Variation in genes controlling warfarin disposition and response in American Indian and Alaska Native people: CYP2C9, VKORC1, CYP4F2, CYP4F11, GGCX

Pharmacogenetics and Genomics

Volumn 25, Issue 7, 2015, Pages 343-353

  Fohner, Alison E ^a   Robinson, Renee ^e   Yracheta, Joseph ^a   Dillard, Denise A ^e   Schilling, Brian ^e   Khan, Burhan ^e   Hopkins, Scarlett ^f   Boyer, Bert B ^f   Black, Jynene ^f   Wiener, Howard ^g   Tiwari, Hemant K ^g   Gordon, Adam ^b   Nickerson, Deborah ^b   Tsai, Jesse M ^c   Farin, Federico M ^c   Thornton, Timothy A ^d   Rettie, Allan E ^a   Thummel, Kenneth E ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b Departments of Genome Sciences   (United States)

^c Departments of Environmental and Occupational Health Sciences   (United States)

^d Cancer Research Center   (United States)

^e SOUTHCENTRAL FOUNDATION   (United States)

^f UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^g UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

Coumadin; cytochrome P450; indigenous populations; individualized therapy; personalized medicine; underserved populations

Indexed keywords

CYTOCHROME P450; CYTOCHROME P450 2C9; CYTOCHROME P450 4F11; CYTOCHROME P450 4F2; UNCLASSIFIED DRUG; VITAMIN K DEPENDENT CARBOXYLASE; VITAMIN K EPOXIDE REDUCTASE; VKORC1 PROTEIN; WARFARIN; ANTICOAGULANT AGENT; CYP2C9 PROTEIN, HUMAN; CYP4F11 PROTEIN, HUMAN; CYP4F2 PROTEIN, HUMAN; CYTOCHROME P450 FAMILY 4; GLUTAMYL CARBOXYLASE; LIGASE; VITAMIN K GROUP; VKORC1 PROTEIN, HUMAN;

ADULT; ALASKA NATIVE; AMERICAN INDIAN; ARTICLE; DRUG DISPOSITION; DRUG RESPONSE; ENZYME ACTIVITY; FEMALE; GENE FREQUENCY; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; PHARMACOGENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ALASKA; ANTAGONISTS AND INHIBITORS; GENE LINKAGE DISEQUILIBRIUM; GENETIC VARIATION; GENETICS;

ALASKA; ALASKA NATIVES; ANTICOAGULANTS; CARBON-CARBON LIGASES; CYTOCHROME P-450 CYP2C9; CYTOCHROME P450 FAMILY 4; FEMALE; GENE FREQUENCY; GENETIC VARIATION; GENOTYPE; HUMANS; INDIANS, NORTH AMERICAN; LINKAGE DISEQUILIBRIUM; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; VITAMIN K; VITAMIN K EPOXIDE REDUCTASES; WARFARIN;

EID: 84931058500     PISSN: 17446872     EISSN: 17446880     Source Type: Journal    
DOI: 10.1097/FPC.0000000000000143     Document Type: Article

References (58)

1. Shin J. Clinical pharmacogenomics of warfarin and clopidogrel. J Pharm Pract 2012; 25:428-438.
2. Bhathena A, Spear BB. Pharmacogenetics: improving drug and dose selection. Curr Opin Pharmacol 2008; 8:639-646.
3. Thummel KE, Lin YS. Sources of interindividual variability. Methods Mol Biol 2014; 1113:363-415.
4. Eichelbaum M, Ingelman-Sundberg M, Evans WE. Pharmacogenomics and individualized drug therapy. Annu Rev Med 2006; 57:119-137.
5. Smart A, Martin P. The promise of pharmacogenetics: assessing the prospects for disease and patient stratification. Stud Hist Philos Biol Biomed Sci 2006; 37:583-601.
6. Boyer BB, Dillard D, Woodahl EL, Whitener R, Thummel KE, Burke W. Ethical issues in developing pharmacogenetic research partnerships with American Indigenous communities. Clin Pharmacol Ther 2011; 89:343-345.
7. Fohner A, Muzquiz LI, Austin MA, Gaedigk A, Gordon A, Thornton T, et al. Pharmacogenetics in American Indian populations: analysis of CYP2D6, CYP3A4, CYP3A5, and CYP2C9 in the Confederated Salish and Kootenai Tribes. Pharmacogenet Genomics 2013; 23:403-414.
8. Shaw JL, Robinson R, Starks H, Burke W, Dillard DA. Risk, reward, and the double-edged sword: perspectives on pharmacogenetic research and clinical testing among Alaska Native people. Am J Public Health 2013; 103:2220-2225.
9. Horner RD, Day GM, Lanier AP, Provost EM, Hamel RD, Trimble BA. Stroke mortality among Alaska Native people. Am J Public Health 2009; 99:1996-2000.
10. Go AS, Mozaffarian D, Roger VL, Benjamin EJ, Berry JD, Blaha MJ, et al. Executive summary: heart disease and stroke statistics-2014 update: a report from the American Heart Association. Circulation 2014; 129:399-410.
11. Howard BV, Metzger JS, Killer KR, Jolly SE, Asay ED, Wang H, et al. Allcause, cardiovascular, and cancer mortality in western Alaska Native people: Westen Alaska Tribal Collaborative for Health (WATCH). Am J Public Health 2014; 104:1334-1340.
12. Stafford RS, Singer DE. Recent national patterns of warfarin use in atrial fibrillation. Circulation 1998; 97:1231-1233.
13. Birman-Deych E, Radford MJ, Nilasena DS, Gage BF. Use and effectiveness of warfarin in Medicare beneficiaries with atrial fibrillation. Stroke 2006; 37:1070-1074.
14. Shapiro SS. Treating thrombosis in the 21st century. N Engl J Med 2003; 349:1762-1764.
15. Hart RG, Pearce LA, Aguilar MI. Meta-analysis: antithrombotic therapy to prevent stroke in patients who have nonvalvular atrial fibrillation. Ann Intern Med 2007; 146:857-867.
16. Schilling B. Anticoagulation care for Alaska native customer-owners within the Nuka model of care, 7th ed. La Jolla, CA: Dawn AC Anticoagulation Management Software North American User Group Meeting; 2013.
17. Daly AK. Pharmacogenetics of the major polymorphic metabolizing enzymes. Fundam Clin Pharmacol 2003; 17:27-41.
18. Daly AK. Pharmacogenetics of the cytochromes P450. Curr Top Med Chem 2004; 4:1733-1744.
19. Ingelman-Sundberg M, Sim SC, Gomez A, Rodriguez-Antona C. Influence of cytochrome P450 polymorphisms on drug therapies: pharmacogenetic, pharmacoepigenetic and clinical aspects. Pharmacol Ther 2007; 116:496-526.
20. Zanger UM, Turpeinen M, Klein K, Schwab M. Functional pharmacogenetics/genomics of human cytochromes P450 involved in drug biotransformation. Anal Bioanal Chem 2008; 392:1093-1108.
21. McDonagh EM, Whirl-Carrillo M, Garten Y, Altman RB, Klein TE. From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med 2011; 5:795-806.
22. Alaska Department of Labor and Workforce Development RaAS. Alaska population overview: 2012 estimates; 2013. p. 128.
23. Bourgain C, Zhang Q. Kinship and inbreeding coefficients computation in general pedigrees, 1.1 ed. Boston, MA: Free Software Foundation Inc.; 2009.
24. Manachaikul A, Mychaleckyi JC, Rich SS, Daly K, Sale M, Chen W-M. Robust relationship inference in genome-wise association studies. Bioinformatics 2010; 26:2867-2873.
25. Rieder MJ, Taylor SL, Clark AG, Nickerson DA. Sequence variation in the human angiotensin converting enzyme. Nat Genet 1999; 22:59-62.
26. Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8:195-202.
27. Nickerson DA, Tobe VO, Taylor SL. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res 1997; 25:2745-2751.
28. Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet 2006; 38:375-381.
29. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186-194.
30. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods 2010; 7:248-249.
31. Grantham R. Amino acid difference formula to help explain protein evolution. Science 1974; 185:862-864.
32. McPeek MS, Wu X, Ober C. Best linear unbiased allele-frequency estimation in complex pedigrees. Biometrics 2004; 60:359-367.
33. Krauss ME. Alaska native languages: past, present, and future. Fairbanks, AK: Alaska Native Language Center; 1980.
34. Krauss ME. Alaska ANLCUo, Research AIoSE. Indigenous peoples and languages of Alaska. Fairbanks: Alaska Native Language Center, University of Alaska Fairbanks; 2011.
35. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. 1000 Genomes Project Consortium. An integrated map of genetic variation from 1092 human genomes. Nature 2012; 491:56-65.
36. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005; 21:263-265.
37. Maekawa K, Fukushima-Uesaka H, Tohkin M, Hasegawa R, Kajio H, Kuzuya N, et al. Four novel defective alleles and comprehensive haplotype analysis of CYP2C9 in Japanese. Pharmacogenet Genomics 2006; 16:497-514.
38. Shu Y, Leabman MK, Feng B, Mangravite LM, Huang CC, Stryke D, et al. Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1. Proc Natl Acad Sci USA 2003; 100:5902-5907.
39. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001; 29:308-311.
40. Limdi NA, Wiener H, Goldstein JA, Acton RT, Beasley TM. Influence of CYP2C9 and VKORC1 on warfarin response during initiation of therapy. Blood Cells Mol Dis 2009; 43:119-128.
41. Limdi NA, Wadelius M, Cavallari L, Eriksson N, Crawford DC, Lee MT, et al. Warfarin pharmacogenetics: a single VKORC1 polymorphism is predictive of dose across 3 racial groups. Blood 2010; 115:3827-3834.
42. 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 2008; 82:495-500.
43. Alsmadi O, John SE, Thareja G, Hebbar P, Antony D, Behbehani K, Thanaraj TA. Genome at juncture of early human migration: a systematic analysis of two whole genomes and thirteen exomes from Kuwaiti population subgroup of inferred Saudi Arabian tribe ancestry. PLoS One 2014; 9:e99069.
44. Wadelius M, Chen LY, Downes K, Ghori J, Hunt S, Eriksson N, et al. Common VKORC1 and GGCX polymorphisms associated with warfarin dose. Pharmacogenomics J 2005; 5:262-270.
45. King CR, Deych E, Milligan P, Eby C, Lenzini P, Grice G, et al. Gammaglutamyl carboxylase and its influence on warfarin dose. Thromb Haemost 2010; 104:750-754.
46. Kimura R, Miyashita K, Kokubo Y, Akaiwa Y, Otsubo R, Nagatsuka K, et al. Genotypes of vitamin K epoxide reductase, gamma-glutamyl carboxylase, and cytochrome P450 2C9 as determinants of daily warfarin dose in Japanese patients. Thromb Res 2007; 120:181-186.
47. Vijayasarathy C, Sui R, Zeng Y, Yang G, Xu F, Caruso RC, et al. Molecular mechanisms leading to null-protein product from retinoschisin (RS1) signalsequence mutants in X-linked retinoschisis (XLRS) disease. Hum Mutat 2010; 31:1251-1260.
48. Gannage-Yared MH, Makrythanasis P, Chouery E, Sobacchi C, Mehawej C, Santoni FA, et al. Exome sequencing reveals a mutation in DMP1 in a family with familial sclerosing bone dysplasia. Bone 2014; 68:142-145.
49. Farrow EG, Davis SI, Ward LM, Summers LJ, Bubbear JS, Keen R, et al. Molecular analysis of DMP1 mutants causing autosomal recessive hypophosphatemic rickets. Bone 2009; 44:287-294.
50. Caridi G, Dagnino M, Lugani F, Shalev SA, Campagnoli M, Galliano M, et al. A novel mutation in the albumin gene (c.1Agt;C) resulting in analbuminemia. Eur J Clin Invest 2013; 43:72-78.
51. Dai DP, Xu RA, Hu LM, Wang SH, Geng PW, Yang JF, et al. CYP2C9 polymorphism analysis in Han Chinese populations: building the largest allele frequency database. Pharmacogenomics J 2014; 14:85-92.
52. Wester MR, Yano JK, Schoch GA, Yang C, Griffin KJ, Stout CD, Johnson EF. The structure of human cytochrome P450 2C9 complexed with flurbiprofen at 2.0-A resolution. J Biol Chem 2004; 279:35630-35637.
53. Niinuma Y, Saito T, Takahashi M, Tsukada C, Ito M, Hirasawa N, Hiratsuka M. Functional characterization of 32 CYP2C9 allelic variants. Pharmacogenomics J 2014; 14:107-114.
54. Roth JA, Boudreau D, Fujii MM, Farin FM, Rettie AE, Thummel KE, Veenstra DL. Genetic risk factors for major bleeding in patients treated with warfarin in a community setting. Clin Pharmacol Ther 2014; 95:636-643.
55. Consortium IWP. Estimation of the warfarin dose with clinical and pharmacogenetic data. N Engl J Med 2009; 360:753-764.
56. Rieder MJ, Reiner AP, Gage BF, Nickerson DA, Eby CS, McLeod HL, et al. Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. N Engl J Med 2005; 352:2285-2293.
57. Nahar R, Saxena R, Deb R, Parakh R, Shad S, Sethi PK, et al. CYP2C9, VKORC1, CYP4F2, ABCB1 and F5 variants: influence on quality of longterm anticoagulation. Pharmacol Rep 2014; 66:243-249.
58. Edson KZ, Prasad B, Unadkat JD, Suhara Y, Okano T, Guengerich FP, et al. Cytochrome P450-dependent catabolism of vitamin K: omega-hydroxylation catalyzed by human CYP4F2 and CYP4F11. Biochemistry 2013; 52:8276-8285.