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HelpTest Code PGXQP Focused Pharmacogenomics Panel, Varies
Additional Codes
Epic# -
LAB000 (enter test name into comments)
Cerner name(s):
- Miscellaneous Sendout
Specimen Required
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 reflex testing for 2D6 sequencing and will stop after initial 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 50 ng/mcL.
2. Provide concentration of DNA and volume on tube.
Specimen Stability Information: Frozen (preferred) 1 year/Ambient/Refrigerated
Forms
1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available:
-Informed Consent for Genetic Testing (T576)
-Informed Consent for Genetic Testing-Spanish (T826)
2. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:
-Neurology Specialty Testing Client Test Request (T732)
-Therapeutics Test Request (T831)
-Cardiovascular Test Request (T724)
-Renal Diagnostics Test Request (T830)
Secondary ID
610057Useful For
Preemptive or reactive genotyping of patients for pharmacogenomic purposes
Providing an assessment for genes with strong drug-gene associations
Genetics Test Information
This test includes targeted testing to evaluate the following genes:
CYP1A2, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, SLCO1B1, VKORC1, CYP4F2, and rs12777823.
CYP2D6 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 an ambiguous phenotype results from tier 1 testing. Approximately 3% of samples require tier 2 testing.
Testing Algorithm
If a specimen requires follow-up for CYP2D6, then reflex testing will be performed as appropriate at an additional charge.
For more information see CYP2D6 Comprehensive Cascade Testing Algorithm.
Special Instructions
Method Name
Real Time Polymerase Chain Reaction (RT-PCR) with Allelic Discrimination Analysis/PCR followed by DNA Sequencing, when appropriate
Reporting Name
Focused Pharmacogenomics Panel, VSpecimen Type
VariesSpecimen Minimum Volume
Whole Blood: 1 mL
Saliva, extracted DNA: see Specimen Required
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 suitability.Clinical Information
This panel provides a comprehensive analysis for multiple genes with strong drug phenotype associations. Each sample is tested for specific variations with known functional impact. Pharmacogenomic data for the following specific variants are reviewed and reported (if present):
-CYP1A2 *1F, *1K, *6, and *7
-CYP2C9 *2, *3, *4, *5, *6, *8, *9, *11, *12, *13, *14, *15, *16, *17, *18, *25, *26, *28, *30, *33, and *35
-CYP2C19 *2, *3, *4, *5, *6, *7, *8, *9, *10, *17, and *35
-CYP2D6 *2, *3, *4, *4N, *5, *6, *7, *8, *9, *10, *11, *12, *13, *14A (now known as *114), *14B (now known as *14), *15, *17, *29, *35, *36, *41, *59, *68, and CYP2D6 gene duplication; additional CYP2D6 variants may be detected through the reflex testing process
-CYP3A4 *8, *11, *12, *13, *16, *17, *18, *22, and *26
-CYP3A5 *3, *6, *7, *8, and *9
-CYP4F2 *3
-rs12777823G>A
-SLCO1B1 rs4149056 (*5)
-VKORC1 c. -1639G>A, c.85G>T, c.106G>T, c.121G>T, c.134T>C, c.172A>G, c.196G>A, c.358C>T, and c.383T>G
Based on the results of each assay, a genotype is assigned, and a phenotype is predicted for each gene. Assessment of multiple genes may assist the ordering clinician with personalized drug recommendations, avoidance of adverse drug reactions, and optimization of drug treatment.
Reference Values
An interpretive report will be provided.
Interpretation
An interpretive report will be provided, which focuses on only drugs and genes with published pharmacogenomic practice guidance by the Clinical Pharmacogenetics Implementation Consortium, other professional organizations or where strong FDA guidance has been issued in drug labels.
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
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. Genetic test results in patients who have undergone liver transplantation may not accurately reflect the patient's genetic status for the genes on this panel.
This test is not designed to provide specific dosing recommendations and is to be used as an aid to clinical decision making only. Results should be used along with other clinical and laboratory data. Drug-label guidance should be used when dosing patients with medications regardless of the predicted phenotype.
For additional information, see the following tests:
-1A2Q / Cytochrome P450 1A2 Genotype, Varies
-2C9QT / Cytochrome P450 2C9 Genotype, Varies
-2C19R / Cytochrome P450 2C19 Genotype, Varies
-2D6Q / Cytochrome P450 2D6 Comprehensive Cascade, Varies
-3A4Q / Cytochrome P450 3A4 Genotype, Varies
-3A5Q / Cytochrome P450 3A5 Genotype, Varies
-SLC1Q / Solute Carrier Organic Anion Transporter Family Member 1B1 (SLCO1B1) Genotype, Statin, Varies
-WARSQ / Warfarin Response Genotype, Varies
Clinical Reference
1. Ji Y, Skierka JM, Blommel JH, et al. 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. 2016;18(3):438-445. doi:10.1016/j.jmoldx.2016.01.003
2. Samwald M, Xu H, Blagec K, et al. Incidence of exposure of patients in the United States to multiple drugs for which pharmacogenomic guidelines are available. PLoS One. 2016;11(10):e0164972. doi:10.1371/journal.pone.0164972
3. Clinical Pharmacogenetic Implementation Committee (CPIC): Genes-Drugs. CPIC; Accessed October 25, 2023. Available at https://cpicpgx.org/genes-drugs/
4. Pharmacogenomics Knowledgebase (PharmGKB). Accessed October 25, 2023. Available at www.pharmgkb.org/
5. Crews KR, Monte AA, Huddart R, et al. Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2D6, OPRM1, and COMT Genotypes and Select Opioid Therapy. Clin Pharmacol Ther. 2021;110(4):888-896. doi: 10.1002/cpt.2149
Method Description
Genomic DNA is extracted from whole blood or saliva. Genotyping for each allele 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)
CYP2D6 Copy Number Assay:
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 to10 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)
2D6 Sequencing Assays (Tier 2, as needed):
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 Friday
Report Available
3 to 14 daysSpecimen Retention Time
Whole blood/Saliva: 2 weeks; Extracted DNA: 2 monthsPerforming 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
0029U
0071U (if appropriate)
0072U (if appropriate)
0073U (if appropriate)
0074U (if appropriate)
0075U (if appropriate)
0076U (if appropriate)
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| PGXQP | Focused Pharmacogenomics Panel, V | 82118-1 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 610185 | CYP1A2 Genotype | 72884-0 |
| 610186 | CYP1A2 Phenotype | 94254-0 |
| 610187 | CYP2C19 Genotype | 57132-3 |
| 610188 | CYP2C19 Phenotype | 79714-2 |
| 610570 | CYP2C19 Activity Score | 104667-1 |
| 610189 | CYP2C9 Genotype | 46724-1 |
| 610190 | CYP2C9 Phenotype | 79716-7 |
| 610571 | CYP2C9 Activity Score | 104668-9 |
| 610191 | CYP2D6 Genotype | 40425-1 |
| 610192 | CYP2D6 Phenotype | 79715-9 |
| 610572 | CYP2D6 Activity Score | 104669-7 |
| 610193 | CYP3A4 Genotype | 81139-8 |
| 610194 | CYP3A4 Phenotype | 81145-5 |
| 610195 | CYP3A5 Genotype | 81140-6 |
| 610196 | CYP3A5 Phenotype | 79717-5 |
| 610197 | SLCO1B1 Genotype | 93412-5 |
| 610198 | SLCO1B1 Phenotype | 79722-5 |
| 610199 | Warfarin CYP2C9 Genotype | 46724-1 |
| 610201 | Warfarin VKORC1 Resistance Genotype | 50722-8 |
| 610200 | Warfarin VKORC1 Promoter Genotype | 50722-8 |
| 614000 | Warfarin CYP2C9 and VKORC1 Promoter Phenotype | 54451-0 |
| 610202 | Warfarin CYP4F2 *3 Genotype | 93197-2 |
| 610203 | Warfarin rs12777823 Genotype | 93198-0 |
| 610204 | Interpretation | 69047-9 |
| 610205 | Additional Information | 48767-8 |
| 610206 | Method | 85069-3 |
| 610207 | Disclaimer | 62364-5 |
| 610208 | 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 |