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Genetic polymorphisms in warfarin and tacrolimus-related genes VKORC1, CYP2C9 and CYP3A5 in the Greek-Cypriot population
© Hadjipanagi et al.; licensee BioMed Central Ltd. 2014
- Received: 9 May 2013
- Accepted: 1 March 2014
- Published: 5 March 2014
Two variants in the gene encoding the cytochrome P450 2C9 enzyme (CYP2C9) are considered the most significant genetic risk factors associated with bleeding after warfarin prescription. A variant in the vitamin K epoxide reductase (VKORC1) has been also associated by several studies with warfarin response. Another variant in the P450 3A5 enzyme (CYP3A5) gene is known to affect the metabolism of many drugs, including tacrolimus.
We conducted a population genetic study in 148 unrelated healthy Greek-Cypriot volunteers (through PCR-RFLP assays), in order to determine the frequencies of the above pharmacogenetics variants and to compare allele frequencies with those in other major ethnic groups. The allele frequencies of CYP2C9*2, CYP2C9*3 and CYP3A5*3 were found to be 0.162, 0.112 and 0.943 respectively, whereas VKORC1 - 1639A was 0.534. The latter frequency differs significantly when compared with Caucasians, Asians and Africans (p < 0.001) and is still significant when compared with the geographically and culturally closely related to Greek-Cypriots, Hellenes of Greece (p = 0.01). Interestingly ~18% of our population are carriers of four or three risk alleles regarding warfarin sensitivity, therefore they have a high predisposition for bleeding after taking high or even normal warfarin doses.
Our data show no significant difference in the frequency of CYP2C9 and CYP3A5 allelic variants when compared to the Caucasian population, but differ significantly when compared with Africans and Asians (p < 0.001). Also, the frequency of variant VKORC1 - 1639A differs between Greek-Cypriots and every other population we compared. Finally, about 1/5 Greek-Cypriots carry three or four risk alleles and ~50% of them carry at least two independent risk alleles regarding warfarin sensitivity, a potentially high risk for over-anticoagulation.
- Population genetics
There are genetic variations in genes encoding for the hepatic CYP450 metabolizing enzymes that can lead to undesirable drug reactions or inadequate response to commonly prescribed doses, either because of reduced or enhanced enzyme activity, respectively . Testing for the activity of the CYP450 enzymes and isoforms before a patient receives a specific medication can provide valuable information concerning the initial dose. Molecular genetic testing is advantageous and more cost-effective compared to enzymatic methods due to methodological simplicity.
It is notable that in August 2007, the FDA label for warfarin, a frequently used anti-coagulant drug, was updated to highlight the benefit of genetic testing to predict warfarin response. This was renewed on February 2010 (http://www.fda.gov/). Candidate-gene association studies have identified two genes responsible for the main proportion of warfarin response: CYP2C9, which codes for the enzyme cytochrome CYP450 2C9 that metabolizes S-warfarin  and VKORC1, which codes for warfarin’s target, vitamin K epoxide reductase . CYP2C9*2 (Arg 144 to Cys) and CYP2C9*3 (Ile 359 to Leu) are recognized as the main CYP2C9 variants in humans, affecting negatively the enzyme activity [4, 5]. In order to avoid high risk for bleeding, these polymorphisms must be taken into account before warfarin treatment . Warfarin-dosing algorithms that incorporate CYP2C9 and VKORC1 genetic profile seem to predict pretty accurately the required warfarin dose for each patient [7, 8].
The CYP3A5 gene represents the major extrahepatic isoform of CYP3A gene family and in association with CYP3A4 are responsible for the metabolism of over 50% of all the clinically used drugs . Some studies pay special attention at the frequent CYP3A5*3 allele and tacrolimus dosing , a frequently used immunosuppressant drug. It is recommended that homozygous CYP3A5*3/*3 patients receive roughly a 50% lower initial tacrolimus dose than patients with at least one wild type CYP3A5*1 allele as a result of the difference observed in oral clearance [10, 11].
According to the available bibliography, it is more than evident that different human populations can differ significantly in genetic allelic frequencies for drug metabolism genes . The purpose of the present study was to investigate for the first time the prevalence of the most common allelic variants of VKORC1, CYP2C9 and CYP3A5 in a representative sample of the Greek-Cypriot population, and to compare these data with existing published data from other populations.
Genomic DNA isolated from whole peripheral blood  from 148 male healthy unrelated Greek-Cypriot subjects over 20 years old, was used for this study. The population of Greek-Cypriots is 660,000 (census of 2011), therefore the number of 148 individuals represents adequately our population. The subjects were selected according to their origin, aiming at even geographical coverage of all the provinces of Cyprus, including mountainous areas, thereby avoiding population stratification. We enrolled only male subjects for this study due to the fact we had more information about their geographic origin in contrast with females, because of their participation in another phylogenetics project. The DNA samples were used after they were anonymized. Our research project has been approved by the Cyprus National Bioethics Committee. Informed consent was obtained from all subjects. Research carried out on volunteers of this study was in compliance with the Helsinki Declaration.
Molecular genetic analysis
In this study we directly tested our sample group only for the four following genetic variants: VKORC1 g.-1639G/A, CYP2C9*2, CYP2C9*3 and CYP3A5*3. We did not test specifically for the wild type CYP2C9*1 allele, the frequency of which was inferred from the absence of the two variants tested. The genetic polymorphisms were genotyped by PCR-RFLP assays. Details of the methods regarding the VKORC1 g.-1639G/A, CYP2C9*2 and CYP3A5*3 polymorphisms are described elsewhere [14–16]. For the CYP2C9*3 polymorphism, the following primers were designed and used for amplification:
CYP2C9-3_For: 5’ ACACAGATGCTGTGGTGCACGAGGTCCAGAGG TAC 3’
CYP2C9-3_Rev: 5’ CTGGAAACAAGAGAAAGTCCAGTTAAACTGCCATAC 3’
The forward primer was modified by substitution of the fourth nucleotide from the 3’ end, from A to G (italics and bold), so that upon amplification a restriction recognition site for BanI is created. The digestion products were analyzed by electrophoresis on 3.5% agarose gels. The CYP2C9*3 allele is represented by the 225 bp and 31 bp bands, whereas wild type allele is represented by the uncut 256 bp band.
Comparison of population allele frequencies was performed through Pearson chi-square test, using SPSSv.15 statistical package (IBM, USA). The significance level, alpha, was set to 0.05. Hardy-Weinberg equilibrium was tested for all the analyzed polymorphisms through an Excel based application (Microsoft Office 2007).
Results and discussion
Genotype distribution of the four pharmacogenetics variants in the Greek-Cypriot population
Genotypic combinations of the three genotyped variants related with warfarin, in 148 Greek-Cypriot individuals
VKORC1 -AG + GG
VKORC1 -AG + GG
CYP2C9*1/*2 + *2/*2
VKORC1 -AG + GG
It has been proven that CYP2C9*2 and *3 cause a reduction in S-warfarin clearance (10-fold variation observed from CYP2C9*11 to CYP2C9*33) activity (*1/*1 > *1/*2 > *1/*3 > *2/*2 > *2/*3 > *3/*3). The effect of the CYP2C9*3/*3 genotype is the most severe one with clearance of S-warfarin being 10% of the wild type genotype . VKORC1 encoded enzyme interacts with warfarin, so the enzyme levels can affect sensitivity to warfarin. Jorgensen et al. , reviewed recently almost all the available bibliography and found that CYP2C9*3 and VKORC1 variants are significant for warfarin dose determination for most ethnic populations . Sconce et al.  showed clearly (giving also a useful algorithm for warfarin dose determination) that the three significant variants of the aforementioned genes have additive properties .
Allele frequencies of the four studied pharmacogenetic variants in Cyprus and comparison with other populations
No of tested chromosomes
(P < 0.001)
(P = 0.296)
(P = 0.002)
(P = 0.526)
(P < 0.001)
(P < 0.0001)
(P < 0.001)
(P < 0.001)
(P < 0.001)
(P < 0.001)
(P < 0.001)
(P < 0.001)
Hellenes from Greece
(P = 0.010)
(P = 0.183)
(P = 0.144)
(P = 0.957)
This research project was covered from internal University of Cyprus funds to CD (Chapter 3/311).
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