Rare genetic variants in cellular transporters, metabolic enzymes, and nuclear receptors can be important determinants of interindividual differences in drug response

Genetics in Medicine

Volumn 19, Issue 1, 2017, Pages 20-29

  Kozyra, Mikael ^a   Ingelman Sundberg, Magnus ^a   Lauschke, Volker M ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

drug development; genetic variation; personalized medicine; pharmacogenes; rare variants

Indexed keywords

ABC TRANSPORTER; ABCC12 PROTIEN; CELL NUCLEUS RECEPTOR; CYBR1 PROTEIN; CYTOCHROME P450 1A1; CYTOCHROME P450 1A2; CYTOCHROME P450 2A6; CYTOCHROME P450 2B6; CYTOCHROME P450 2C19; CYTOCHROME P450 2C8; CYTOCHROME P450 2C9; CYTOCHROME P450 2D6; CYTOCHROME P450 2E1; CYTOCHROME P450 2J2; CYTOCHROME P450 3A4; CYTOCHROME P450 3A5; CYTOCHROME P450 4F2; CYTOCHROME P450 FAMILY 4; DRUG; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 2; PPARA PROTEIN; PROTEIN; SLC TRANSPORTER; SOLUTE CARRIER ORGANIC ANION TRANSPORTER 1B3; UNCLASSIFIED DRUG; VKORC1 PROTEIN; CELL RECEPTOR; PHARMACOLOGICAL BIOMARKER;

AFRICAN; ARTICLE; CONTROLLED STUDY; CULTURAL DIVERSITY; DRUG EFFICACY; DRUG RESPONSE; ETHNIC DIFFERENCE; EUROPEAN; EXON; GENE FREQUENCY; GENETIC DIFFERENCE; GENETIC IDENTIFICATION; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; SINGLE NUCLEOTIDE POLYMORPHISM; SOCIAL DETERMINANTS OF HEALTH; WHOLE EXOME SEQUENCING; BLACK PERSON; CAUCASIAN; DRUG INACTIVATION; EXOME; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HUMAN GENOME PROJECT; PERSONALIZED MEDICINE; PHARMACOKINETICS; POPULATION GENETICS;

AFRICAN CONTINENTAL ANCESTRY GROUP; BIOMARKERS, PHARMACOLOGICAL; EUROPEAN CONTINENTAL ANCESTRY GROUP; EXOME; EXONS; GENETIC VARIATION; GENETICS, POPULATION; GENOME-WIDE ASSOCIATION STUDY; HUMAN GENOME PROJECT; HUMANS; INACTIVATION, METABOLIC; PHARMACOKINETICS; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECISION MEDICINE; RECEPTORS, CYTOPLASMIC AND NUCLEAR;

EID: 85009205080     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2016.33     Document Type: Article

References (40)

1. Ingelman-Sundberg M. Pharmacogenomic biomarkers for prediction of severe adverse drug reactions. N Engl J Med 2008;358:637-639.
2. Tufts Center for the Study of Drug Development. How the Tufts Center for the Study of Drug Development pegged the cost of a new drug at 2.6 billion. 18 November2014. http://csdd.tufts.edu/files/uploads/cost-study-backgrounder. pdf.
3. Frueh FW, Amur S, Mummaneni P, et al. Pharmacogenomic biomarker information in drug labels approved by the United States food and drug administration: prevalence of related drug use. Pharmacotherapy 2008;28:992-998.
4. Ehmann F, Caneva L, Prasad K, et al. Pharmacogenomic information in drug labels: European Medicines Agency perspective. Pharmacogenomics J 2015;15:201-210.
5. Moaddeb J, Haga SB. Pharmacogenetic testing: current evidence of clinical utility. Ther Adv Drug Saf 2013;4:155-169.
6. Fujikura K, Ingelman-Sundberg M, Lauschke VM. Genetic variation in the human cytochrome P450 supergene family. Pharmacogenet Genomics 2015;25:584-594.
7. Pirmohamed M. Personalized pharmacogenomics: predicting efficacy and adverse drug reactions. Annu Rev Genomics Hum Genet 2014;15:349-370.
8. Franke RM, Gardner ER, Sparreboom A. Pharmacogenetics of drug transporters. Curr Pharm Des 2010;16:220-230.
9. Roundhill EA, Fletcher JI, Haber M, Norris MD. Clinical relevance of multidrugresistance-proteins (MRPs) for anticancer drug resistance and prognosis. In: Efferth T (ed). Resistance to Targeted ABC Transporters in Cancer. Springer: Heidelberg, Germany, 2015;27-52.
10. Oshiro C, Mangravite L, Klein T, Altman R. PharmGKB very important pharmacogene: SLCO1B1. Pharmacogenet Genomics 2010;20:211-216.
11. Niemi M, Backman JT, Kajosaari LI, et al. Polymorphic organic anion transporting polypeptide 1B1 is a major determinant of repaglinide pharmacokinetics. Clin Pharmacol Ther 2005;77:468-478.
12. The SEARCH Collaborative Group. SLCO1B1 variants and statin-induced myopathy-A genomewide study. N Engl J Med 2008;359:789-799.
13. Kalliokoski A, Neuvonen M, Neuvonen PJ, Niemi M. The effect of SLCO1B1 polymorphism on repaglinide pharmacokinetics persists over a wide dose range. Br J Clin Pharmacol 2008;66:818-825.
14. Guillemette C. Pharmacogenomics of human UDP-glucuronosyltransferase enzymes. Pharmacogenomics J 2003;3:136-158.
15. Iyer L, Das S, Janisch L, et al. UGT1A1 28 polymorphism as a determinant of irinotecan disposition and toxicity. Pharmacogenomics J 2002;2:43-47.
16. Hayes JD, Flanagan JU, Jowsey IR. Glutathione transferases. Annu Rev Pharmacol Toxicol 2005;45:51-88.
17. Bonifazi F, Storci G, Bandini G, et al. Glutathione transferase-A2 S112T polymorphism predicts survival, transplant-related mortality, busulfan and bilirubin blood levels after allogeneic stem cell transplantation. Haematologica 2014;99:172-179.
18. James MO, Ambadapadi S. Interactions of cytosolic sulfotransferases with xenobiotics. Drug Metab Rev 2013;45:401-414.
19. Cook I, Wang T, Falany CN, Leyh TS. High accuracy in silico sulfotransferase models. J Biol Chem 2013;288:34494-34501.
20. Edavana VK, Dhakal IB, Yu X, Williams S, Kadlubar S. Sulfation of 4-hydroxy toremifene: individual variability, isoform specificity, and contribution to toremifene pharmacogenomics. Drug Metab Dispos 2012;40:1210-1215.
21. Omiecinski CJ, Vanden Heuvel JP, Perdew GH, Peters JM. Xenobiotic metabolism, disposition, and regulation by receptors: from biochemical phenomenon to predictors of major toxicities. Toxicol Sci 2011;120(suppl 1):S49-S75.
22. Tennessen JA, Bigham AW, O'Connor TD, et al.; Broad GO; Seattle GO; NHLBI Exome Sequencing Project. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012;337:64-69.
23. 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491:56-65.
24. Drögemöller BI, Wright GE, Niehaus DJ, Emsley R, Warnich L. Next-generation sequencing of pharmacogenes: a critical analysis focusing on schizophrenia treatment. Pharmacogenet Genomics 2013;23:666-674.
25. Yue P, Melamud E, Moult J. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 2006;7:166.
26. Coulon S, Gaillard PH, Chahwan C, McDonald WH, Yates JR 3rd, Russell P. Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Mol Biol Cell 2004;15:71-80.
27. Tukey RH, Strassburg CP. Human UDP-glucuronosyltransferases: metabolism, expression, and disease. Annu Rev Pharmacol Toxicol 2000;40:581-616.
28. Nelson MR, Wegmann D, Ehm MG, et al. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 2012;337:100-104.
29. Allikmets R, Dean M. Bringing age-related macular degeneration into focus. Nat Genet 2008;40:820-821.
30. Pussegoda K, Ross CJ, Visscher H, et al.; CPNDS Consortium. Replication of TPMT and ABCC3 genetic variants highly associated with cisplatin-induced hearing loss in children. Clin Pharmacol Ther 2013;94:243-251.
31. Arimany-Nardi C, Koepsell H, Pastor-Anglada M. Role of SLC22A1 polymorphic variants in drug disposition, therapeutic responses, and drug-drug interactions. Pharmacogenomics J 2015;15:473-487.
32. Frischmeyer PA, Dietz HC. Nonsense-mediated mRNA decay in health and disease. Hum Mol Genet 1999;8:1893-1900.
33. 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 2010;10: 191-199.
34. Voora D, Shah SH, Reed CR, et al. Pharmacogenetic predictors of statinmediated low-density lipoprotein cholesterol reduction and dose response. Circ Cardiovasc Genet 2008;1:100-106.
35. Ramsey LB, Bruun GH, Yang W, et al. Rare versus common variants in pharmacogenetics: SLCO1B1 variation and methotrexate disposition. Genome Res 2012;22:1-8.
36. Campbell MC, Tishkoff SA. African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet 2008;9:403-433.
37. Nies AT, Koepsell H, Winter S, et al. Expression of organic cation transporters OCT1 (SLC22A1) and OCT3 (SLC22A3) is affected by genetic factors and cholestasis in human liver. Hepatology 2009;50:1227-1240.
38. Hartman, E., Grieve, R., Ramsahai, R. & Sekhon, J. S. From sample average treatment effect to population average treatment effect on the treated: combining experimental with observational studies to estimate population treatment effects. J R Stat Soc Ser A 2015;178:757-778.
39. Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. The real cost of sequencing: higher than you think! Genome Biol 2011;12:125.
40. Snyder MW, Adey A, Kitzman JO, Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat Rev Genet 2015;16:344-358.