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Test Code PGXQP Focused Pharmacogenomics Panel, Varies


Specimen Required


Patient Preparation: A previous hematopoietic stem cell transplant from an allogenic donor will interfere with testing. For information about testing patients who have received a hematopoietic stem cell transplant, call 800-533-1710.

 

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) 4 days/Refrigerated 4 days/Frozen 4 days

Additional Information:

1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2. To ensure minimum volume and concentration of DNA is met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

 

Specimen Type: Cord blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send cord blood specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 4 days/Frozen 4 days

Additional Information:

1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.

2. To ensure minimum volume and concentration of DNA is met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.

3. While a properly collected cord blood sample may not be at risk for maternal cell contamination, unanticipated complications may occur during collection. Therefore, maternal cell contamination studies are recommended to ensure the test results reflect that of the patient tested and are available at an additional charge. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.

 

Specimen Type: Saliva

Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.

Supplies: Saliva Collection Kit (T786)

Specimen Volume: 2 Swabs

Collection Instructions: Collect and send specimen per kit instructions.

Specimen Stability Information: Ambient (preferred) 30 days/Refrigerated 30 days

Additional Information: Saliva specimens are acceptable but not recommended. Due to lower quantity/quality of DNA yielded from saliva, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.

 

Specimen Type: Extracted DNA

Container/Tube:

Preferred: Screw Cap Micro Tube, 2 mL with skirted conical base

Acceptable: Matrix tube, 1mL

Collection Instructions:

1. The preferred volume is at least 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

Additional Information: DNA must be extracted in a CLIA-certified laboratory or equivalent and must be extracted from a specimen type listed as acceptable for this test (including applicable anticoagulants). Our laboratory has experience with Chemagic, Puregene, Autopure, MagnaPure, and EZ1 extraction platforms and cannot guarantee that all extraction methods are compatible with this test. If testing fails, one repeat will be attempted, and if unsuccessful, the test will be reported as failed and a charge will be applied. If applicable, specific gene regions that were unable to be interrogated due to DNA quality will be noted in the report.


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

610057

Useful For

Preemptive or reactive genotyping of patients for pharmacogenomic purposes

 

Providing an assessment for genes with strong drug-gene associations

 

Assisting in the management of patients with complex medication regimens

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. Reflex sequencing is limited to the minimum number of reactions that are required to define the patient’s genotype.

Testing Algorithm

If a specimen requires follow-up for CYP2D6, then reflex testing will be performed as appropriate at an additional charge.

 

For cord blood specimens, maternal cell contamination testing may be performed at an additional charge.

 

For more information see CYP2D6 Comprehensive Cascade Testing Algorithm.

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, V

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time
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 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

Specimens may contain donor DNA if obtained from patients who received non-leukocyte reduced 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 April 4, 2025. Available at https://cpicpgx.org/genes-drugs/

4. Pharmacogenomics Knowledgebase (PharmGKB). Accessed April 4, 2025. 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. This assay uses three probes which detect copy number in the promoter, intron 6, and exon 9 of the CYP2D6 gene. 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

Varies

Report Available

3 to 14 days

Specimen Retention Time

Whole blood: 28 days (if available); Saliva: 30 days (if available); Extracted DNA: 3 months

Performing 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
MATCC Maternal Cell Contamination, B Yes No