Psychotropic Pharmacogenomics Gene Panel - Clinical Genetic Test - GTR

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Psychotropic Pharmacogenomics Gene Panel

Clinical Genetic Test

offered by

Mayo Clinic Laboratories

View lab's test page

GTR Test Accession: GTR000593350.3

CAP

PHARMACOGENOMIC

Last updated in GTR: 2024-04-29

Last annual review date for the lab: 2024-05-28

At a Glance

Test purpose:

Drug Response; Therapeutic management

Conditions (1):

Drug metabolism or response

Genes (22):

ADRA2A (10q25.2); ANKK1 (11q23.2); CHRNA3 (15q25.1); COMT (22q11.21); CYP1A2 (15q24.1) more...

Methods (3):

Molecular Genetics - Targeted variant analysis: Fragment analysis; Real-time PCR with SYBR Green; SNP Detection

Target population:

Individuals needing preemptive or reactive genotyping for pharmacogenomic purposes.

Clinical validity:

Not provided

Clinical utility:

Guidance for selecting a drug therapy and/or dose

Ordering Information

Offered by:

Mayo Clinic Laboratories
View lab's website
View lab's test page

Test short name:

PSYQP

Specimen Source:

Isolated DNA
Peripheral (whole) blood
Saliva
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Dentist
Licensed Physician
Nurse Practitioner
Physician Assistant
Public Health Mandate
Registered Nurse

Test Order Code:

PSYQP
View other test codes

LOINC codes:

**LOINC codes notice

Lab contact:

Elyse Love, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
gcmolgen@mayo.edu
1-800-533-1710

Contact Policy:

Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.

How to Order:

https://www.mayocliniclabs.com/test-catalog/Specimen/610060
Order URL

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Based on applicable state law

Test strategy:

Testing for CYP2D6 is done in 2 tiers when needed. Tier 1 uses a 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, … View more

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Conditions

Total conditions: 1

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 22

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 3

Method Category

Test method

Instrument

Targeted variant analysis

Fragment analysis

Targeted variant analysis

Real-time PCR with SYBR Green

Targeted variant analysis

SNP Detection

QuantStudio 12K Flex

Clinical Information

Test purpose:

Drug Response; Therapeutic management

Clinical utility:

Guidance for selecting a drug therapy and/or dose

View citations (2)

Pharmacogenomics knowledge for personalized medicine. Whirl-Carrillo M, et al. Clin Pharmacol Ther. 2012;92(4):414-7. doi:10.1038/clpt.2012.96. PMID: 22992668.
Clinical Pharmacogenetics Implementation Consortium. Accessed April 29, 2024. https://cpicpgx.org/

Target population:

Individuals needing preemptive or reactive genotyping for pharmacogenomic purposes.

View citations (2)

Pharmacogenomics knowledge for personalized medicine. Whirl-Carrillo M, et al. Clin Pharmacol Ther. 2012;92(4):414-7. doi:10.1038/clpt.2012.96. PMID: 22992668.
Clinical Pharmacogenetics Implementation Consortium. Accessed April 29, 2024. https://cpicpgx.org/

Research:

Is research allowed on the sample after clinical testing is complete?
Research testing is only performed under IRB approved protocol with an opt-out policy in place.

Recommended fields not provided:

Clinical validity, What is the protocol for interpreting a variation as a VUS?, Are family members with defined clinical status recruited to assess significance of VUS without charge?, Will the lab re-contact the ordering physician if variant interpretation changes?, Sample negative report, Sample positive report

Technical Information

Test Procedure:

Genomic DNA is extracted from the sample. Genotyping for the following genes is performed using a PCR-based 5'-nuclease assay. Fluorescently labeled detection probes anneal to the target DNA: ANKK1, ADRA2, CHRNA3, COMT, CYP1A2, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, DRD2, EPHX1, GRIK4, HTR2A, HTR2C, MTHFR, OPRM1, SCN1A, and UGT2B15. PCR … Genomic DNA is extracted from the sample. Genotyping for the following genes is performed using a PCR-based 5'-nuclease assay. Fluorescently labeled detection probes anneal to the target DNA: ANKK1, ADRA2, CHRNA3, COMT, CYP1A2, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, DRD2, EPHX1, GRIK4, HTR2A, HTR2C, MTHFR, OPRM1, SCN1A, and UGT2B15. 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, Applied Biosystems Revision A.0 January 2014) Amplification for the HLA-B*15:02 and HLA-A*31:01 alleles and an internal control gene is performed by real-time PCR in the presence of SYBR Green, which fluoresces when bound to double-stranded DNA. A genotype is assigned based on the allele-specific SYBR Green fluorescent signals that are detected.(Unpublished Mayo method) SLC6A4 is performed utilizing PCR amplification of the region surrounding the polymorphism followed by size separation of the products.(Lesch KP, Bengel D, Heils A, et al: Association of anxiety-related traits with a polymorphism in the serotonin transporter gene regulatory region. Science 1996;274:1527-1530) 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 Revision B, Applied Biosystems, Carlsbad, CA) 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) View more

Test Platform:

Other

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

Accuracy and analytical sensitivity for targeted simple variant(s) (SNVs and INDELs): (>99%). Accuracy and specificity for del/dup detection: (>99%).

Assay limitations:

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 … View more

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Formal PT program

PT Provider:
American College of Medical Genetics / College of American Pathologists, ACMG/CAP

Recommended fields not provided:

Test Confirmation, Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, Description of PT method, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Category: FDA exercises enforcement discretion

Additional Information

Reviews:

PubMed Clinical Queries

Clinical resources:

Consumer resources:

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.