Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for Pharmacogenomics

BMC Genetics

Volumn 15, Issue , 2014, Pages

  Li, Jing ^a   Lao, Xingzhen ^b   Zhang, Chao ^a   Tian, Lei ^a   Lu, Dongsheng ^a   Xu, Shuhua ^a  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b CHINA PHARMACEUTICAL UNIVERSITY   (China)

Author keywords

ADME genes; African Americans; Drug response heterogeneity; Genetic admixture; Genetic diversity

Indexed keywords

BREAST CANCER RESISTANCE PROTEIN; CYTOCHROME P450 1A1; CYTOCHROME P450 1A2; CYTOCHROME P450 2C19; CYTOCHROME P450 2C8; CYTOCHROME P450 2C9; CYTOCHROME P450 2D6; CYTOCHROME P450 2E1; CYTOCHROME P450 3A4; CYTOCHROME P450 3A5; GLUCURONOSYLTRANSFERASE 1A1; GLUCURONOSYLTRANSFERASE 2B7; GLUTATHIONE TRANSFERASE P1; GLUTATHIONE TRANSFERASE T1; MULTIDRUG RESISTANCE PROTEIN 1; ORGANIC ANION TRANSPORTER 1;

AFRICAN AMERICAN; ANCESTRY GROUP; ARTICLE; DIFFERENTIATION; DRUG ABSORPTION; DRUG DISTRIBUTION; DRUG EXCRETION; DRUG METABOLISM; DRUG RESPONSE; ETHNIC DIFFERENCE; GENE EXPRESSION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MUTATION; GENETIC ASSOCIATION; GENETIC DIFFERENCE; GENETIC DRIFT; GENETIC VARIABILITY; HAPLOTYPE; HETEROZYGOSITY; HUMAN; MISSENSE MUTATION; NATURAL SELECTION; PHARMACOGENOMICS; POPULATION; PROTEIN STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICAN AMERICANS; AFRICAN CONTINENTAL ANCESTRY GROUP; ALLELES; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; HAPLOTYPES; HUMANS; PHARMACOGENETICS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84900010583     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-15-52     Document Type: Article

References (48)

1. Shastry BS. Pharmacogenetics and the concept of individualized medicine. Pharmacogenomics J 2006, 6(1):16-21. 10.1038/sj.tpj.6500338, 16302022.
2. Haga SB, LaPointe NM. The potential impact of pharmacogenetic testing on medication adherence. Pharmacogenomics J 2013, 13(6):481-483. 10.1038/tpj.2013.33, 23999596.
3. Sim SC, Kacevska M, Ingelman-Sundberg M. Pharmacogenomics of drug-metabolizing enzymes: a recent update on clinical implications and endogenous effects. Pharmacogenomics J 2013, 13(1):1-11. 10.1038/tpj.2012.45, 23089672.
4. Guessous I, Gwinn M, Khoury MJ. Genome-wide association studies in pharmacogenomics: untapped potential for translation. Genome Med 2009, 1(4):46. 10.1186/gm46, 2684667, 19439031.
5. Ma Q, Lu AY. Pharmacogenetics, pharmacogenomics, and individualized medicine. Pharmacol Rev 2011, 63(2):437-459. 10.1124/pr.110.003533, 21436344.
6. Eichelbaum M, Ingelman-Sundberg M, Evans WE. Pharmacogenomics and individualized drug therapy. Annu Rev Med 2006, 57:119-137. 10.1146/annurev.med.56.082103.104724, 16409140.
7. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic structure of human populations. Science 2002, 298(5602):2381-2385. 10.1126/science.1078311, 12493913.
8. Rosenberg NA. A population-genetic perspective on the similarities and differences among worldwide human populations. Hum Biol 2011, 83(6):659-684. 10.3378/027.083.0601, 3531797, 22276967.
9. Hustert E, Haberl M, Burk O, Wolbold R, He YQ, Klein K, Nuessler AC, Neuhaus P, Klattig J, Eiselt R, Koch I, Zibat A, Brockmoller J, Halpert JR, Zanger UM, Wojnowski L. The genetic determinants of the CYP3A5 polymorphism. Pharmacogenetic 2001, 11(9):773-779.
10. Sistonen J, Fuselli S, Palo JU, Chauhan N, Padh H, Sajantila A. Pharmacogenetic variation at CYP2C9, CYP2C19, and CYP2D6 at global and microgeographic scales. Pharmacogenet Genom 2009, 19(2):170-179.
11. Sabbagh A, Langaney A, Darlu P, Gerard N, Krishnamoorthy R, Poloni ES. Worldwide distribution of NAT2 diversity: Implications for NAT2 evolutionary history. BMC Genet 2008, 9.
12. Dang MT, Hambleton J, Kayser SR. The influence of ethnicity on warfarin dosage requirement. Ann Pharmacother 2005, 39(6):1008-1012. 10.1345/aph.1E566, 15855242.
13. 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(3):243-257. 10.1517/17425250902800153, 19331590.
14. Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, Hirbo JB, Awomoyi AA, Bodo JM, Doumbo O, Ibrahim M, Juma AT, Kotze MJ, Lema G, Moore JH, Mortensen H, Nyambo TB, Omar SA, Powell K, Pretorius GS, Smith MW, Thera MA, Wambebe C, Weber JL, Williams SM. The genetic structure and history of Africans and African Americans. Science 2009, 324(5930):1035-1044. 10.1126/science.1172257, 2947357, 19407144.
15. Pillai G, Davies G, Denti P, Steimer JL, McIlleron H, Zvada S, Chigutsa E, Ngaimisi E, Mirza F, Tadmor B, Holford NH. Pharmacometrics: opportunity for reducing disease burden in the developing world: the case of Africa. CPT pharmacometrics Syst pharmacol. 2013, 2:e69. 10.1038/psp.2013.45, 3828009, 23985967.
16. Jin W, Xu S, Wang H, Yu Y, Shen Y, Wu B, Jin L. Genome-wide detection of natural selection in African Americans pre- and post-admixture. Genome Res 2012, 22(3):519-527. 10.1101/gr.124784.111, 3290787, 22128132.
17. Zakharia F, Basu A, Absher D, Assimes TL, Go AS, Hlatky MA, Iribarren C, Knowles JW, Li J, Narasimhan B, Sidney S, Southwick A, Myers RM, Quertermous T, Risch N, Tang H. Characterizing the admixed African ancestry of African Americans. Genome Biol 2009, 10(12):R141. 10.1186/gb-2009-10-12-r141, 2812948, 20025784.
18. Cornuet JM, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 1996, 144(4):2001-2014. 1207747, 8978083.
19. Stumpf MP. Haplotype diversity and SNP frequency dependence in the description of genetic variation. Eur J Hum Genet 2004, 12(6):469-477. 10.1038/sj.ejhg.5201179, 15026785.
20. Vijayan NN, Mathew A, Balan S, Natarajan C, Nair CM, Allencherry PM, Banerjee M. Antipsychotic drug dosage and therapeutic response in schizophrenia is influenced by ABCB1 genotypes: a study from a south Indian perspective. Pharmacogenomics 2012, 13(10):1119-1127. 10.2217/pgs.12.86, 22909202.
21. Kato M, Fukuda T, Serretti A, Wakeno M, Okugawa G, Ikenaga Y, Hosoi Y, Takekita Y, Mandelli L, Azuma J, Kinoshita T. ABCB1 (MDR1) gene polymorphisms are associated with the clinical response to paroxetine in patients with major depressive disorder. Prog Neuro Biol Psychoph 2008, 32(2):398-404.
22. Leschziner GD, Andrew T, Pirmohamed M, Johnson MR. ABCB1 genotype and PGP expression, function and therapeutic drug response: a critical review and recommendations for future research. Pharmacogenomics J 2007, 7(3):154-179. 10.1038/sj.tpj.6500413, 16969364.
23. Soyama A, Saito Y, Hanioka N, Maekawa K, Komamura K, Kamakura S, Kitakaze M, Tomoike H, Ueno K, Goto Y, Kimura H, Katoh M, Sugai K, Saitoh O, Kawai M, Ohnuma T, Ohtsuki T, Suzuki C, Minami N, Kamatani N, Ozawa S, Sawada J. Single nucleotide polymorphisms and haplotypes of CYP1A2 in a Japanese population. Drug Metabolism Pharmacokinet 2005, 20(1):24-33.
24. Lin KM, Tsou HH, Tsai IJ, Hsiao MC, Hsiao CF, Liu CY, Shen WW, Tang HS, Fang CK, Wu CS, Lu SC, Kuo HW, Liu SC, Chan HW, Hsu YT, Tian JN, Liu YL. CYP1A2 genetic polymorphisms are associated with treatment response to the antidepressant paroxetine. Pharmacogenomics 2010, 11(11):1535-1543. 10.2217/pgs.10.128, 21121774.
25. Popat RA, Van Den Eeden SK, Tanner CM, Kamel F, Umbach DM, Marder K, Mayeux R, Ritz B, Ross GW, Petrovitch H, Topol B, McGuire V, Costello S, Manthripragada AD, Southwick A, Myers RM, Nelson LM. Coffee, ADORA2A, and CYP1A2: the caffeine connection in Parkinson's disease. Eur J Neurol 2011, 18(5):756-765. 10.1111/j.1468-1331.2011.03353.x, 3556904, 21281405.
26. Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genetics 2009, 5(6):e1000519. 10.1371/journal.pgen.1000519, 2689842, 19543370.
27. Ingman M, Kaessmann H, Paabo S, Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature 2000, 408(6813):708-713. 10.1038/35047064, 11130070.
28. Serre D, Paabo SP. Evidence for gradients of human genetic diversity within and among continents. Genome Res 2004, 14(9):1679-1685. 10.1101/gr.2529604, 515312, 15342553.
29. Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, De The G, Essex M, Sankale JL, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, et al. A high-density admixture map for disease gene discovery in african americans. Am J Hum Genet 2004, 74(5):1001-1013. 10.1086/420856, 1181963, 15088270.
30. Pena SD. The fallacy of racial pharmacogenomics. Braz J Biol Res 2011, 44(4):268-275.
31. Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, . Genomes Project C, Abecasis GR An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491(7422):56-65. 10.1038/nature11632, 3498066, 23128226, Genomes Project C, Abecasis GR.
32. Browning BL, Browning SR. Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. Genet Epidemiol 2007, 31(6):606-606.
33. Ke X, Taylor MS, Cardon LR. Singleton SNPs in the human genome and implications for genome-wide association studies. Eur J Hum Genet 2008, 16(4):506-515. 10.1038/sj.ejhg.5201987, 18197193.
34. Li J, Zhang L, Zhou H, Stoneking M, Tang K. Global patterns of genetic diversity and signals of natural selection for human ADME genes. Hum Mol Genet 2011, 20(3):528-540. 10.1093/hmg/ddq498, 21081654.
35. Daly TM, Dumaual CM, Miao X, Farmen MW, Njau RK, Fu DJ, Bauer NL, Close S, Watanabe N, Bruckner C, Hardenbol P, Hockett RD. Multiplex assay for comprehensive genotyping of genes involved in drug metabolism, excretion, and transport. Clin Chem 2007, 53(7):1222-1230. 10.1373/clinchem.2007.086348, 17510302.
36. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35(Database issue):D61-D65. 1716718, 17130148.
37. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010, 26(16):2069-2070. 10.1093/bioinformatics/btq330, 2916720, 20562413.
38. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 2012, 22(9):1790-1797. 10.1101/gr.137323.112, 3431494, 22955989.
39. Whirl-Carrillo M, McDonagh EM, Hebert JM, Gong L, Sangkuhl K, Thorn CF, Altman RB, Klein TE. Pharmacogenomics Knowledge for Personalized Medicine. Clin Pharmacol Ther 2012, 92(4):414-417. 10.1038/clpt.2012.96, 3660037, 22992668.
40. Sankararaman S, Sridhar S, Kimmel G, Halperin E. Estimating local ancestry in admixed populations. Am J Hum Genet 2008, 82(2):290-303. 10.1016/j.ajhg.2007.09.022, 2664993, 18252211.
41. Maples BK, Gravel S, Kenny EE, Bustamante CD. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am J Hum Genet 2013, 93(2):278-288. 10.1016/j.ajhg.2013.06.020, 3738819, 23910464.
42. Churchhouse C, Marchini J. Multiway admixture deconvolution using phased or unphased ancestral panels. Genet Epidemiol 2013, 37(1):1-12. 10.1002/gepi.21692, 23136122.
43. Thomas MG, Weale ME, Jones AL, Richards M, Smith A, Redhead N, Torroni A, Scozzari R, Gratrix F, Tarekegn A, Wilson JF, Capelli C, Bradman N, Goldstein DB. Founding mothers of Jewish communities: Geographically separated Jewish groups were independently founded by very few female ancestors. Am J Hum Genet 2002, 70(6):1411-1420. 10.1086/340609, 379128, 11992249.
44. Birnbaum ZW, Tingey FH. One-Sided Confidence Contours for Probability Distribution Functions. Ann Math Stat 1951, 22(4):592-596.
45. Weir BS, Cockerham CC. Estimating F-Statistics for the Analysis of Population-Structure. Evolution 1984, 38(6):1358-1370.
46. Shriver MD, Kennedy GC, Parra EJ, Lawson HA, Sonpar V, Huang J, Akey JM, Jones KW. The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. Hum Genomics 2004, 1(4):274-286. 10.1186/1479-7364-1-4-274, 3525267, 15588487.
47. Voight BF, Kudaravalli S, Wen XQ, Pritchard JK. A map of recent positive selection in the human genome. PloS Biol 2006, 4(4):659-659.
48. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Res 2005, 15(11):1566-1575. 10.1101/gr.4252305, 1310644, 16251466.