JM et al. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res. 21(6), 830-839 (2011).
58. Cha PC, Mushiroda T, Takahashi A et al. High-resolution SNP and haplotype maps of the human gamma-glutamyl carboxylase gene (GGCX) and association study between polymorphisms in GGCX and the warfarin maintenance dose requirement of the Japanese population. J. Hum. Genet. 52(10), 856-864 (2007). (Pubitemid 47512854)
59. Kidd JM, Cooper GM, Donahue WF et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453(7191), 56-64 (2008). (Pubitemid 351630326)
60. Pautas E, Moreau C, Gouin-Thibault I et al. Genetic factors (VKORC1, CYP2C9, EPHX1, and CYP4F2) are predictor variables for warfarin response in very elderly, frail inpatients. Clin. Pharmacol. Ther. 87(1), 57-64 (2010).
61. Ciccacci C, Paolillo N, di Fusco D, Novelli G, Borgiani P. EPHX1 polymorphisms are not associated with warfarin response in an Italian population. Clin. Pharmacol. Ther. 89(6), 791; author reply 792 (2011).
62. Ouahchi K, Lindeman N, Lee C. Copy number variants and pharmacogenomics. Pharmacogenomics 7(1), 25-29 (2006).
63. Johansson I, Ingelman-Sundberg M. CNVs of human genes and their implication in pharmacogenetics. Cytogenet. Genome Res. 123(1-4), 195-204 (2008).
64. Dhawan D, Padh H. Pharmacogenetics: technologies to detect copy number variations. Curr. Opin. Mol. Ther. 11(6), 670-680 (2009).
65. He Y, Hoskins JM, Mcleod HL. Copy number variants in pharmacogenetic genes. Trends Mol. Med. 17(5), 244-251 (2011).
66. Zhu Q, Ge D, Maia JM et al. A genome-wide comparison of the functional properties of rare and common genetic variants in humans. Am. J. Hum. Genet. 88(4), 458-468 (2011).