The Environmental Genome Project: Reference polymorphisms for drug metabolism genes and genome-wide association studies

Drug Metabolism Reviews

Volumn 40, Issue 2, 2008, Pages 241-261

  Rieder, Mark J ^a   Livingston, Robert J ^a   Stanaway, Ian B ^a   Nickerson, Deborah A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Environmental Genome Project; Genome wide association; Genotyping; Linkage disequilibrium; Phase I cytochrome P450; SNPs

Indexed keywords

CYTOCHROME P450; ISOENZYME;

CYP1A1 GENE; CYP1A2 GENE; CYP1B1 GENE; CYP2B6 GENE; CYP2E1 GENE; CYP3A4 GENE; CYP3A5 GENE; DRUG METABOLISM; ENVIRONMENTAL FACTOR; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HUMAN; HUMAN GENOME; PHENOTYPE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; BIOTRANSFORMATION; DNA MICROARRAY; DNA SEQUENCE; ENVIRONMENT; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENETIC DATABASE; GENETIC PREDISPOSITION; GENETICS; GENOMICS; METHODOLOGY; PHARMACOGENETICS; PROGRAM DEVELOPMENT;

BIOTRANSFORMATION; CYTOCHROME P-450 ENZYME SYSTEM; DATABASES, GENETIC; ENVIRONMENT; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETIC RESEARCH; GENOMICS; GENOTYPE; HUMANS; ISOENZYMES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHARMACOGENETICS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROGRAM DEVELOPMENT; SEQUENCE ANALYSIS, DNA;

EID: 44649121538     PISSN: 03602532     EISSN: 10979883     Source Type: Journal    
DOI: 10.1080/03602530801952880     Document Type: Review

References (66)

1. Barrett, J. C., Cardon, L. R. (2006). Evaluating coverage of genome-wide association studies. Nat. Genet. 6:659-662.
2. Bhangale, T. R., Stephens, M., Nickerson, D. A. (2006). Automating resequencing-based detection of insertion-deletion polymorphisms. Nat. Genet. 12:1457-1462.
3. Bosch, T. M., Meijerman, I., Beijnen, J. H., Schellens, J. H. (2006). Genetic polymorphisms of drug-metabolising enzymes and drug transporters in the chemotherapeutic treatment of cancer. Clin. Pharmacokinet. 3:253-285.
4. Carlson, C. S., Eberle, M. A., Rieder, M. J., Smith, J. D., Kruglyak, L., Nickerson, D. A. (2003). Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat. Genet. 33:518-521.
5. Carlson, C. S., Eberle, M. A., Rieder, M. J., Yi, Q., Kruglyak, L., Nickerson, D. A. (2004). Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 1:106-120.
6. Chanock, S. J., Manolio, T., Boehnke, M., Boerwinkle, E., Hunter, D. J., Thomas, G., et al. (2007). Replicating genotype-phenotype associations. Nature 7145:655-660.
7. Chowbay, B., Zhou, S., Lee, E. J. (2005). An interethnic comparison of polymorphisms of the genes encoding drug-metabolizing enzymes and drug transporters: experience in Singapore. Drug Metab. Rev. 2:327-378.
8. Clark, A. G., Hubisz, M. J., Bustamante, C. D., Williamson, S. H., Nielsen, R. (2005). Ascertainment bias in studies of human genome-wide polymorphism. Genome Res. 11:1496-1502.
9. Collins, F. S., Brooks, L. D., Chakravarti, A. (1998). A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 12:1229-1231.
10. Conrad, D. F., Jakobsson, M., Coop, G., Wen, X., Wall, J. D., Rosenberg, N. A., et al. (2006). A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat. Genet, 11:1251-1260.
11. Daly, A. K. (2006). Significance of the minor cytochrome P450 3A isoforms. Clin Pharmacokinet. 1:13-31.
12. de Bakker, P. I., Burtt, N. P., Graham, R. R., Guiducci, C., Yelensky, R., Drake, J. A., et al. (2006). Transferability of tag SNPs in genetic association studies in multiple populations. Nat. Genet. 11:1298-1303.
13. de Bakker, P. I., Yelensky, R., Pe'er, I., Gabriel, S. B., Daly, M. J., Altshuler, D. (2005). Efficiency and power in genetic association studies. Nat.. Genet. 11:1217-1223.
14. Duerr, R. H., Taylor, K. D., Brant, S. R., Rioux, J. D., Silverberg, M. S., Daly, M. J., et al. (2006). A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 5804:1461-1463.
15. Easton, D. F., Pooley, K. A., Dunning, A. M., Pharoah, P. D., Thompson, D., Ballinger, D. G., et al. (2007). Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 7148:1087-1093.
16. Eichler, E. E., Nickerson, D. A., Altshuler, D., Bowcock, A. M., Brooks, L. D., Carter, N. P., et al. (2007). Completing the map of human genetic variation. Nature 7141:161-165.
17. Ekins, S., Wrighton, S. A. (1999). The role of CYP2B6 in human xenobiotic metabolism. Drug Metab. Rev. 3:719-754.
18. Evans, W. E., Relling, M. V. (2004). Moving towards individualized medicine with pharmacogenomics. Nature 6990:464-468.
19. Fan, J. B., Chee, M. S., Gunderson, K. L. (2006). Highly parallel genomic assays. Nat. Rev. Genet. 8:632-644.
20. Field, S. F., Howson, J. M., Smyth, D. J., Walker, N. M., Dunger, D. B., Todd, J. A. (2007). Analysis of the type 2 diabetes gene, TCF7L2, in 13,795 type 1 diabetes cases and control subjects. Diabetologia 1:212-213.
21. Fodor, S. P., Read, J. L., Pirrung, M. C., Stryer, L., Lu, A. T., Solas, D. (1991). Light-directed, spatially addressable parallel chemical synthesis. Science 4995:767-773.
22. Goldstein, D. B., Tate, S. K., Sisodiya, S. M. (2003). Pharmacogenetics goes genomic. Nat. Rev. Genet. 12:937-947.
23. Gonzalez, J. R., Armengol, L., Sole, X., Guino, E., Mercader, J. M., Estivill, X., et al. (2007). SNPassoc: an R package to perform whole genome association studies. Bioinformatics 5:644-645.
24. Gudmundsson, J., Sulem, P., Manolescu, A., Amundadottir, L. T., Gudbjartsson, D., Helgason, A., et al. (2007). Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat. Genet. 5:631-637.
25. Gunderson, K. L., Kuhn, K. M., Steemers, F. J., Ng, P., Murray, S. S., Shen, R. (2006a). Whole-genome genotyping of haplotype tag single nucleotide polymorphisms. Pharmacogenomics 4:641-648.
26. Gunderson, K. L., Steemers, F. J., Ren, H., Ng, P., Zhou, L., Tsan, C., et al. (2006b). Whole-genome genotyping. Meth. Enzymol. 410:359-376.
27. Haines, J. L., Hauser, M. A., Schmidt, S., Scott, W. K., Olson, L. M., Gallins, P., et al. (2005). Complement factor H variant increases the risk of age-related macular degeneration. Science 5720:419-421.
28. Helgadottir, A., Thorleifsson, G., Manolescu, A., Gretarsdottir, S., Blondal, T., Jonasdottir, A., et al. (2007). A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 5830:1491-1493.
29. Hodgson, E., Rose, R. L. (2007). The importance of cytochrome P450 2B6 in the human metabolism of environmental chemicals. Pharmacol. Ther. 2:420-428.
30. Ingelman-Sundberg, M., Daly, A. K., Oscarson, M., Nebert, D. W. (2000). Human cytochrome P450 (CYP) genes: recommendations for the nomenclature of alleles. Pharmacogenetics 1:91-93.
31. Kruglyak, L., Nickerson, D. A. (2001). Variation is the spice of life. Nat. Genet 3:234-236.
32. Kuehl, P., Zhang, J., Lin, Y., Lamba, J., Assem, M., Schuetz, J., et al. (2001). Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression. Nat. Genet. 4:383-391.
33. Lamba, J. K., Lin, Y. S., Schuetz, E. G., Thummel, K. E. (2002). Genetic contribution to variable human CYP3A-mediated metabolism. Adv. Drug Deliv.Rev. 10:1271-1294.
34. Lang, T., Klein, K., Fischer, J., Nussler, A. K., Neuhaus, P., Hofmann, U., et al. (2001). Extensive genetic polymorphism in the human CYP2B6 gene with impact on expression and function in human liver. Pharmacogenetics 5:399-415.
35. Lewis, D. F. (2004). 57 varieties: the human cytochromes P450. Pharmacogenomics (3):305-318.
36. Lieber, C. S. (1997). Cytochrome P-4502E1: its physiological and pathological role. Physiol. Rev. 2:517-544.
37. Livingston, R. J., von Niederhausern, A., Jegga, A. G., Crawford, D. C., Carlson, C. S., Rieder, M. J., et al. (2004). Pattern of sequence variation across 213 environmental response genes. Genome Res. 10A:1821-1831.
38. Marchini, J., Howie, B., Myers, S., McVean, G., Donnelly, P. (2007). A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 7:906-913.
39. McPherson, R., Pertsemlidis, A., Kavaslar, N., Stewart, A., Roberts, R., Cox, D. R., et al. (2007). A common allele on chromosome 9 associated with coronary heart disease. Science 5830:1488-1491.
40. Murray, M. (2006). Altered CYP expression and function in response to dietary factors: potential roles in disease pathogenesis. Curr. Drug Metab. 1:67-81.
41. Nebert, D. W., Dalton, T. P. (2006). The role of cytochrome P450 enzymes in endogenous signalling pathways and environmental carcinogenesis. Nat. Rev. Cancer 12:947-960.
42. Nebert, D. W., Dalton, T. P., Okey, A. B., Gonzalez, F. J. (2004). Role of aryl hydrocarbon receptor-mediated induction of the CYP1 enzymes in environmental toxicity and cancer. J. Biol. Chem. 23:23847-23850.
43. Olden, K., Wilson, S. (2000). Environmental health and genomics: visions and implications. Nat. Rev. Genet. 2:149-153.
44. Pe'er, I., Chretien, Y. R., de Bakker, P. I., Barrett, J. C., Daly, M. J., Altshuler, D. M. (2006a). Biases and reconciliation in estimates of linkage disequilibrium in the human genome. Am. J. Hum. Genet. 4:588-603.
45. Pe'er, I., de Bakker, P. I., Maller, J., Yelensky, R., Altshuler, D., Daly, M. J. (2006b). Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat. Genet. 6:663-667.
46. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 3:559-575.
47. Rioux, J. D., Xavier, R. J., Taylor, K. D., Silverberg, M. S., Goyette, P., Huett, A., et al. (2007). Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat. Genet. 5:596-604.
48. Rodriguez-Antona, C., Ingelman-Sundberg, M. (2006). Cytochrome P450 pharmacogenetics and cancer. Oncogene 11:1679-1691.
49. Roy, J. N., Lajoie, J., Zijenah, L. S., Barama, A., Poirier, C., Ward, B. J., et al. (2005). CYP3A5 genetic polymorphisms in different ethnic populations. Drug Metab. Dispos. 7:884-887.
50. Rushmore, T. H., Kong, A. N. (2002). Pharmacogenomics, regulation and signaling pathways of phase I and II drug metabolizing enzymes. Curr. Drug Metab. 5:481-490.
51. Sadee, W., Dai, Z. (2005). Pharmacogenetics/genomics and personalized medicine. Hum. Mol. Genet. R207-214.
52. Saxena, R., Voight, B. F., Lyssenko, V., Burtt, N. P., de Bakker, P. I., Chen, H., et al. (2007). Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 5829:1331-1336.
53. Servin, B., Stephens, M. (2007). Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet. 7:e114.
54. Shriver, M. D., Mei, R., Parra, E. J., Sonpar, V., Halder, I., Tishkoff, S. A., et al. (2005). Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics 2:81-89.
55. Sladek, R., Rocheleau, G., Rung, J., Dina, C., Shen, L., Serre, D., et al. (2007). A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 7130:881-885.
56. Solus, J. F., Arietta, B. J., Harris, J. R., Sexton, D. P., Steward, J. Q., McMunn, C., et al. (2004). Genetic variation in eleven phase I drug metabolism genes in an ethnically diverse population. Pharmacogenomics 7:895-931.
57. Stephens, M., Sloan, J. S., Robertson, P. D., Scheet, P., Nickerson, D. A. (2006). Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat. Genet. 3:375-381.
58. Stranger, B. E., Nica, A. C., Forrest, M. S., Dimas, A., Bird, C. P., Beazley, C., et al. (2007). Population genomics of human gene expression. Nat Genet 39:1217-1224.
59. The International HapMap Consortium. (2003). The International HapMap Project. Nature 426:789-796.
60. The International HapMap Consortium. (2005). A haplotype map of the human genome. Nature 693:1299-1320.
61. The Wellcome Trust Consortium. (2007). Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661-678.
62. Thummel, K. E., Wilkinson, G. R. (1998). In vitro and in vivo drug interactions involving human CYP3A. Annu. Rev. Pharmacol. Toxicol. 38:389-430.
63. Todd, J. A., Walker, N. M., Cooper, J. D., Smyth, D. J., Downes, K., Plagnol, V., et al. (2007). Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat. Genet. 7:857-864.
64. Wilkinson, G. R. (2005). Drug metabolism and variability among patients in drug response. N. Engl. J. Med.. 21:2211-2221.
65. Xie, H. G., Wood, A. J., Kim, R. B., Stein, C. M., Wilkinson, G. R. (2004). Genetic variability in CYP3A5 and its possible consequences. Pharmacogenomics 3:243-272.
66. Zeggini, E., Rayner, W., Morris, A. P., Hattersley, A. T., Walker, M., Hitman, G. A., et al. (2005). An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated data sets. Nat. Genet. 12:1320-1322.