Ethnic variability in the allelic distribution of pharmacogenes between Korean and other populations

Pharmacogenetics and Genomics

Volumn 22, Issue 12, 2012, Pages 829-836

  Kim, In Wha ^a   Kim, Kyung Im ^a   Chang, Hyeu Jin ^a   Yeon, Bora ^b   Bang, Seo Jin ^a   Park, Taesung ^a,b   Kwon, Ji Sun ^c   Kim, Sangsoo ^c   Oh, Jung Mi ^a  

^a Seoul National University   (South Korea)

^b Interdisciplinary Program in Bioinformatics   (South Korea)

^c Soongsil University   (South Korea)

Author keywords

ethnic difference; genetic variation; genome wide association study; pharmacogenomics; single nucleotide polymorphism

Indexed keywords

ADULT; AGED; ARTICLE; ASIAN; CAUCASIAN; CHINESE; CONTROLLED STUDY; ETHNIC DIFFERENCE; ETHNIC GROUP; GENE FREQUENCY; GENETIC DATABASE; HAPLOTYPE MAP; HUMAN; JAPANESE; KOREAN; NIGERIAN; NORMAL HUMAN; PHARMACOGENETICS; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84870352723     PISSN: 17446872     EISSN: 17446880     Source Type: Journal    
DOI: 10.1097/FPC.0b013e328358dd70     Document Type: Article

References (48)

1. Jung J, Kang H, Cho YS, Oh JH, Ryu MH, Chung HW, et al. Gene flow between the Korean peninsula and its neighboring countries. PLoS One 2010; 5:e11855.
2. Daly AK. Genome-wide association studies in pharmacogenomics. Nat Rev Genet 2010; 11:241-246.
3. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001; 29:308-311. (Pubitemid 32054478)
4. Chen J, Teo YY, Toh DS, Sung C. Interethnic comparisons of important pharmacology genes using SNP databases: potential application to drug regulatory assessments. Pharmacogenomics 2010; 11:1077-1094.
5. Suarez-Kurtz G, Pena S, Hutz MH. Application of the F(ST) statistics to explore pharmacogenomic diversity in the Brazilian population. Pharmacogenomics 2012; 13:771-777.
6. Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 2008; 40:955-962.
7. Frayling TM. Genome-wide association studies provide new insights into type 2 diabetes aetiology. Nat Rev Genet 2007; 8:657-662. (Pubitemid 47281993)
8. Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, Lindgren CM, et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 2007; 316:889-894. (Pubitemid 46764279)
9. Hughes AE, Orr N, Esfandiary H, Diaz-Torres M, Goodship T, Chakravarthy U. A common CFH haplotype, with deletion of CFHR1 and CFHR3, is associated with lower risk of age-related macular degeneration. Nat Genet 2006; 38:1173-1177. (Pubitemid 44470363)
10. Eriksson N, Macpherson JM, Tung JY, Hon LS, Naughton B, Saxonov S, et al. Web-based, participant-driven studies yield novel genetic associations for common traits. PLoS Genet 2010; 6:e1000993.
11. Sanna S, Jackson AU, Nagaraja R, Willer CJ, Chen WM, Bonnycastle LL, et al. Common variants in the GDF5-UQCC region are associated with variation in human height. Nat Genet 2008; 40:198-203. (Pubitemid 351171401)
12. Wu R, Tong C, Wang Z, Mauger D, Tantisira K, Szefler SJ, et al. A conceptual framework for pharmacodynamic genome-wide association studies in pharmacogenomics. Drug Discov Today 2011; 16:884-890.
13. Tanaka Y, Nishida N, Sugiyama M, Kurosaki M, Matsuura K, Sakamoto N, et al. Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet 2009; 41:1105-1109.
14. Shuldiner AR, O'Connell JR, Bliden KP, Gandhi A, Ryan K, Horenstein RB, et al. Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy. JAMA 2009; 302:849-857.
15. Takeuchi F, McGinnis R, Bourgeois S, Barnes C, Eriksson N, Soranzo N, et al. A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose. PLoS Genet 2009; 5:e1000433.
16. Link E, Parish S, Armitage J, Bowman L, Heath S, Matsuda F, et al. SLCO1B1 variants and statin-induced myopathy-a genomewide study. N Engl J Med 2008; 359:789-799.
17. International HapMap Consortium. A haplotype map of the human genome. Nature 2005; 437:1299-1320.
18. Cho YS, Go MJ, Kim YJ, Heo JY, Oh JH, Ban HJ, et al. A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits. Nat Genet 2009; 41:527-534.
19. Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 2007; 39:906-913. (Pubitemid 47014502)
20. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. (Pubitemid 30257031)
21. Nam D, Kim J, Kim SY, Kim S. GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res 2010; 38:W749-W754.
22. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010; 38:D355-D360.
23. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012; 40:D109-D114.
24. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005; 102:15545-15550. (Pubitemid 41528093)
25. 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.
26. Han K, Kim K-z, Park T. Unbalanced sample size effect on the genome-wide population differentiation studies Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference; 18 December 2010; Hong Kong; pp. 347-352.
27. Wright S. Variability within and among natural populations. Chicago, IL: University of Chicago Press; 1978.
28. R Development Core Team. R: a language and environment for statistical computing, reference index version 2.14.1. ISBN 3-900051-07-0. Vienna, Austria: R Foundation for Statistical Computing. Available at: http://www.R-project.org; 2005.
29. Yasuda SU, Zhang L, Huang SM. The role of ethnicity in variability in response to drugs: focus on clinical pharmacology studies. Clin Pharmacol Ther 2008; 84:417-423.
30. Scott SA, Sangkuhl K, Gardner EE, Stein CM, Hulot JS, Johnson JA, et al. Clinical Pharmacogenetics Implementation Consortium guidelines for cytochrome P450-2C19 (CYP2C19) genotype and clopidogrel therapy. Clin Pharmacol Ther 2011; 90:328-332.
31. Johnson JA, Gong L, Whirl-Carrillo M, Gage BF, Scott SA, Stein CM, et al. Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and VKORC1 genotypes and warfarin dosing. Clin Pharmacol Ther 2011; 90:625-629.
32. Swen JJ, Nijenhuis M, de Boer A, Grandia L, Maitland-van der Zee AH, Mulder H, et al. Pharmacogenetics: from bench to byte-an update of guidelines. Clin Pharmacol Ther 2011; 89:662-673.
33. Relling MV, Gardner EE, Sandborn WJ, Schmiegelow K, Pui CH, Yee SW, et al. Clinical Pharmacogenetics Implementation Consortium guidelines for thiopurine methyltransferase genotype and thiopurine dosing. Clin Pharmacol Ther 2011; 89:387-391.
34. Lim J, Kim YJ, Yoon Y, Kim SO, Kang H, Park J, et al. Comparative study of the linkage disequilibrium of an ENCODE region, chromosome 7p15, in Korean, Japanese, and Han Chinese samples. Genomics 2006; 87:392-398. (Pubitemid 43214511)
35. He M, Gitschier J, Zerjal T, de Knijff P, Tyler-Smith C, Xue Y. Geographical affinities of the HapMap samples. PLoS One 2009; 4:e4684.
36. Teixeira D, Vargens D, Principe A, Oliveira E, Amorim A, Prrata MJ, et al. High prevalence of the GSTM3A/B polymorphism in sub-Sarahan African populations. Braz J Med Biol Res 2010; 43:677-680.
37. Cho HJ, Sohn KH, Park HM, Lee KH, Choi B, Kim S, et al. Factors affecting the interindividual variability of warfarin dose requirement in adult Korean patients. Pharmacogenomics 2007; 8:329-337. (Pubitemid 46585496)
38. D'Andrea G, D'Ambrosio RL, Di Perna P, Chetta M, Santacroce R, Brancaccio V, et al. A polymorphism in the VKORC1 gene is associated with an interindividual variability in the dose-anticoagulant effect of warfarin. Blood 2005; 105:645-649. (Pubitemid 40070748)
39. Rodrigo E, Ruiz JC, Angeles de Cos M, Ruiz J, Gago M, Pinera C, et al. Correlation of C0 and C2 levels with cyclosporine side effects in kidney transplantation. Transplant Proc 2009; 41:2328-2331.
40. Hesselink DA, van Schaik RH, van der Heiden IP, van der Werf M, Gregoor PJ, Lindemans J, et al. Genetic polymorphisms of the CYP3A4, CYP3A5, and MDR-1 genes and pharmacokinetics of the calcineurin inhibitors cyclosporine and tacrolimus. Clin Pharmacol Ther 2003; 74:245-254. (Pubitemid 37083100)
41. Brennan P, Lewis S, Hashibe M, Bell DA, Boffetta P, Bouchardy C, et al. Pooled analysis of alcohol dehydrogenase genotypes and head and neck cancer: a HuGE review. Am J Epidemiol 2004; 159:1-16. (Pubitemid 38049416)
42. Grant BF, Stinson FS, Dawson DA, Chou SP, Dufour MC, Compton W, et al. Prevalence and co-occurrence of substance use disorders and independent mood and anxiety disorders: results from the National Epidemiologic Survey on Alcohol and Related Conditions. Arch Gen Psychiatry 2004; 61:807-816. (Pubitemid 39031120)
43. Phan VH, Moore MM, McLachlan AJ, Piquette-Miller M, Xu H, Clarke SJ. Ethnic differences in drug metabolism and toxicity from chemotherapy. Expert Opin Drug Metab Toxicol 2009; 5:243-257.
44. Mialet Perez J, Rathz DA, Petrashevskaya NN, Hahn HS, Wagoner LE, Schwartz A, et al. Beta 1-adrenergic receptor polymorphisms confer differential function and predisposition to heart failure. Nat Med 2003; 9:1300-1305. (Pubitemid 37279854)
45. Sandilands AJ, O'Shaughnessy KM. The functional significance of genetic variation within the beta-adrenoceptor. Br J Clin Pharmacol 2005; 60:235-243. (Pubitemid 41224130)
46. Sekine I, Yamamoto N, Nishio K, Saijo N. Emerging ethnic differences in lung cancer therapy. Br J Cancer 2008; 99:1757-1762.
47. O'Donnell PH, Dolan ME. Cancer pharmacoethnicity: ethnic differences in susceptibility to the effects of chemotherapy. Clin Cancer Res 2009; 15:4806-4814.
48. The International Conference on Harmonisation of Technical Requirements for Pharmaceuticals for Human Use. ICH E5(R1): ethnic factors in the acceptability of foreign clinical data. Available at: www.ich.org/[Accessed 11 March 1998].