Genotype and risk of major bleeding during warfarin treatment

Genetic polymorphisms and major bleeding risk during vitamin K antagonists treatment: The BLEEDS case-cohort

BACKGROUND

Major bleeding occurs annually in 1%-3% of patients on vitamin K antagonists (VKAs), despite close monitoring. Genetic variants in proteins involved in VKA response may affect this risk.

AIM

To determine the association of genetic variants (cytochrome P450 enzymes 2C9 [CYP2C9] and 4F2 [CYP4F2], gamma-glutamyl carboxylase [GGCX]) with major bleeding in VKA users, separately and combined, including vitamin K epoxide reductase complex subunit-1 (VKORC1).

METHODS

A case-cohort study was established within the BLEEDS cohort, which includes 16,570 patients who initiated VKAs between 2012 and 2014. We selected all 326 major bleeding cases that occurred during 17,613 years of follow-up and a random subcohort of 978 patients. We determined variants in CYP2C9, CYP4F2, GGCX, VKORC1 and evaluated the interaction between variant genotypes. Hazard ratios for major bleeding with 95% confidence intervals (95% CI) were estimated by weighted Cox regression.

RESULTS

Genotype was determined in 256 cases and 783 subcohort members. Phenprocoumon was the most prescribed VKA for both cases and the subcohort (78% and 75%, respectively). Patients with major bleeding were slightly older than subcohort patients. CYP4F2-TT carriership was associated with a 1.6-fold (95% CI 0.9-2.8) increased risk of major bleeding compared with CC-alleles, albeit not statistically significant. For the CYP2C9 and GGCX variants instead, the major bleeding risk was around unity. Carrying at least two variant genotypes in CYP2C9 (poor metabolizer), CYP4F2-TT, and VKORC1-AA was associated with a 4.0-fold (95%CI 1.4-11.4) increased risk, while carriers of both CYP4F2-TT and VKORC1-AA had a particularly increased major bleeding risk (hazard ratio 6.7, 95% CI 1.5-29.8) compared with carriers of CC alleles in CYP4F2 and GG in VKORC1. However, the number of major bleeding cases in carriers of multiple variants was few (8 and 5 patients, respectively).

CONCLUSIONS

CYP4F2 polymorphism was associated with major bleeding, especially in combination with VKORC1 genetic variants. These variants could be considered to further personalize anticoagulant treatment.

Machine learning analysis of bleeding status in venous thromboembolism patients

Background

Anticoagulation therapy is the mainstay of therapy for patients with venous thromboembolism (VTE). However, continuing or stopping anticoagulants after the first 3 to 6 months is a difficult decision that requires ascertainment of the risk of bleeding and recurrent VTE. Despite the development of several statistical models to predict bleeding, the benefit of machine learning (ML) models has not been investigated in depth.

Objectives

To assess the benefits of ML algorithms in bleeding risk evaluation in VTE patients and gain insight into their baseline information.

Methods

The baseline clinical, demographic, and genotype information was collected for 2542 patients with VTE who were on extended anticoagulation therapy. Six unsupervised dimensionality reduction and clustering ML algorithms were used to visualize and cluster the data for patients with major bleeding (118 patients) and nonbleeders. Eight supervised ML algorithms were trained and compared with the previously derived clinical models using a 5-fold nested cross-validation scheme.

Results

The baseline dataset for bleeders and nonbleeders showed a high degree of similarity. Two novel clusters were discovered within the dataset for bleeders based on the presence of isolated pulmonary embolism or isolated deep vein thrombosis, though the difference in bleeding risks was not statistically significant (P = .32). The supervised analysis showed that the ML and clinical models have similar discrimination (c-statistics, ∼62%) and calibration performance (Brier score, ∼0.045).

Conclusion

The clinical variables recorded at baseline are not distinctive enough to improve bleeding prediction beyond the performance of the existing models, and other strategies or data modalities should be considered.

Real-world evidence that among atrial fibrillation patients warfarin is associated with reduced nonelective admissions compared with those on DOACs

BACKGROUND

Randomized trials show inconsistent estimates on risks of direct-acting oral anticoagulants (DOACs) versus warfarin in bleeding and mortality for atrial fibrillation (AF) patients. Trials are confounded by additional DOAC adherence support, while warfarin has a low time in therapeutic range. Few real-world studies compared emergency hospitalization risk between DOAC and warfarin users in AF. This study aimed to determine emergency hospitalization risk for AF patients on DOACs or warfarin in real-world settings.

METHODS

A tapered-matched real-world cohort extracted data from 412 English general practices' primary care records linked with emergency department (ED) and hospitalization data from the ECLIPSE database. AF patients with new DOAC or warfarin prescriptions were included. The primary outcome was all-cause ED attendance; the secondary outcomes were ED re-attendance, nonelective hospitalization, and rehospitalization within 12 months. Weighted Cox regression estimated relative risk difference.

RESULTS

39 201 DOAC patients were matched with 13 145 warfarin patients. DOAC patients had a 25% higher likelihood of attending ED (odds ratio 1.25; 95% confidence interval [CI] 1.01-1.55). DOAC use also associated with higher ED re-attendance, nonelective hospitalization, and rehospitalization within 12 months: 1.41 (95% CI 1.00-1.98), 1.26 (1.00-1.57), and 1.54 (1.01-2.34), respectively, with p-values < .05.

CONCLUSIONS

DOACs for AF thromboprophylaxis are associated with the increased risk of ED attendance, recurrent hospitalization, and numerical rise in ED re-attendance and first nonelective hospitalization compared to warfarin. However, these real-world data cannot establish if this difference results from medication adherence, lack of regular DOAC clinic monitoring, unmeasured confounders, or fundamental agent efficacy disparities.

A Physiological-Based Pharmacokinetic Model Embedded with a Target-Mediated Drug Disposition Mechanism Can Characterize Single-Dose Warfarin Pharmacokinetic Profiles in Subjects with Various CYP2C9 Genotypes under Different Cotreatments

Warfarin, a commonly prescribed oral anticoagulant medication, is highly effective in treating deep vein thrombosis and pulmonary embolism. However, the clinical dosing of warfarin is complicated by high interindividual variability in drug exposure and response and its narrow therapeutic index. CYP2C9 genetic polymorphism and drug-drug interactions (DDIs) are substantial contributors to this high variability of warfarin pharmacokinetics (PK), among numerous factors. Building a physiology-based pharmacokinetic (PBPK) model for warfarin is not only critical for a mechanistic characterization of warfarin PK but also useful for investigating the complicated dose-exposure relationship of warfarin. Thus, the objective of this study was to develop a PBPK model for warfarin that integrates information regarding CYP2C9 genetic polymorphisms and their impact on DDIs. Generic PBPK models for both S- and R-warfarin, the two enantiomers of warfarin, were constructed in R with the mrgsolve package. As expected, a generic PBPK model structure did not adequately characterize the warfarin PK profile collected up to 15 days following the administration of a single oral dose of warfarin, especially for S-warfarin. However, following the integration of an empirical target-mediated drug disposition (TMDD) component, the PBPK-TMDD model well characterized the PK profiles collected for both S- and R-warfarin in subjects with different CYP2C9 genotypes. Following the integration of enzyme inhibition and induction effects, the PBPK-TMDD model also characterized the PK profiles of both S- and R-warfarin in various DDI settings. The developed mathematic framework may be useful in building algorithms to better inform the clinical dosing of warfarin. SIGNIFICANCE STATEMENT: The present study found that a traditional physiology-based pharmacokinetic (PBPK) model cannot sufficiently characterize the pharmacokinetic profiles of warfarin enantiomers when warfarin is administered as a single dose, but a PBPK model with a target-mediated drug disposition mechanism can. After incorporating CYP2C9 genotypes and drug-drug interaction information, the developed model is anticipated to facilitate the understanding of warfarin disposition in subjects with different CYP2C9 genotypes in the absence and presence of both cytochrome P450 inhibitors and cytochrome P450 inducers.

Association of VKORC1 and CYP2C9 single-nucleotide polymorphisms with warfarin dose adjustment in Saudi patients

OBJECTIVES

Despite its wide usage, warfarin therapy remains challenging due to its narrow therapeutic index, inter-individual response variability, and risk of bleeding. Previous reports have suggested that polymorphisms in VKORC1 and CYP2C9 genes could influence warfarin therapy. Herein, we investigated whether VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 gene polymorphisms are associated with warfarin dose adjustment and related bleeding events.

METHODS

This cross-sectional study was conducted on Saudi adults receiving warfarin for more than 1 month. Their demographics and relevant clinical data were obtained. Genotyping for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*2 genotypes was performed.

RESULTS

Patients who are homozygous for the mutant T allele VKORC1 T/T required the lowest warfarin daily maintenance dose, compared to VKORC1 C/T and VKORC1 C/C. Similarly, there was a significant reduction in warfarin daily maintenance dose among CYP2C9*1/*3 and CYP2C9*1/*2 groups compared to CYP2C9*1/*1. However, we found no significant correlation between the studied polymorphisms and warfarin-associated bleeding.

CONCLUSIONS

Similar to other populations, the VKORC1 and CYP2C9 gene polymorphisms are significantly associated with warfarin dosage in Saudi patients. The presence of at least one copy of the mutant alleles for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 is associated with a significant reduction in warfarin maintenance dose.

The Impact of CYP2C9*11 Allelic Variant on the Pharmacokinetics of Phenytoin and (S)-Warfarin

Cytochrome P450 2C9 (CYP2C9) is responsible for the oxidative metabolism of about 15% of commonly used drugs, some of which are characterized by a narrow therapeutic window. CYP2C9 is highly polymorphic, and over 60 alleles have been described. CYP2C9*2 and CYP2C9*3 are the most common polymorphisms among White patients and both are associated with decreased activity. The evidence concerning the functional importance of less frequent variant alleles is scarce. The objective of the current study was to characterize the in vivo activity of CYP2C9 among carriers of CYP2C9*11, one of the "African" alleles and the fourth most common CYP2C9 variant allele among White patients by using two prototype substrates, phenytoin and (S)-warfarin. Single 300-mg phenytoin and 20-mg warfarin doses were given to 150 healthy Ethiopian Jewish participants who were nonsmokers, at least one week apart. (S)-warfarin oral clearance and phenytoin metabolic ratio (PMR) derived from the ratio of 5-(4-hydroxyphenyl)-5-phenylhydantoin in 24-hour urine collection to plasma phenytoin 12 hours (PMR 24/12) or 24 hours (PMR 24/24) post dosing, were used as markers of CYP2C9 activity. PMR 24/12 and PMR 24/24 were reduced by 50% and 62.2%, respectively, among carriers of CYP2C9*1/*11 (n = 13) as compared with carriers of CYP2C9*1/*1 (n = 127) (false discovery rate (FDR) q < 0.001). The respective decrease in (S)-warfarin oral clearance was 52.6% (FDR q < 0.001). In conclusion, the enzyme encoded by CYP2C9*11 is characterized by a more than 50% decrease in the enzymatic activity, resembling the extent of decrease associated with CYP2C9*3 ("no-function allele"). Among patients of African ancestry, CYP2C9*11 genetic analysis should be considered prior to prescribing of narrow therapeutic window drugs such as phenytoin, warfarin, nonsteroidal anti-inflammatory drugs, or siponimod.

Association of VKORC1 and CYP2C9 single-nucleotide polymorphisms with warfarin dose adjustment in Saudi patients

OBJECTIVES

Despite its wide usage, warfarin therapy remains challenging due to its narrow therapeutic index, inter-individual response variability, and risk of bleeding. Previous reports have suggested that polymorphisms in VKORC1 and CYP2C9 genes could influence warfarin therapy. Herein, we investigated whether VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 gene polymorphisms are associated with warfarin dose adjustment and related bleeding events.

METHODS

This cross-sectional study was conducted on Saudi adults receiving warfarin for more than 1 month. Their demographics and relevant clinical data were obtained. Genotyping for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*2 genotypes was performed.

RESULTS

Patients who are homozygous for the mutant T allele VKORC1 T/T required the lowest warfarin daily maintenance dose, compared to VKORC1 C/T and VKORC1 C/C. Similarly, there was a significant reduction in warfarin daily maintenance dose among CYP2C9*1/*3 and CYP2C9*1/*2 groups compared to CYP2C9*1/*1. However, we found no significant correlation between the studied polymorphisms and warfarin-associated bleeding.

CONCLUSIONS

Similar to other populations, the VKORC1 and CYP2C9 gene polymorphisms are significantly associated with warfarin dosage in Saudi patients. The presence of at least one copy of the mutant alleles for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 is associated with a significant reduction in warfarin maintenance dose.

Inter-phenotypic differences in CYP2C9 and CYP2C19 metabolism: Bayesian meta-regression of human population variability in kinetics and application in chemical risk assessment

Quantifying variability in pharmacokinetics (PK) and toxicokinetics (TK) provides a science-based approach to refine uncertainty factors (UFs) for chemical risk assessment. In this context, genetic polymorphisms in cytochromes P450 (CYPs) drive inter-phenotypic differences and may result in reduction or increase in metabolism of drugs or other xenobiotics. Here, an extensive literature search was performed to identify PK data for probe substrates of the human polymorphic isoforms CYP2C9 and CYP2C19. Relevant data from 158 publications were extracted for markers of chronic exposure (clearance and area under the plasma concentration-time curve) and analysed using a Bayesian meta-regression model. Enzyme function (EF), driven by inter-phenotypic differences across a range of allozymes present in extensive and poor metabolisers (EMs and PMs), and fraction metabolised (Fm), were identified as exhibiting the highest impact on the metabolism. The Bayesian meta-regression model provided good predictions for such inter-phenotypic differences. Integration of population distributions for inter-phenotypic differences and estimates for EF and Fm allowed the derivation of CYP2C9- and CYP2C19-related UFs which ranged from 2.7 to 12.7, and were above the default factor for human variability in TK (3.16) for PMs and major substrates (Fm >60%). These results provide population distributions and pathway-related UFs as conservative in silico options to integrate variability in CYP2C9 and CYP2C19 metabolism using in vitro kinetic evidence and in the absence of human data. The future development of quantitative extrapolation models is discussed with particular attention to integrating human in vitro and in vivo PK or TK data with pathway-related variability for chemical risk assessment.

Prediction and treatment of bleeding in patients under anticoagulant treatment

Major bleeding is a common complication of anticoagulant treatment. Risk assessment tools are relevant in the management of patients with atrial fibrillation and venous thromboembolism. The combination of clinical, biological and genetic markers is incorporated to build predictive scores to help in the decision process about intensity and duration of treatment. The optimal management of bleeding involves the application of predictive scores in combination with anticoagulant reversal strategies.

Comparison of CYP2C9 Activity in Ethiopian and Non-Ethiopian Jews Using Phenytoin as a Probe

The pharmacokinetics of CYP2C9 substrates is characterized by substantial interethnic variability. The objective of the study was to compare CYP2C9 activity by using Phenytoin Metabolic Ratio (PMR) between Ethiopian and non-Ethiopian Jews. PMR was derived from the ratio of p-HPPH in 24 h urine collection to plasma phenytoin, 12 h (PMR24/12) or 24 h (PMR24/24) after the administration of 300 mg phenytoin. Analysis of CYP2C9*2, *3, *5, *6, *8, and *11 was carried by direct sequencing. PMR was significantly correlated with CYP2C9 genotype in both groups (p < 0.002). Mean PMR values were similar among Ethiopians and non-Ethiopians despite the fact that the fraction of non-carriers of CYP2C9 variant alleles was significantly different (85 vs. 53%, respectively, p < 0.001). However, among non-carriers of CYP2C9*2, *3, *5, *6, *8, and *11 variant alleles, PMR24/12 and PMR24/24 values were 30 and 34% greater respectively in the non-Ethiopians group (p < 0.001). In conclusion-CYP2C9 activity as measured by PMR is similar in Ethiopian and non-Ethiopian Jews. However, among non-carriers of CYP2C9 variant alleles accounting for 85% of Ethiopian Jews, CYP2C9 activity is decreased by approximately one third as compared with non-Ethiopian Jews. Unique genetic CYP2C9 polymorphisms occurring only in Ethiopians may account for this difference.

Genetic Factors Influencing Warfarin Dose in Black-African Patients: A Systematic Review and Meta-Analysis

Warfarin is the most commonly used oral anticoagulant in sub-Saharan Africa. Dosing is challenging due to a narrow therapeutic index and high interindividual variability in dose requirements. To evaluate the genetic factors affecting warfarin dosing in black-Africans, we performed a meta-analysis of 48 studies (2,336 patients). Significant predictors for CYP2C9 and stable dose included rs1799853 (CYP2C9*2), rs1057910 (CYP2C9*3), rs28371686 (CYP2C9*5), rs9332131 (CYP2C9*6), and rs28371685 (CYP2C9*11) reducing dose by 6.8, 12.5, 13.4, 8.1, and 5.3 mg/week, respectively. VKORC1 variants rs9923231 (-1639G>A), rs9934438 (1173C>T), rs2359612 (2255C>T), rs8050894 (1542G>C), and rs2884737 (497T>G) decreased dose by 18.1, 21.6, 17.3, 11.7, and 19.6 mg/week, respectively, whereas rs7294 (3730G>A) increased dose by 6.9 mg/week. Finally, rs12777823 (CYP2C gene cluster) was associated with a dose reduction of 12.7 mg/week. Few studies were conducted in Africa, and patient numbers were small, highlighting the need for further work in black-Africans to evaluate genetic factors determining warfarin response.

Has the introduction of direct oral anticoagulants (DOACs) in England increased emergency admissions for bleeding conditions? A longitudinal ecological study

OBJECTIVE

There is concern about long-term safety of direct oral coagulants (DOACs) in clinical practice. Our aim was to investigate whether the introduction of DOACs compared with vitamin-K antagonists in England was associated with a change in admissions for bleeding or thromboembolic complications.

SETTING

5508 General practitioner (GP) practices in England between 2011 and 2016.

PARTICIPANTS

All GP practices in England with a registered population size of greater than 1000 that had data for all 6 years.

MAIN OUTCOME MEASURE

The rate of emergency admissions to hospital for bleeding or thromboembolism, per 100 000 population for each GP practice in England.

MAIN EXPOSURE MEASURE

The annual number of DOAC items prescribed for each GP practice population as a proportion of all anticoagulant items prescribed.

DESIGN

This longitudinal ecological study used panel regression models to investigate the association between trends in DOAC prescribing within GP practice populations and trends in emergency admission rates for bleeding and thromboembolic conditions, while controlling for confounders.

RESULTS

For each additional 10% of DOACs prescribed as a proportion of all anticoagulants, there was a 0.9% increase in bleeding complications (rate ratio 1.008 95% CI 1.003 to 1.013). The introduction of DOACs between 2011 and 2016 was associated with additional 4929 (95% CI 2489 to 7370) emergency admissions for bleeding complications. Increased DOAC prescribing was associated with a slight decline in admission for thromboembolic conditions.

CONCLUSION

Our data show that the rapid increase in prescribing of DOACs after changes in National Institute for Health and Care Excellence guidelines in 2014 may have been associated with a higher rate of emergency admissions for bleeding conditions. These consequences need to be considered in assessing the benefits and costs of the widespread use of DOACs.

Oral Anticoagulant Therapy-When Art Meets Science

Anticoagulant treatment is extremely important and frequently encountered in the therapy of various cardiovascular diseases. Vitamin K antagonists (VKA) are in use for the prevention and treatment of arterial and venous thromboembolism, despite the introduction of new direct-acting oral anticoagulants (NOAC). The VKA still have the clear recommendation in patients with a mechanical prosthetic heart valve replacement or moderate to severe mitral stenosis of the rheumatic origin, in deep vein thrombosis associated with congenital thrombophilia, and in cases where NOAC are prohibited by social condition (financial reason) or by comorbidities (extreme weight, severe renal or liver disease). VKA dosing required to reach the targeted therapeutic range varies largely between patients (inter-individual variability). This inter-individual variability depends on multiple environmental factors such as age, mass, diet, etc. but it is also influenced by genetic determinism. About 30 genes implicated in the metabolism coumarins derivatives were identified, the most important being CYP2C9 and VKORC, each with several polymorphisms. Herein, we review the data regarding genetic alterations in general and specific populations, highlight the diagnosis options in particular cases presenting with genetic alteration causing higher sensitivity and/or resistance to VKA therapy and underline the utility of NOAC in solving such rare and difficult problems.

A Rare Combination of CYP2C9*3/*3 and VKORC1 1639AA in a Patient Who Had Myxoma and Thromboembolism

We report a case of intolerance to warfarin. A 20-year-old woman with toe pain was diagnosed with myxoma with multiple systemic embolisms. She was prescribed warfarin for remaining embolic pain after myxoma excision and mitral annuloplasty. Even on 1 mg of warfarin, the international normalized ratio was much increased. The patient was found to have cytochrome P450 2C9 (CYP2C9)*3/*3 and vitamin K epoxide reductase complex subunit 1 (VKORC1) 1639AA genotype, which is extremely rare in Koreans. Based on this result, we assessed the potential risks and benefits of warfarin and decided to switch to aspirin because the risk of bleeding was considered to be too high.

Opportunities and Challenges in Cardiovascular Pharmacogenomics: From Discovery to Implementation

This review will provide an overview of the principles of pharmacogenomics from basic discovery to implementation, encompassing application of tools of contemporary genome science to the field (including areas of apparent divergence from disease-based genomics), a summary of lessons learned from the extensively studied drugs clopidogrel and warfarin, the current status of implementing pharmacogenetic testing in practice, the role of genomics and related tools in the drug development process, and a summary of future opportunities and challenges.

Pharmacogenomics

Genomic medicine, which uses DNA variation to individualise and improve human health, is the subject of this Series of papers. The idea that genetic variation can be used to individualise drug therapy-the topic addressed here-is often viewed as within reach for genomic medicine. We have reviewed general mechanisms underlying variability in drug action, the role of genetic variation in mediating beneficial and adverse effects through variable drug concentrations (pharmacokinetics) and drug actions (pharmacodynamics), available data from clinical trials, and ongoing efforts to implement pharmacogenetics in clinical practice.

Association between four microRNA binding site-related polymorphisms and the risk of warfarin-induced bleeding complications

Bleeding is the most serious complication of warfarin anticoagulation therapy and is known to occur even at patients with therapeutic international normalized ratio (INR) range. Recently, it has been shown that microRNAs play a significant role in pharmacogenetics by regulating genes that are critical for drug function. Interaction between microRNAs and these target genes could be affected by single-nucleotide polymorphisms (SNPs) located in microRNA-binding sites. This study focused on 3′-untranslated region (3′-UTR) SNPs of the genes involved in the warfarin action and the occurrence of bleeding complications in an Iranian population receiving warfarin. A total of 526 patients under warfarin anticoagulation therapy with responding to the therapeutic dose and maintenance of the INR in the range of 2.0-3.5 in three consecutive blood tests were included in the study. Four selected 3'-UTR SNPs (rs12458, rs7294, rs1868774 and rs34669593 located in GATA4, VKORC1, CALU and GGCX genes, respectively) with the potential to disrupt/eliminate or enhance/create microRNA-binding site were genotyped using a simple PCR-based restriction fragment length polymorphism (PCR-RFLP) method. Patients with the rs12458 AT or TT genotypes of the GATA4 gene had a lower risk of bleeding compared to patients with the AA genotype (adjusted OR: 0.478, 95% CI: 0.285-0.802, P= 0.005, OR: 0.416, 95% CI: 0.192-0.902, P= 0.026, respectively). 3'-UTR polymorphisms in other genes were not significantly associated with the risk of bleeding complications. In conclusion, the SNP rs12458A>T in the 3′UTR region of GATA4 is associated with the incidence of warfarin-related bleeding at target range of INR, likely by altering microRNA binding and warfarin metabolism. Further genetics association studies are needed to validate these findings before they can be implemented in clinical settings.

PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison

Background

Pharmacogenomics (PGx) studies how genomic variations impact variations in drug response phenotypes. Knowledge in pharmacogenomics is typically composed of units that have the form of ternary relationships gene variant – drug – adverse event. Such a relationship states that an adverse event may occur for patients having the specified gene variant and being exposed to the specified drug. State-of-the-art knowledge in PGx is mainly available in reference databases such as PharmGKB and reported in scientific biomedical literature. But, PGx knowledge can also be discovered from clinical data, such as Electronic Health Records (EHRs), and in this case, may either correspond to new knowledge or confirm state-of-the-art knowledge that lacks “clinical counterpart” or validation. For this reason, there is a need for automatic comparison of knowledge units from distinct sources.

Results

In this article, we propose an approach, based on Semantic Web technologies, to represent and compare PGx knowledge units. To this end, we developed PGxO, a simple ontology that represents PGx knowledge units and their components. Combined with PROV-O, an ontology developed by the W3C to represent provenance information, PGxO enables encoding and associating provenance information to PGx relationships. Additionally, we introduce a set of rules to reconcile PGx knowledge, i.e. to identify when two relationships, potentially expressed using different vocabularies and levels of granularity, refer to the same, or to different knowledge units. We evaluated our ontology and rules by populating PGxO with knowledge units extracted from PharmGKB (2701), the literature (65,720) and from discoveries reported in EHR analysis studies (only 10, manually extracted); and by testing their similarity. We called PGxLOD (PGx Linked Open Data) the resulting knowledge base that represents and reconciles knowledge units of those various origins.

Conclusions

The proposed ontology and reconciliation rules constitute a first step toward a more complete framework for knowledge comparison in PGx. In this direction, the experimental instantiation of PGxO, named PGxLOD, illustrates the ability and difficulties of reconciling various existing knowledge sources.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2693-9) contains supplementary material, which is available to authorized users.

VKORC1 variants as significant predictors of warfarin dose in Emiratis

Purpose: Variability in response to warfarin is one of the main obstacles challenging its use in clinical practice. Vitamin K epoxide reductase complex (VKORC) is the target enzyme of warfarin, and variations in the form of single nucleotide polymorphisms (SNPs) in VKORC1, coding for this enzyme, are known to cause resistance to warfarin treatment. This study aimed to explore VKORC1 variants in Emirati patients receiving warfarin treatment and to correlate their genotypes at the studied SNPs to their maintenance warfarin dose.

Patients and methods: Sanger sequencing of the majority of the VKORC1 gene was applied to samples from 90 patients and 117 normal individuals recruited from Tawam Hospital, Al-Ain, UAE. Genotypes at the following variants were determined (rs9923231, rs188009042, rs61742245, rs17708472, rs9934438, rs8050894, rs2359612, rs7294). Statistical analysis was applied, including ANOVA, cross-tabulation, and multiple linear regression analysis, to determine the ability of nongenetic factors (age and gender) and genetic factors (VKORC1 genotypes) to explain variability in warfarin dose in patients.

Results: Different frequencies of minor alleles were detected in the selected SNPs. Significant variation among genotypes at six VKORC1 variants were identified (rs9923231, rs9934438, rs8050894, rs2359612, rs7294). The main predictors for warfarin dose were rs9923231, age, and rs61742245 with 50.7% of the average warfarin dose in our sample could be explained by a regression model built on these three factors.

Conclusion: This is the first report of the explanatory power of VKORC1 genotypes and nongenetic factors (age and gender) on warfarin dose among Emiratis. Also, this study highlighted the positive effect of considering rare pharmacogenomic variants on explaining warfarin dose variability.

Aspects of Modern Biobank Activity - Comprehensive Review

Biobanks play an increasing role in contemporary research projects. These units meet all requirements to regard them as a one of the most innovative and up-to-date in the field of biomedical research. They enable conducting wide-scale research by the professional collection of biological specimens and correlated clinical data. Pathology units may be perceived roots of biobanking. The review aims at describing the concept of biobanks, their model of function and scientific potential. It comprises the division of biobanks, sample preservation methods and IT solutions as well as guidelines and recommendations for management of a vast number of biological samples and clinical data. Therefore, appropriate standard operating procedures and protocols are outlined. Constant individualization of diagnostic process and treatment procedures creates the niche for translational units. Thus, the role of biobanks in personalized medicine was also specified. The exceptionality of biobanks poses some new ethical-legal issues which have various solutions, in each legal system, amongst the world. Finally, distribution and activity of European biobanks are mentioned.

Pharmacogenetics of vitamin K antagonists and bleeding risk prediction in atrial fibrillation

BACKGROUND

Polymorphisms in the vitamin K epoxide reductase complex 1 (VKORC1) and cytochrome P450 2C9 (CYP2C9) genes increase the bleeding risk in anticoagulated atrial fibrillation (AF) patients. Here, we aimed to investigate whether VKORC1 and CYP2C9 polymorphisms improved the predictive performance for major bleeding using the HAS-BLED score.

MATERIAL AND METHODS

We recruited 652 consecutive AF patients stable on vitamin K antagonist (INR 2.0-3.0) during at least the previous 6 months. A baseline venous blood sample was obtained for DNA extraction. We gave an extra point to the HAS-BLED score if the patient was a simultaneous carrier of the VKORC1 and CYP2C9 polymorphisms related to bleeding, and we called this modified score "GEN|HAS-BLED." During a median follow-up of 7.6 years (IQR 5.6-8.0), all major bleeding events were recorded.

RESULTS

During follow-up, 106 (16.2%) patients experienced a major bleeding (2.81%/y; 42 intracranial haemorrhages and 44 gastrointestinal bleeding) and 24 (3.7%) died from major bleeding (0.48%/y). Cox regression analyses demonstrated a significant association between HAS-BLED or GEN|HAS-BLED and major bleeds, both as continuous or categorical scores. Comparison of receiver operating characteristic (ROC) curves shows that original HAS-BLED clinical score had better predictive ability than GEN|HAS-BLED (0.660, 95% CI 0.622-0.696 vs 0.645, 95% CI 0.607-0.682; P = .030). Discrimination and reclassification analyses showed that GEN|HAS-BLED did not improve sensitivity compared with the original score and even showed significant negative reclassification.

CONCLUSION

Adding pharmacogenetic factors (ie polymorphisms of the VKORC1 and CYP2C9 genes) to the HAS-BLED score does not improve the prediction or discrimination performance for major bleeding.

Benefit of Preemptive Pharmacogenetic Information on Clinical Outcome

The development of new knowledge around the genetic determinants of variable drug action has naturally raised the question of how this new knowledge can be used to improve the outcome of drug therapy. Two broad approaches have been taken: a point-of-care approach in which genotyping for specific variant(s) is undertaken at the time of drug prescription, and a preemptive approach in which multiple genetic variants are typed in an individual patient and the information archived for later use when a drug with a "pharmacogenetic story" is prescribed. This review addresses the current state of implementation, the rationale for these approaches, and barriers that must be overcome. Benefits to pharmacogenetic testing are only now being defined and will be discussed.

Incidence and characteristics of major bleeding among rivaroxaban users with renal disease and nonvalvular atrial fibrillation

OBJECTIVE

Patients with nonvalvular atrial fibrillation (AF) and renal disease (RD) who receive anticoagulation therapy appear to be at greater risk of major bleeding (MB) than AF patients without RD. As observed in past studies, anticoagulants are frequently withheld from AF patients with RD due to concerns regarding bleeding. The objective of this study was to evaluate the incidence and pattern of MB in those with RD, as compared to those without RD, in a population of rivaroxaban users with nonvalvular AF.

METHODS

Electronic medical records of over 10 million patients from the Department of Defense Military Health System were queried to identify rivaroxaban users with nonvalvular AF. A validated algorithm was used to identify MB-related hospitalizations. RD was defined through diagnostic codes present within 6 months prior to the bleeding date for MB cases and end of study participation for non-MB patients. Data were collected on patient characteristics, comorbidities, MB management, and outcomes.

RESULTS

Overall, 44,793 rivaroxaban users with nonvalvular AF were identified. RD was present among 6,921 patients (15.5%). Patients with RD had a higher rate of MB than those without RD, 4.52 per 100 person-years versus 2.54 per 100 person-years, respectively. The fatal bleeding outcome rate (0.09 per 100 person-years) was identical between those with and without RD.

CONCLUSION

In this post-marketing study of 44,793 rivaroxaban users with nonvalvular AF, RD patients experienced a higher MB rate than those without RD. The higher rate of MB among those with RD may be due to the confounding effects of comorbidities.

Quality of anticoagulation control and hemorrhage risk among African American and European American warfarin users

OBJECTIVE

We evaluated whether percent time in target range (PTTR), risk of over-anticoagulation [international normalized ratio (INR)>4], and risk of hemorrhage differ by race. As PTTR is a strong predictor of hemorrhage risk, we also determined the influence of PTTR on the risk of hemorrhage by race.

PARTICIPANTS AND METHODS

Among 1326 warfarin users, PTTR was calculated as the percentage of interpolated INR values within the target range of 2.0-3.0. PTTR was also categorized as poor (PTTR<60%), good (60≤PTTR<70%), or excellent (PTTR≥70%) anticoagulation control. Over-anticoagulation was defined as INR more than 4 and major hemorrhages included serious, life-threatening, and fatal bleeding episodes. Logistic regression and survival analyses were carried out to evaluate the association of race with PTTR (≥60 vs. <60) and major hemorrhages, respectively.

RESULTS

Compared with African Americans, European Americans had higher PTTR (57.6 vs. 49.1%; P<0.0001) and were more likely to attain 60≤PTTR<70% (22.9 vs. 13.1%; P<0.001) or PTTR of at least 70% (26.9 vs. 18.2%; P=0.001). Older (>65 years) patients without venous thromboembolism indication and chronic kidney disease were more likely to attain PTTR of at least 60%. After accounting for clinical and genetic factors, and PTTR, African Americans had a higher risk of hemorrhage [hazard ratio (HR)=1.58; 95% confidence interval (CI): 1.04-2.41; P=0.034]. Patients with 60≤PTTR<70% (HR=0.62; 95% CI: 0.38-1.02; P=0.058) and PTTR of at least 70% (HR=0.27; 95% CI: 0.15-0.49; P<0.001) had a lower risk of hemorrhage compared with those with PTTR less than 60%.

CONCLUSION

Despite the provision of warfarin management through anticoagulation clinics, African Americans achieve a lower overall PTTR and have a significantly higher risk of hemorrhage. Personalized medicine interventions tailored to African American warfarin users need to be developed.

The Influence of Big (Clinical) Data and Genomics on Precision Medicine and Drug Development

Drug development continues to be costly and slow, with medications failing due to lack of efficacy or presence of toxicity. The promise of pharmacogenomic discovery includes tailoring therapeutics based on an individual's genetic makeup, rational drug development, and repurposing medications. Rapid growth of large research cohorts, linked to electronic health record (EHR) data, fuels discovery of new genetic variants predicting drug action, supports Mendelian randomization experiments to show drug efficacy, and suggests new indications for existing medications. New biomedical informatics and machine-learning approaches advance the ability to interpret clinical information, enabling identification of complex phenotypes and subpopulations of patients. We review the recent history of use of "big data" from EHR-based cohorts and biobanks supporting these activities. Future studies using EHR data, other information sources, and new methods will promote a foundation for discovery to more rapidly advance precision medicine.

Influence of genetic and non-genetic factors on acenocoumarol maintenance dose requirement in a Tunisian population

PURPOSE

We aimed to study potential variables involved in interindividual variability to acenocoumarol (AC) response in order to establish a pharmacogenetic algorithm (PA) that includes clinical and genetic factors to predict adequate AC dose to stabilize anticoagulation in a cohort of Tunisian patients.

METHODS

Genotyping of the CYP2C9, VKORC1, CYP4F2, and CALU polymorphisms was conducted on 246 patients using PCR-RFLP technique. AC normalized maintenance dose (NMD): ((mean maintenance dose/international normalized ratio (INR)) equilibrium) was calculated. The statistical study was carried out with SPSS V20.

RESULTS

A significant correlation was found between age, BMI, and daily AC dose (r = - 0.397; p < 0.001 and r = 0.215; p = 0.001, respectively). The carriers of mutated alleles CYP2C9*2 or CYP2C9*3 or VKORC1 haplotypes (H1 and H7) were associated with AC hyper-sensibility. After adjustment to potential covariates, these patients presented supra-therapeutic INR during treatment period and needed low AC dose (ORs* = 0.28 [0.06-0.60], p = 0.004; ORs* = 0.12 [0.04-0.05], p < 0.001; ORs* = 0.45 [0.24-0.84], p = 0.01; and ORs* = 0.28 [0.06-0.98], p = 0.049, respectively). However, carriers of VKORC1 haplotypes (H3 and H12) or mutated alleles CYP4F2 (rs2108622) or CALU (rs1043550) tend to resist to treatment, hence long period of therapy initiation, and must be treated with high AC dose (ORs* = 2.67 [81.12-5.91], p = 0.013; ORs* = 8.76 [1.07-76.26], p = 0.019; ORs* = 3.12 [1.01-9.63], p = 0.047; and ORs* = 3.96 [1.41-11.09], p = 0.009, respectively). A final multivariate regression model explained 48.1% of the global interindividual variability in AC dose requirement.

CONCLUSION

The PA demonstrated that VKORC1 and CYP2C9 polymorphisms contribution was more important than clinical factors. Applying the PA would allow dose adjustment to treat patients in a personalized manner.

A post-marketing assessment of major bleeding in total hip and total knee replacement surgery patients receiving rivaroxaban

BACKGROUND

Rivaroxaban is a novel oral anticoagulant indicated for prophylaxis against deep vein thrombosis and pulmonary embolism in patients undergoing total hip replacement (THR) or total knee replacement (TKR) surgery.

OBJECTIVE

To evaluate major bleeding (MB) in THR/TKR patients receiving post-operative rivaroxaban.

METHODS

Electronic medical records of nearly 10 million US Department of Defense (DoD) beneficiaries were queried from 1 January 2013 through 30 June 2015. Using the validated Cunningham case-finding algorithm, post-surgical MB events in rivaroxaban users were identified and analyzed. The incidence of MB was determined, and descriptive statistics were used to compare patient characteristics and other covariates in those with and without MB. Two additional methods were used to explore and identify bleeding cases that were not considered MB events per the study case-finding algorithm.

RESULTS

A total of 12,429 patients received THR and/or TKR surgery, and were post-operatively prescribed rivaroxaban. Nine patients had MB, yielding an incidence proportion of 0.07% (95% CI 0.02-0.13). The alternative case-finding methods found bleeding incidences of 0.46% and 0.21%, though it is not clear whether these are clinical MB cases, since the alternative methods were not validated.

CONCLUSIONS

The incidence of MB in this retrospective analysis is lower than that observed in the clinical trials of rivaroxaban. Whether this is due to lower real-world MB rates or challenges with case-finding algorithms is unclear.

Integrating genotypes in the SAMe-TT2R2 score for the prediction of anticoagulation control in Chinese patients with atrial fibrillation on warfarin

INTRODUCTION

The SAMe-TT₂R₂ score has been proposed to predict whether patients with atrial fibrillation (AF) would be well anti-coagulated with warfarin or not. However, it might over-estimate the number of patients under suboptimal warfarin treatment in non-Caucasians. This study was designed to modify the SAMe-TT₂R₂ score with genotypes and validate it in Chinese AF patients treated with warfarin.

MATERIAL AND METHODS

Consented Chinese-Han patients (n=510) with AF under the treatment of warfarin for at least 3months were randomly divided into a derivation (n=310) and a validation cohort (n=200). For each patient, CYP2C9*3 and VKORC1 -1639 A/G genotyping was performed, and the time in therapeutic range (TTR) was calculated over this period.

RESULTS

The modified SAMe-TT₂R₂ score was established by adding "warfarin genotype bins" to replace "the non-white race" variable. In the validation cohort, the discrimination performance of the modified score for good anticoagulation control (TTR≥70%) was significantly improved (c- index increased from 0.60 to 0.67). Significantly increased risks of major bleedings (HR: 4.91; 95% CI: 1.03-23.37; adjusted p=0.04) and all bleedings (HR: 1.93; 95% CI: 1.14-3.25; adjusted p=0.01) were found in patients with modified scores ≥2, as compared with patients with modified scores of 0-1.

CONCLUSIONS

The modified SAMe-TT₂R₂ score could improve the ability for the identification of good anticoagulation control, and the prediction of major bleeding events in Chinese patients with AF treated by warfarin.

A comparative study of different methods for automatic identification of clopidogrel-induced bleedings in electronic health records

Electronic health records (EHRs) linked with biobanks have been recognized as valuable data sources for pharmacogenomic studies, which require identification of patients with certain adverse drug reactions (ADRs) from a large population. Since manual chart review is costly and time-consuming, automatic methods to accurately identify patients with ADRs have been called for. In this study, we developed and compared different informatics approaches to identify ADRs from EHRs, using clopidogrel-induced bleeding as our case study. Three different types of methods were investigated: 1) rule-based methods; 2) machine learning-based methods; and 3) scoring function-based methods. Our results show that both machine learning and scoring methods are effective and the scoring method can achieve a high precision with a reasonable recall. We also analyzed the contributions of different types of features and found that the temporality information between clopidogrel and bleeding events, as well as textual evidence from physicians' assertion of the adverse events are helpful. We believe that our findings are valuable in advancing EHR-based pharmacogenomic studies.

Genetic determinants of variability in warfarin response after the dose-titration phase

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.

Comparison of the Incidence of Major Bleeding With Rivaroxaban Use Among Nonvalvular Atrial Fibrillation Patients With Versus Without Diabetes Mellitus

Diabetes mellitus (DM) is a common co-morbidity in those with nonvalvular atrial fibrillation (NVAF). Most patients with DM and NVAF have a CHA₂DS₂-VASc score of ≥1 and should be considered for oral anticoagulation therapy for stroke prevention per treatment guidelines. The most important risk associated with anticoagulation is bleeding, which may be higher in those with NVAF plus DM. Our objective was to evaluate the incidence and characteristics of major bleeding (MB) in rivaroxaban users diagnosed with NVAF, further comparing those with DM versus those without DM, in a real-world clinical setting. Electronic medical records of >10 million patients from the Department of Defense Military Health System were queried to identify rivaroxaban users with NVAF over a 2.5-year period. Major bleeding-related hospitalization was identified by a validated case-finding algorithm. Patient characteristics, incidence and management of MB, and fatal outcomes were assessed by DM status. Of 44,793 rivaroxaban users with NVAF, 12,039 (26.9%) had DM, who were more likely men, younger, with more co-morbidity and higher CHA₂DS₂-VASc scores. Major bleeding incidence was higher among those with DM compared with those without, 3.68 (95% confidence interval [CI] 3.37 to 4.03) versus 2.51 (95% CI 2.34 to 2.69) per 100 person-years, and intracranial bleeding incidence was 0.19 (95% CI 0.13 to 0.28) versus 0.25 (95% CI 0.20 to 0.31) per 100 person-years. Fatal outcomes were rare for both cohorts, 0.09 per 100 person-years. In conclusion, in this post-marketing study of 44,793 rivaroxaban users with NVAF, patients with DM had more co-morbidities and higher incidence of MB compared with those without DM.

Pharmacogenetic Implementation Lessons From the "Real World"

The manuscript "Anticoagulation Endpoints With Clinical Implementation of Warfarin Pharmacogenetic Dosing in a Real- World Setting: A Proposal for a New Pharmacogenetic Dosing Approach" describes process outcomes in an institutional program to use pharmacogenetic testing to optimize warfarin dose in a cohort of 257 patients of diverse ancestries. The strengths and weaknesses of the approach and program are discussed, along with the current and potential future status of warfarin as a model for pharmacogenetic testing.

VKORC1 and CYP2C9 polymorphisms related to adverse events in case-control cohort of anticoagulated patients

Vitamin K antagonists (VKAs) are highly effective but have a narrow therapeutic index and require routine monitoring of the INR. The primary aim of pharmacogenetics (PGx) is to optimize patient care, achieving drug treatments that are personalized according to the genetic profile of each patient. The best-characterized genes involved in VKA PGx involve pharmacokinetics (VKORC1) and pharmacodynamics (CYP2C9) of VKA metabolism. The role of these genes in clinical outcomes (bleeding and thrombosis) during oral anticoagulant (OAC) therapy is controversial. The aim of the present study was to evaluate any potential association between genotype VKORC1 and CYP2C9 and adverse events (hemorrhagic and/or thrombotic), during initiation and long-term VKA treatment, in Caucasian patients. Furthermore, we aimed to determine if the concomitant prescription of other selected drugs affected the association between genotype and adverse events.We performed a retrospective, matched case-control study to determine associations between multiple gene variants, drug intake, and any major adverse effects in anticoagulated patients, monitored in 2 Italian anticoagulation clinics.Our results show that anticoagulated patients have a high risk of adverse events if they are carriers of 1 or more genetic polymorphisms in the VKORC1 (rs9923231) and CYP2C9 (rs1799853 and rs1057910) genes.Information on CYP2C9 and VKORC1 variants may be useful to identify individualized oral anticoagulant treatment for each patient, improve management and quality of VKA anticoagulation control, and monitor drug surveillance in pharmacovigilance programs.

CHA2DS2-VASc Scores and Major Bleeding in Patients With Nonvalvular Atrial Fibrillation Who Are Receiving Rivaroxaban

STUDY OBJECTIVE

Assessing stroke risk associated with nonvalvular atrial fibrillation depends on the evaluation of patient characteristics and clinical features. Clinicians must determine that the net clinical benefit from anticoagulation therapy outweighs its risk, namely, bleeding. Risk assessment for stroke is commonly performed by calculating a CHA₂DS₂-VASc (congestive heart failure/left ventricular dysfunction, hypertension, ≥75 years, diabetes mellitus, previous stroke or transient ischemic attack or thromboembolism, vascular disease, aged 65 to 74 years, sex female) score. It is possible that CHA₂DS₂-VASc scores also have a relationship with the incidence of major bleeding. We examined the relationship between CHA₂DS₂-VASc scores and major bleeding in rivaroxaban users with nonvalvular atrial fibrillation.

METHODS

Electronic medical records of more than 10 million patients from the Department of Defense Military Health System were queried to identify patients with nonvalvular atrial fibrillation who received rivaroxaban from January 1, 2013, to June 30, 2015. Baseline characteristics of the study population were described by CHA₂DS₂-VASc scores and major bleeding status; major bleeding incidence was evaluated by CHA₂DS₂-VASc score category and for each CHA₂DS₂-VASc component.

RESULTS

Overall, 44,793 patients met the inclusion criteria for this analysis. The major bleeding incidence rate was 2.84 (95% confidence interval 2.69 to 3.00) per 100 person-years. The incidence of major bleeding increased from 0.30 to 5.40 per 100 person-years among patients with a CHA₂DS₂-VASc score of 0 to 5 or higher, respectively. Fatal outcomes among patients with major bleeding were positively correlated with CHA₂DS₂-VASc scores; patients with higher scores had higher mortality rates. The CHA₂DS₂-VASc component with the highest major bleeding incidence was for vascular disease, 5.69 (95% confidence interval 5.18 to 6.24) per 100 person-years.

CONCLUSION

Higher CHA₂DS₂-VASc scores are associated with increased incidence of major bleeding in nonvalvular atrial fibrillation patients receiving rivaroxaban.

CYP2C9, CYPC19 and CYP2D6 gene profiles and gene susceptibility to drug response and toxicity in Turkish population

Pharmacogenetics is a vast field covering drug discovery research, the genetic basis of pharmacokinetics and dynamics, genetic testing and clinical management in diseases. Pharmacogenetic approach usually focuses on variations of drug transporters, drug targets, drug metabolizing enzymes and other biomarker genes. Cytochrome P450 (CYP) enzymes, an essential source of variability in drug-response, play role in not only phase I-dependent metabolism of xenobiotics but also metabolism of endogenous compounds such as steroids, vitamins and fatty acids. CYP2C9, CYP2C19 and CYP2D6 enzymes being highly polymorphic are responsible for metabolism of a variety of drug groups. In the study, it was determined the genotype and allele frequency of CYP2C9∗2, CYP2C19∗3, CYP2C19∗2, CYP2C19∗3, CYP2C19∗17, CYP2D6∗9 and CYP2D6∗41, very common and functional single-nucleotide polymorphisms (SNPs), in healthy volunteers. The genotype distributions were consistent with the Hardy-Weinberg equilibrium in the population (p > 0.05). It is believed that the determination of polymorphisms in the enzymes may be beneficial in order to prevention or reduction in adverse effects and death. The recessive allele frequencies of CYP2C9∗2, CYP2C19∗3, CYP2C19∗2, CYP2C19∗3, CYP2C19∗17, CYP2D6∗9 and CYP2D6∗41 were 11, 13, 12, 13, 25, 4 and 15%, respectively. According to the obtained results, the carriers of CYP2D6∗9 variant allele should be received higher doses of the drugs metabolizing with this enzyme in Turkish population, while the carriers of other variant alleles do not generally have any requirement of dose regimen.

Phenome-Wide Association Studies as a Tool to Advance Precision Medicine

Beginning in the early 2000s, the accumulation of biospecimens linked to electronic health records (EHRs) made possible genome-phenome studies (i.e., comparative analyses of genetic variants and phenotypes) using only data collected as a by-product of typical health care. In addition to disease and trait genetics, EHRs proved a valuable resource for analyzing pharmacogenetic traits and developing reverse genetics approaches such as phenome-wide association studies (PheWASs). PheWASs are designed to survey which of many phenotypes may be associated with a given genetic variant. PheWAS methods have been validated through replication of hundreds of known genotype-phenotype associations, and their use has differentiated between true pleiotropy and clinical comorbidity, added context to genetic discoveries, and helped define disease subtypes, and may also help repurpose medications. PheWAS methods have also proven to be useful with research-collected data. Future efforts that integrate broad, robust collection of phenotype data (e.g., EHR data) with purpose-collected research data in combination with a greater understanding of EHR data will create a rich resource for increasingly more efficient and detailed genome-phenome analysis to usher in new discoveries in precision medicine.

Influence of the CYP4F2 polymorphism on the risk of hemorrhagic complications in coumarin-treated patients

Objectives:

To evaluate the impact of the CYP4F2 polymorphism on bleeding complications and over-anticoagulation due to coumarin.

Methods:

A comprehensive literature search was performed to look for eligible studies published prior to February 2015 in EMBASE and PubMed. References were strictly identified by inclusion and exclusion criteria, and authors of primary studies were consulted for additional information and data. Revman 5.3 software was used to analyze the impact of the CYP4F2 polymorphism on hemorrhagic complications and over-anticoagulation events (international normalized ratio >4).

Results:

Eight studies involving 3,101 samples met the specified inclusion criteria. Compared with wild-type homozygotes (CYP4F2*1*1), carriers of the CYP4F2*3 variant had no significant effects on total bleeding events (odds ratio [OR]: 0.86; 95% confidence interval [CI]: 0.71-1.05; p=0.15), major hemorrhage complications in coumarin users (OR: 0.80; 95% CI: 0.64-1.01; p=0.06). Patients carried CYP4F2*3 also had nonsignificant associations with the risk of over-anticoagulation (relative risk [RR]: 079; 95% CI: 0.59-1.06; p=0.12). We found a lower risk in patients with homozygotes for CYP4F2*3, but there was no statistical significance (RR: 0.66; 95% CI: 0.43-1.01; p=0.05).

Conclusion:

This meta-analysis indicated the impact of the CYP4F2 polymorphism on bleeding complications and over-anticoagulation in coumarin-treated patients failed to reach the level of statistical significance. However, large-scale and well designed studies are necessary to determine conclusively the association between the CYP4F2 polymorphism and hemorrhage risk.

Integrating electronic health record genotype and phenotype datasets to transform patient care

The Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009 mandates the development and implementation of electronic health record (EHR) systems across the country. While a primary goal is to improve the care of individual patients, EHRs are also key enabling resources for a vision of individualized (or personalized or precision) medicine: the aggregation of multiple EHRs within or across healthcare systems should allow discovery of patient subsets that have unusual and definable clinical trajectories that deviate importantly from the expected response in a "typical" patient. The spectrum of such personalized care can then extend from prevention to choice of medication to intensity or nature of follow-up.

International warfarin genotype-guided dosing algorithms in the Turkish population and their preventive effects on major and life-threatening hemorrhagic events

AIM

To determine the accuracy of international warfarin pharmacogenetic algorithms developed on large multiethnic cohorts (comprising more than 1000 subjects) to predict therapeutic warfarin doses in Turkish patients.

MATERIALS & METHODS

We investigated two Turkish warfarin-treated cohorts: patients with no history of hemorrhagic or thromboembolic event and patients with major and life-threatening hemorrhagic events.

RESULTS

International pharmacogenetic algorithms showed good performances in predicting the therapeutic dose of patients with no history of bleedings, but they did not significantly detect the incorrect warfarin dose of patients with major and life-threatening hemorrhagic events.

CONCLUSION

Although genetic information can predict the therapeutic warfarin dose, the accuracy of the international pharmacogenetic algorithms is not sufficient to be used for warfarin screening in Turkish patients.

Extracting research-quality phenotypes from electronic health records to support precision medicine

The convergence of two rapidly developing technologies - high-throughput genotyping and electronic health records (EHRs) - gives scientists an unprecedented opportunity to utilize routine healthcare data to accelerate genomic discovery. Institutions and healthcare systems have been building EHR-linked DNA biobanks to enable such a vision. However, the precise extraction of detailed disease and drug-response phenotype information hidden in EHRs is not an easy task. EHR-based studies have successfully replicated known associations, made new discoveries for diseases and drug response traits, rapidly contributed cases and controls to large meta-analyses, and demonstrated the potential of EHRs for broad-based phenome-wide association studies. In this review, we summarize the advantages and challenges of repurposing EHR data for genetic research. We also highlight recent notable studies and novel approaches to provide an overview of advanced EHR-based phenotyping.

Is dabigatran efficacy enough to prevent stroke in atrial fibrillation patient with high CHADS2 score during peri-procedural catheter radiofrequency ablation? A case report with literature review

Atrial fibrillation (AF) is a major cause of thromboembolic (TE) events including stroke and transient ischemic attacks, catheter radiofrequency ablation (CA) has been demonstrated to effectively eliminate AF in majority of patients. During the peri-procedural CA of AF, dabigatran, a reversible direct thrombin inhibitor, has been proved as safe and efficacy as warfarin in the prevention of thromboembolic complication. However, for patients with CHADS2 score ≥3, sometimes dabigatran may not be an ideal substitute of warfarin. The current study presents delayed stroke occurred in a middle-aged AF patient with high CHADS2 score who had undergone successful CA of AF being on dabigatran, trans esophageal echocardiogram (TEE) detected a clot in the left atrium appendage (LAA) and magnetic resonance image (MRI) indicated stroke of left basal ganglia, therefore anticoagulant was switched to warfarin with well controlled international normalization ratio (INR) ranging from 2.0-3.0 and the patient eventually recovered without any TE events during the subsequent follow-up.