Journal List > Lab Med Online > v.6(4) > 1057318

Kim, Yun, Kim, Song, Woo, Lee, Lee, Cho, Ji, Chae, Lee, and Chun: Clinical Pharmacogenetic Testing and Application: Laboratory Medicine Clinical Practice Guidelines Part 2

Abstract

Pharmacogenetics is a rapidly evolving field and the number of pharmacogenetic tests for clinical use is steadily increasing. However, incorrect or inadequate implementation of pharmacogenetic tests in clinical practice may result in a rise in medical costs and adverse outcomes in patients. This document suggests guidelines for the clinical application, interpretation, and reporting of pharmacogenetic test results based on a literature review and the collection of evidence-based expert opinions. The clinical laboratory practice guidelines encompass the clinical pharmacogenetic tests covered by public medical insurance in Korea. Technical, ethical, and regulatory issues related to clinical pharmacogenetic tests have also been addressed. In particular, this document comprises the following pharmacogenetic tests: CYP2C9 and VKORC1 for warfarin, CYP2C19 for clopidogrel, CYP2D6 for tricyclic antidepressants, codeine, tamoxifen, and atomoxetine, NAT2 for isoniazid, UGT1A1 for irinotecan, TPMT for thio-purines, EGFR for tyrosine kinase inhibitors, ERBB2 (HER2) for erb-b2 receptor tyrosine kinase 2-targeted therapy, and KRAS for anti-epidermal growth factor receptor drugs. These guidelines would help improve the usefulness of pharmacogenetic tests in routine clinical settings.

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Table 1.
CYP2C9 alleles and enzyme activity [11]
Allele Constituted by genotypes at: Amino acid changes Enzymatic activity
∗1 Reference allele   Normal
∗2 C>T at rs1799853 R144C Decreased
∗3 A>C at rs1057910 I359L Decreased
∗4 T>C at rs56165452 I359T Decreased
∗5 C>G at rs28371686 D360E Decreased
∗6 delA at rs9332131 273 frame shift Null
∗7 C>A at rs67807361 L19I  
∗8 G>A at rs7900194 R150H Decreased
∗9 A>G at rs2256871 H251R  
∗11 C>T at rs28371685 R335W Decreased
∗12 C>T at rs9332239 P489S Decreased
∗13 T>C at rs72558187 L90P Decreased
∗14 G>A at rs72558189 R125H Decreased
∗15 C>A at rs72558190 S162X Null
∗16 A>C at rs72558192 T299A Decreased
∗17 1144C>T P382S Decreased
∗18 A>C at rs1057910, A>C at rs72558193, A>T at rs1057911 I359L; D397A Decreased
∗25 delAGAAATGGAA at rs72558188 118 frame shift Null
∗33 G>A at rs72558184 R132Q Decreased
Table 2.
Allele frequencies (%) of CYP2C9 and VKORC1
Allele White [6] Asian [6] Black [6] Korean [105-110] Chinese [111-118] Japanese [119-123]
CYP2C9∗2 13 0 3 0 0 0
CYP2C9∗3 7 4 2 4-5 2-9 2
VKORC1 −1639G>A (rs9923231) or 1173C>T (rs9934438) 39 91 11 87-94 88-93 86-92
Table 3.
Recommended warfarin doses (mg/day) to achieve a therapeutic international normalized ratio based on CYP2C9 and VKORC1 genotypes using the warfarin product insert approved by the United States Food and Drug Administration
VKORC1 −1639G>A CYP2C9∗1/∗1 CYP2C9∗1/∗2 CYP2C9∗1/∗3 CYP2C9∗2/∗2 CYP2C9∗2/∗3 CYP2C9∗3/∗3
GG 5-7 5-7 3-4 3-4 3-4 0.5-2
GA 5-7 3-4 3-4 3-4 0.5-2 0.5-2
AA 3-4 3-4 0.5-2 0.5-2 0.5-2 0.5-2
Table 4.
Representative warfarin dosing algorithms
  International Warfarin Pharmacogenetic Consortium (IWPC) algorithm Gage algorithm
Derivation cohort, total/Asian (n) 4,043/1,229 1,015/NA
Validation cohort, total/Asian (n) 1,009/300 292/NA
Variables in the dosing equation Age (decades), height (cm), weight (kg), VKORC1 genotype (-1639G>A), CYP2C9 genotype (∗2, ∗3), race (Asian, black/ African American, missing, or mixed), enzyme inducer (carbamazepine, phenytoin, rifampin, or rifampicin) status, amiodarone status VKORC1 genotype (-1639G>A), BSA, CYP2C9 genotype (∗2, ∗3), Age (decades), target INR, per 0.5 increase, amiodarone status, current smoker, race (African American), DVT/PE
Output Square root of weekly warfarin dose Daily dose
Internet source http://www.warfarindosing.org, http://www.pharmgkb.org http://www.warfarindosing.org

Abbreviations: BSA, body surface area in meters; DVT, deep vein thrombosis; INR, international normalized ration; PE, pulmonary embolism.

Table 5.
Frequencies (%) of CYP2C19 alleles
Allele White [124, 125] African American [124, 125] Hispanic [124] Ashkenazi Jewish [124] Asian [30] Korean [40-47]
∗1 84-87.1 75-82 85 83 60-62 60.0-65.3
∗2 12-12.9 12-25.0 10 12 29-35 26.0-30.3
∗3 0 0 - - 2.4-8.9 6.8-10.1
∗4 0.3 0 0 0.45 0-0.5 0
∗5 - - - - 0-0.6 -
∗6 - - - - 0 0
∗7 - - - - - -
∗8 0.4 0.3 0 0.15 0 0
∗17 - - - - 0.3 1.2-1.5
Table 6.
Assigning likely CYP2C19 phenotypes based on genotypes [31]
Likely phenotype Genotypes Examples of diplotypes
Ultra-rapid metabolizer: normal or increased activity (~5-30% of patients) An individual carrying 2 increased-activity alleles (∗17), or 1 functional allele (∗1) plus 1 increased-activity allele (∗17) ∗1/∗17, ∗17/∗17
Extensive metabolizer: homozygous wild-type or An individual carrying 2 functional (∗1) alleles ∗1/∗1
normal activity (~35-50% of patients)    
Intermediate metabolizer: heterozygote or intermediate An individual carrying 1 functional allele (∗1) plus 1 loss-of- ∗1/∗2, ∗1/∗3
activity (~18-45% of patients) function allele (∗2-∗8)  
Poor metabolizer: homozygous variant, mutant, low, or deficient activity (~2-15% of patients) An individual carrying 2 loss-of-function alleles (∗2-∗8) ∗2/∗2, ∗2/∗3, ∗3/∗3
Table 7.
Clopidogrel therapy based on CYP2C19 phenotype for ACS/PCI patients initiating antiplatelet therapy [31]
Phenotype (genotype) Implications for clopidogrel Therapeutic recommendations
Ultra-rapid metabolizer (UM) (∗1/∗17, ∗17/∗17) and extensive metabolizer (EM) (∗1/∗1) Normal (EM) or increased (UM) platelet inhibition; normal (EM) or decreased (UM) residual platelet aggregationa Clopidogrel label-recommended dosage and administration
Intermediate metabolizer (IM) (∗1/∗2, ∗1/∗3, ∗2/∗17) Reduced platelet inhibition; increased residual platelet aggrega- Prasugrel or other alternative therapy (if no
  tion; increased risk for adverse cardiovascular events contraindication)
Poor metabolizer (PM) (∗2/∗2, ∗2/∗3, ∗3/∗3) Significantly reduced platelet inhibition; increased residual plate- Prasugrel or other alternative therapy (if no
  let aggregation; increased risk for adverse cardiovascular events contraindication)

a The CYP2C19∗17 allele may be associated with an increased risk of bleeding.

Table 8.
Frequencies of CYP2D6 alleles (%)
Allele East Asian [50] Korean [126] Korean [54] Europe [50] African [50] South/Central Asian [50] Oceanian [50]
∗1 34.17 33.25 32.32 53.63 39.23 53.70 70.15
∗2 12.82 10.13 10.88 26.91 20.12 31.90 1.20
∗3 0.00 0.00 - 1.32 0.03 0.00 0.00
∗4 0.42 0.25 - 18.50 3.36 6.56 1.13
∗5 5.61 6.13 5.61 2.69 6.07 2.54 4.95
∗10 42.31 45.00 45.58 3.16 6.77 19.76 1.60
∗41 1.97 1.88 2.24 8.56 10.94 10.50 0.00
∗2xN 0.38 0.50 0.99 1.27 1.56 0.50 0.00
∗1xN 0.28 0.13 0.07 0.80 1.47 0.50 11.83
Table 9.
Assignment of likely phenotypes based on diplotypes of CYP2D6 [49, 127]
Likely phenotype Activity score Genotypes Examples of diplotypes
Ultra-rapid metabolizer (~1-2%) > 2.0 An individual carrying duplications of functional alleles (∗1/∗1)xN, (∗1/∗2)xN, (∗2/∗2)xN
Extensive metabolizer (~77-92%) 1.0-2.0 An individual carrying 2 functional alleles or 1 functional and ∗1/∗1, ∗1/∗2, ∗2/∗2, 1/∗9, ∗1/∗41, ∗1/∗5, ∗1/∗4
    1 nonfunctional allele or 1 functional and 1 reduced function allele  
Intermediate metabolizer (~2-11%) 0.5 An individual carrying 1 reduced function and 1 nonfunctional allele or ∗4/∗41, ∗5/∗9, ∗4/∗10, ∗41/∗41
    2 reduced function alleles  
Poor metabolizer (~5-10%) 0 An individual carrying no functional alleles ∗4/∗4, ∗3/∗4, ∗5/∗5, ∗5/∗6
Table 10.
Dosing recommendations for amitriptyline and nortriptyline based on CYP2D6 phenotype [49]
Phenotype Implication Therapeutic recommendation
Ultra-rapid metabolizer Increased metabolism of tricyclics to less active compounds when compared with extensive metabolizers. Avoid tricyclic use due to potential lack of efficacy. Consider an alternative drug not metabolized by CYP2D6.
  Lower plasma concentrations will increase the probability If a tricyclic is warranted, consider increasing the starting dose. Utilize therapeu-
  of pharmacotherapy failure. tic drug monitoring to guide dose adjustments.
Extensive metabolizer Normal metabolism of tricyclics. Initiate therapy with recommended starting dose.
Intermediate metabolizer Reduced metabolism of tricyclics to less active compounds when compared with extensive metabolizers. Consider a 25% reduction of the recommended starting dose. Utilize therapeutic drug monitoring to guide dose adjustments.
  Higher plasma concentrations will increase the probability of side effects.  
Poor metabolizer (~5-10%) Greatly reduced metabolism of tricyclics to less active compounds when compared with extensive metabolizers. Avoid tricyclic use due to the potential for side effects. Consider an alternative drug not metabolized by CYP2D6.
  Higher plasma concentrations will increase the probability of side effects. If a tricyclic is warranted, consider a 50% reduction of the recommended starting dose. Utilize therapeutic drug monitoring to guide dose adjustments.
Table 11.
Frequencies of NAT2 alleles (%)
Allele Cambo- Japanese Korean Korean Korean Europe- African
Allele dian [69] [71] [70] [71] [72] an [71] [71]
∗4 40.1 69.3 65.7 62.4 62.3 - 8.9
∗5 11.3 - 1.6 - 1.9 53.3 71.6
∗6 31.4 22.7 20.1 22.4 21.2 - -
∗7 17.2 - 11.5 15.2 13.5 - -
∗11 - - - - - 44.4 19.4
∗12 - - 0.8 - 0.5 - -
∗13 - 8.0 0.1 - 0.7 2.3 -
Table 12.
Assignment of likely phenotypes based on diplotypes of NAT2 [68, 70]
Likely phenotype Genotype Examples of diplotypes
Normal/high activity (rapid acetylator) 2 rapid NAT2 alleles (∗4, ∗11, ∗12, ∗13) ∗4/∗4, ∗4/∗12, ∗4/∗13, etc.
Intermediate activity (intermediate acetylator) 1 rapid NAT2 allele and 1 slow NAT2 allele ∗4/∗5, ∗4/∗6, ∗4/∗7, etc.
Low activity (slow acetylator) 2 slow NAT2 alleles (∗5, ∗6, ∗7) ∗6/∗6, ∗7/∗7, ∗6/∗7, ∗5/∗6, ∗5/∗7, etc.
Table 13.
Frequencies of UGT1A1 alleles (%)
Allele Asian [128] Korean [129] Korean [130] Korean [131] Korean [132] Korean [133] White [128] Black [128]
∗6 15.7 21.3 18.6 15.5 22.2 19.3 0.7 0.0
∗28 9.7 12.7 10.4 10.3 9.5 11.4 38.8 44.6
Table 14.
Assignment of likely phenotypes based on diplotypes of UGT1A1
Likely phenotype Genotype Examples of diplotypes
Homozygous wild (normal/high activity) Two functional alleles (∗1) ∗1/∗1
Heterozygote (intermediate activity, intermediate metabolizer) One functional (∗1) and one reduced function allele (∗6, ∗28) ∗1/∗6, ∗1/∗28
Compound heterozygote [134] (low activity, poor metabolizer) One reduced function allele (∗6) and another reduced function allele (∗28) ∗6/∗28
Homozygous variant (low activity, poor metabolizer) Two reduced function alleles (∗6, ∗28) ∗6/∗6, ∗28/∗28
Table 15.
Frequencies of TPMT alleles (%)
Allele Asian [82] Korean [40] Korean [41] Korean [42] Korean [43] Korean [44] Korean [45] Korean [87] Caucasian [82]
∗1 98.35 98.88 97.51 98.95 98.78 96.19 96.00 96.44 95.73
∗2 0 0 0 0 0 0 1.00 0 0.19
∗3A 0.01 0 0 0 0 0 0.50 0 3.56
∗3B 0 0 0 0 0 0 0 0 0.05
∗3C 1.57 0.88 1.75 1.05 1.22 2.54 2.50 1.44 0.42
∗6 0.07 0.25 0.73 - - 1.27 - 0.17 -
Table 16.
Assignment of likely thiopurine S-methyltransferase phenotypes based on genotypes [23]
Likely phenotype Genotypes Examples of diplotypes
Homozygous wild-type or normal high activity (constitutes ~86-97% of patients) An individual carrying two or more functional (∗1) alleles ∗1/∗1
Heterozygote or intermediate activity (~3-14% of patients) An individual carrying one functional allele (∗1) plus one nonfunctional allele (∗2, ∗3A, ∗3B, ∗3C, or ∗4) ∗1/∗2, ∗1/∗3A, ∗1/∗3B, ∗1/∗3C, ∗1/∗4
Homozygous variant, mutant, low, or deficient activity (~1 in 178 to 1 in 3,736 patients) An individual carrying two nonfunctional alleles (∗2, ∗3A, ∗3B, ∗3C, or ∗4) ∗3A/∗3A, ∗2/∗3A, ∗3C/∗3A, ∗3C/∗4, ∗3C/∗2, ∗3A/∗4
Table 17.
Drug sensitivity according to genetic variations in EGFR
Major genetic variation Nomenclature Phenotype
G719S (exon 18) NM_005228.3:c.2155G<A, NP_005219.2:p.Gly719Ser TKI sensitivity
G719C (exon 18) NM_005228.3:c.2155G<T, NP_005219.2:p.Gly719Cys TKI sensitivity
G719A (exon 18) NM_005228.3:c.2155G<C, NP_005219.2:p.Gly719Ala TKI sensitivity
In-frame deletions (exon 19) NM_005228.3:c.2235_2249del15, NP_005219.2:p.Glu746_Ala750del TKI sensitivity
  NM_005228.3:c.2236_2250del15, NP_005219.2:p.Glu746_Ala750del TKI sensitivity
  NM_005228.3:c.2239_2248delinsC, NP_005219.2:p.Leu747_Ala750delinsPro NM_005228.3:c.2240_2257del18, NP_005219.2:p.Leu747_Pro753delinsSer TKI sensitivity TKI sensitivity
T790M (exon 20) NM_005228.3:c.2369C>T, NP_005219.2:p.Thr790Met TKI resistance
L858R (exon 21) NM_005228.3:c.2573T>G, NP_005219.2:p.Leu858Arg TKI sensitivity
L861Q (exon 21) NM_005228.3: c.2582T>A, NP_005219.2:p.Leu861Gln TKI sensitivity
Table 18.
Number and type of mutations, affected codons, and corresponding altered amino acids in exon 2, codons 12 and 13 of the KRAS gene, analyzed separately for specimens derived from primary tumors and metastases [104]
Codon Type of point mutation Frequency of mutations in primary tumors (n=879)(% of all tumors) Frequency of mutations in metastases (n =139) (% of all tumors)
12 c.35G>A (p.G12D) c.35G>T (p.G12V) 123 (14.0%) 78 (8.9%) 21 (15.1%) 9 (6.5%)
  c.34G>T (p.G12C) 29 (3.3%) 3 (2.2%)
  c.34G>A (p.G12S) c.35G>C (p.G12A) 21 (2.4%) 21 (2.4%) 5 (3.6%) 3 (2.2%)
  c.34G>C (p.G12R) c.34G>A, c.35G4T (p.G12I) 4 (0.5%) 1 (0.1%) 1 (0.7%) Not reported
  c.34G>T, c.35G4T (p.G12F) 1 (0.1%) 1 (0.7%)
13 c.38G>A (p.G13D) c.37G>T (p.G13C) 68 (7.7%) 2 (0.2%) Not reported 7 (5.0%)
  c.37G>C (p.G13R) 1 (0.1%) 1 (0.7%)
Wild type 530 (60.3%) 88 (63.3%)
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