Test Catalog

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) 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.

 

See CYP2D6 Comprehensive Cascade Testing Algorithm.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

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.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Focused Pharmacogenomics Panel, V

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.

 

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: 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)/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)

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

Blood: 1 mL

Saliva, extracted DNA: see Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

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 (preferred)

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) 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.

 

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, *2A, *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, *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, *5, *6, *7, *8, and *9

-CYP4F2 *3

-rs12777823G>A

-SLCO1B1 rs4149056 variant found in the *5, *15, and *17 alleles, and rs4149015 found in the *17 and *21 alleles

-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 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
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Samples may contain donor DNA if obtained from patients who received non-leukoreduced blood transfusions or allogeneic hematopoietic stem cell transplantation. Results from samples 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 May;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 Oct 20;11(10):e0164972. doi: 10.1371/journal.pone.0164972

3. Clinical Pharmacogenetic Implementation Committee (CPIC): Genes-Drugs. CPIC; Accessed October 14, 2020. Available at https://cpicpgx.org/genes-drugs/

4. Pharmacogenomics Knowledgebase (PharmGKB). Accessed October 14, 2020. 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 Oct;110(4):888-896. doi: 10.1002/cpt.2149

Special Instructions
Library of PDFs including pertinent information and forms related to the test

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.(Instruction manual: TaqMan SNP Genotyping Assay User's Guide. Applied Biosystems; Revision A.0, 01/2014)

 

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 B)

 

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

Supplemental RE

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.

3 to 14 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Whole blood/Saliva: 2 weeks; Extracted DNA: 2 months

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

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 Regional Manager. 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. This test 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.

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 In Process
610189 CYP2C9 Genotype 46724-1
610190 CYP2C9 Phenotype 79716-7
610571 CYP2C9 Activity Score In Process
610191 CYP2D6 Genotype 40425-1
610192 CYP2D6 Phenotype 79715-9
610572 CYP2D6 Activity Score In Process
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

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Create a PDF

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports