Journal List > Lab Med Online > v.6(3) > 1057305

Kim, Yun, Kim, Song, Woo, Lee, Lee, Cho, Ji, Chae, Lee, and Chun: Clinical Pharmacogenetic Testing and Application: Laboratory Medicine Clinical Practice Guidelines Part 1

Abstract

Pharmacogenetics is a rapidly evolving field, and the number of pharmacogenetic tests for clinical use is steadily increasing. However, incorrect or inadequate implementation and use of pharmacogenetic testing in clinical practice may result in an increase in medical costs and adverse patient outcomes. This document contains suggested pharmacogenetic testing guidelines for clinical application, interpretation, and reporting of the results through a literature review and evidence-based expert opinions. The clinical laboratory practice guideline includes clinical pharmacogenetic testing covered by public medical insurance in Korea. Technical, ethical, and regulatory issues related to clinical pharmacogenetic testing are also addressed. This document aims to improve the utility of pharmacogenetic testing in routine clinical settings.

Figures and Tables

Table 1

Classification of pharmacogenetic genes

lmo-6-119-i001
Classification Gene
Drug metabolizing enzyme Phase I CYP superfamily (CYP1A1/2, CYP1B1, CYP2A6, CYP2B6, CYP2C8/9/19, CYP2D6, CYP2E1, CYP3A4/5/7), ALDH, ADH, DPD, NQO1, etc.
Phase II NAT1, NAT2, GSTs, SULTs, COMT, TPMT, UGTs, etc.
Drug transporter ABC transporter (ABCB1, ABCC1/2, ABCG2), SLC transporter (SLC21A3/6/8/9, SLC22A1/2/3/6/7/8/11)
Drug target DNA repair (XRCC1/3, APEX1, ERCC1/2, BRCA1), TYMS, EGFR, KRAS, etc.
Table 2

Pharmacogenetic target genes and level of evidence according to the international guideline and study results

lmo-6-119-i002
Gene Drug Category LOE* Guideline and reference
ANKK1 Antipsychotics Toxicity/ADR 1B Mol Psychiatry. 2007;12:794
BCR/ABL1 Imatinib, Dasatinib, Nilotinib, Bosutinib Efficacy - CLSI, Clinical chemistry textbook
Eur J Clin Pharmacol. 2013;69:S17
BRAF Vemurafenib, Cetuximab Efficacy - N Engl J Med. 2011;364:2507
J Clin Oncol. 2008;26:5705
CFTR Ivacaftor Efficacy 1A Pharmacol Ther. 2014;95(6):592-7
COMT Cisplatin Toxicity/ADR 1B Nat Genet. 2009;41:1345
CYP2C19 Clopidogrel Dosage, Efficacy, Toxicity/ADR 1A CPIC (High), DPWG (3, 4)
CYP2C9 Warfarin Dosage, Toxicity/ADR 1A NACB (A-II), CLSI, CPIC (High)
CYP2D6 Antidepressants, Tamoxifen, Atomoxetine Dosage, Efficacy, Toxicity/ADR 1A/2A NACB (B-III; tamoxifen, atomoxetine)
CPIC (high, moderate; antidepressants), DPWG (3, 4)
CYP3A5 Tacrolimus Dosage 1B DPWG (4)
CYP4F2 Acenocoumarol Dosage 1B J Thromb Haemost. 2013;11:1200
DPYD Pyrimidine analogs Toxicity/ADR 1B CPIC (Weak, Moderate, High), DPWG (3)
EGFR Erlotinib, Gefitinib Efficacy 1B J Thorac Oncol. 2012;7:1490
EML4/ALK Crizotinib Efficacy - N Engl J Med. 2010;363:1734
ERBB2 HER2/neu Inhibitor Efficacy 3 NACB (B-II)
ESR1 Exemestane Efficacy - Eur J Clin Pharmacol. 2013;69:S17
Breast Cancer Res Treat. 2013;138:807
FIP1L1/PDGFRA Imatinib Efficacy - Haematologica. 2007;92:1173
FLOT1 Carbamazepine Toxicity/ADR 1B Epilepsia. 2008;49:2087
G6PD  Dapsone Toxicity/ADR 1B Pharmacogenet Genomics. 2012;22:219
GRIK4  Citalopram Efficacy 1B Am J Psychiatry. 2007;164:1181
GSTA1  Anticancer drug Toxicity/ADR 3 Clinical chemistry textbook
Pharmacogenomics. 2012;13:171
GSTM1 Isoniazid Toxicity/ADR 3 Clinical chemistry textbook
J Clin Pharm Ther. 2012;37:712
GSTM3 Anticancer drug Toxicity/ADR 3 Pharmacogenomics J. 2010;10:54
GSTP1 Anticancer drug Efficacy, Toxicity/ADR 2A/3 Clinical chemistry textbook
J Clin Oncol. 2010;28:3227
GSTT1 Thalidomide Toxicity/ADR 3 Leuk Res. 2011;35:1178
HLA-B Abacavir, Allopurinol Toxicity/ADR 1A NACB (A-II; abacavir), CPIC (High)
IFNL3 Peginterferon Efficacy 1A/1B J Viral Hepat. 2013;20:e107
c-KIT Imatinib Efficacy - CLSI, Clinical chemistry textbook
Proc Natl Acad Sci USA. 2009;106:1542
KRAS EGFR inhibitor Efficacy 3 CLSI, Clinical chemistry textbook
Cancer Res. 2006;66:3992
MTHFR Methotrexate Toxicity/ADR 1B Pharmacogenomics. 2013;14:305
NAT2 Isoniazid Toxicity/ADR 2B/3 Clinical chemistry textbook
J Toxicol Sci. 2008;33:187
PDGFRB Imatinib Efficacy - Blood. 2007;109:61
PML/RARA Arsenic Trioxide Efficacy - CLSI, Clinical chemistry textbook
Eur J Clin Pharmacol. 2013;69:S17
SLCO1B1 Simvastatin Toxicity/ADR 1A CPIC (High)
TMEM43 Cisplatin Toxicity/ADR 1B Pharmacogenomics. 2010;11:1377
TPMT Purine analogs Toxicity/ADR 1A NACB (A-I), CPIC (High), DPWG (4)
UGT1A1 Irinotecan Toxicity/ADR 2A, 3, 4 NACB (A-II), DPWG (3)
VKORC1 Warfarin Dosage 1A/1B NACB (A-II), CLSI, CPIC (High)

*Level of evidence [42]: Level 1A, annotation for a variant-drug combination in a CPIC or medical society-endorsed pharmacogenomic guideline, or implemented at a PGRN site or in another major health system. Level 1B, annotation for a variant-drug combination where the preponderance of evidence shows an association. The association must be replicated in more than one cohort with significant P values and preferably will have a strong effect size. Level 2A, annotation for a variant-drug combination that qualifies for level 2B where the variant is within a very important pharmacogene as defined by PharmGKB. The variants in level 2A are in known pharmacogenes; therefore, functional significance is more likely. Level 2B, annotation for a variant-drug combination with moderate evidence of an association. The association must be replicated but some studies may not show statistical significance, and/or the effect size may be small. Level 3, annotation for a variant-drug combination based on a single significant (not yet replicated) annotation for a variant-drug combination evaluated in multiple studies but lacking clear evidence of an association. Level 4, annotation based on a case report, non-significant study, or in vitro, molecular, or functional assay evidence only (https://www.pharmgkb.org/).

Abbreviations: LOE, level of evidence; ADR, adverse drug reaction; NACB, National Academy of Clinical Biochemistry [19]; CLSI, Clinical and Laboratory Standards Institute, MM19AE [18]; Clinical chemistry textbook, Tietz Textbook of Clinical Chemistry and Molecular Diagnostics. 5th ed. Elsevier [37]; CPIC, Clinical Pharmacogenetics Implementation Consortium [383940]; DPWG, Dutch Pharmacogenetics Working Group [41].

Table 3

Classification and grade of reagents and instruments related to pharmacogenetic tests

lmo-6-119-i003
Table 4

Pharmacogenetic tests in the medical insurance reimbursement list

lmo-6-119-i004

Notes

This article is available from http://www.labmedonline.org

References

1. Kawachi MH, Bahnson RR, Barry M, Busby JE, Carroll PR, Carter HB, et al. NCCN clinical practice guidelines in oncology: prostate cancer early detection. J Natl Compr Canc Netw. 2010; 8:240–262.
2. Mohler J, Bahnson RR, Boston B, Busby JE, D'Amico A, Eastham JA, et al. NCCN clinical practice guidelines in oncology: prostate cancer. J Natl Compr Canc Netw. 2010; 8:162–200.
3. Zelenetz AD, Abramson JS, Advani RH, Andreadis CB, Byrd JC, Czuczman MS, et al. NCCN clinical practice guidelines in oncology: non-Hodgkin's lymphomas. J Natl Compr Canc Netw. 2010; 8:288–334.
4. Appell ML, Berg J, Duley J, Evans WE, Kennedy MA, Lennard L, et al. Nomenclature for alleles of the thiopurine methyltransferase gene. Pharmacogenet Genomics. 2013; 23:242–248.
crossref
5. Edwards MS, Chadda SD, Zhao Z, Barber BL, Sykes DP. A systematic review of treatment guidelines for metastatic colorectal cancer. Colorectal Dis. 2012; 14:e31–e47.
crossref
6. Dalen P, Dahl ML, Bernal Ruiz ML, Nordin J, Bertilsson L. 10-Hydroxylation of nortriptyline in white persons with 0, 1, 2, 3, and 13 functional CYP2D6 genes. Clin Pharmacol Ther. 1998; 63:444–452.
crossref
7. Weinshilboum R, Wang L. Pharmacogenomics: bench to bedside. Nat Rev Drug Discov. 2004; 3:739–748.
crossref
8. Nichols J, Altaie S, Cooper G, Glavina P, Halim A, Hatjimihail A, et al. Laboratory quality control based on risk management; approved guideline. EP23-A. Wayne, PA: Clinical and Laboratory Standards Institute;2011.
9. Njoroge SW, Nichols JH. Risk management in the clinical laboratory. Ann Lab Med. 2014; 34:274–278.
crossref
10. Nolte F, Hill CE. Polymerase chain reaction and other nucleic acid amplification technology. In : McPherson RA, Pincus MR, editors. Henry's clinical diagnosis and management by laboratory methods. 22nd ed. Philadelphia, PA: Elsevier Saunders;2011. p. 1271–1281.
11. Kim MS. Method for genetic testing. The Korean Society for Laboratory Medicine. Laboratory medicine. 5th ed. Seoul: Panmun education;2014. p. 1003–1013.
12. Seoung MW, Lee ST. Genomic test. The Korean Society for Laboratory Medicine. Laboratory medicine. 5th ed. Seoul: Panmun education;2014. p. 1015–1026.
13. Murdock DG, Wallace DC. PNA-mediated PCR clamping. Applications and methods. Methods Mol Biol. 2002; 208:145–164.
crossref
14. BIOETHICS AND SAFETY ACT. Act No. 11844.
15. Ki CS, Hong YJ. Quality assurance in molecular diagnosis. The Korean Society for laboratory medicine. Laboratory Medicine. 5th ed. Seoul: Panmun education;2014. p. 1039–1044.
16. Min WK. Laboratory quality management. The Korean Society for Laboratory Medicine. Laboratory Medicine. 5th ed. Seoul: Panmun education;2014. p. 41–48.
17. The Korean Society for Laboratory Medicine/Laboratory Medicine Foundation. The Korean Society for Laboratory Medicine/Laboratory Medicine Foundation. Good laboratory inspection checklist: molecular tests. 2015.
18. Clinical and Laboratory Standards Institute. Establishing molecular testing in clinical laboratory environments: CLSI document MM19-A. Wayne, PA: Clinical and Laboratory Standards Institute;2011.
19. Valdes R, Payne DA, Linder MW. Laboratory analysis and application of pharmacogenetics to clinical practice. Laboratory medicine practice guideline. The national academy of clinical biochemistry;2010.
20. Korean Institute of Genetic Testing Evaluation. Korean Institute of Genetic Testing Evaluation inspection checklist for molecular genetic tests. Korean Institute of Genetic Testing Evaluation;2015.
21. College of American Pathologists. Molecular Pathology Checklist. College of American Pathologists Commission on Laboratory Accreditation;2013.
22. American College of Medical Genetics. Standards and guidelines for clinical genetics laboratories. American College of Medical Genetics;2008.
23. Lee SY. Pharmacogenetic testing. The Korean Society for Laboratory Medicine. Laboratory Medicine. 5th ed. Seoul: Panmun education;2014. p. 1101–1106.
24. Flockhart DA, O'Kane D, Williams MS, Watson MS, Gage B, Gandolfi R, et al. Pharmacogenetic testing of CYP2C9 and VKORC1 alleles for warfarin. Genet Med. 2008; 10:139–150.
crossref
25. Notification No. 2015-18 of the Ministry of Food & Drugs safety.
26. Notification No. 2014-178 of the Ministry of Food & Drugs safety.
27. Enforcement regulations No. 310 of the Ministry of Food & Drugs safety.
28. Notification No. 2014-125 of the Ministry of Health & Welfare.
29. MEDICAL SERVICE ACT. Act No. 13108.
30. Notification No. 2014-189 of the Ministry of Health & Welfare.
31. Notification No. 2015-25 of the Ministry of Health & Welfare.
32. MEDICAL TECHNICIANS, ETC. Act No. 11102.
33. Enforcement decree of the Act on MEDICAL TECHNICIANS, ETC. Enforcement decree of the Act No. 26130.
34. Enforcement decree of the Act on BIOETHICS AND SAFETY ACT. Enforcement decree of the Act No. 25840.
35. Enforcement regulations of the Act on BIOETHICS AND SAFETY ACT. Enforcement regulations of the Ministry of Health & Welfare No. 283.
36. Notification No. 2013-81 of the Ministry of Health & Welfare.
37. Burtis C, Ashwood E, Bruns D. Tietz Textbook of Clinical Chemistry and Molecular Diagnostics. 5th ed. Elsevier;2012.
38. Relling MV, Gardner EE, Sandborn WJ, Schmiegelow K, Pui CH, Yee SW, et al. Clinical Pharmacogenetics Implementation Consortium guidelines for thiopurine methyltransferase genotype and thiopurine dosing. Clin Pharmacol Ther. 2011; 89:387–391.
crossref
39. Relling MV, Gardner EE, Sandborn WJ, Schmiegelow K, Pui CH, Yee SW, et al. Clinical pharmacogenetics implementation consortium guidelines for thiopurine methyltransferase genotype and thiopurine dosing: 2013 update. Clin Pharmacol Ther. 2013; 93:324–325.
crossref
40. Johnson JA, Gong L, Whirl-Carrillo M, Gage BF, Scott SA, Stein CM, et al. Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and VKORC1 genotypes and warfarin dosing. Clin Pharmacol Ther. 2011; 90:625–629.
crossref
41. Swen JJ, Nijenhuis M, de Boer A, Grandia L, Maitland-van der Zee AH, Mulder H, et al. Pharmacogenetics: from bench to byte--an update of guidelines. Clin Pharmacol Ther. 2011; 89:662–673.
crossref
42. Whirl-Carrillo M, McDonagh EM, Hebert JM, Gong L, Sangkuhl K, Thorn CF, et al. Pharmacogenomics knowledge for personalized medicine. Clin Pharmacol Ther. 2012; 92:414–417.
crossref
TOOLS
Similar articles