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Test Code PGXQP Focused Pharmacogenomics Panel, Varies


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


Useful 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.

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

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

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 days

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