PGX Genotyping

For detection of CYP2C9, VKORC1, and CYP4F2 variants affecting warfarin metabolism

Clinical Background

 Warfarin is one of the most commonly used oral anticoagulant worldwide and is prescribed for the treatment and prevention of thrombotic disorders. Although highly efficacious, warfarin’s narrow therapeutic index and wide interindividual variability make its dosing challenging (CPIC guidelines).  Metabolizer phenotypes can be predicted by the genotype.  The clinical impact of the warfarin genotype can be influenced by other metabolic pathways, and other non-genetic factors (eg, other medications, diet). Epidemiology

 Variant frequency is ethnicity dependent.  The CYP2C9carrier frequency is approximately 20% in Caucasians, 5% in African Americans, and 4% in Asians.  The VKORC1 carrier frequency is approximately is approximately 39% in Caucasians, 91% in Asians, and 11% in African-Americans. Genetics

 The CYP2C9 is located on 10q23.33.  The VKORC1 gene is located on chromosome 16p11.2.  The CYP4F2 gene is located on chromosome 19p13.11.  Inheritance is autosomal recessive. Indications for Ordering

 Pre-therapeutic testing to identify individuals who should avoid, or may require unconventional doses of medications metabolized by CYP2C9, VKORC1, and CYP4F2. Interpretation

 Standard INR monitoring is still required.

Indiana University School of Medicine Division of Diagnostic Genomics - Laboratory 975 West Walnut Street, IB247 Indianapolis, IN. 46202-5251 Tel. 317-274-0143

 Calculating a warfarin dose based on genotype and other clinical findings is available (eg, www.warfarindosing.org).  If no variants are detected, this suggests *1 allele and normal enzymatic activity.  If one decreased functional or non-functional variant is detected, intermediate-to-normal enzymatic activity is predicted.  If two non-functional variants are present on opposite allele, this predicts low enzymatic activity and a poor metabolizer phenotype.  Individuals who are CYP4F2*3/*3 may require approximately 1 mg/day more warfarin.  Genotype results should be interpreted in context of the individual clinical situation. Consultation with a clinical pharmacy professional is recommended.

Recommended daily warfarin doses (mg/day) to achieve a therapeutic INR based on CYP2C9 and VKORC1 genotype using the warfarin product insert approved by the United States Food and Drug Administration: VKORC1 CYP2C9*1/*1 CYP2C9*1/*2 CYP2C9*1/*3 CYP2C9*2/*2 CYP2C9*2/*3 CYP2C9*3/ Genotype (- *3 1639G>A, rs9923231)

GG 5-7 5-7 3-4 3-4 3-4 0.5-2

GA 5-7 3-4 3-4 3-4 0.5-2 0.5-2

AA 3-4 3-4 0.5-2 0.5-2 0.5-2 0.5-2

Reproduced from updated warfarin (Coumadin®) product label.

Methodology

 Realtime Polymerase chain reaction (PCR) and microarray analysis  Variants tested include:

Variants in CYP2C9 Assay

Predicted enzyme Allele variant dbSNP activity

*1 Assumed when no variant detected normal

*2 c.430C>T rs1799853 Decreased function

Indiana University School of Medicine Division of Diagnostic Genomics - Pharmacogenomics Laboratory 975 West Walnut Street, IB247 Indianapolis, IN. 46202-5251 Tel. 317-274-0143

*3 c.1075A>C rs1057910 Decreased function

*5 c.1080C>G rs28371686 Decreased function

*6 c.818delA rs9332131 Non-functional

*8 c.449G>A rs7900194 Decreased function

*11 c.1003C>T rs28371685 Decreased function

Variant in VKORC1 Assay

Predicted enzyme Allele variant dbSNP activity

*1 Assumed when no variant detected normal

*2/*7RE c.-1639G>A rs9923231

Variant in CYP4F2 Assay

Predicted enzyme Allele variant dbSNP activity

*1 Assumed when no variant detected normal

*3 c.18000G>A rs2108622 Decreased function

Indiana University School of Medicine Division of Diagnostic Genomics - Pharmacogenomics Laboratory 975 West Walnut Street, IB247 Indianapolis, IN. 46202-5251 Tel. 317-274-0143