Test Catalog

Test ID: PGXFP    
Focused Pharmacogenomics Panel

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 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, *14A, *14B, and *15. 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 in Special Instructions.

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, *14B,*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 that 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 in Special Instructions. 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 heterologous blood transfusions or allogeneic blood or marrow 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 blood or marrow 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. Drug-label guidance should be used when dosing patients with medications regardless of the predicted phenotype.

 

For additional information, see the following test IDs:

1A2V / Cytochrome P450 1A2 Genotype

2C9GV / Cytochrome P450 2C9 Genotype

2C19V / Cytochrome P450 2C19 Genotype

2D6CV / Cytochrome P450 2D6 (CYP2D6) Comprehensive Cascade

3A4V / Cytochrome P450 3A4 Genotype

3A5V / Cytochrome P450 3A5 Genotype

SLC1V / Solute Carrier Organic Anion Transporter Family Member 1B1 (SLCO1B1) Genotype, Statin

WARSV / Warfarin Response Genotype

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

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

3. Clinical Pharmacogenetic Implementation Committee Gene-Drug Table. Accessed 5/4/2017. Available at https://cpicpgx.org/genes-drugs/

4. Pharmacogenomics Knowledgebase (PharmGKB). Accessed 5/4/2017. Available at www.pharmgkb.org/

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