Test Id : PGXQP
Focused Pharmacogenomics Panel, Varies
Useful For
Suggests clinical disorders or settings where the test may be helpful
Preemptive or reactive genotyping of patients for pharmacogenomic purposes
Providing an assessment for genes with strong drug-gene associations
Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request
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.
Reflex Tests
Lists tests that may or may not be performed, at an additional charge, depending on the result and interpretation of the initial 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 |
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
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.
Method Name
A short description of the method used to perform the test
Real Time Polymerase Chain Reaction (RT-PCR) with Allelic Discrimination Analysis/PCR followed by DNA Sequencing, when appropriate
NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.
Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test
Aliases
Lists additional common names for a test, as an aid in searching
CYP1A2
CYP2C19
CYP2C9
CYP2D6
CYP3A4
CYP3A5
CYP4F2
Cytochrome P450
Gene Panel
P450 Genotyping
PGx Focused Panel
Pharmacogenetic Panel
Selection of right medication
Pre-emptive genotyping
SLCO1B1
VKORC1
WARFSEN
1A2
2C19
2C9
2D6
3A4
3A5
4F2
1B1
OATP1B1
RS 12777823
SLC01B1
WARFARIN RESISTANCE
WARFARIN SENSITIVITY
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
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.
Specimen Type
Describes the specimen type validated for testing
Varies
Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing
Submit only 1 of the following specimens:
Specimen Type: Whole blood
Container/Tube:
Preferred: Lavender top (EDTA)
Acceptable: None
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
Special Instructions
Library of PDFs including pertinent information and forms related to the test
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)
Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the testing laboratory. The minimum volume is sufficient for one attempt at testing.
Whole Blood: 1 mL
Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected
Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included
Specimen Type | Temperature | Time | Special Container |
---|---|---|---|
Varies | Varies |
Useful For
Suggests clinical disorders or settings where the test may be helpful
Preemptive or reactive genotyping of patients for pharmacogenomic purposes
Providing an assessment for genes with strong drug-gene associations
Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request
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
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
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.
Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test
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
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.
An interpretive report will be provided.
Interpretation
Provides information to assist in interpretation of the test results
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 US Food and Drug Administration 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
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances
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
Recommendations for in-depth reading of a clinical nature
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 November 14, 2024. Available at https://cpicpgx.org/genes-drugs/
4. Pharmacogenomics Knowledgebase (PharmGKB). Accessed November 14, 2024. 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
Describes how the test is performed and provides a method-specific reference
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)
PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information
Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.
Monday through Friday
Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.
Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded
Performing Laboratory Location
Indicates the location of the laboratory that performs the test
Fees :
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.
- Authorized users can sign in to Test Prices for detailed fee information.
- Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
- Prospective clients should contact their account representative. For assistance, contact Customer Service.
Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.
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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.
CPT codes are provided by the performing laboratory.
CPT codes are provided by the performing laboratory.
0029U
0071U (if appropriate)
0072U (if appropriate)
0073U (if appropriate)
0074U (if appropriate)
0075U (if appropriate)
0076U (if appropriate)
LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.
Test Id | Test Order Name | Order LOINC Value |
---|---|---|
PGXQP | Focused Pharmacogenomics Panel, V | 82118-1 |
Result Id | Test Result Name |
Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
|
---|---|---|
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 |
610207 | Disclaimer | 62364-5 |
610208 | Reviewed by | 18771-6 |
610206 | Method | 85069-3 |