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Test Code WARSV Warfarin Response Genotype


Advisory Information


If patient is using medications other than warfarin, the preferred test is 2C9GV / Cytochrome P450 2C9 Genotype, which tests for only the CYP2C9 gene.



Specimen Required


Multiple genotype tests can be performed on a single specimen after a single extraction. See Multiple Genotype Test List in Special Instructions for a list of tests that can be ordered together.

 

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 specimen in original tube.

Specimen Stability Information: Ambient (preferred)/Refrigerated

 

Specimen Type: Saliva

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

Supplies: DNA Saliva Collection Kit (T786)

Container/Tube: Saliva Swab Collection Kit (T786: fees apply)

Specimen Volume: 1 swab

Collection Instructions: Collect and send specimen per kit instructions.

Specimen Stability Information: Ambient

 

Specimen Type: 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. Include concentration and volume on tube.

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


Forms

1. New York Clients-Informed consent is required. Please document on the request form or electronic order that a copy is on file. An Informed Consent for Genetic Testing (T576) is available in Special Instructions.

2. If not ordering electronically, complete, print, and send a Pharmacogenomics Test Request Form (T797) with the specimen (https://www.mayomedicallaboratories.com/it-mmfiles/pharmacogenomics-test-request-form-mc0767-15.pdf)

Useful For

Identifying patients who may require warfarin dosing adjustments(3,4) including:

-Patients being started on a first prescription for warfarin

-Patients who have previously been prescribed warfarin and have required multiple dosing adjustments to maintain the international normalized ratio in the target range

-Patients with a history of thrombosis or bleeding when taking warfarin

Genetics Test Information

This test is used for assessing CYP2C9, VKORC1, CYP4F2, and rs12777863 for variants affecting the metabolism of warfarin (Coumadin). This assay should be ordered on patients who are receiving warfarin for the first time or who are experiencing difficulties in maintaining the international normalized ratio (INR) in the therapeutic range.

Method Name

Real-Time Polymerase Chain Reaction (PCR) with Allelic Discrimination Analysis

Reporting Name

Warfarin Response Genotype

Specimen Type

Varies

Specimen Minimum Volume

Blood: 0.4 mL
Saliva: 1 swab

Specimen Stability Information

Specimen Type Temperature Time
Varies Varies

Reject Due To

Hemolysis

NA

Lipemia

NA

Icterus

NA

Other

NA

Clinical Information

Warfarin is a Coumarin-based drug commonly utilized in anticoagulation therapy to prevent thrombosis due to inherited and acquired hemostatic disorders. The drug is also used in a number of other medical conditions and treatments including atrial fibrillation and hip replacement surgery. Warfarin acts by interfering with the metabolism of vitamin K, which is necessary for production of key coagulation factors. Warfarin inhibits vitamin K recycling by blocking its metabolism at the vitamin K-epoxide intermediate; thereby decreasing the amount of available vitamin K. Warfarin has a narrow therapeutic window; undermedicating increases the risk for thrombosis and overmedicating increases the risk for cerebrovascular accidents. Warfarin therapy has one of the highest rates of severe adverse drug reactions.

 

Warfarin is dosed using nongenetic factors including gender, weight, and age, and is monitored by coagulation testing in order to maintain the international normalized ratio (INR) within specific limits. However, warfarin metabolism is highly variable and dependent upon genetic factors. Variants within 3 genes and 1 intragenic locus are known to affect the metabolism of warfarin and the dose needed to maintain the correct serum drug level and degree of anticoagulation.

 

The CYP2C9 gene encodes the cytochrome P450 2C9 (CYP2C9) enzyme that primarily metabolizes the more active isomer of warfarin (S-warfarin) to inactive products. Some CYP2C9 variants result in decreased enzymatic activity and may lead to increases in serum warfarin and over-medicating, driving the INR above the therapeutic target.

 

The second gene (VKORC1) encodes vitamin K epoxide reductase complex subunit-1 (VKORC1), a small transmembrane protein of the endoplasmic reticulum that is part of the vitamin K cycle and the target of warfarin therapy.(1) Vitamin K epoxide, a by-product of the carboxylation of blood coagulation factors, is reduced to vitamin K by VKORC1. A VKORC1 promoter variant leads to decreased expression of the gene, resulting in reduced availability of vitamin K. This may cause increases in serum warfarin and overmedicating, driving the INR above the therapeutic target.  In addition, there are variations in VKORC1 that lead to warfarin resistance that are tested by this assay. These variations are rare.

 

CYP4F2 metabolizes reduced vitamin K to hydroxyl-vitamin K1, thus removing it from the pathways involved in the activation of clotting factors impacted by warfarin.  In individuals who self-identify as being of non-African ancestry, carriers of the CYP4F2*3 (C.1297G->A; rs2108622) variant may need a small (5%-10%) warfarin dosage increase to achieve therapeutic goals.

 

The rs12777823G->A variant is located intragenic in the CYP2C locus on chromosome 10. The A allele has been associated with the need for a 10% to 15% decrease in dose in individuals who self-identify as being of African ancestry.

 

CYP2C9:

CYP2C9 metabolizes a wide variety of drugs including warfarin and phenytoin. (Note that if testing is desired for other CYP2C9 substrates, order 2C9GV / Cytochrome P450 2C9 Genotype.

 

A number of specific CYP2C9 variants result in enzymatic deficiencies. The following information outlines the relationship between the variants detected in this assay and their effect on the activity of the enzyme (Table 1):

 Table 1:

CYP2C9 Allele

cDNA Nucleotide Change

Effect on Enzyme Metabolism

*1

None (wild type)

Normal activity

*2

430C->T

Reduced activity

*3

1075A->C

No activity

*4

1076T->C

Reduced activity

*5

1080C->G

Reduced activity

*6

818delA

No activity

*8

449G->A

Substrate specific

*9

752A->G

Reduced activity

*11

1003C->T

Reduced activity

*12

1465C->T

Reduced activity

*13

269C->T

Minimal activity

*14

374G->A

Minimal activity

*15

485C->A

No activity

*16

895A->G

Minimal activity

*17

1144C->T

Reduced activity

*18

1190A->C

No activity

*25

353_362del

No activity

*26

389C->G

Minimal activity

*28

641A->T

Minimal activity

*30

1429G->A

Minimal activity

*33

395G->A

Minimal activity

*35

374G->T + 430C->T

No activity

 

VKORC1:

The c.-1639 promoter variant is located in the second nucleotide of an E-Box (CANNTG) and its presence disrupts the consensus sequence, reducing promoter activity. In vitro experiments show a 44% higher transcription level of the G versus the A allele.(1) The c.-1639 G->A nucleotide change results in decreased gene expression and reduced enzyme activity.  This test also determines the genotype for multiple other loci within VKORC1 that have been associated with warfarin resistance. The mechanism by which these variations cause warfarin resistance is not clearly understood.

 

 Table 2: Additional Variants Tested

Gene/SNV

cDNA Nucleotide Change

Effect on Enzyme Metabolism

VKORC1

-1639G->A

Warfarin sensitivity

VKORC1

85G->T

Warfarin resistance

VKORC1

106G->T

Warfarin resistance

VKORC1

121G->T

Warfarin resistance

VKORC1

134T->C

Warfarin resistance

VKORC1

172A->G

Warfarin resistance

VKORC1

196G->A

Warfarin resistance

VKORC1

358C->T

Warfarin resistance

VKORC1

383T->G

Warfarin resistance

CYP4F2*3

1297G->A

Warfarin resistance

rs12777823G->A(a)

 

Warfarin sensitivity

a. rs12777823G->A is an intergenic single nucleotide variant (SNV)

 

Warfarin dosing may require adjustment depending on the genotypes identified and the predicted phenotype. Patients who have high warfarin sensitivity may benefit from greatly reduced warfarin dosage or by transitioning to another comparable medication.(2) Similarly, in rare instances, individuals with VKORC1 warfarin resistance variants, may require a higher warfarin dose or may benefit from selection of an alternate medication.

Reference Values

An interpretive report will be provided.

Interpretation

An interpretive report will be provided that includes assay information, genotype, and an interpretation indicating the patient's predicted warfarin response.

 

The CYP2C9 and CYP4F2 genotypes, with associated star alleles, are assigned using standard allelic nomenclature as published by the Human Cytochrome P450 (CYP) Allele Nomenclature Database Committee.(5)

 

Individuals without a detectable alteration in CYP2C9 or CYP4F2 will be designated as CYP2C9*1/*1 or CYP4F2*1/*1

 

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.

 

Individuals who have variants in 1 or more gene tested by this assay may require more frequent monitoring of international normalized ratio (INR) to maintain the INR in the target range.

 

Drug-drug interactions and drug/metabolite inhibition must be considered when prescribing warfarin. Warfarin metabolism may be inhibited through drug-drug interactions, including amiodarone and some statins. It is important to interpret the results of testing and dose adjustments in the context of hepatic and renal function and patient age.

Cautions

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 pre-transplant DNA specimen is recommended for testing. 

 

CYP2C9, VKORC1, CYP4F2, and rs12777823 genetic test results in patients who have undergone liver transplantation may not accurately reflect the patient's CYP2C9 or VKORC1 status.

 

This method may not detect all variants that impact warfarin sensitivity or resistance. Therefore, absence of a detectable variant does not rule out the possibility that a patient has an altered CYP2C9 or VKORC1 metabolism due to other variants that cannot be detected with this method. Furthermore, when 2 or more variants are identified, the cis-/trans- status (whether the variants are on the same or opposite chromosomes) is not always known.  

Method Description

Genomic DNA is extracted from whole blood or saliva. Genotyping for the alleles is performed using a 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.(User Guide: TaqMan SNP Genotyping Assay, Applied Biosystems Revision A.0 January 2014)

Day(s) and Time(s) Performed

Monday through Friday; 8 a.m.

Analytic Time

3 days (Not reported Saturday or Sunday)

Specimen Retention Time

Whole Blood/Saliva swab: 2 weeks; Extracted DNA: 2 months

Performing Laboratory

Mayo Medical Laboratories in Rochester

Test Classification

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 U.S. Food and Drug Administration.

CPT Code Information

0030U

LOINC Code Information

Test ID Test Order Name Order LOINC Value
WARSV Warfarin Response Genotype In Process

 

Result ID Test Result Name Result LOINC Value
BA0251 CYP2C9 Genotype In Process
BA0248 VKORC1 Genotype In Process
BA0232 Additional VKORC1 Variants 82939-0
BA0254 CYP4F2 *3 Genotype In Process
BA0257 rs12777823 Genotype In Process
BA0234 Interpretation In Process
BA0260 Additional Information 48767-8
BA0236 Method 49549-9
BA0237 Disclaimer 62364-5
BA0238 Reviewed by 18771-6