Comparison between MassARRAY and pyrosequencing for CYP2C19 and ABCB1 gene variants of clopidogrel efficiency genotyping

Clinical and cost-effectiveness of clopidogrel resistance genotype testing after ischaemic stroke or transient ischaemic attack: a systematic review and economic model

Background

Stroke or transient ischaemic attack patients are at increased risk of secondary vascular events. Antiplatelet medications, most commonly clopidogrel, are prescribed to reduce this risk. Factors including CYP2C19 genetic variants can hinder clopidogrel metabolism. Laboratory-based or point-of-care tests can detect these variants, enabling targeted treatment.

Objective

To assess the effectiveness of genetic testing to identify clopidogrel resistance in people with ischaemic stroke or transient ischaemic attack. Specific objectives: Do people tested for clopidogrel resistance, and treated accordingly, have a reduced risk of secondary vascular events? Do people with loss-of-function alleles associated with clopidogrel resistance have a reduced risk of secondary vascular events if treated with alternative interventions compared to clopidogrel? Do people with loss-of-function alleles associated with clopidogrel resistance have an increased risk of secondary vascular events when treated with clopidogrel? What is the accuracy of point-of-care tests for detecting variants associated with clopidogrel resistance? What is the technical performance and cost of CYP2C19 genetic tests? Is genetic testing for clopidogrel resistance cost-effective compared with no testing?

Design

Systematic review and economic model.

Results

Objective 1: Two studies assessed secondary vascular events in patients tested for loss-of-function alleles and treated accordingly. They found a reduced risk, but confidence intervals were wide (hazard ratio 0.50, 95% confidence interval 0.09 to 2.74 and hazard ratio 0.53, 95% confidence interval 0.24 to 1.18). Objective 2: Seven randomised controlled trials compared clopidogrel with alternative treatment in people with genetic variants. Ticagrelor was associated with a lower risk of secondary vascular events than clopidogrel (summary hazard ratio 0.76, 95% confidence interval 0.65 to 0.90; two studies). Objective 3: Twenty-five studies compared outcomes in people with and without genetic variants treated with clopidogrel. People with genetic variants were at an increased risk of secondary vascular events (hazard ratio 1.72, 95% confidence interval 1.43 to 2.08; 18 studies). There was no difference in bleeding risk (hazard ratio 0.98, 95% confidence interval 0.68 to 1.40; five studies). Objective 4: Eleven studies evaluated Genomadix Cube accuracy; no studies evaluated Genedrive. Summary sensitivity and specificity against laboratory reference standards were both 100% (95% confidence interval 94% to 100% and 99% to 100%). Objective 5: Seventeen studies evaluated technical performance of point-of-care tests. Test failure rate ranged from 0.4% to 19% for Genomadix Cube. A survey of 8/10 genomic laboratory hubs revealed variation in preferred technologies for testing, and cost per test ranging from £15 to £250. Most laboratories expected test failure rate to be < 1%. Additional resources could enhance testing capacity and expedite turnaround times. Objective 6: Laboratory and point-of-care CYP2C19 testing strategies were cost-saving and increase quality-adjusted life-years compared with no testing. Both strategies gave similar costs, quality-adjusted life-years and expected net monetary benefit.

Conclusions

Our results suggest that CYP2C19 testing followed by tailored treatment is likely to be effective and cost-effective in both populations.

Future work

Accuracy and technical performance of Genedrive. Test failure rate of Genomadix Cube in a National Health Service setting. Value of testing additional loss-of-function alleles. Appropriateness of treatment dichotomy based on loss-of-function alleles.

Limitations

Lack of data on Genedrive. No randomised 'test-and-treat' studies of dipyramidole plus aspirin.

Study registration

This study is registered as PROSPERO CRD42022357661.

Funding

This award was funded by the National Institute for Health and Care Research (NIHR) Evidence Synthesis programme (NIHR award ref: NIHR135620) and is published in full in Health Technology Assessment; Vol. 28, No. 57. See the NIHR Funding and Awards website for further award information.

A novel AllGlo probe-quantitative PCR method for detecting single nucleotide polymorphism in CYP2C19 to evaluate the antiplatelet activity of clopidogrel

CYP2C19 gene has multiple single nucleotide polymorphism (SNP), which is the major determinant for clopidogrel treatment responses. Therefore, CYP2C19 SNP detection is essential for predicting clopidogrel efficacy. Currently, there is still no quick and effective method for routine detection of common CYP2C19 SNPs in clinical laboratories, which is critically needed prior to clopidogrel treatment. AllGlo™ based quantitative PCR was used to develop a novel genotyping method for CYP2C19 SNP detection, termed CyPAllGlo. The performance of CyPAllGlo was compared with that of the commonly used fluorescence in situ hybridization (FISH) method, and the data was verified by DNA sequencing. CyPallGlo was used to identify CYP2C19 polymorphisms in 363 patients with coronary heart disease. The univariate analysis was used to access the antiplatelet efficacy of clopidogrel in patients. The associations between CYP2C19 polymorphisms and clopidogrel efficacy were analyzed. Using CyPAllGlo to detect CYP2C19*2 and CYP2C19*3 alleles was highly specific and fast. The detection limit was approximately 0.07 µg/µl and 0.7 µg/µl for CYP2C19*2 and CYP2C19*3, respectively. The consistency between FISH and CyPAllGlo were 98.07% for CYP2C19*2 and 99.17% for CYP2C19*3. DNA sequencing showed that the accuracy of CyPAllGlo was 100%. The analysis time for the whole CyPAllGlo procedure was approximately 60 min. Univariate analysis showed that the anticoagulation efficacy of clopidogrel was related to patient age, CYP2C19 genotype, metabolic phenotype, and LDL level. The logistic regression analysis showed that the genotype of CYP2C19 and metabolic phenotype was the two risk factors for clopidogrel antiplatelet ineffectiveness. This novel CyPAllGlo is a rapid and accurate method for detection of CYP2C19 SNP. The specificity and consistency of CyPAllGlo are comparable with that of widely used DNA sequencing. These findings provide valuable rapid method for predicting clopidogrel efficacy, which can be quickly translated to improve personalized precision medicine for coronary heart disease treatment.

Genomic profile of diabetic retinopathy in a north indian cohort

BACKGROUND

Diabetic Retinopathy (DR) is one of the major microvascular complications of diabetes. Being a complex disease, it is important to delineate the genetic and environmental factors that influence the susceptibility to DR in a population. Therefore, the present study was designed to investigate the role of genetic and lifestyle risk factors associated with DR susceptibility in a North-Indian population.

METHODS

A total of 848 subjects were enrolled, comprising of DR cases (n = 414) and healthy controls (n = 434). The Sequenom MassARRAY technology was used to perform target genome analysis of 111 SNPs across 57 candidate genes and 14 intergenic region SNPs that are involved in the metabolic pathways associated with type 2 diabetes (T2D) and DR. Allele, genotype and haplotype frequencies were determined and compared among cases and controls. Logistic regression models were used to determine genotype-phenotype and phenotype-phenotype correlations.

RESULTS

The strongest association was observed with TCF7L2 rs12255372 T allele [p < 0.0001; odds ratio (OR) = 1.81 (1.44-2.27)] and rs11196205 C allele [p < 0.0008; OR = 1.62 (1.32-1.99)]. Genotype-phenotype and phenotype-phenotype correlations were found in the present study.

CONCLUSION

Our study provides strong evidence of association between the TCF7L2 variants and DR susceptibility.

Screening of single nucleotide polymorphisms within HLA region related to hematopoietic stem cell transplantation using MassARRAY technology

A growing number of studies showed that single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA)-related genes were associated with the outcome of hematopoietic stem cell transplantation (HSCT). Thus, other SNPs located nearby the classical HLA genes must be considered in HSCT. We evaluated the clinical feasibility of MassARRAY by comparing to Sanger sequencing. The PCR amplicons with each one of the 17 loci that were related to the outcomes of HSCT published by our previous study were transferred onto a SpectroCHIP Array for genotyping by mass spectrometry. The sensitivity of MassARRAY was 97.9% (614/627) and the specificity was 100% (1281/1281), where the positive predictive value (PPV) was 100% (614/614) and the negative predictive value (NPV) was 99.0% (1281/1294). MassARRAY is high-throughput, which can accurately analyze multiple SNPs at the same time. Based on these properties, we proposed that it could be an efficient method to match the genotype between the graft and the recipient before transplantation.

Population pharmacokinetics of oxcarbazepine 10-monohydroxy derivative in Chinese adult epileptic patients

OBJECTIVE

Oxcarbazepine (OXC) is metabolised to active 10-monohydroxy derivative (MHD) after oral administration. Using this fact we aimed to develop an MHD population pharmacokinetic (PPK) model in Chinese adult epileptic patients to facilitate the clinical implementation of model-guided individualised drug therapy.

METHODS

We collected blood samples from Chinese adult epileptic patients taking OXC at the Second Affiliated Hospital of Zhejiang University School of Medicine. We used high performance liquid chromatography (HPLC-MS/MS) with tandem mass spectrometry to detect MHD concentrations in the blood samples. We collected various data from patients including their demographic, pathological, and physiological information. MassARRAY method was used to detect ABCC2, ABCB1, SCN8A, SCN1A, SCN2A, SCN3A, UGT1A9, and UGT2B7 gene polymorphisms. We used a nonlinear mixed-effects modelling method to develop the PPK model and we predicted dosing regimens through simulation.

RESULT

In total we collected 164 blood samples from 118 patients. We found that a one-compartment model with first-order absorption better described the in vivo MHD pharmacokinetics. UGT2B7 gene (rs7439366) site mutation and the combined use of valproic acid enhanced the MHD clearance rate. We divided patients into groups based on the UGT2B7 genotype and whether they were also using valproic acid at the same time. Individualised OXC dosing regimens were proposed for different subgroups of patients.

CONCLUSION

In Chinese adult epileptic patients, individualised drug administration can be facilitated using a PPK model of OXC.

TRIAL REGISTRATION NUMBER

ChiCTR-OOC-17012141.

Molecular Genetic Techniques in Biomarker Analysis Relevant for Drugs Centrally Approved in Europe

On the basis of scientific evidence, information on the option, recommendation or requirement to test for pharmacogenetic or pharmacogenomic biomarkers is incorporated in the Summary of Product Characteristics of an increasing number of drugs in Europe. A screening of the Genetic Testing Registry (GTR) showed that a variety of molecular genetic testing methods is currently offered worldwide in testing services with regard to according drugs and biomarkers. Thereby, among the methodology indicated in the screened GTR category ‘Molecular Genetics’, next-generation sequencing is applied for identification of the largest proportion of evaluated biomarkers that are relevant for therapeutic management of centrally approved drugs in Europe. However, sufficient information on regulatory clearances, clinical utility, analytical and clinical validity of applied methods is rarely provided.

Towards next-generation personalization of tacrolimus treatment: a review on advanced diagnostic and therapeutic approaches

The benefit of personalized medicine is that it allows the customization of drug therapy - maximizing efficacy while avoiding side effects. Genetic polymorphisms are one of the major contributors to interindividual variability. Currently, the only gold standard for applying personalized medicine is dose titration. Because of technological advancements, converting genotypic data into an optimum dose has become easier than in earlier years. However, for many medications, determining a personalized dose may be difficult, leading to a trial-and-error method. On the other hand, the technologically oriented pharmaceutical industry has a plethora of smart drug delivery methods that are underutilized in customized medicine. This article elaborates the genetic polymorphisms of tacrolimus as case study, and extensively covers the diagnostic and therapeutic technologies which aid in the delivery of personalized tacrolimus treatment for better clinical outcomes, thereby providing a new strategy for implementing personalized medicine.

A meta-analysis of effects of CYP2C9 and CYP2C19 polymorphisms on phenytoin pharmacokinetic parameters

Aim: Phenytoin is metabolized through CYP2C9 and CYP2C19. Polymorphisms of CYP2C9 and CYP2C19 may increase plasma concentration and side effects. Materials & methods: Systematic review and meta-analysis were performed to evaluate the effects of CYP2C9 and CYP2C19 polymorphism on pharmacokinetic parameters. PubMed, Science Direct, Cochrane library, and Thai databases were systematically searched. Results: Eight observational studies, comprising a total of 633 patients were included. Michaelis-Menten constant was significantly higher in the polymorphism of CYP2C9IM/CYP2C19EM and CYP2C9IM/CYP2C19IM groups as compared with the control groups (CYP2C9EM/CYP2C19EM) at 2.16 and 1.55 mg/l (p < 0.00001, p < 0.0001). The maximum rate of action was significantly lower in the control groups as compared with the polymorphism of CYP2C9IM/CYP2C19EM and CYP2C9IM/CYP2C19IM groups at 3.10 and 3.53 mg/kg/day (p = 0.00001, <0.0001). Conclusion: The dosage regimen for patients in the CYP2C9IM group to achieve phenytoin therapeutic levels was 2.1-3.4 mg/kg/day.

MASS SPECTROMETRY-BASED PERSONALIZED DRUG THERAPY

Personalized drug therapy aims to provide tailored treatment for individual patient. Mass spectrometry (MS) is revolutionarily involved in this area because MS is a rapid, customizable, cost-effective, and easy to be used high-throughput method with high sensitivity, specificity, and accuracy. It is driving the formation of a new field, MS-based personalized drug therapy, which currently mainly includes five subfields: therapeutic drug monitoring (TDM), pharmacogenomics (PGx), pharmacomicrobiomics, pharmacoepigenomics, and immunopeptidomics. Gas chromatography-MS (GC-MS) and liquid chromatography-MS (LC-MS) are considered as the gold standard for TDM, which can be used to optimize drug dosage. Matrix-assisted laser desorption ionization-time of flight-MS (MALDI-TOF-MS) significantly improves the capability of detecting biomacromolecule, and largely promotes the application of MS in PGx. It is becoming an indispensable tool for genotyping, which is used to discover and validate genetic biomarkers. In addition, MALDI-TOF-MS also plays important roles in identity of human microbiome whose diversity can explain interindividual differences of drug response. Pharmacoepigenetics is to study the role of epigenetic factors in individualized drug treatment. MS can be used to discover and validate pharmacoepigenetic markers (DNA methylation, histone modification, and noncoding RNA). For the emerging cancer immunotherapy, personalized cancer vaccine has effective immunotherapeutic activity in the clinic. MS-based immunopeptidomics can effectively discover and screen neoantigens. This article systematically reviewed MS-based personalized drug therapy in the above mentioned five subfields. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Development and validation of T-ARMS-PCR to detect CYP2C19*17 allele

Background

CYP2C19*17 (rs12248560) is a functional single nucleotide polymorphism (SNP) in the CYP2C19 gene. It has been shown that CYP2C19*17 is associated with the clinical outcome of some drugs metabolized by CYP2C19 and a decreased risk of some diseases. The aim of this study was to develop a reliable and simple method to detect this polymorphism.

Methods

Tetra‐primer amplification refractory mutation system‐polymerase chain reaction (T‐ARMS‐PCR) was used to detect the CYP2C19*17 polymorphism. A total of 93 samples were screened by this method, and the results of T‐ARMS‐PCR were validated by DNA sequencing.

Results

There were 91 samples with the CC genotype (97.8%) and two samples with the CT genotype (2.2%). The frequency of the C allele was 98.9%, and the frequency of the T allele was 1.1%. The DNA sequencing results were completely concordant with the T‐ARMS‐PCR results.

Conclusion

T‐ARMS‐PCR can detect the CYP2C19*17 polymorphism with high accuracy, low costs, and a simple process.