Clinical pharmacology and pharmacogenetics in a genomics era: The DMET platform

Pharmacogenomics

Volumn 11, Issue 1, 2010, Pages 89-103

  Sissung, Tristan M ^a   English, Bevin C ^a   Venzon, David ^a   Figg, William D ^a   Deeken, John F ^b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

Author keywords

DMET; Genome wide association study; Pharmacogenetics; Pharmacokinetics; Toxicity

Indexed keywords

ALDEHYDE DEHYDROGENASE; ALFENTANIL; ALPRAZOLAM; AMFEBUTAMONE; AMITRIPTYLINE; ARTEMISININ; ATOMOXETINE; CARBAMAZEPINE; CARRIER PROTEIN; CATECHOL METHYLTRANSFERASE; CISPLATIN; CLOPIDOGREL; COUMARIN; CYCLOPHOSPHAMIDE; CYTOCHROME P450 2A6; CYTOCHROME P450 2B6; CYTOCHROME P450 2C19; CYTOCHROME P450 2C9; CYTOCHROME P450 2D6; CYTOCHROME P450 3A4; CYTOCHROME P450 3A5; DIHYDROPYRIMIDINE DEHYDROGENASE; DRUG METABOLIZING ENZYME; FLUOROURACIL; GLUTATHIONE TRANSFERASE P1; IFOSFAMIDE; LEVODOPA; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE (PHOSPHATE) DEHYDROGENASE (QUINONE); TEGAFUR; UNINDEXED DRUG;

CLINICAL PHARMACOLOGY; DRUG ABSORPTION; DRUG DISTRIBUTION; DRUG ELIMINATION; DRUG METABOLISM; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; INDIVIDUALIZATION; MEDICAL DECISION MAKING; METHODOLOGY; PATIENT CARE; PHARMACOGENETICS; PHENOTYPE; POLYMERASE CHAIN REACTION; REVIEW; TREATMENT OUTCOME;

DATABASES, FACTUAL; ENZYMES; GENES; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INDIVIDUALIZED MEDICINE; PHARMACEUTICAL PREPARATIONS; PHARMACOGENETICS; PHARMACOLOGY, CLINICAL;

EID: 73549120609     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/pgs.09.154     Document Type: Review

References (57)

1. Zhou SF, Di YM, Chan E et al.: Clinical pharmacogenetics and potential application in personalized medicine. Curr. Drug Metab. 9, 738-784 (2008). Thorough review of the current status of personalized medicine.
2. Zanger U, Turpeinen M, Klein K, Schwab M: Functional pharmacogenetics/ genomics of human cytochromes P450 involved in drug biotransformation. Anal. Bioanal. Chem. 392, 1093-1108 (2008).
3. Walko C, McLeod H: Pharmacogenomic progress in individualized dosing of key drugs for cancer patients. Nat. Clin. Pract. Oncol. 6, 153-162 (2009).
4. Mattison L, Fourie J, Hirao Y et al.: The uracil breath test in the assessment of dihyrdropyrimidine dehydrogenase activity: pharmacokinetic relationship between expired 13CO2 and plasma [2-13C]dihydrouracil. Clin. Cancer Res. 12, 549-555 (2006).
5. Kurnik D, Wood A, Wilkinson G: The erythromycin breath test reflects P-glycoprotein function independently of cytochrome P450 3A activity. Clin. Pharmacol. Ther. 80, 238-234 (2006).
6. 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, 1022-1027 (2008).
7. Daly AK, Donaldson PT, Bhatnagar P et al.: HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat. Genet. 41, 816-819 (2009).
8. Link E, Parish S, Armitage J et al.: SLCO1B1 variants and statin-induced myopathy - genomewide study. N. Engl. J. Med. 359, 789-799 (2008).
9. Nelson MR, Bacanu SA, Mosteller M et al.: Genome-wide approaches to identify pharmacogenetic contributions to adverse drug reactions. Pharmacogenomics J. 9, 23-33 (2009).
10. Parkinson A: Biotransformation of xenobiotics. In: Casarett and Doull's Toxicology: The Basic Science of Poisons. Klaassen CD (Ed.). McGraw-Hill, NY, USA 133-224 (2001).
11. Deeken J: The Affymetrix DMET platform and pharmacogenetics in drug development. Curr. Opin. Mol. Ther. 11, 260-268 (2009).
12. van Schaik RH: CYP450 pharmacogenetics for personalizing cancer therapy. Drug resistance update: reviews and commentaries in antimicrobial and anticancer chemotherapy. Drug Resist. Updat. 11, 77-98 (2008). Comprehensive review of CYP450s in pharmacogenetics.
13. Sissung TM, Gardner ER, Gao R, Figg WD: Pharmacogenetics of membrane transporters: a review of current approaches. Methods Mol. Biol. 448, 41-62 (2008).
14. Kindla J, Fromm MF, Konig J: In vitro evidence for the role of OATP and OCT uptake transporters in drug-drug interactions. Expert Opin. Drug Metab. Toxicol. 5,489-500 (2009).
15. Heist RS, Christiani D: EGFR-targeted therapies in lung cancer: predictors of response and toxicity. Pharmacogenomics 10, 59-68 (2009).
16. Drazen JM, Yandava CN, Dube L et al.: Pharmacogenetic association between ALOX5 promoter genotype and the response to anti-asthma treatment. Nat. Genet. 22, 168-170 (1999).
17. Timsit YE, Negishi M: CAR and PXR: the xenobiotic-sensing receptors. Steroids 72, 231-246 (2007).
18. Zhang B, Xie W, Krasowski MD: PXR: axenobiotic receptor of diverse function implicated in pharmacogenetics. Pharmacogenomics 9, 1695-1709 (2008).
19. Corvol H, Dc Giacomo A, Eng C et al.: Genetic ancestry modifies pharmacogenetic gene-gene interaction for asthma. Pharmacogenet. Genomics 19, 489-496 (2009).
20. Rodrigues-Lima F, Dairou J, Dupret JM: Effect of environmental substances on the activity of arylamine N-acetyltransferases. Curr. Drug Metab. 9, 505-509 (2008).
21. von Mutius E: Gene-environment interactions in asthma. J. Allergy Clin. Immunol. 123, 3-11; quiz 2-3 (2009).
22. Lusis AJ, Fogelman AM, Fonarow GC: Genetic basis of atherosclerosis: part II: clinical implications. Circulation 110, 2066-2071 (2004).
23. Wu X, Gu J, Spitz MR: Strategies to Identify Pharmacogenomic Biomarkers: Candidate Gene, Pathway-Based, and Genome-Wide Approaches. 1st Edition. Humana Press, NJ, USA (2008). Comprehensive book chapter comparing candidate gene, pathway based and genome-wide association study approaches in genetic association studies.
24. Evans WE, Horner M, Chu YQ, Kalwinsky D, Roberts WM: Altered mercaptopurine metabolism, toxic effects, and dosage requirement in a thiopurine methyltransferase-deficient child with acute lymphocytic leukemia. J. Pediatr. 119, 985-989 (1991).
25. Lennard L, Lewis IJ, Michelagnoli M, Lilleyman JS: Thiopurine methyltransfe rase deficiency in childhood lymphoblastic leukaemia: 6-mercaptopurine dosage strategies. Med. Pediatr. Oncol. 29, 252-255 (1997).
26. Relling MV, Hancock ML, Boyett JM, Pui CH, Evans WE: Prognostic importance of 6-mercaptopurine dose intensity in acute lymphoblastic leukemia. Blood 93, 2817-2823 (1999).
27. Ando Y, Saka H, Ando M et al.: Polymorphisms of UDP-glucuronosyltransferase gene and irinotecan toxicity: a pharmacogenetic analysis. Cancer Res. 60,6921-6926(2000).
28. Innocenti F, Undevia SD, Iyer L et al.: Genetic variants in the UDP-glucuronosyltransferase 1A1 gene predict the risk of severe neutropenia of irinotecan. J Clin. Oncol. 22, 1382-1388 (2004).
29. Marcuello E, Altes A, Menoyo A, Del Rio E, Gomez-Pardo M, Baiget M: UGT1A1 gene variations and irinotecan treatment in patients with metastatic colorectal cancer. Br. J. Cancer 91,678-682(2004).
30. Rouits E, Boisdron-Celle M, Dumont A, Guerin O, Morel A, Gamelin E: Relevance of different UGT1A1 polymorphisms in irinotecan-induced toxicity: a molecular and clinical study of 75 patients. Clin. Cancer Res. 10, 5151-5159 (2004).
31. Pullarkat ST, Stoehlmacher J, Ghaderi V et al.: Thymidylate synthase gene polymorphism determines response and toxicity of 5-FU chemotherapy. Pharmacogenomics J. 1, 65-70 (2001).
32. Villafranca E, Okruzhnov Y, Dominguez MA et al.: Polymorphisms of the repeated sequences in the enhancer region of the thymidylate synthase gene promoter may predict downstaging after preoperative chemoradiation in rectal cancer. J. Clin. Oncol. 19, 1779-1786 (2001).
33. Goekkurt E, Hoehn S, Wolschke C et al.: Polymorphisms of glutathione S-transferases (GST) and thymidylate synthase (TS) - novel predictors for response and survival in gastric cancer patients. Br. J. Cancer 94, 281-286 (2006).
34. Gurubhagavatula S, Liu G, Park S et al.: XPD and XRCC1 genetic polymorphisms are prognostic factors in advanced non-small-cell lung cancer patients treated with platinum chemotherapy. J. Clin. Oncol. 22,2594-2601 (2004).
35. Park DJ, Stoehlmacher J, Zhang W, Tsao-Wei DD, Groshen S, Lenz HJ: A Xeroderma pigmentosum group D gene polymorphism predicts clinical outcome to platinum-based chemotherapy in patients with advanced colorectal cancer. Cancer Res. 61, 8654-8658 (2001).
36. Ruzzo A, Graziano F, Kawakami K et al.: Pharmacogenetic profiling and clinical outcome of patients with advanced gastric cancer treated with palliative chemotherapy. J. Clin. Oncol. 24, 1883-1891 (2006).
37. Stoehlmacher J, Ghaderi V, Iobal S et al.: A polymorphism of the XRCC1 gene predicts for response to platinum based treatment in advanced colorectal cancer. Anticancer Res. 21,3075-3079(2001).
38. Zhou W, Gurubhagavatula S, Liu G et al.: Excision repair cross-complementation group 1 polymorphism predicts overall survival in advanced non-small cell lung cancer patients treated with platinum-based chemotherapy. Clin. Cancer Res. 10, 4939-4943 (2004).
39. Borges S, Desta Z, Li L et al.: Quantitative effect of CYP2D6 genotype and inhibitors on tamoxifen metabolism: implication for optimization of breast cancer treatment. Clin. Pharmacol. Ther. 80, 61-74 (2006).
40. Anglicheau D, Legendre C, Beaune P, Thervet E: Cytochrome p450 3A polymorphisms and immunosuppressive drugs: an update. Pharmacogenomics 8, 835-849 (2007).
41. Ryan SG: Regression to the truth: replication of association in pharmacogenetic studies. Pharmacogenomics 4,201-207(2003).
42. Eeles RA, Kote-Jarai Z, Giles GG et al.: Multiple newly identified loci associated with prostate cancer susceptibility. Nat. Genet. 40,316-321 (2008).
43. Rafnar T, Sulem P, Stacey SN et al.: Sequence variants at the TERT-CLPTM1L locus associate with many cancer types. Nat. Genet. 41,221-227(2009).
44. Thomas G, Jacobs KB, Yeager M et al.: Multiple loci identified in a genome-wide association study of prostate cancer. Nat. Genet. 40,310-315 (2008).
45. Cordell HJ: Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum. Mol. Genet. 11, 2463-2468 (2002).
46. Baker SD, Verweij J, Cusatis GA et al.: Pharmacogenetic pathway analysis of docetaxel elimination. Clin. Pharmacol. Ther. 85, 155-163 (2009).
47. Dahut WL, Gulley JL, Arlen PM et al.: Randomized phase II trial of docetaxel plus thalidomide in androgen-independent prostate cancer. J. Clin. Oncol. 22, 2532-2539(2004).
48. Deeken JF, Cormier T, Price DK et al.: A pharmacogenetic study of docetaxel and thalidomide in patients with castration-resistant prostate cancer using the DMET genotyping platform. Pharmacogenomics J. (In press).
49. Caldwell MD, Awad T, Johnson JA et al.: CYP4F2 genetic variant alters required warfarin dose. Blood 111, 4106-4112 (2008). First discovery of the role of variants in CYP4F2 in association with warfarin dosing.
50. Borgiani P, Ciccacci C, Forte V et al.: CYP4F2 genetic variant (rs2108622) significantly contributes to warfarin dosing variability in the Italian population. Pharmacogenomics 10, 261-266 (2009).
51. Mega JL, Close SL, Wiviott SD et al.: Cytochrome p-450 polymorphisms and response to Clopidogrel. N. Engl. J. Med. 360, 354-362 (2009). First discovery of the role of variants in CYP2C19 and CYP2B6 in clopidogrel therapy.
52. Drews J: Drug discovery: a historical perspective. Science 287, 1960-1964 (2000).
53. Schneider BP, Wang M, Radovich M et al.: Association of vascular endothelial growth factor and vascular endothelial growth factor receptor-2 genetic polymorphisms with outcome in a trial of paclitaxel compared with paclitaxel plus bevacizumab in advanced breast cancer: ECOG 2100. J. Clin. Oncol. 26, 4672-4678 (2008).
54. Website that defined the initial SNP selection of DMET www.pharmaadme.org/joomla/ (Accessed 28 October, 2009)
55. A comprehensive source that curates pharmacogenetics relationships www.pharmgkb.org (Accessed 28 October, 2009)
56. DMET™ Plus Premier Pack allele translation reports: summary of comprehensive drug disposition genotyping into commonly recognized allele names www.affymetrix.com/support/technical/whitepapers/dmet-plus-translation.pdf (Accessed 28 October, 2009)
57. Single-sample analysis methodology for the DMET™ Plus Product www.affymetrix.com/support/technical/whitepapers/dmet-plus-algorithm- whitepapervl.pdf (Accessed 28 October, 2009)