Frequency of DPYD gene variants and phenotype inference in a Southern Brazilian population

Fluoropyrimidines are chemotherapy drugs that may cause severe adverse events, and their metabolism occurs by dihydropyrimidine deydrogenase (DPD), coded by DPYD. Variants in the DPYD were associated to a greater risk of toxicity. Our aim was to determine the frequency of the most relevant DPYD alleles according to CPIC guidelines (DPYD*2A-rs3918290, DPYD*13-rs55886062, rs67376798, and HapB3-rs75017182) in a sample of 800 healthy Southern Brazilians. Frequencies for rs3918290, rs75017182, and rs67376798 were 0.25%, 1.06%, and 0.38%, respectively. No rs55886062 allele was detected. In total, 3.4% of individuals were classified as intermediate metabolizers. Frequencies for rs3918290, rs55886062, and rs67376798 were similar to those found in non-Finnish Europeans; however, rs75017182 was less frequent when compared to non-Finnish Europeans, but more frequent than in Africans and East Asians. rs3918290 and rs67376798 also presented higher frequency when compared to Africans. The Latino population was the only one that did not differ from our sample in any variant analyzed. The frequencies for all the other populations (non-Finnish European, African, South Asian, and East Asian) presented differences from our sample in at least one variant. rs115232898 was not analyzed in the present study. Cost-effective studies should be performed to evaluate the implementation of these tests in the clinical practice in the Southern Brazil.

Machine Learning for Prediction of Stable Warfarin Dose in US Latinos and Latin Americans

Populations used to create warfarin dose prediction algorithms largely lacked participants reporting Hispanic or Latino ethnicity. While previous research suggests nonlinear modeling improves warfarin dose prediction, this research has mainly focused on populations with primarily European ancestry. We compare the accuracy of stable warfarin dose prediction using linear and nonlinear machine learning models in a large cohort enriched for US Latinos and Latin Americans (ULLA). Each model was tested using the same variables as published by the International Warfarin Pharmacogenetics Consortium (IWPC) and using an expanded set of variables including ethnicity and warfarin indication. We utilized a multiple linear regression model and three nonlinear regression models: Bayesian Additive Regression Trees, Multivariate Adaptive Regression Splines, and Support Vector Regression. We compared each model’s ability to predict stable warfarin dose within 20% of actual stable dose, confirming trained models in a 30% testing dataset with 100 rounds of resampling. In all patients (n = 7,030), inclusion of additional predictor variables led to a small but significant improvement in prediction of dose relative to the IWPC algorithm (47.8 versus 46.7% in IWPC, p = 1.43 × 10⁻¹⁵). Nonlinear models using IWPC variables did not significantly improve prediction of dose over the linear IWPC algorithm. In ULLA patients alone (n = 1,734), IWPC performed similarly to all other linear and nonlinear pharmacogenetic algorithms. Our results reinforce the validity of IWPC in a large, ethnically diverse population and suggest that additional variables that capture warfarin dose variability may improve warfarin dose prediction algorithms.

PharmVar GeneFocus: CYP2C9

The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C9 gene. Genetic variation within the CYP2C9 gene locus impacts the metabolism or bioactivation of many clinically important drugs, including nonsteroidal anti-inflammatory drugs, phenytoin, antidiabetic agents, and angiotensin receptor blockers. Variable CYP2C9 activity is of particular importance regarding efficacy and safety of warfarin and siponimod as indicated in their package inserts. This GeneFocus provides a comprehensive overview and summary of CYP2C9 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium.

Polymorphism of the CYP2C9 and VKORC1 genes in patients on the public health system of a municipality in Southern Brazil

Background

Genetic factors can be responsible for part of the populational and interindividual differences observed in warfarin users.

Objectives

To identify occurrence of polymorphisms of the CYP2C9 and VKORC1 genes in patients taking warfarin and relate these profiles to their medication dosages and the Time in Therapeutic Range (TTR).

Methods

Monthly interviews were conducted for data collection. Data were collected on demographic characteristics and medications in use, especially warfarin, including reason for prescription and weekly dose. TTR was calculated as the percentage of days with international normalized ratio (INR) between 2 and 3. The CYP2C9 and VKORC1 genes were analyzed at a Human Genetics Laboratory.

Results

49 patients (74.2%) had polymorphisms of the CYP2C9 and/or VKORC1 genes; the remaining 17 (25.8%) did not have these polymorphisms. The average weekly dose of warfarin was lower among those who had a polymorphism for any of the genes compared to those who did not, with a significant difference (p = 0.035). The mean TTR was also lower among patients with polymorphism. However, the difference between the two groups was not significant for this variable (p = 0.438).

Conclusions

An association was observed between the polymorphisms and the warfarin doses taken by the patients. However, there was no association with adverse events or the time spent within the therapeutic range in this sample.

Risk factors associated with the development of oral mucositis in pediatric oncology patients: Systematic review and meta-analysis

OBJECTIVES

Oral mucositis (OM) is an acute toxicity related to cancer treatment. This systematic review aimed to identify potential risk factors associated with the development of OM in pediatric cancer patients.

METHODS

A search was performed in four electronic databases to identify studies that analyzed risk factors for OM in pediatric cancer patients.

RESULTS

Nineteen articles were included. The incidence of OM ranged from 20% to 80.4%. Chemotherapeutic agents were potential risk factors for OM in eight (42%) studies. Hematological, hepatic, and renal parameters were also considered in eight (42%) studies, while specific individual factors were reported in five (26.3%) studies. Baseline disease, oral microbiota, genetic profile, and biomarkers were reported in four (21.5%) studies each. Meta-analysis showed that groups submitted to high-risk chemotherapy for OM had a 2.79-fold increased risk of OM.

CONCLUSIONS

Identifying risk factors for OM is essential in order to allow individualized and early prevention treatment.

Variants p.Pro2063Ser and p.Arg324* co-segregate in type 3 von Willebrand disease patients from Southern Brazil

INTRODUCTION

von Willebrand factor (VWF) is a multimeric plasma glycoprotein that plays an important role in haemostasis. von Willebrand disease (VWD) is an inherited heterogeneous bleeding disorder caused by either a quantitative or qualitative defect of VWF. Type 3 VWD, the most severe form of the disease, leads to complete quantitative VWF deficiency.

AIM

The present study aims to investigate the molecular pathogenesis of type 3 VWD patients from Southern Brazil.

METHODS

The VWF gene was sequenced in 26 cases clinically diagnosed with type 3 VWD by next-generation sequencing using Ion Torrent PGM.

RESULTS

In 25 patients, we were able to identify both disease-causing variants. We identified 72 different variants: 31 intronic and 41 exonic. Five novel variants were found: c.6976+5G>T; c.6885_6886insC; c.3378C>T (p.Cys1126); c.3346_3347insCCA; and c.2503G>T (p.Glu835*). Variants p.Pro2063Ser and p.Arg324* co-segregated in 17 patients, 15 of them in homozygosity.

CONCLUSION

Our results may contribute to the discussion on whether the variant p.Pro2063Ser is pathogenic or not. Finally, the presence of a common haplotype in patients bearing these two variants suggests a founder effect for this variant in our region.

Effect of CYP4F2, VKORC1, and CYP2C9 in Influencing Coumarin Dose: A Single-Patient Data Meta-Analysis in More Than 15,000 Individuals

The cytochrome P450 (CYP)4F2 gene is known to influence mean coumarin dose. The aim of the present study was to undertake a meta-analysis at the individual patients level to capture the possible effect of ethnicity, gene-gene interaction, or other drugs on the association and to verify if inclusion of CYP4F2*3 variant into dosing algorithms improves the prediction of mean coumarin dose. We asked the authors of our previous meta-analysis (30 articles) and of 38 new articles retrieved by a systematic review to send us individual patients' data. The final collection consists of 15,754 patients split into a derivation and validation cohort. The CYP4F2*3 polymorphism was consistently associated with an increase in mean coumarin dose (+9% (95% confidence interval (CI) 7-10%), with a higher effect in women, in patients taking acenocoumarol, and in white patients. The inclusion of the CYP4F2*3 in dosing algorithms slightly improved the prediction of stable coumarin dose. New pharmacogenetic equations potentially useful for clinical practice were derived.

Influence of pharmacogenetic polymorphisms and demographic variables on metformin pharmacokinetics in an admixed Brazilian cohort

AIMS

To identify pharmacogenetic and demographic variables that influence the systemic exposure to metformin in an admixed Brazilian cohort.

METHODS

The extreme discordant phenotype was used to select 106 data sets from nine metformin bioequivalence trials, comprising 256 healthy adults. Eleven single-nucleotide polymorphisms in SLC22A1, SLC22A2, SLC47A1 SLC47A2 and in transcription factor SP1 were genotyped and a validated panel of ancestry informative markers was used to estimate the individual proportions of biogeographical ancestry. Two-step (univariate followed by multivariate) regression modelling was developed to identify covariates associated with systemic exposure to metformin, accessed by the area under the plasma concentration-time curve, between 0 and 48 h (AUC_0-48h ), after single oral doses of metformin (500 or 1000 mg).

RESULTS

The individual proportions of African, Amerindian and European ancestry varied widely, as anticipated from the structure of the Brazilian population The dose-adjusted, log-transformed AUC_0-48h 's (ng h ml^-1  mg^-1 ) differed largely in the two groups at the opposite ends of the distribution histogram, namely 0.82, 0.79-0.85 and 1.08, 1.06-1.11 (mean, 95% confidence interval; P = 6.10^-26 , t test). Multivariate modelling revealed that metformin AUC_0-48h increased with age, food and carriage of rs12208357 in SLC22A1 but was inversely associated with body surface area and individual proportions of African ancestry.

CONCLUSIONS

A pharmacogenetic marker in OCT1 (SLC22A1 rs12208357), combined with demographic covariates (age, body surface area and individual proportion of African ancestry) and a food effect explained 29.7% of the variability in metformin AUC_0-48h .

Influence of the CYP2C9*3 allele on the pharmacological interaction between warfarin and simvastatin

A letter in response to: Andersson ML, Eliasson E, Lindh JD. A clinically significant interaction between warfarin and simvastatin is unique to carriers of the CYP2C9*3 allele. Pharmacogenomics 13(7), 757–762 (2012).

Risk factors for hypertensive disorders of pregnancy in southern Brazil

OBJECTIVE

The aim of the study was to identify the frequency of risk factors for hypertensive disorders in pregnancy in Southern Brazil.

METHODS

The study included 161 patients with hypertensive disorders and 169 control subjects matched by age and ethnicity. The frequency of the risk factors was compared by Fisher's exact test, chi-square and Student's t test. A multivariate logistic regression analysis assessed the independent role of clinical, social and demographic factors which were associated with occurrence of the hypertensive disease in pregnancy in the univariate analysis.

RESULTS

Patients enrolled in the study were predominantly Caucasian (73%) and the mean age was 29. In the multivariate analysis, the variables associated were: family history of preeclampsia (p = 0.001; OR = 3.88; 95% CI = 1.77-8.46), diabetes (p = 0.021; OR = 3.87; 95% CI = 1.22-12.27) and chronic hypertension (p = 0.002; OR = 7.05; 95% CI = 1.99-24.93).

CONCLUSION

The risk factors associated with hypertensive disorders in pregnancy appear to be similar to those reported in other countries. The knowledge of the risk factors could be helpful in a prenatal care.

Influence of genetic, biological and pharmacological factors on warfarin dose in a Southern Brazilian population of European ancestry

AIMS

To investigate the influence of polymorphisms in CYP2C9, VKORC1, CYP4F2 and F2 genes on warfarin dose-response and develop a model including genetic and non-genetic factors for warfarin dose prediction needed for each patient.

METHODS

A total of 279 patients of European ancestry on warfarin medication were investigated. Genotypes for -1639G>A, 1173C>T, and 3730G>A SNPs in the VKORC1 gene, CYP2C9*2 and CYP2C9*3, 1347C>T in the CYP4F2 gene and 494C>T in the F2 gene were determined by allelic discrimination with Taqman 5'-nuclease assays.

RESULTS

The CYP2C9*2 and CYP2C9*3 polymorphisms in the CYP2C9 gene, -1639G>A and 1173C>T in the VKORC1 gene and 494C>T in the F2 gene are responsible for lower anticoagulant doses. In contrast, 1347C>T in the CYP4F2 gene and 3730G>A in the VKORC1 gene are responsible for higher doses of warfarin. An algorithm including genetic, biological and pharmacological factors that explains 63.3% of warfarin dose variation was developed.

CONCLUSION

The model suggested has one of the highest coefficients of determination among those described in the literature.

Relationship between polymorphisms in thrombophilic genes and preeclampsia in a Brazilian population

The purpose of this study was to evaluate the thrombophilic genes in pregnant women with and without preeclampsia independently or in combination. In a prospective case-control study, we investigated four polymorphisms in thrombophilic genes in 75 women with mild or severe preeclampsia and 145 women with normal pregnancy. The genotype frequencies were assessed and the odds ratio (OR) calculated. When we analyzed the polymorphisms independently and the development of preeclampsia, no association was observed [methylenetetrahydrofolate reductase (MTHFR) 677TT genotype, OR 2.07, 95% confidence interval (CI) 0.99-4.30; prothrombin mutation (F II) (GA or AA genotypes) OR 8.11, 95% CI 0.89-73.92; factor V Leiden (FV Leiden) OR 3.94, 95% CI 0.35-44.23; plasminogen activator inhibitor (PAI-1) 4G/4G genotype, OR 1.63, 95% CI 0.87-3.05] not even with severe preeclampsia subgroup analysis. However, when we investigated a possible interaction among these polymorphisms on the development of the preeclampsia, the OR for having one risk genotype, one or two genotype risk factors and two genotype risk factors compared to those without genotype risk factors were 1.97 (95% CI 1.08-3.59), 2.21 (95% CI 1.25-3.92) and 4.27 (95% CI 1.3-13.9), respectively. In conclusion, in the population analyzed, the presence of the genotype risk factors alone does not seem to be associated with the development of preeclampsia even in the severe presentation form. However, an interaction among the MTHFR, F II, FV and PAI-1 gene polymorphisms on the development of the preeclampsia was indicated.