Retrospective evidence for clinical validity of expanded genetic model in warfarin dose optimization in a South Indian population

Development and validation wise assessment of genotype guided warfarin dosing algorithm in Indian population

OBJECTIVES

A study was conducted to develop and validate the warfarin pharmacogenetic dose optimization algorithm considering the clinical pharmacogenetic implementation consortium (CPIC) recommendations for the Asian ethnicity population.

METHODS

The present prospective observational study recruited warfarin-receiving patients. We collected a three ml blood sample for VKORC1, CYP2C9*2, CYP2C9*3, and CYP4F2 polymorphism assessment during the follow-up visits. Clinical history, sociodemographic and warfarin dose details were noted.

RESULTS

The study recruited 300 patients (250 in derivation and 50 in validation timed cohort) receiving warfarin therapy. The baseline characteristics were similar in both cohorts. BMI, presence of comorbidity, VKORC1, CYP2C9*2, and CYP2C9*3 were identified as covariates significantly affecting the warfarin weekly maintenance dose (p<0.001 for all) and the same were included in warfarin pharmacogenetic dose optimization algorithm building. The algorithm built-in the present study showed a good correlation with Gage (r=0.57, p<0.0001), and IWPC (r=0.51, p<0.0001) algorithms, widely accepted in western side of the globe. The receiver operating characteristic curve analysis showed a sensitivity of 73 %, a positive predictive value of 96 %, and a specificity of 89 %. The algorithm correctly identified the validation cohort's warfarin-sensitive, intermediate reacting, and resistant patient populations.

CONCLUSIONS

Validation and comparisons of the warfarin pharmacogenetic dose optimization algorithm have made it ready for the clinical trial assessment.

Pharmacogenetic variants influence vitamin K anticoagulant dosing in patients with mechanical prosthetic heart valves

Background: Vitamin K antagonists (VKAs) are class I oral anticoagulants that are widely prescribed following surgical heart valve implantation. The objective of this study was to quantify the relative effects of VKORC1, CYP2C9 and CYP4F2 genotypes in predicting VKA dosing. Materials & methods: A total of 506 South Indian patients with mechanical prosthetic heart valves who were prescribed oral VKAs, such as warfarin or acenocoumarol, were genotyped. The discriminatory ability of mutant genotypes to predict dose categories and bleeding events was assessed using regression analysis. Results: The VKORC1 rs9923231, CYP2C9*3 and CYP4F2*3 mutant genotypes significantly influenced VKA-dose requirements and explained 27.47% of the observed dose variation. Conclusion: These results support pharmacogenetic screening for initial VKA dosing among South Indian patients with mechanical prosthetic heart valves.

Pharmacogenetic determinants of warfarin in the Indian population

BACKGROUND

Several studies optimized the warfarin dose based on CYP2C9*2, CYP2C9*3, VKORC1 -1639 G > A, CYP4F2 V433M. But, the information on the rare variants is lacking. In this study, we have explored the prevalence of common and rare pharmacogenetic determinants of warfarin and determined their damaging nature.

METHODS

We have analyzed 2000 healthy adults using the Infinium global screening array (GSA) for 15 pharmacogenetic determinants of warfarin. In addition, we have elucidated the impact of these variants on protein function, stability, dynamics, evolutionary preservation, and ligand binding propensity.

RESULTS

The GSA Analysis has revealed that CYP4F2 V433M (MAF: 39.425%), VKORC1 -1639 G > A (MAF: 20.5%), CYP2C9*3 (MAF:9.925%), and CYP2C9*2 (MAF:4.575%) are common, while CYP2C9*14 (MAF: 1.475%), CYP2C9*4 (0.175%), CYP2C9*5 (0.125%), and CYP2C9*11 (0.125%) are rare. Position-specific evolutionary preservation (PSEP) analysis has revealed that CYP2C9*4 is possibly damaging, while CYP2C9*5, CYP2C9*11, and CYP2C9*14 are probably damaging. CYP2C9*4 has high thermolability (-10.14 kcal/mol). Among the rare CYP2C9 variants, CYP2C9*4 and CYP2C9*11 exert destabilizing effects and may have increased molecular flexibility, while CYP2C9*5 and CYP2C9*14 exert stabilizing effects and may have decreased molecular flexibility. DNase I footprint analysis has revealed the loss of the E-box consensus sequence due to VKORC1 -1639 G > A polymorphism.

CONCLUSION

CYP2C9*2, CYP2C9*3, VKORC1 -1639 G > A and CYP4F2 V433M are common; CYP2C9*4, CYP2C9*5, CYP2C9*11, and CYP2C9*14 variants are rare in Indian subjects. All the CYP2C9 variants are found to be damaging. DNase I footprint analysis provided the mechanistic rationale for the association of VKORC1 -1639 G > A with warfarin sensitivity.

Value of VKORC1 (-1639G>A) rs9923231 genotyping in predicting warfarin dose: A replication study in South Indian population

OBJECTIVE

Warfarin is the most commonly prescribed oral anticoagulant, although having a narrow therapeutic index and wide interindividual variability. The aim of this study was to replicate the utility of VKORC1 (-1639G>A) rs9923231 genotyping in predicting the mean daily dose and to evaluate its ability to categorize warfarin-treated patients to high-, intermediate-, or low-dose categories in the South Indian population.

MATERIALS AND METHODS

A cohort of 222 warfarin-treated patients was genotyped using restriction fragment length polymorphism method. The influence of the rs9923231 polymorphism on the variations in the mean daily dose was compared using one-way analysis of variance and linear regression analysis. Discriminatory ability of the rs9923231 polymorphism to group the patients into ordered dose categories was assessed by estimating the proportional odds ratios using the ordered logit regression analysis.

RESULTS

The frequency of AA genotype and A allele in the study sample was found to be 1.8% and 9.23%, respectively, which was similar to reports from other South Indian populations. The mean daily dose required to achieve the optimum international normalized ratio was significantly lower in AA homozygous genotype carriers (3.99 ± 1.67 mg/day) and GA heterozygous (4.26 ± 1.57 mg/day) compared to the GG genotype carriers (5.51 ± 2.13 mg/day), p = 0.003. The A allele carriers (GA+AA genotypes) had a 3.23 higher odds of being grouped as a low-dose requiring category compared to non-carriers (95% CI 1.49-6.98, p = 0.003).

CONCLUSIONS

These preliminary results strongly support the use of VKORC1 (-1639G>A) rs9923231 polymorphism for genetically guided initial warfarin dosing in South Indian patients with heart valve replacements.

Artificial neural network-based pharmacogenomic algorithm for warfarin dose optimization

AIM

To develop more precise pharmacogenomic algorithm for prediction of safe and effective dose of warfarin.

MATERIALS & METHODS

An artificial neural network (ANN) algorithm was developed by using age, gender, BMI, plasma vitamin K levels, thyroid status and ten genetic variables as the inputs and therapeutic warfarin dose as the output. Hyperbolic tangent function was used to build an ANN architecture.

RESULTS

This model explained 93.5% variability in warfarin dosing and predicted warfarin dose accurately in 74.5% patients whose international normalized ratio (INR) was less than 2.0 and in 83.3% patients whose INR was more than 3.5. This algorithm reduced the out-of-range INRs (odds ratio [OR]: 0.49; 95% CI: 0.30-0.79; p = 0.003), the rate of adverse drug reactions (OR: 0.00; 95% CI: 0.00-1.21; p = 0.06) and time to reach first therapeutic INR (OR: 6.73; 95% CI: 2.17-22.31; p < 0.0001). This algorithm was found to be applicable in both euthyroid and hypothyroid status. S-warfarin/7-hydroxywarfarin ratio was found to increase in subjects with CYP2C9*2 and CYP2C9*3 justifying the warfarin sensitivity attributed to these variants.

CONCLUSION

An application of ANN for warfarin dosing improves predictability and provides safe and effective dosing.

Impact of polymorphisms of the GGCX gene on maintenance warfarin dose in Chinese populations: Systematic review and meta-analysis

The meta-analysis was conducted to investigate the impact of gamma-glutamyl carboxylase (GGCX) on maintenance warfarin dose. 8 studies were included, focusing on the impact of GGCX single nucleotide polymorphisms (SNPs) on mean daily warfarin dose (MDWD). GGCX (rs699664; AA versus GG, GA versus GG, A versus GG) and GGCX (rs12714145; GA versus GG, AA versus GG, A versus GG) showed no significant differences on mean daily warfarin dose (MDWD). This meta-analysis was the first to report the relationship between GGCX SNPs and MDWD in Chinese populations. No evidence could be found in the relationship between SNPs of GGCX (rs699664 and rs12714145) and maintenance warfarin dose.

Mechanistic insights into the effect of CYP2C9*2 and CYP2C9*3 variants on the 7-hydroxylation of warfarin

AIM

To evaluate the impact of CYP2C9*2 and CYP2C9*3 variants on binding and hydroxylation of warfarin.

MATERIALS & METHODS

Multiple linear regression model of warfarin pharmacokinetics was developed from the dataset of patients (n = 199). Pymol based in silico models were developed for the genetic variants.

RESULTS

CYP2C9*2 and CYP2C9*3 variants exhibited high warfarin/7-hydroxywarfarin (multiple linear regression model), dose-dependent disruption of hydrogen bonds with warfarin, dose-dependent increase in the distance between C7 of S-warfarin and Fe-O of CYP2C9, dose-dependent decrease in the glide scores (in silico).

CONCLUSION

CYP2C9*2 and CYP2C9*3 variants result in disruption of hydrogen bonding interactions with warfarin and longer distance between C7 and Fe-O thus impairing warfarin 7-hydroxylation due to lower binding affinity of warfarin. Original submitted 7 May 2014; Revision submitted 30 October 2014.

An acenocoumarol dosing algorithm exploiting clinical and genetic factors in South Indian (Dravidian) population

OBJECTIVE

The objective of this study was to determine the influence of CYP2C9, VKORC1, CYP4F2, and GGCX genetic polymorphisms on mean daily dose of acenocoumarol in South Indian patients and to develop a new pharmacogenetic algorithm based on clinical and genetic factors.

METHODS

Patients receiving acenocoumarol maintenance therapy (n = 230) were included in the study. Single nucleotide polymorphisms (SNP) of CYP2C9, VKORC1, CYP4F2, and GGCX were genotyped by real-time polymerase chain reaction (RT-PCR) method.

RESULTS

The mean daily acenocoumarol maintenance dose was found to be 3.7 ± 2.3 (SD) mg/day. The CYP2C9 *1*2, CYP2C9 *1*3, and CYP2C9 *2*3 variant genotypes significantly reduced the dose by 56.7 % (2.0 mg), 67.6 % (1.6 mg), and 70.3 % (1.5 mg) than wild-type carriers 4.1 mg, p < 0.0001. The genetic variants of CYP2C9 and GGCX (rs11676382) were found to be associated with lower acenocoumarol dose, whereas CYP4F2 (rs2108622) was associated with higher doses. Age, body mass index (BMI), variation of CYP2C9, VKORC1, CYP4F2, and GGCX were the major determinants of acenocoumarol maintenance dose, accounting for 61.8 % of its variability (adjusted r (2) = 0.615, p < 0.0001). Among the VKORC1 variants, rs9923231 alone contributed up to 28.6 % of the acenocoumarol dose variation.

CONCLUSION

VKORC1 rs9923231 polymorphism had the highest impact on acenocoumarol daily dose. A new pharmacogenetic algorithm was established to determine the acenocoumarol dose in South Indian population.

Methodological issues in the development of a pharmacogenomic algorithm for warfarin dosing: comparison of two regression approaches

Aim: To ascertain whether multiple polynomial regression (MPR) has any advantage over multiple linear regression (MLR) in developing pharmacogenomic algorithms. Materials & methods: Two pharmacogenomic algorithms were developed based on MPR and MLR models from a warfarin pharmacogenomic data set (derivation cohort [n = 125] and validation cohort [n = 115]). Results: The MPR model showed better correlation with therapeutic dose (r = 0.62 vs 0.52); better diagnostic utility in distinguishing the warfarin-sensitive and warfarin-resistant patients (area under the receiver operating characteristic curves: 0.89 vs 0.81); and lower rate of underestimation (13.9 vs 20%) compared with the MLR model. Rate of overestimation was higher in the MPR than the MLR (10 vs 6.7%) model. Conclusion: The MPR approach has advantages over the MLR approach in predicting accurate and safe dose.

Original submitted 12 December 2013; Revision submitted 24 March 2014

Effect of CYP2C9, VKORC1, CYP4F2 and GGCX genetic variants on warfarin maintenance dose and explicating a new pharmacogenetic algorithm in South Indian population

OBJECTIVE

To determine the influence of genetic polymorphisms on warfarin maintenance dose and to explicate an algorithm using the pharmacogenetic and clinical factors to determine the maintenance and/or starting dose of warfarin in South Indian patients receiving warfarin therapy.

METHODS

Patients receiving stabilized warfarin therapy (n=257) were included in the study. Single nucleotide polymorphisms (SNPs) of CYP2C9 (rs1799853 and rs1057910), VKORC1 (rs9923231, rs7196161, rs2884737, rs9934438, rs8050894, rs2359612 and rs7294), CYP4F2 (rs2108622) and GGCX (rs11676382) were genotyped by the quantitative real time-PCR method.

RESULTS

The mean daily maintenance dose of warfarin was found to be 4.7 ± 2.1 mg/day. Patients with the CYP2C9*1/*2, *1/*3 and *2/*3 variant genotypes required a 51.0 (2.8 mg), 60.9 (2.3 mg) and 62.2 % (2.2 mg) lower daily maintenance dose of warfarin, respectively, than those patients with the CYP2C9*1/*1 wild-type genotype (5.2 mg) (p<0.0001). The genetic variants of CYP2C9, VKORC1 and GGCX were associated with decreased warfarin dose, except for rs7196161, rs7294 and rs2108622 which were associated with an increased warfarin dose. Genetic variations of CYP2C9 (*2 and *3), VKORC1 (rs9923231, rs7294, rs9934438 and rs2359612), CYP4F2, GGCX and non-genetic factors such as age, body weight, clinical status (post mechanical valve replacement) could explain up to 62.1 % of the overall variation (adjusted r (2) 60.2 %, p<0.0001) in warfarin maintenance dose.

CONCLUSION

Genetic polymorphisms of CYP2C9, VKORC1, CYP4F2 and GGCX are important predictive factors of warfarin maintenance dose, and the developed algorithm will be useful to predict the required maintenance and/or starting warfarin dose in South Indian populations.

Optimal dosing of warfarin and other coumarin anticoagulants: the role of genetic polymorphisms

Coumarin anticoagulants, which include warfarin, acenocoumarol and phenprocoumon, are among the most widely prescribed drugs worldwide. There is now a large body of published data showing that genotype for certain common polymorphisms in the genes encoding the target vitamin K epoxide reductase (G-1639A/C1173T) and the main metabolizing enzyme CYP2C9 (CYP2C9*2 and *3 alleles) are important determinants of the individual coumarin anticoagulant dose requirement. Additional less common polymorphisms in these genes together with polymorphisms in other genes relevant to blood coagulation such as the cytochrome P450 CYP4F2, gamma-glutamyl carboxylase, calumenin and cytochrome P450 oxidoreductase may also be significant predictors of dose, especially in ethnic groups such as Africans where there have been fewer genetic studies compared with European populations. Using relevant genotypes to calculate starting dose may improve safety during the initiation period. Various algorithms for dose calculation, which also take patient age and other characteristics into consideration, have been developed for all three widely used coumarin anticoagulants and are now being tested in ongoing large randomised clinical trials. One recently completed study has provided encouraging results suggesting that calculation of warfarin dose on the basis of individual patient genotype leads to few adverse events and a higher proportion of time within the therapeutic coagulation rate window, but these findings still need confirmation.