Analysis of Genetic Variation in CYP450 Genes for Clinical Implementation

Liuh Ling Goh, Chia Wei Lim, Wey Cheng Sim, Li Xian Toh, Khai Pang Leong, Liuh Ling Goh, Chia Wei Lim, Wey Cheng Sim, Li Xian Toh, Khai Pang Leong

Abstract

Background: Genetic determinants of drug response remain stable throughout life and offer great promise to patient-tailored drug therapy. The adoption of pharmacogenetic (PGx) testing in patient care requires accurate, cost effective and rapid genotyping with clear guidance on the use of the results. Hence, we evaluated a 32 SNPs panel for implementing PGx testing in clinical laboratories.

Methods: We designed a 32-SNP panel for PGx testing in clinical laboratories. The variants were selected using the clinical annotations of the Pharmacogenomics Knowledgebase (PharmGKB) and include polymorphisms of CYP2C9, CYP2C19, CYP2D6, CYP3A5 and VKORC1 genes. The CYP2D6 gene allele quantification was determined simultaneously with TaqMan copy number assays targeting intron 2 and exon 9 regions. The genotyping results showed high call rate accuracy according to concordance with genotypes identified by independent analyses on Sequenome massarray and droplet digital PCR. Furthermore, 506 genomic samples across three major ethnic groups of Singapore (Malay, Indian and Chinese) were analysed on our workflow.

Results: We found that 98% of our study subjects carry one or more CPIC actionable variants. The major alleles detected include CYP2C9*3, CYP2C19*2, CYP2D6*10, CYP2D6*36, CYP2D6*41, CYP3A5*3 and VKORC1*2. These translate into a high percentage of intermediate (IM) and poor metabolizer (PM) phenotypes for these genes in our population.

Conclusion: Genotyping may be useful to identify patients who are prone to drug toxicity with standard doses of drug therapy in our population. The simplicity and robustness of this PGx panel is highly suitable for use in a clinical laboratory.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1. Frequency of metabolizer groups in…
Fig 1. Frequency of metabolizer groups in 3 major ethnic groups of Singapore population.
(A) CYP2C9 (B) CYP2C19 and (C) CYP2D6.
Fig 2. The frequencies of actionable diplotypes…
Fig 2. The frequencies of actionable diplotypes for each drug-gene rule.
The definition of actionable diplotypes is defined as follows: (i) warfarin, CYP2C9 *2 or *3 heterozygote or homozygote with VKORC1 GA or AA genotype and CYP2C9*1 with VKORC1 AA genotype; (ii) clopidogrel, CYP2C19*2, *3 and *6; (iii) codeine, CYP2D6 poor and intermediate metabolizers; (iv) tacrolimus, CYP3A5*1 heterozygote or homozygote.

References

    1. Weinshilboum RM, Wang L (2006) Pharmacogenetics and pharmacogenomics: development, science, and translation. Annu Rev Genomics Hum Genet 7: 223–245. 10.1146/annurev.genom.6.080604.162315
    1. Wang L, McLeod HL, Weinshilboum RM (2011) Genomics and drug response. N Engl J Med 364: 1144–1153. 10.1056/NEJMra1010600
    1. Green ED, Guyer MS, National Human Genome Research I (2011) Charting a course for genomic medicine from base pairs to bedside. Nature 470: 204–213. 10.1038/nature09764
    1. Sim SC, Kacevska M, Ingelman-Sundberg M (2013) Pharmacogenomics of drug-metabolizing enzymes: a recent update on clinical implications and endogenous effects. Pharmacogenomics J 13: 1–11. 10.1038/tpj.2012.45
    1. Wu AC, Fuhlbrigge AL (2008) Economic evaluation of pharmacogenetic tests. Clin Pharmacol Ther 84: 272–274. 10.1038/clpt.2008.127
    1. Relling MV, Evans WE (2015) Pharmacogenomics in the clinic. Nature 526: 343–350. 10.1038/nature15817
    1. Furge LL, Guengerich FP (2006) Cytochrome P450 enzymes in drug metabolism and chemical toxicology: An introduction. Biochem Mol Biol Educ 34: 66–74. 10.1002/bmb.2006.49403402066
    1. van der Weide J, Steijns LS (1999) Cytochrome P450 enzyme system: genetic polymorphisms and impact on clinical pharmacology. Ann Clin Biochem 36 (Pt 6): 722–729.
    1. Wadelius M, Pirmohamed M (2007) Pharmacogenetics of warfarin: current status and future challenges. Pharmacogenomics J 7: 99–111. 10.1038/sj.tpj.6500417
    1. Johnson JA, Gong L, Whirl-Carrillo M, Gage BF, Scott SA, Stein CM, et al. (2011) Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and VKORC1 genotypes and warfarin dosing. Clin Pharmacol Ther 90: 625–629. 10.1038/clpt.2011.185
    1. Gurbel PA, Bliden KP, Antonino MJ, Stephens G, Gretler DD, Jurek MM, et al. (2010) The effect of elinogrel on high platelet reactivity during dual antiplatelet therapy and the relation to CYP2C19*2 genotype: first experience in patients. J Thromb Haemost 8: 43–53. 10.1111/j.1538-7836.2009.03648.x
    1. Furuta T, Shirai N, Sugimoto M, Nakamura A, Hishida A, Ishizaki T (2005) Influence of CYP2C19 pharmacogenetic polymorphism on proton pump inhibitor-based therapies. Drug Metab Pharmacokinet 20: 153–167.
    1. Thorn CF, Whirl-Carrillo M, Leeder JS, Klein TE, Altman RB (2012) PharmGKB summary: phenytoin pathway. Pharmacogenet Genomics 22: 466–470. 10.1097/FPC.0b013e32834aeedb
    1. Birdwell KA, Decker B, Barbarino JM, Peterson JF, Stein CM, Sadee W, et al. (2015) Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for CYP3A5 Genotype and Tacrolimus Dosing. Clin Pharmacol Ther 98: 19–24. 10.1002/cpt.113
    1. Lamba JK, Lin YS, Schuetz EG, Thummel KE (2002) Genetic contribution to variable human CYP3A-mediated metabolism. Adv Drug Deliv Rev 54: 1271–1294.
    1. Ingelman-Sundberg M (2004) Pharmacogenetics of cytochrome P450 and its applications in drug therapy: the past, present and future. Trends Pharmacol Sci 25: 193–200. 10.1016/j.tips.2004.02.007
    1. Crews KR, Caudle KE, Dunnenberger HM, Sadhasivam S, Skaar TC (2015) Considerations for the Utility of the CPIC Guideline for CYP2D6 Genotype and Codeine Therapy. Clin Chem 61: 775–776. 10.1373/clinchem.2014.237412
    1. Hicks JK, Bishop JR, Sangkuhl K, Muller DJ, Ji Y, Leckband SG, et al. (2015) Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2D6 and CYP2C19 Genotypes and Dosing of Selective Serotonin Reuptake Inhibitors. Clin Pharmacol Ther 98: 127–134. 10.1002/cpt.147
    1. Zhou SF (2009) Polymorphism of human cytochrome P450 2D6 and its clinical significance: Part I. Clin Pharmacokinet 48: 689–723. 10.2165/11318030-000000000-00000
    1. Kimura S, Umeno M, Skoda RC, Meyer UA, Gonzalez FJ (1989) The human debrisoquine 4-hydroxylase (CYP2D) locus: sequence and identification of the polymorphic CYP2D6 gene, a related gene, and a pseudogene. Am J Hum Genet 45: 889–904.
    1. Sim SC, Ingelman-Sundberg M (2013) Update on allele nomenclature for human cytochromes P450 and the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Database. Methods Mol Biol 987: 251–259. 10.1007/978-1-62703-321-3_21
    1. Sistonen J, Fuselli S, Levo A, Sajantila A (2005) CYP2D6 genotyping by a multiplex primer extension reaction. Clin Chem 51: 1291–1295. 10.1373/clinchem.2004.046466
    1. Ji Y, Skierka JM, Blommel JH, Moore BE, VanCuyk DL, Bruflat JK, et al. (2016) Preemptive Pharmacogenomic Testing for Precision Medicine: A Comprehensive Analysis of Five Actionable Pharmacogenomic Genes Using Next-Generation DNA Sequencing and a Customized CYP2D6 Genotyping Cascade. J Mol Diagn 18: 438–445. 10.1016/j.jmoldx.2016.01.003
    1. Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, et al. (2011) High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 83: 8604–8610. 10.1021/ac202028g
    1. Ramamoorthy A, Flockhart DA, Hosono N, Kubo M, Nakamura Y, Skaar TC (2010) Differential quantification of CYP2D6 gene copy number by four different quantitative real-time PCR assays. Pharmacogenet Genomics 20: 451–454. 10.1097/FPC.0b013e32833a1083
    1. Brunham LR, Chan SL, Li R, Aminkeng F, Liu X, Saw WY, et al. (2014) Pharmacogenomic diversity in Singaporean populations and Europeans. Pharmacogenomics J 14: 555–563. 10.1038/tpj.2014.22
    1. Chan MY, Tan K, Tan HC, Huan PT, Li B, Phua QH, et al. (2012) CYP2C19 and PON1 polymorphisms regulating clopidogrel bioactivation in Chinese, Malay and Indian subjects. Pharmacogenomics 13: 533–542. 10.2217/pgs.12.24
    1. Tan DS, Yeo AH, Ho HK, Wee HL, Ong HY (2014) Asian study of clopidogrel (ASCLOP) responsiveness: the contributions of genetic and non-genetic factors. Int J Cardiol 171: e21–23. 10.1016/j.ijcard.2013.11.126
    1. Lim JS, Chen XA, Singh O, Yap YS, Ng RC, Wong NS, et al. (2011) Impact of CYP2D6, CYP3A5, CYP2C9 and CYP2C19 polymorphisms on tamoxifen pharmacokinetics in Asian breast cancer patients. Br J Clin Pharmacol 71: 737–750. 10.1111/j.1365-2125.2011.03905.x
    1. Scott SA, Sangkuhl K, Stein CM, Hulot JS, Mega JL, Roden DM, et al. (2013) Clinical Pharmacogenetics Implementation Consortium guidelines for CYP2C19 genotype and clopidogrel therapy: 2013 update. Clin Pharmacol Ther 94: 317–323. 10.1038/clpt.2013.105
    1. Crews KR, Gaedigk A, Dunnenberger HM, Klein TE, Shen DD, Callaghan JT, et al. (2012) Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for codeine therapy in the context of cytochrome P450 2D6 (CYP2D6) genotype. Clin Pharmacol Ther 91: 321–326. 10.1038/clpt.2011.287

Source: PubMed

Sponsors and Collaborators

Medical Conditions

Drug Interventions

3
Subscribe