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Integrated analysis of genetic variation and gene expression reveals novel variant for increased warfarin dose requirement in African Americans.
Hernandez W, Gamazon ER, Aquino-Michaels K, Smithberger E, O'Brien TJ, Harralson AF, Tuck M, Barbour A, Cavallari LH, Perera MA
(2017) J Thromb Haemost 15: 735-743
MeSH Terms: Adult, African Americans, Aged, Algorithms, Calcium-Binding Proteins, Cohort Studies, Cytochrome P-450 CYP2C9, Female, Gene Expression Profiling, Gene Expression Regulation, Genetic Variation, Genotype, Humans, Linkage Disequilibrium, Liver, Male, Middle Aged, Pharmacogenetics, Precision Medicine, Quantitative Trait Loci, Thromboembolism, Vitamin K Epoxide Reductases, Warfarin
Show Abstract · Added April 13, 2017
Essentials Genetic variants controlling gene regulation have not been explored in pharmacogenomics. We tested liver expression quantitative trait loci for association with warfarin dose response. A novel predictor for increased warfarin dose response in African Americans was identified. Precision medicine must take into account population-specific variation in gene regulation.
SUMMARY - Background Warfarin is commonly used to control and prevent thromboembolic disorders. However, because of warfarin's complex dose-requirement relationship, safe and effective use is challenging. Pharmacogenomics-guided warfarin dosing algorithms that include the well-established VKORC1 and CYP2C9 polymorphisms explain only a small proportion of inter-individual variability in African Americans (AAs). Objectives We aimed to assess whether transcriptomic analyses could be used to identify regulatory variants associated with warfarin dose response in AAs. Patients/Methods We identified a total of 56 expression quantitative trait loci (eQTLs) for CYP2C9, VKORC1 and CALU derived from human livers and evaluated their association with warfarin dose response in two independent AA warfarin patient cohorts. Results We found that rs4889606, a strong cis-eQTL for VKORC1 (log Bayes Factor = 12.02), is significantly associated with increased warfarin daily dose requirement (β = 1.1; 95% confidence interval [CI] 0.46 to 1.8) in the discovery cohort (n = 305) and in the replication cohort (β = 1.04; 95% CI 0.33 -1.7; n = 141) after conditioning on relevant covariates and the VKORC1 -1639G>A (rs9923231) variant. Inclusion of rs4889606 genotypes, along with CYP2C9 alleles, rs9923231 genotypes and clinical variables, explained 31% of the inter-patient variability in warfarin dose requirement. We demonstrate different linkage disequilibrium patterns in the region encompassing rs4889606 and rs9923231 between AAs and European Americans, which may explain the increased dose requirement found in AAs. Conclusion Our approach of interrogating eQTLs identified in liver has revealed a novel predictor of warfarin dose response in AAs. Our work highlights the utility of leveraging information from regulatory variants mapped in the liver to uncover novel variants associated with drug response and the importance of population-specific research.
© 2017 International Society on Thrombosis and Haemostasis.
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23 MeSH Terms
STRATEGIES FOR EQUITABLE PHARMACOGENOMIC-GUIDED WARFARIN DOSING AMONG EUROPEAN AND AFRICAN AMERICAN INDIVIDUALS IN A CLINICAL POPULATION.
Wiley LK, Vanhouten JP, Samuels DC, Aldrich MC, Roden DM, Peterson JF, Denny JC
(2017) Pac Symp Biocomput 22: 545-556
MeSH Terms: Adult, African Americans, Aged, Algorithms, Anticoagulants, Cohort Studies, Computational Biology, Cytochrome P-450 CYP2C9, European Continental Ancestry Group, Female, Gene Frequency, Humans, Male, Middle Aged, Models, Genetic, Pharmacogenomic Variants, Polymorphism, Single Nucleotide, Vitamin K Epoxide Reductases, Warfarin
Show Abstract · Added March 14, 2018
The blood thinner warfarin has a narrow therapeutic range and high inter- and intra-patient variability in therapeutic doses. Several studies have shown that pharmacogenomic variants help predict stable warfarin dosing. However, retrospective and randomized controlled trials that employ dosing algorithms incorporating pharmacogenomic variants under perform in African Americans. This study sought to determine if: 1) including additional variants associated with warfarin dose in African Americans, 2) predicting within single ancestry groups rather than a combined population, or 3) using percentage African ancestry rather than observed race, would improve warfarin dosing algorithms in African Americans. Using BioVU, the Vanderbilt University Medical Center biobank linked to electronic medical records, we compared 25 modeling strategies to existing algorithms using a cohort of 2,181 warfarin users (1,928 whites, 253 blacks). We found that approaches incorporating additional variants increased model accuracy, but not in clinically significant ways. Race stratification increased model fidelity for African Americans, but the improvement was small and not likely to be clinically significant. Use of percent African ancestry improved model fit in the context of race misclassification.
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19 MeSH Terms
Genetic determinants of variability in warfarin response after the dose-titration phase.
Iwuchukwu OF, Ramirez AH, Shi Y, Bowton EA, Kawai VK, Schildcrout JS, Roden DM, Denny JC, Stein CM
(2016) Pharmacogenet Genomics 26: 510-516
MeSH Terms: Adult, African Americans, Aged, Aged, 80 and over, Anticoagulants, Calcium-Binding Proteins, Carbon-Carbon Ligases, Cytochrome P-450 CYP2C9, Cytochrome P450 Family 4, Epoxide Hydrolases, European Continental Ancestry Group, Female, Humans, International Normalized Ratio, Male, Middle Aged, Pharmacogenomic Variants, Vitamin K Epoxide Reductases, Warfarin
Show Abstract · Added March 14, 2018
OBJECTIVES - Genetic factors contribute considerably toward variability in warfarin dose requirements and are important in the dose-titration phase; their effects on the stability of anticoagulation later in therapy are not known.
METHODS - Using deidentified electronic medical records linked to a DNA-biobank, we studied 140 African-Americans and 943 European-Americans after the warfarin dose-titration phase. We genotyped 12 single nucleotide polymorphisms in genes (CYP2C9, VKORC1, CYP4F2, GGCX, EPHX1, CALU) associated with altered warfarin dose requirements and tested their associations with international normalized ratio variability (INRVAR) and percent time in therapeutic range in European-Americans and African-Americans.
RESULTS - One allele copy of rs2108622 in CYP4F2 was associated with a 15% [95% confidence interval (CI): 1-26, P=0.03] decrease in the median INRVAR in European-Americans. In African-Americans, GGCX variants rs11676382 and rs699664 were associated with 4.16-fold (95% CI: 1.45-11.97, P=0.009) and 1.50-fold (95% CI: 1.07-2.08, P=0.02) changes in the median INRVAR per variant allele copy, respectively; rs11676382 was also significantly associated with a 23.19% (95% CI: 5.89-40.48, P=0.01) decrease in time in therapeutic range. The total variation in INRVAR explained by both clinical factors and rs2108622 was 5.2% for European-Americans. In African-Americans, the inclusion of GGCX variants rs11676382 and rs699664, and the CYP2C9*8 variant rs7900194 explained ∼29% of the variation in INRVAR.
CONCLUSION - The stability of anticoagulation after the warfarin dose-titration phase is differentially affected by variants in CYP4F2 in European-Americans and GGCX loci in African-Americans.
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19 MeSH Terms
A prognostic model based on readily available clinical data enriched a pre-emptive pharmacogenetic testing program.
Schildcrout JS, Shi Y, Danciu I, Bowton E, Field JR, Pulley JM, Basford MA, Gregg W, Cowan JD, Harrell FE, Roden DM, Peterson JF, Denny JC
(2016) J Clin Epidemiol 72: 107-15
MeSH Terms: Adult, Age Factors, Aged, Clopidogrel, Decision Support Systems, Clinical, Drug Utilization, Electronic Health Records, Female, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Longitudinal Studies, Male, Middle Aged, Models, Statistical, Pharmacogenetics, Predictive Value of Tests, Prognosis, Program Evaluation, Proportional Hazards Models, Reproducibility of Results, Risk Factors, Sex Factors, Ticlopidine, United States, Warfarin
Show Abstract · Added March 14, 2018
OBJECTIVES - We describe the development, implementation, and evaluation of a model to pre-emptively select patients for genotyping based on medication exposure risk.
STUDY DESIGN AND SETTING - Using deidentified electronic health records, we derived a prognostic model for the prescription of statins, warfarin, or clopidogrel. The model was implemented into a clinical decision support (CDS) tool to recommend pre-emptive genotyping for patients exceeding a prescription risk threshold. We evaluated the rule on an independent validation cohort and on an implementation cohort, representing the population in which the CDS tool was deployed.
RESULTS - The model exhibited moderate discrimination with area under the receiver operator characteristic curves ranging from 0.68 to 0.75 at 1 and 2 years after index dates. Risk estimates tended to underestimate true risk. The cumulative incidences of medication prescriptions at 1 and 2 years were 0.35 and 0.48, respectively, among 1,673 patients flagged by the model. The cumulative incidences in the same number of randomly sampled subjects were 0.12 and 0.19, and in patients over 50 years with the highest body mass indices, they were 0.22 and 0.34.
CONCLUSION - We demonstrate that prognostic algorithms can guide pre-emptive pharmacogenetic testing toward those likely to benefit from it.
Copyright © 2016 Elsevier Inc. All rights reserved.
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25 MeSH Terms
Genotype and risk of major bleeding during warfarin treatment.
Kawai VK, Cunningham A, Vear SI, Van Driest SL, Oginni A, Xu H, Jiang M, Li C, Denny JC, Shaffer C, Bowton E, Gage BF, Ray WA, Roden DM, Stein CM
(2014) Pharmacogenomics 15: 1973-83
MeSH Terms: Adult, Aged, Biological Specimen Banks, Cytochrome P-450 CYP2C9, Cytochrome P-450 Enzyme System, Cytochrome P450 Family 4, Dose-Response Relationship, Drug, Ethnic Groups, Female, Gene Frequency, Genetic Association Studies, Genetic Variation, Genotype, Hemorrhage, Humans, Male, Middle Aged, Risk Factors, Vitamin K Epoxide Reductases, Warfarin
Show Abstract · Added January 23, 2015
AIM - To determine whether genetic variants associated with warfarin dose variability were associated with increased risk of major bleeding during warfarin therapy.
MATERIALS & METHODS - Using Vanderbilt's DNA biobank we compared the prevalence of CYP2C9, VKORC1 and CYP4F2 variants in 250 cases with major bleeding and 259 controls during warfarin therapy.
RESULTS - CYP2C9*3 was the only allele that differed significantly among cases (14.2%) and controls (7.8%; p = 0.022). In the 214 (85.6%) cases with a major bleed 30 or more days after warfarin initiation, CYP2C9*3 was the only variant associated with bleeding (adjusted odds ratio: 2.05; 95% CI: 1.04, 4.04).
CONCLUSION - The CYP2C9*3 allele may double the risk of major bleeding among patients taking warfarin for 30 or more days.
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20 MeSH Terms
Genetic variant in folate homeostasis is associated with lower warfarin dose in African Americans.
Daneshjou R, Gamazon ER, Burkley B, Cavallari LH, Johnson JA, Klein TE, Limdi N, Hillenmeyer S, Percha B, Karczewski KJ, Langaee T, Patel SR, Bustamante CD, Altman RB, Perera MA
(2014) Blood 124: 2298-305
MeSH Terms: African Americans, Algorithms, Alleles, Anticoagulants, Cohort Studies, Exome, Folic Acid, Geography, Haplotypes, Homeostasis, Humans, Pharmacogenetics, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Sequence Analysis, DNA, Warfarin
Show Abstract · Added April 13, 2017
The anticoagulant warfarin has >30 million prescriptions per year in the United States. Doses can vary 20-fold between patients, and incorrect dosing can result in serious adverse events. Variation in warfarin pharmacokinetic and pharmacodynamic genes, such as CYP2C9 and VKORC1, do not fully explain the dose variability in African Americans. To identify additional genetic contributors to warfarin dose, we exome sequenced 103 African Americans on stable doses of warfarin at extremes (≤ 35 and ≥ 49 mg/week). We found an association between lower warfarin dose and a population-specific regulatory variant, rs7856096 (P = 1.82 × 10(-8), minor allele frequency = 20.4%), in the folate homeostasis gene folylpolyglutamate synthase (FPGS). We replicated this association in an independent cohort of 372 African American subjects whose stable warfarin doses represented the full dosing spectrum (P = .046). In a combined cohort, adding rs7856096 to the International Warfarin Pharmacogenetic Consortium pharmacogenetic dosing algorithm resulted in a 5.8 mg/week (P = 3.93 × 10(-5)) decrease in warfarin dose for each allele carried. The variant overlaps functional elements and was associated (P = .01) with FPGS gene expression in lymphoblastoid cell lines derived from combined HapMap African populations (N = 326). Our results provide the first evidence linking genetic variation in folate homeostasis to warfarin response.
© 2014 by The American Society of Hematology.
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17 MeSH Terms
The impact of age and CYP2C9 and VKORC1 variants on stable warfarin dose in the paediatric population.
Vear SI, Ayers GD, Van Driest SL, Sidonio RF, Stein CM, Ho RH
(2014) Br J Haematol 165: 832-5
MeSH Terms: Adolescent, Age Factors, Alleles, Anticoagulants, Aryl Hydrocarbon Hydroxylases, Child, Child, Preschool, Cross-Sectional Studies, Cytochrome P-450 CYP2C9, Genetic Variation, Genotype, Humans, Infant, Pharmacogenetics, Retrospective Studies, Vitamin K Epoxide Reductases, Warfarin
Show Abstract · Added March 10, 2014
The influence of genetic variation on warfarin dose requirement is limited for paediatric patients. We performed a retrospective, cross-sectional study to examine the effect of variant CYP2C9 and VKORC1 genotypes on warfarin dose in 100 children. Those with VKORC1 genotype AA required 48% of the dose of homozygous wild-type (GG, P < 0·0001). Patients with any variant CYP2C9 allele required 71% of the dose for wild-type (P = 0·001). The effect of variant VKORC1 alleles tended to vary with age, suggesting developmental ontogeny may influence warfarin sensitivity. Age, CYP2C9 genotype, VKORC1 genotype and age:VKORC1 interaction accounted for 53% of warfarin dose variability.
© 2014 John Wiley & Sons Ltd.
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17 MeSH Terms
Pulmonary embolism after total joint arthroplasty: cost and effectiveness of four treatment modalities.
Raphael IJ, McKenzie JC, Zmistowski B, Brown DB, Parvizi J, Austin MS
(2014) J Arthroplasty 29: 933-7
MeSH Terms: Aged, Aged, 80 and over, Anticoagulants, Arthroplasty, Replacement, Costs and Cost Analysis, Female, Heparin, Humans, Male, Middle Aged, Pulmonary Embolism, Retrospective Studies, Treatment Outcome, Vena Cava Filters, Warfarin
Show Abstract · Added March 5, 2014
Pulmonary embolism (PE) treatment relies on therapeutic anticoagulation and may be associated with severe complications. Inferior vena cava filters (IVCFs) are used as an alternative/adjunct to anticoagulation. In this study we evaluate 4 treatment protocols for clinical efficacy and cost. We reviewed over 27,000 total joint arthroplasty (TJA) patients. We retrospectively identified 294 patients with a documented, symptomatic PE within 90 days of surgery. All patients were treated with warfarin postoperatively. In addition, for the acute management, patients were divided into four treatment groups: (1) IVCF only, (2) IVCF with heparin, (3) heparin only and (4) no treatment. Complication rates, hospital stay and PE recurrence are reported. Among patients who received warfarin, IVCF was associated with fewer complications and lower overall hospital costs compared to the use of heparin for the treatment of PE after TJA.
© 2014.
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15 MeSH Terms
Applied pharmacogenomics in cardiovascular medicine.
Weeke P, Roden DM
(2014) Annu Rev Med 65: 81-94
MeSH Terms: Adrenergic beta-Antagonists, Antihypertensive Agents, Antithrombins, Aryl Hydrocarbon Hydroxylases, Cardiovascular Diseases, Clopidogrel, Cytochrome P-450 CYP2C19, Cytochrome P-450 CYP2C9, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Liver-Specific Organic Anion Transporter 1, Organic Anion Transporters, Pharmacogenetics, Polymorphism, Single Nucleotide, Precision Medicine, Ticlopidine, Vitamin K Epoxide Reductases, Warfarin
Show Abstract · Added March 7, 2014
Interindividual heterogeneity in drug response is a central feature of all drug therapies. Studies in individual patients, families, and populations over the past several decades have identified variants in genes encoding drug elimination or drug target pathways that in some cases contribute substantially to variable efficacy and toxicity. Important associations of pharmacogenomics in cardiovascular medicine include clopidogrel and risk for in-stent thrombosis, steady-state warfarin dose, myotoxicity with simvastatin, and certain drug-induced arrhythmias. This review describes methods used to accumulate and validate these findings and points to approaches--now being put in place at some centers--to implementing them in clinical care.
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18 MeSH Terms
Vitamin K intake, body mass index and warfarin maintenance dose.
Kabagambe EK, Beasley TM, Limdi NA
(2013) Cardiology 126: 214-8
MeSH Terms: Aged, Aged, 80 and over, Anticoagulants, Body Mass Index, Female, Humans, Male, Middle Aged, Pharmacogenetics, Prospective Studies, Vitamin K, Warfarin
Show Abstract · Added May 19, 2014
BACKGROUND - Warfarin inhibits vitamin K-dependent coagulation factors. Being fat-soluble, the availability of vitamin K may vary according to body fat. We hypothesized that body mass index (BMI), a proxy of body fat, may interact with vitamin K intake in determining a warfarin maintenance (WM) dose.
METHODS - Patients with data on vitamin K intake, potential confounders and WM dose (n = 172) were included in linear regression models to test whether BMI modifies the relation between vitamin K intake and WM dose.
RESULTS - Warfarin loading dose correlated with the maintenance dose (r = 0.36, p < 0.0001) but was not significantly associated with WM dose in analyses adjusted for vitamin K epoxide reductase (VKORC1) and cytochrome P450 2C9 (CYP2C9) genotypes. In fully adjusted models, BMI was associated (p = 0.001) with WM dose but vitamin K was only marginally positively associated (p = 0.06) with WM dose. We found no interaction (p > 0.05) between BMI and vitamin K intake with regard to WM dose. Inclusion of vitamin K intake in the model only slightly improved the amount of variance (1.1%) explained by age, gender, BMI, race, physical activity, energy intake and VKORC1 and CYP2C9 genotypes.
CONCLUSION - Our data suggest that body fat does not affect the relation between vitamin K intake and WM dose.
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12 MeSH Terms