A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose

Abstract

We report the first genome-wide association study (GWAS) whose sample size (1,053 Swedish subjects) is sufficiently powered to detect genome-wide significance (p<1.5×10−7) for polymorphisms that modestly alter therapeutic warfarin dose. The anticoagulant drug warfarin is widely prescribed for reducing the risk of stroke, thrombosis, pulmonary embolism, and coronary malfunction. However, Caucasians vary widely (20-fold) in the dose needed for therapeutic anticoagulation, and hence prescribed doses may be too low (risking serious illness) or too high (risking severe bleeding). Prior work established that ∼30% of the dose variance is explained by single nucleotide polymorphisms (SNPs) in the warfarin drug target VKORC1 and another ∼12% by two non-synonymous SNPs (*2, *3) in the cytochrome P450 warfarin-metabolizing gene CYP2C9. We initially tested each of 325,997 GWAS SNPs for association with warfarin dose by univariate regression and found the strongest statistical signals (p<10−78) at SNPs clustering near VKORC1 and the second lowest p-values (p<10−31) emanating from CYP2C9. No other SNPs approached genome-wide significance. To enhance detection of weaker effects, we conducted multiple regression adjusting for known influences on warfarin dose (VKORC1, CYP2C9, age, gender) and identified a single SNP (rs2108622) with genome-wide significance (p = 8.3×10−10) that alters protein coding of the CYP4F2 gene. We confirmed this result in 588 additional Swedish patients (p<0.0029) and, during our investigation, a second group provided independent confirmation from a scan of warfarin-metabolizing genes. We also thoroughly investigated copy number variations, haplotypes, and imputed SNPs, but found no additional highly significant warfarin associations. We present power analysis of our GWAS that is generalizable to other studies, and conclude we had 80% power to detect genome-wide significance for common causative variants or markers explaining at least 1.5% of dose variance. These GWAS results provide further impetus for conducting large-scale trials assessing patient benefit from genotype-based forecasting of warfarin dose.

Worldwide allele frequency distribution of four polymorphisms associated with warfarin dose requirements

“…After correcting for the effects of VKORC1 and CYP2C9, a recent genome-wide association study on Swedish patients has confirmed the association of rs2108622 with warfarin dose. 9 However, another study by Zhang et al 24 in the United Kingdom concluded that there was no clear association between this polymorphism and stable warfarin dose. Our study indicates that the derived T allele is present at relatively high frequencies in most worldwide populations.…”

“…3,10 Previous studies have demonstrated that two genes, VKORC1 and CYP2C9, which are involved in the vitamin K-dependent clotting pathway, explain an additional 30-54% of variance observed in warfarin dosing. 6,9,11 Warfarin exists as a mixture of two stereoisomers, R and S. 8,12 S-warfarin is approximately three times as active as the R-enantiomer 12 and works by antagonizing the vitamin K-dependent clotting pathway. Vitamin K epoxide reductase subunit 1 (VKORC1), having a major role in the vitamin K pathway, is the target protein of warfarin.…”

“…Recent research has identified a third gene, CYP4F2 as influencing an individual's sensitivity to warfarin. 9,19,20 CYP4F2 codes for a vitamin K 1 oxidase that causes a decrease in the metabolism of vitamin K 1 . 21 Several studies have shown that carriers of the derived T allele at the non-synonymous SNP rs2108622 require higher warfarin doses than subjects with the ancestral C allele.…”

“…22 Studies on European populations have indicated that CYP4F2 rs2108622 may account for an additional 1-7% of observed variation in warfarin dosing. 9,22,23 The effect of this CYP4F2 polymorphism seems to be substantially smaller than the effect of the VKORC1 and CYP2C9 variants, and the clinical relevance of CYP4F2 has recently been questioned. 24 The traditional approach for warfarin dosing is based on an initial fixed dose, followed by stabilization through trial and error.…”

Warfarin pharmacogenetics: development of a dosing algorithm for Omani patients

“…9,16,22 Furthermore, three genome-wide association studies failed to find any additional genetic loci other than those herein studied (CYP2C9, CYP4F2 and VKORC1) with regard to influence on warfarin dose requirement. 23,24 In conclusion, in this first report on the impact of genetic, clinical and demographic factors involved in warfarin dose requirement in the Omani patients, a significant percentage of variability still (around 37%) awaits explanation. Similar to the Brazilian patients with mixed ethnicities, a general warfarin dosing algorithm like the IWPC performed poorly in this microgeographically defined, ethnically admixed Omani patient.…”