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HelpTest Code 2D6Q Cytochrome P450 2D6 Comprehensive Cascade, Varies
Ordering Guidance
This test is not for use in assessing for autoimmune hepatitis. Autoantibodies for the CYP2D6 enzyme are found in many cases of autoimmune hepatitis; order LKM / Liver/Kidney Microsome Type 1 Antibodies, Serum for autoimmune hepatitis assessment.
Testing is available as the single gene assay (this test) and as a part of a psychotropic or focused pharmacogenomics panel.
If multiple pharmacogenomic genotype testing is desired, order PGXQP / Focused Pharmacogenomics Panel, Varies.
If genotype testing for psychotropic medications is desired, order PSYQP / Psychotropic Pharmacogenomics Gene Panel, Varies.
Specimen Required
Multiple genotype tests can be performed on a single specimen after a single extraction. See Multiple Genotype Test List for a list of tests that can be ordered together.
Submit only 1 of the following specimens:
Specimen Type: Whole blood
Container/Tube: Lavender top (EDTA)
Specimen Volume: 3 mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send whole blood specimen in original tube. Do not aliquot.
Specimen Stability Information: Ambient (preferred) 9 days/Refrigerated 30 days
Specimen Type: Saliva
Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.
Supplies: Saliva Swab Collection Kit (T786)
Specimen Volume: 1 swab
Collection Instructions: Collect and send specimen per kit instructions.
Additional Information: Due to lower concentration of DNA yielded from saliva, testing cannot proceed to tier 2 sequencing and will stop after tier 1 testing is complete.
Specimen Stability Information: Ambient 30 days
Specimen Type: Extracted DNA
Container/Tube: 2 mL screw top tube
Specimen Volume: 100 mcL (microliters)
Collection Instructions:
1. The preferred volume is 100 mcL at a concentration of 75 ng/mcL.
2. Include concentration and volume on tube.
Specimen Stability Information: Frozen (preferred) 1 year/Ambient/Refrigerated
Useful For
Providing information relevant to tamoxifen, codeine, and tramadol, as well as other medications metabolized by cytochrome P450 2D6
Determining the exact genotype when other methods fail to generate this information or if genotype-phenotype discord is encountered clinically
Identifying precise genotype when required (eg, drug trials, research protocols)
Identifying novel variants that may interfere with drug metabolism (when reflex to sequencing is performed)
Genetics Test Information
Testing is done in 2 tiers when needed. Tier 1 uses a polymerase chain reaction (PCR)-based 5'-nuclease assay to determine the variants present. All samples also have copy number determined by PCR-based 5'-nuclease assay. Testing in tier 1 allows for the detection of all common CYP2D6 variants (eg, *2, *3, *4, *5, *6, *7, *8, *9, *10, *17, *29, *35, *41, *59) and rarer alleles such as *11, *12, *14, *15, and *114. Duplications and multiplications of alleles are also identified. Unitary and tandem CYP2D7-2D6 (*13) alleles and CYP2D6-2D7 (eg, *4N, *36, and *68) alleles can also be detected. Tier 2 testing involves sequencing using fluorescent dye-terminator chemistry and is only done if tier 1 testing results are ambiguous. Approximately 3% of samples require tier 2 testing.
Testing Algorithm
Tier 2 testing will be performed only if an ambiguous phenotype is identified by tier 1 testing. The number of sequencing tests needed to determine the phenotype will vary depending on the tier 1 result.
For more information see CYP2D6 Comprehensive Cascade Testing Algorithm.
Special Instructions
Method Name
Tier 1: Real Time Polymerase Chain Reaction (PCR)
Tier 2: Polymerase Chain Reaction (PCR) followed by DNA Sequence Analysis
Reporting Name
CYP2D6 Genotype Cascade, VSpecimen Type
VariesSpecimen Minimum Volume
Blood: 1 mL
Saliva: 1 swab
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Varies | Varies | ||
Reject Due To
All specimens will be evaluated at Mayo Clinic Laboratories for test suitabilityClinical Information
The cytochrome P450 (CYP) family of enzymes is a group of oxidative/dealkylating enzymes localized in the microsomes of many tissues including the intestines and liver. One of the CYP enzymes, CYP2D6, is wholly or partially responsible for the metabolism of many commonly prescribed drugs.
The CYP2D6 gene is highly variable with over 100 named alleles. The gene may be deleted, duplicated, and multiplied, and can have multiple sequence variations. In addition, some individuals have genes that are hybrids of CYP2D6 and the CYP2D7 pseudogene. Some individuals have CYP2D6 variants that result in synthesis of an enzyme with decreased or absent catalytic activity. These individuals may process CYP2D6-metabolized medications more slowly. CYP2D6 duplications and multiplications involving active alleles may result in ultrarapid metabolism of CYP2D6-metabolized drugs. CYP2D6 genotype results are used to predict metabolizer phenotypes.(See Table 1)
Table 1. Enzyme Activity of Individual Star Alleles
|
Enzyme activity |
Examples of CYP2D6 star alleles |
|
Normal (extensive) metabolism |
*1, *2, *35 |
|
Decreased activity |
*9, *10, *14, *17, *29, and *41, *59 |
|
No or null activity |
*3, *4, *4N, *5, *6, *7, *8, *11, *12, *13, *15, *36, *68, *114 |
CYP2D6 phenotype is predicted based upon the number of functional, partially functional, and nonfunctional alleles present in a sample.
Phenotyping is derived from the Pharmacogene Variation Consortium website (1), the Clinical Pharmacogenetics Implementation Consortium website (2), published guidelines (3-8), and an exhaustive review of the CYP2D6 literature (9-10).
There are instances where a precise phenotype prediction is not possible, and in these instances, a range of possible phenotypes will be given. Individuals without a detectable gene alteration will have the predicted phenotype of an extensive drug metabolizer and are designated as CYP2D6*1/*1.
Drugs that are metabolized through CYP2D6 may require dosage adjustment based on the individual patient's genotype. Patients who are poor metabolizers may require lower than usual doses to achieve optimal response in the case of drugs that are inactivated by the CYP2D6 enzyme and higher than usual doses in the case of drugs that are activated by CYP2D6 enzyme. Alternatively, patients who are ultrarapid metabolizers may benefit from increased doses in the case of drugs that are inactivated by CYP2D6 enzyme and lower doses in the case of drugs that are activated by CYP2D6. In the absence of clear guidance from FDA on dosing for various metabolizer phenotypes, patients with either ultrarapid or poor metabolism may benefit by switching to comparable alternate medications not primarily metabolized by CYP2D6 or by therapeutic drug monitoring where applicable.
Overall, this test provides a comprehensive CYP2D6 genotype result for patients, ensuring a more accurate phenotype prediction. This assay has clinical significance for patients taking or considering medications activated (eg, codeine, tramadol, and tamoxifen) or inactivated (eg, antidepressants and antipsychotics) by the CYP2D6 enzyme.
Sequential tier testing associated with this test will be initiated until the least ambiguous phenotype possible is determined.
Reference Values
A comprehensive interpretive report will be provided.
Interpretation
A comprehensive interpretive report will be provided, which combines the results of all tier testing utilized to obtain the final genotype.
The genotype, with associated star alleles, is assigned using standard allelic nomenclature as published by the Pharmacogene Variation (PharmVar) Consortium.(1)
For the CYP2D6 copy number variation assay, the reportable copy number range is 0 to 4 copies for each of the CYP2D6 region assessed.
Novel variants will be classified based on known, predicted, or possible effect on gene function and reported with interpretive comments detailing their potential or known significance.
For additional information regarding pharmacogenomic genes and their associated drugs, see Pharmacogenomic Associations Tables. This resource also includes information regarding enzyme inhibitors and inducers, as well as potential alternate drug choices.
Cautions
Rare variants may be present that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings (phenotype), additional testing should be considered.
Specimens may contain donor DNA if obtained from patients who received non-leukoreduced blood transfusions or allogeneic hematopoietic stem cell transplantation. Results from specimens obtained under these circumstances may not accurately reflect the recipient's genotype. For individuals who have received blood transfusions, the genotype usually reverts to that of the recipient within 6 weeks. For individuals who have received allogeneic hematopoietic stem cell transplantation, a pretransplant DNA specimen is recommended for testing.
CYP2D6 genetic test results in patients who have undergone liver transplantation may not accurately reflect the patient's CYP2D6 status.
This method may not detect all CYP2D6 variants that result in altered CYP2D6 activity. Therefore, absence of a detectable variant does not rule out the possibility that a patient has altered CYP2D6 metabolism due to other CYP2D6 variants that cannot be detected with this method. Furthermore, when 2 or more variants are identified, the cis-/trans- status (whether the variants are on the same or opposite chromosomes) is not always known.
A complicating factor in correlating CYP2D6 genotype with phenotype is that many drugs or their metabolites are inhibitors of CYP2D6 catalytic activity. Selective-serotonin reuptake inhibitors (SSRI), as well as some tricyclic antidepressants (TCA) and other drugs, may reduce CYP2D6 catalytic activity. Patients in all metabolizer categories, except poor metabolizer, may have CYP2D6 enzyme activity inhibited by a variety of medications or their metabolites. Consequently, an individual may require a lower medication dose than predicted by genotyping alone. It is important to interpret the results of testing in the context of other coadministered drugs.
CYP2D6 alleles with decreased function may metabolize different drugs at different rates, ranging from normal to poor, but the literature on this is incomplete at this time.
This test is not designed to provide specific dosing or drug selection recommendations and is to be used as an aid to clinical decision making only. Drug-label guidance should be used when dosing patients with medications regardless of the predicted phenotype.
Method Description
Genomic DNA is extracted from whole blood or saliva.
Genotype Assay (Tier 1):
Genotyping is performed using a polymerase chain reaction (PCR)-based 5'-nuclease assay. Fluorescently labeled detection probes anneal to the target DNA. PCR is used to amplify the section of DNA that contains the variant. If the detection probe is an exact match to the target DNA, the 5'-nuclease polymerase degrades the probe, the reporter dye is released from the effects of the quencher dye, and a fluorescent signal is detected. Genotypes are assigned based on the allele-specific fluorescent signals that are detected.(Unpublished Mayo method)
Copy Number Assay (Tier 1):
This assay utilizes a duplex real-time PCR, which includes 1 copy number probe and a reference assay per reaction. Each copy number probe detects the genomic sequence of interest and the reference assay detects a sequence that is known to be present in 2 copies in a diploid genome. Relative quantitation is used to determine the relative copy number of the target of interest in a genomic DNA (gDNA) sample normalized to 10 ng/mcL for each probe. Each probe is normalized to the known copy number of the reference sequence, and compared to a calibrator sample with known copies of the target sequence included with each run.(Package insert: Taqman Copy Number Assays. Applied Biosystems; Revision D, 02/2019)
Sequencing Assays (Tier 2):
The CYP2D6 allele of interest is amplified by PCR. The PCR product is then purified and sequenced in both directions using fluorescent dye-terminator chemistry. Sequencing products are separated on an automated sequencer and trace files analyzed for variations in the exons and intron/exon boundaries of all 9 exons using mutation detection software and visual inspection.(Unpublished Mayo method)
Day(s) Performed
Monday through Thursday
Report Available
3 to 16 daysPerforming Laboratory
Mayo Clinic Laboratories in Rochester
Test Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.CPT Code Information
0070U
0071U (if appropriate)
0076U (if appropriate)
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| 2D6Q | CYP2D6 Genotype Cascade, V | 47403-1 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 610103 | CYP2D6 Genotype | 40425-1 |
| 610104 | CYP2D6 Phenotype | 79715-9 |
| 610569 | CYP2D6 Activity Score | 104669-7 |
| 610105 | Interpretation | 69047-9 |
| 610106 | Additional Information | 48767-8 |
| 610107 | Method | 85069-3 |
| 610108 | Disclaimer | 62364-5 |
| 610109 | Reviewed by | 18771-6 |
Reflex Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| 2D61Z | CYP2D6 Full Gene Sequence | No, (Bill Only) | No |
| 2D62Z | CYP2D6 GEN CYP2D6-2D7 Hybrid | No, (Bill Only) | No |
| 2D63Z | CYP2D6 GEN CYP2D7-2D6 Hybrid | No, (Bill Only) | No |
| 2D64Z | CYP2D6 Nonduplicated Gene | No, (Bill Only) | No |
| 2D65Z | CYP2D6 5' Gene DUP/MLT | No, (Bill Only) | No |
| 2D66Z | CYP2D6 3' Gene DUP/MLT | No, (Bill Only) | No |