1
|
Narasimhalu K, Chan J, Ang YK, De Silva DA, Tan KB. Empiric treatment with aspirin and ticagrelor is the most cost-effective strategy in patients with minor stroke or transient ischemic attack. Int J Stroke 2024; 19:209-216. [PMID: 37679898 DOI: 10.1177/17474930231202374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
BACKGROUND Patients with minor ischemic stroke or transient ischemic attacks (TIAs) are often treated with dual antiplatelet therapy regimens as part of secondary stroke prevention. Clopidogrel, an antiplatelet used in these regimens, is metabolized into its active form by the CYP2C19 enzyme. Patients with loss of function (LOF) mutations in CYP2C19 are at risk for poorer secondary outcomes when prescribed clopidogrel. AIMS We aimed to determine the cost-effectiveness of three different treatment antiplatelet regimens in ischemic stroke populations with minor strokes or TIAs and how these treatment regimens are influenced by the LOF prevalence in the population. METHODS Markov models were developed to look at the cost-effectiveness of empiric treatment with aspirin and clopidogrel versus empiric treatment with aspirin and ticagrelor, versus genotype-guided therapy for either 21 or 30 days. Effect ratios were obtained from the literature, and incidence rates and costs were obtained from the national data published by the Singapore Ministry of Health. The primary endpoints were the incremental cost-effectiveness ratios (ICERs). RESULTS Empiric treatment with aspirin and ticagrelor was the most cost-effective treatment. Genotype-guided therapy was more cost-effective than empiric aspirin and clopidogrel if the LOF was above 48%. Empiric ticagrelor and aspirin was cost saving when compared to genotype-guided therapy. Results in models of dual antiplatelet therapy for 30 days were similar. CONCLUSION This study suggests that in patients with minor stroke and TIA planned for dual antiplatelet regimens, empiric ticagrelor and aspirin is the most cost-effective treatment regimen. If ticagrelor is not available, genotype-guided therapy is the most cost-effective treatment regimen if the LOF prevalence in the population is more than 48%.
Collapse
Affiliation(s)
- Kaavya Narasimhalu
- Department of Neurology (SGH Campus), National Neuroscience Institute, Singapore
| | - Jeremy Chan
- Department of Neurology (SGH Campus), National Neuroscience Institute, Singapore
| | - Yoong Kwei Ang
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
- School of Public Health, National University of Singapore, Singapore
| | - Deidre Anne De Silva
- Department of Neurology (SGH Campus), National Neuroscience Institute, Singapore
| | - Kelvin Bryan Tan
- School of Public Health, National University of Singapore, Singapore
- Policy, Research and Evaluation Division, Ministry of Health, Singapore
| |
Collapse
|
2
|
Targeted next-generation sequencing of genes involved in Warfarin Pharmacodynamics and pharmacokinetics pathways using the Saudi Warfarin Pharmacogenetic study (SWAP). THE PHARMACOGENOMICS JOURNAL 2023:10.1038/s41397-023-00300-3. [PMID: 36739459 DOI: 10.1038/s41397-023-00300-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 01/15/2023] [Accepted: 01/26/2023] [Indexed: 02/06/2023]
Abstract
BACKGROUND Warfarin is an oral anticoagulant commonly used for treatment and prophylaxis against thromboembolic events. Warfarins's narrow therapeutic index window is one of the main challenges in clinical practice; thus, it requires frequent monitoring and dose adjustment to maintain patients' therapeutic range. Warfarin dose variation and response are attributed to several inter-and intra-individuals factors, including genetic variants in enzymes involved in warfarin pharmacokinetics (PK) and pharmacodynamics (PD) pathways. Thus, we aim to utilize the next-generation sequencing (NGS) approach to identify rare and common genetic variants that might be associated with warfarin responsiveness. METHOD AND RESULTS A predesigned NGS panel that included 16 genes involved in Warfarin PK/PD pathways was used to sequence 786 patients from the Saudi Warfarin Pharmacogenetic Cohort (SWAP). Identified variants were annotated using several annotation tools to identify the pathogenicity and allele frequencies of these variants. We conducted variants-level association tests with warfarin dose. We identified 710 variants within the sequenced genes; 19% were novel variants, with the vast majority being scarce variants. The genetic association tests showed that VKORC1 (rs9923231, and rs61742245), CYP2C9 (rs98332238, rs9332172, rs1057910, rs9332230, rs1799853, rs1057911, and rs9332119), CYP2C19 (rs28399511, and rs3758581), and CYP2C8 (rs11572080 and rs10509681) were significantly associated with warfarin weekly dose. Our model included genetics, and non-genetic factors explained 40.1% of warfarin dose variation. CONCLUSION The study identifies novel variants associated with warfarin dose in the Saudi population. These variants are more likely to be population-specific variants, suggesting that population-specific studies should be conducted before adopting a universal warfarin genotype-guided dosing algorithm.
Collapse
|
3
|
Narasimhalu K, Ang YK, Tan DSY, De Silva DA, Tan KB. Cost Effectiveness of Genotype-Guided Antiplatelet Therapy in Asian Ischemic Stroke Patients: Ticagrelor as an Alternative to Clopidogrel in Patients with CYP2C19 Loss of Function Mutations. Clin Drug Investig 2020; 40:1063-1070. [PMID: 32959334 DOI: 10.1007/s40261-020-00970-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Patients with ischemic stroke are often treated with clopidogrel monotherapy as part of secondary stroke prevention. The prevalence of loss of function (LOF) mutations in the CYP2C19 gene is higher in Asians than in Western populations. Patients with loss of function (LOF) mutations are at risk for poorer secondary outcomes when prescribed clopidogrel. OBJECTIVE We aimed to determine the cost effectiveness of genotype-guided antiplatelet therapy in an Asian population with the aim of prescribing ticagrelor as an alternative to patients with LOF mutations. METHODS Markov models were developed to look at the cost effectiveness of genetic testing of CYP2C19, with patients who screened positive for LOF alleles being switched to ticagrelor compared to universal clopidogrel treatment. Effect ratios were obtained from the literature and incidence rates and costs were obtained from the national data published by the Singapore Ministry of Health. Lifetime costs and quality-adjusted life-years (QALYs) were calculated. The primary endpoints were the incremental cost-effectiveness ratios (ICERs). RESULTS The prevalence of the LOF mutations was 61% in the population, with 65% of ethnic Chinese, 60% of ethnic Indian, and 53% of ethnic Malay patients having LOF mutations. Based on this prevalence, the overall ICER of genetic testing was S$33,839/QALY with ICERS of S$30,755/QALY, S$33,177/QALY, and S$41,470/QALY for Chinese, Indians, and Malays, respectively. CONCLUSION This study suggests that it is cost effective to screen for LOF mutations in the CYP2C19 gene in ischemic stroke populations, with ticagrelor as a substitute for clopidogrel in those with LOF mutations.
Collapse
Affiliation(s)
- Kaavya Narasimhalu
- Department of Neurology (SGH Campus), National Neuroscience Institute, Outram Road, 169608, Singapore, Singapore.
| | - Yoong Kwei Ang
- Policy, Research and Evaluation Division, Ministry of Health, Singapore, Singapore
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Doreen Su Yin Tan
- Policy, Research and Evaluation Division, Ministry of Health, Singapore, Singapore
- Khoo Teck Puat Hospital, Singapore, Singapore
| | - Deidre Anne De Silva
- Department of Neurology (SGH Campus), National Neuroscience Institute, Outram Road, 169608, Singapore, Singapore
| | - Kelvin Bryan Tan
- Policy, Research and Evaluation Division, Ministry of Health, Singapore, Singapore
- School of Public Health, National University of Singapore, Singapore, Singapore
| |
Collapse
|
4
|
Zhang J, Wang H, Niu G, Liu Y, Wang Y, Zhang L, Pei Y, Zhu H, Dai P, Chen C. Deciphering DMET genetic data: comprehensive assessment of Northwestern Han, Tibetan, Uyghur populations and their comparison to eleven 1000 genome populations. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 46:S1176-S1185. [PMID: 30688101 DOI: 10.1080/21691401.2018.1533849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We investigated the allele frequencies of drug absorption, distribution, metabolism and elimination (ADME)-related drug-metabolizing enzymes and transporters (DMET) genes in the Northwestern Han, Tibetan and Uyghur populations and compared the related genes in these three populations with those in eleven 1000 Genome populations. We examined 1936 single nucleotide polymorphisms of 225 DMET genes involved in ADME processes and found 732, 679 and 804 sites were polymorphic in Han, Tibetan and Uyghur. Tibetan differed from Han in only four sites (p < .05), whereas Uyghur differed from Han and Tibetan in 24 and 21 sites, respectively (p < .05). The distributions of 1058 genotyping data of 245 individuals from Han, Tibetan and Uyghur were compared with 1207 other individuals from the eleven 1000 Genomes populations. The top four populations in Han that exhibited the smallest pairwise Fst values were CHB, Tibetan, CHD and JPT; those in Tibetan were Han, CHB, Uyghur and CHD; and those in Uyghur were Han, Tibetan, GIH and CEU. MEGA results revealed that CHB, CHD, JPT, Han, Tibetan and Uyghur were grouped in cluster 1. GIH, MEX, CEU and TSI were grouped in cluster 2. MKK, ASW, LWK and YRI were grouped in cluster 3.
Collapse
Affiliation(s)
- Jiayi Zhang
- a College of Life Science , Northwest University , Xi'an , China
| | - Huijuan Wang
- a College of Life Science , Northwest University , Xi'an , China
| | - Geng Niu
- a College of Life Science , Northwest University , Xi'an , China
| | - Yongkang Liu
- a College of Life Science , Northwest University , Xi'an , China
| | - Yanxia Wang
- a College of Life Science , Northwest University , Xi'an , China
| | - Lirong Zhang
- a College of Life Science , Northwest University , Xi'an , China
| | - Yanrui Pei
- a College of Life Science , Northwest University , Xi'an , China
| | - Hongli Zhu
- a College of Life Science , Northwest University , Xi'an , China.,b National Engineering Research Center for Miniaturized Detection Systems , Northwest University , Xi'an , China
| | - Penggao Dai
- a College of Life Science , Northwest University , Xi'an , China.,b National Engineering Research Center for Miniaturized Detection Systems , Northwest University , Xi'an , China
| | - Chao Chen
- a College of Life Science , Northwest University , Xi'an , China.,b National Engineering Research Center for Miniaturized Detection Systems , Northwest University , Xi'an , China
| |
Collapse
|
5
|
Lam YWF. Economic Evaluation of Pharmacogenomic Testing. Pharmacogenomics 2019. [DOI: 10.1016/b978-0-12-812626-4.00014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
6
|
Jin LH, Kim BH, Lee JH, Lee K, Kwack K, Yim SV. Screening study for genetic polymorphisms affecting pharmacokinetics of talniflumate. Transl Clin Pharmacol 2017; 25:166-172. [PMID: 32095470 PMCID: PMC7033407 DOI: 10.12793/tcp.2017.25.4.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 11/19/2022] Open
Abstract
Talniflumate is a phthalidyl ester of niflumic acid, which has potent analgesic and anti-inflammatory effects and is widely used to treat inflammatory disorders, such as rheumatoid arthritis. To screen the possible genetic factors affecting the pharmacokinetics (PK) of talniflumate, 23 male Korean volunteers were enrolled from two separate bioequivalence studies. All subjects received 740 mg (two tablets) talniflumate in a standard 2×2 cross-over model in a randomized order. For the genetic study, PK parameters of the reference drug were used. We used Illumina Human610Quad v1.0 DNA Analysis BeadChip for whole genome single nucleotide polymorphism (SNP) analysis and whole genome genotyping data were processed by linear regression analysis for PK parameters. Whole genome analysis revealed 1498 significant SNPs (P < 0.0001) for Cmax, 65 significant SNPs (P < 0.0001) for T max, and 1491 significant SNPs (P < 0.0001) for AUC inf. For clinical pharmacological purposes, we selected SNPs from drug metabolizing enzymes and transporters, and analyzed the PK parameters of various genotypes. Two SNPs (rs11165069 from ABCA4 (p=0.00002); rs17847036 from CYP2C9 (p=0.000001)) showed significant associations with talniflumate C max. In the T max group, two SNPs (rs3787555 from CYP24A1 (p=0.00035); rs2275034 from ABCA4 (p=0.000587)) showed significant associations with talniflumate T max. In the AUC inf group, two SNPs (rs11165069 from ABCA4 (p=0.00002); rs12461006 from SLC1A6 (p=0.00008)) exhibited significant associations with talniflumate absorption. These results show that genetic factors could affect the PK parameters, and provide information that may be used in the development of personalized talniflumate therapy.
Collapse
Affiliation(s)
- Li Hua Jin
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Bo-Hyung Kim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Kidong Lee
- Department of BioMedical Science, College of Life Science, CHA University, SeongNam 13488, Republic of Korea
| | - KyuBum Kwack
- Department of BioMedical Science, College of Life Science, CHA University, SeongNam 13488, Republic of Korea
| | - Sung-Vin Yim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| |
Collapse
|
7
|
Angiolillo DJ, Ferreiro JL, Jakubowski JA, Winters KJ, Effron MB, Duvvuru S, Costigan TM, Sundseth SS, Walker JR, Saucedo JF, Kleiman NS, Varenhorst C, Braun OÖ. Enhanced active metabolite generation and platelet inhibition with prasugrel compared to clopidogrel regardless of genotype in thienopyridine metabolic pathways. Thromb Haemost 2017; 110:1223-31. [DOI: 10.1160/th13-03-0263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 08/09/2013] [Indexed: 12/29/2022]
Abstract
SummaryClopidogrel response varies according to the presence of genetic polymorphisms. The CYP2C19*2 allele has been associated with impaired response; conflicting results have been reported for CYP2C19*17, ABCB1, and PON1 genotypes. We assessed the impact of CYP2C19, PON1, and ABCB1 polymorphisms on clopidogrel and prasugrel pharmacodynamic (PD) and pharmacokinetic (PK) parameters. Aspirin-treated patients (N=194) with coronary artery disease from two independent, prospective, randomised, multi-centre studies comparing clopidogrel (75 mg) and prasugrel (10 mg) were genotyped and classified by predicted CYP2C19 metaboliser phenotype (ultra metabolisers [UM] = *17 carriers; extensive metabolisers [EM] = *1/1 homozygotes; reduced metabolisers [RM] = *2 carriers). ABCB1 T/T and C/T polymorphisms and PON1 A/A, A/G and G/G polymorphisms were also genotyped. PD parameters were assessed using VerifyNow® P2Y12 and vasodilator stimulated phosphoprotein (VASP) expressed as platelet reactivity index (PRI) after 14 days of maintenance dosing. Clopidogrel and prasugrel active metabolite (AM) exposure was calculated in a cohort of 96 patients. For clopidogrel, genetic variants in CYP2C19, but not ABCB1 or PON1, affected PK and PD. For prasugrel, none of the measured genetic variants affected PK or PD. Compared with clopidogrel, platelet inhibition with prasugrel was greater even in the CYP2C19 UM phenotype. Prasugrel generated more AM and achieved greater platelet inhibition than clopidogrel irrespective of CYP2C19, ABCB1, and PON1 polymorphisms. The lack of effect from genetic variants on prasugrel AM generation or antiplatelet activity is consistent with previous studies in healthy volunteers and is consistent with improved efficacy in acute coronary syndrome patients managed with percutaneous coronary intervention.
Collapse
|
8
|
Woo HI, Kim SR, Huh W, Ko JW, Lee SY. Association of genetic variations with pharmacokinetics and lipid-lowering response to atorvastatin in healthy Korean subjects. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:1135-1146. [PMID: 28435225 PMCID: PMC5391214 DOI: 10.2147/dddt.s131487] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Statins are effective agents in the primary and secondary prevention of cardiovascular disease, but treatment response to statins varies among individuals. We analyzed multiple genetic polymorphisms and assessed pharmacokinetic and lipid-lowering responses after atorvastatin 80 mg treatment in healthy Korean individuals. Methods Atorvastatin 80 mg was given to 50 healthy Korean male volunteers. Blood samples were collected to measure plasma atorvastatin and lipid concentrations up to 48 hours after atorvastatin administration. Subjects were genotyped for 1,936 drug metabolism and transporter genetic polymorphisms using the Affymetrix DMET plus array. Results The pharmacokinetics and lipid-lowering effect of atorvastatin showed remarkable interindividual variation. Three polymorphisms in the SLCO1B1, SLCO1B3, and ABCC2 genes were associated with either the maximum concentration (Cmax) of atorvastatin or changes in total cholesterol or low-density lipoprotein cholesterol (LDL-C). Minor homozygotes (76.5 ng/mL) of SLCO1B1 c.-910G>A showed higher Cmax than heterozygotes (34.0 ng/mL) and major homozygotes (33.5 ng/mL, false discovery rate P=0.040). Cmax and the area under the plasma concentration curve from hour 0 to infinity (AUC∞) were higher in carriers of the SLCO1B1*17 haplotype that included c.-910G>A than in noncarriers (46.1 vs 32.8 ng/mL for Cmax; 221.5 vs 154.2 ng/mL for AUC∞). SLCO1B3 c.334G>T homozygotes (63.0 ng/mL) also showed higher Cmax than heterozygotes (34.7 ng/mL) and major homozygotes (31.4 ng/mL, FDR P=0.037). A nonsynonymous ABCC2 c.1249G>A was associated with small total cholesterol and LDL-C responses (0.23% and −0.70% for G/A vs −11.9% and −17.4% for G/G). The Cmax tended to increase according to the increase in the number of minor allele of SLCO1B1 c. −910G>A and SLCO1B3 c.334G>T. Conclusion Genetic polymorphisms in transporter genes, including SLCO1B1, SLCO1B3, and ABCC2, may influence the pharmacokinetics and lipid-lowering response to atorvastatin administration.
Collapse
Affiliation(s)
- Hye In Woo
- Department of Laboratory Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Suk Ran Kim
- Clinical Research and Development, Hanmi Pharm. Co., Ltd., Seoul, Korea
| | - Wooseong Huh
- Department of Medicine.,Department of Clinical Pharmacology and Therapeutics
| | - Jae-Wook Ko
- Department of Clinical Pharmacology and Therapeutics
| | - Soo-Youn Lee
- Department of Clinical Pharmacology and Therapeutics.,Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
9
|
Wang Y, Yan BP, Liew D, Lee VWY. Cost-effectiveness of cytochrome P450 2C19 *2 genotype-guided selection of clopidogrel or ticagrelor in Chinese patients with acute coronary syndrome. THE PHARMACOGENOMICS JOURNAL 2017; 18:113-120. [DOI: 10.1038/tpj.2016.94] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/23/2016] [Accepted: 12/08/2016] [Indexed: 01/08/2023]
|
10
|
Berm EJJ, Gout-Zwart JJ, Luttjeboer J, Wilffert B, Postma MJ. A Model Based Cost-Effectiveness Analysis of Routine Genotyping for CYP2D6 among Older, Depressed Inpatients Starting Nortriptyline Pharmacotherapy. PLoS One 2016; 11:e0169065. [PMID: 28033366 PMCID: PMC5199075 DOI: 10.1371/journal.pone.0169065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 12/12/2016] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Genotyping for CYP2D6 has the potential to predict differences in metabolism of nortriptyline. This information could optimize pharmacotherapy. We determined the costs and effects of routine genotyping for old aged Dutch depressed inpatients. METHODS With a decision-tree, we modelled the first 12 weeks of nortriptyline therapy. Direct costs of genotyping, hospitalization, therapeutic drug monitoring and drugs were included. Based on genotype, patients could be correctly, sub-, or supratherapeutically dosed. Improvement from sub- or supratherapeutically dosed patients to correctly dosed patients was simulated, assuming that genotyping would prevent under- or overdosing of patients. In the base case, this improvement was assumed to be 35%. A probabilistic sensitivity analysis (PSA) was performed to determine uncertainty around the incremental cost-effectiveness ratio (ICER). RESULTS In the base case analysis, costs for genotyping were assumed €200 per test with a corresponding ICER at €1 333 000 per QALY. To reach a €50 000 per QALY cut-off, genotyping costs should be decreased towards €40 per test. At genotyping test costs < €35 per test, genotyping was dominant. At test costs of €17 per test there was a 95% probability that genotyping was cost-effective at €50 000 per QALY. CONCLUSIONS CYP2D6 genotyping was not cost-effective at current genotyping costs at a €50 000 per QALY threshold, however at test costs below €40, genotyping could be costs-effective.
Collapse
Affiliation(s)
- Elizabeth J. J. Berm
- University of Groningen, Groningen Institute of Pharmacy, Unit of PharmacoTherapy, -Epidemiology and -Economics (PTE2), Groningen, the Netherlands
| | - Judith J. Gout-Zwart
- University of Groningen, Groningen Institute of Pharmacy, Unit of PharmacoTherapy, -Epidemiology and -Economics (PTE2), Groningen, the Netherlands
- * E-mail:
| | - Jos Luttjeboer
- University of Groningen, Groningen Institute of Pharmacy, Unit of PharmacoTherapy, -Epidemiology and -Economics (PTE2), Groningen, the Netherlands
| | - Bob Wilffert
- University of Groningen, Groningen Institute of Pharmacy, Unit of PharmacoTherapy, -Epidemiology and -Economics (PTE2), Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Clinical Pharmacy and Pharmacology, Groningen, the Netherlands
| | - Maarten J. Postma
- University of Groningen, Groningen Institute of Pharmacy, Unit of PharmacoTherapy, -Epidemiology and -Economics (PTE2), Groningen, the Netherlands
- University Medical Center Groningen (UMCG), Institute for Science in Healthy Aging & HealthcaRE (SHARE), Groningen, the Netherlands
- University Medical Center Groningen (UMCG), Department of Epidemiology, Groningen, the Netherlands
| |
Collapse
|
11
|
Han SM, Park J, Lee JH, Lee SS, Kim H, Han H, Kim Y, Yi S, Cho JY, Jang IJ, Lee MG. Targeted Next-Generation Sequencing for Comprehensive Genetic Profiling of Pharmacogenes. Clin Pharmacol Ther 2016; 101:396-405. [PMID: 27727443 DOI: 10.1002/cpt.532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 12/12/2022]
Abstract
Phenotypic differences in drug responses have been associated with known pharmacogenomic loci, but many remain to be characterized. Therefore, we developed next-generation sequencing (NGS) panels to enable broad and unbiased inspection of genes that are involved in pharmacokinetics (PKs) and pharmacodynamics (PDs). These panels feature repetitively optimized probes to capture up to 114 PK/PD-related genes with high coverage (99.6%) and accuracy (99.9%). Sequencing of a Korean cohort (n = 376) with the panels enabled profiling of actionable variants as well as rare variants of unknown functional consequences. Notably, variants that occurred at low frequency were enriched with likely protein-damaging variants and previously unreported variants. Furthermore, in vitro evaluation of four pharmacogenes, including cytochrome P450 2C19 (CYP2C19), confirmed that many of these rare variants have considerable functional impact. The present study suggests that targeted NGS panels are readily applicable platforms to facilitate comprehensive profiling of pharmacogenes, including common but also rare variants that warrant screening for personalized medicine.
Collapse
Affiliation(s)
- S M Han
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| | - J Park
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| | - J H Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, Korea
| | - S S Lee
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University College of Medicine, Busan, Korea
| | - H Kim
- Celemics Inc, Seoul, Korea
| | - H Han
- Celemics Inc, Seoul, Korea
| | - Y Kim
- Celemics Inc, Seoul, Korea
| | - S Yi
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - J-Y Cho
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - I-J Jang
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | - M G Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
12
|
Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening. Genet Med 2016; 19:357-361. [PMID: 27537706 PMCID: PMC5316383 DOI: 10.1038/gim.2016.105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/16/2016] [Indexed: 12/21/2022] Open
Abstract
PURPOSE The aim of the study was to assess exome data for preemptive pharmacogenetic screening for 203 clinically relevant pharmacogenetic variant positions from the Pharmacogenomics Knowledgebase and Clinical Pharmacogenetics Implementation Consortium and identify copy-number variants (CNVs) in CYP2D6. METHODS We examined the coverage and genotype quality of 203 pharmacogenetic variant positions in 973 exomes compared with five genomes and with five genotyping chip data sets. Then, we determined the agreement of exome and chip genotypes by evaluating concordance in a three-way comparison of exome, genome, and chip-based genotyping at 1,929 variant positions in five individuals. Finally, we evaluated the utility of exomes for detecting CYP2D6 CNVs. RESULTS For 5 individuals examined for 203 pharmacogenetic variants (5 × 203 = 1,015), 998/1,015 were identified by genome, 849/1,015 were identified by exome, and 295/1,015 by genotyping chip. Thirty-six pharmacogenetic star allele variants with moderate to strong Clinical Pharmacogenetics Implementation Consortium (CPIC) therapeutic recommendations were identified in 973 exomes. Exomes had high (98%) genotype concordance with chip-based genotyping. CYP2D6 CNVs were identified in 57/973 exomes. CONCLUSIONS Exomes outperformed the current chip-based assay in detecting more important pharmacogenetic variant positions and CYP2D6 CNVs for preemptive pharmacogenetic screening. Tools should be developed to derive pharmacogenetic variants from exomes.Genet Med 19 3, 357-361.
Collapse
|
13
|
Goh SK, Musafer A, Witkowski T, Muralidharan V, Christophi C, Do H, Dobrovic A. Comparison of 3 Methodologies for Genotyping of Small Deletion and Insertion Polymorphisms. Clin Chem 2016; 62:1012-9. [DOI: 10.1373/clinchem.2016.256388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/16/2022]
Abstract
Abstract
BACKGROUND
The quantification of genomic chimerism is increasingly recognized for its clinical significance after transplantation. Before the measurement of chimerism, accurate genotyping of genetic polymorphisms for informative alleles that can distinguish donor DNA from recipient DNA is essential. The ease of allelic discrimination of small deletion and insertion polymorphisms (DIPs) makes DIPs attractive markers to track chimerism. Current methodologies for the genotyping of DIPs are largely based on “open-tube” approaches. “Closed-tube” approaches involving no or minimal post-PCR handling are preferred. We compared 3 distinct methodologies to determine an optimal platform for DIP genotyping.
METHODS
Genomic DNA from 19 normal individuals was genotyped for 6 small biallelic DIPs using high-resolution melting analysis (HRMA), probe-free droplet digital PCR (ddPCR), and microfluidic electrophoresis of PCR products. For HRMA, 3 different platforms were compared.
RESULTS
Our newly developed probe-free ddPCR approach allowed the genotype of each DIP to be determined by fluorescence intensity based on amplicon size. Microfluidic electrophoresis also allowed genotypes to be determined by amplicon size. HRMA assays allowed the genotype of each DIP to be determined by melting profile. Genotyping results were concordant between the 3 methodologies. HRMA was the most readily performed methodology and was robust across 3 separate HRMA-capable platforms.
CONCLUSIONS
We demonstrated the effectiveness of probe-free ddPCR to accurately genotype small biallelic DIPs. Nevertheless, HRMA proved to be the optimal approach for genotyping small DIPs because closed-tube approaches are preferred owing to rapid and less laborious workflows and least risk of PCR contamination.
Collapse
Affiliation(s)
- Su Kah Goh
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Ashan Musafer
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - Tom Witkowski
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | | | - Christopher Christophi
- Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Victoria, Australia
- Department of Pathology, University of Melbourne, Victoria, Australia
| | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Victoria, Australia
- Department of Pathology, University of Melbourne, Victoria, Australia
| |
Collapse
|
14
|
Economic Evaluations of Pharmacogenetic and Pharmacogenomic Screening Tests: A Systematic Review. Second Update of the Literature. PLoS One 2016; 11:e0146262. [PMID: 26752539 PMCID: PMC4709231 DOI: 10.1371/journal.pone.0146262] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/15/2015] [Indexed: 01/29/2023] Open
Abstract
Objective Due to extended application of pharmacogenetic and pharmacogenomic screening (PGx) tests it is important to assess whether they provide good value for money. This review provides an update of the literature. Methods A literature search was performed in PubMed and papers published between August 2010 and September 2014, investigating the cost-effectiveness of PGx screening tests, were included. Papers from 2000 until July 2010 were included via two previous systematic reviews. Studies’ overall quality was assessed with the Quality of Health Economic Studies (QHES) instrument. Results We found 38 studies, which combined with the previous 42 studies resulted in a total of 80 included studies. An average QHES score of 76 was found. Since 2010, more studies were funded by pharmaceutical companies. Most recent studies performed cost-utility analysis, univariate and probabilistic sensitivity analyses, and discussed limitations of their economic evaluations. Most studies indicated favorable cost-effectiveness. Majority of evaluations did not provide information regarding the intrinsic value of the PGx test. There were considerable differences in the costs for PGx testing. Reporting of the direction and magnitude of bias on the cost-effectiveness estimates as well as motivation for the chosen economic model and perspective were frequently missing. Conclusions Application of PGx tests was mostly found to be a cost-effective or cost-saving strategy. We found that only the minority of recent pharmacoeconomic evaluations assessed the intrinsic value of the PGx tests. There was an increase in the number of studies and in the reporting of quality associated characteristics. To improve future evaluations, scenario analysis including a broad range of PGx tests costs and equal costs of comparator drugs to assess the intrinsic value of the PGx tests, are recommended. In addition, robust clinical evidence regarding PGx tests’ efficacy remains of utmost importance.
Collapse
|
15
|
Integrating dynamic mixed-effect modelling and penalized regression to explore genetic association with pharmacokinetics. Pharmacogenet Genomics 2015; 25:231-8. [PMID: 25751396 PMCID: PMC4387202 DOI: 10.1097/fpc.0000000000000127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
CONTEXT In a previous work, we have shown that penalized regression approaches can allow many genetic variants to be incorporated into sophisticated pharmacokinetic (PK) models in a way that is both computationally and statistically efficient. The phenotypes were the individual model parameter estimates, obtained a posteriori of the model fit and known to be sensitive to the study design. OBJECTIVE The aim of this study was to propose an integrated approach in which genetic effect sizes are estimated simultaneously with the PK model parameters, which should improve the estimate precision and reduce sensitivity to study design. METHODS A total of 200 data sets were simulated under the null and each of the following three alternative scenarios: (i) a phase II study with N=300 participants and n=6 sampling times, wherein six unobserved causal variants affect the drug elimination clearance; (ii) the addition of participants with a residual concentration collected in clinical routine (N=300, n=6 plus N=700, n=1); and (iii) a phase II study (N=300, n=6) in which four unobserved causal variants affect two different model parameters. RESULTS In all scenarios the integrated approach detected fewer false positives. In scenario (i), true-positive rates were low and the stepwise procedure outperformed the integrated approach. In scenario (ii), approaches performed similarly and rates were higher. In scenario (iii), the integrated approach outperformed the stepwise procedure. CONCLUSION A PK phase II study with N=300 lacks the power to detect genetic effects on PK using genetic arrays. Our approach can simultaneously analyse phase II and clinical routine data and identify when genetic variants affect multiple PK parameters.
Collapse
|
16
|
In situ mutation detection and visualization of intratumor heterogeneity for cancer research and diagnostics. Oncotarget 2014; 4:2407-18. [PMID: 24280411 PMCID: PMC3926836 DOI: 10.18632/oncotarget.1527] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Current assays for somatic mutation analysis are based on extracts from tissue sections that often contain morphologically heterogeneous neoplastic regions with variable contents of normal stromal and inflammatory cells, obscuring the results of the assays. We have developed an RNA-based in situ mutation assay that targets oncogenic mutations in a multiplex fashion that resolves the heterogeneity of the tissue sample. Activating oncogenic mutations are targets for a new generation of cancer drugs. For anti-EGFR therapy prediction, we demonstrate reliable in situ detection of KRAS mutations in codon 12 and 13 in colon and lung cancers in three different types of routinely processed tissue materials. High-throughput screening of KRAS mutation status was successfully performed on a tissue microarray. Moreover, we show how the patterns of expressed mutated and wild-type alleles can be studied in situ in tumors with complex combinations of mutated EGFR, KRAS and TP53. This in situ method holds great promise as a tool to investigate the role of somatic mutations during tumor progression and for prediction of response to targeted therapy.
Collapse
|
17
|
Li J, Lao X, Zhang C, Tian L, Lu D, Xu S. Increased genetic diversity of ADME genes in African Americans compared with their putative ancestral source populations and implications for pharmacogenomics. BMC Genet 2014; 15:52. [PMID: 24884825 PMCID: PMC4021503 DOI: 10.1186/1471-2156-15-52] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 04/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND African Americans have been treated as a representative population for African ancestry for many purposes, including pharmacogenomic studies. However, the contribution of European ancestry is expected to result in considerable differences in the genetic architecture of African American individuals compared with an African genome. In particular, the genetic admixture influences the genomic diversity of drug metabolism-related genes, and may cause high heterogeneity of drug responses in admixed populations such as African Americans. RESULTS The genomic ancestry information of African-American (ASW) samples was obtained from data of the 1000 Genomes Project, and local ancestral components were also extracted for 32 core genes and 252 extended genes, which are associated with drug absorption, distribution, metabolism, and excretion (ADME) genes. As expected, the global genetic diversity pattern in ASW was determined by the contributions of its putative ancestral source populations, and the whole profiles of ADME genes in ASW are much closer to those in YRI than in CEU. However, we observed much higher diversity in some functionally important ADME genes in ASW than either CEU or YRI, which could be a result of either genetic drift or natural selection, and we identified some signatures of the latter. We analyzed the clinically relevant polymorphic alleles and haplotypes, and found that 28 functional mutations (including 3 missense, 3 splice, and 22 regulator sites) exhibited significantly higher differentiation between the three populations. CONCLUSIONS Analysis of the genetic diversity of ADME genes showed differentiation between admixed population and its ancestral source populations. In particular, the different genetic diversity between ASW and YRI indicated that the ethnic differences in pharmacogenomic studies are broadly existed despite that African ancestry is dominant in Africans Americans. This study should advance our understanding of the genetic basis of the drug response heterogeneity between populations, especially in the case of population admixture, and have significant implications for evaluating potential inter-population heterogeneity in drug treatment effects.
Collapse
Affiliation(s)
| | | | | | | | | | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| |
Collapse
|
18
|
Erlinge D, James S, Duvvuru S, Jakubowski JA, Wagner H, Varenhorst C, Tantry US, Brown PB, Small D, Moser BA, Sundseth SS, Walker JR, Winters KJ, Gurbel PA. Clopidogrel metaboliser status based on point-of-care CYP2C19 genetic testing in patients with coronary artery disease. Thromb Haemost 2014; 111:943-50. [PMID: 24402637 DOI: 10.1160/th13-09-0767] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 11/26/2013] [Indexed: 01/27/2023]
Abstract
We compared results obtained with the Nanosphere Verigene® System, a novel point-of-care (POC) genetic test capable of analysing 11 CYP2C19 variants within 3 hours, to an established, validated genotyping method (Affymetrix™ DMET+; reference assay) for identifying extensive and reduced metabolisers of clopidogrel. Based on genotyping, patients (N=82) with stable coronary artery disease on clopidogrel 75 mg daily were defined as extensive metabolisers (*1/*1, *1/*17, *17/*17), reduced metabolisers (*1/*2, *1/*8, *2/*2, *2/*3), or of indeterminate metaboliser status (*2/*17). Pharmacokinetic exposure to clopidogrel's active metabolite and pharmacodynamic measures with P2Y12 reaction units (PRU) (VerifyNow®P2Y12 assay) and VASP PRI (PRI) were also assessed. There was a 99.9% overall concordance of marker-level data between the Nanosphere Verigene and DMET+ systems in identifying the CYP2C19 variants and 100% agreement in classifying the patients as extensive (n=59) or reduced metabolisers (n=15). Extensive metabolisers had significantly higher active metabolite exposure than reduced metabolisers (LS means 12.6 ng*h/ml vs 7.7 ng*h/ml; p<0.001). Extensive metabolisers also had lower PRU (LS means 158 vs 212; p=0.003) and VASP PRI (LS means 48% vs 63%, p=0.01) compared to reduced metabolisers. Rates of high on-treatment platelet reactivity were higher in reduced metabolisers compared to extensive metabolisers (VASP PRI ≥ 50%: 79% vs 47%; PRU >235: 33% vs 16%). The Nanosphere Verigene CBS system identified 11 CYP2C19 alleles in less than 3 hours with a high degree of accuracy when compared to a conventional method, and was further validated against pharmacokinetic and pharmacodynamic phenotypes.
Collapse
Affiliation(s)
- David Erlinge
- David Erlinge, Dept. of Cardiology, Lund University, Skane University Hospital, Lund; 221 85 Lund, Sweden, Tel: +46 46172597, Fax: +46 46157857, E-mail:
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Jeon H, Jang IJ, Lee S, Ohashi K, Kotegawa T, Ieiri I, Cho JY, Yoon SH, Shin SG, Yu KS, Lim KS. Apple juice greatly reduces systemic exposure to atenolol. Br J Clin Pharmacol 2013; 75:172-9. [PMID: 22574741 DOI: 10.1111/j.1365-2125.2012.04324.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIM Fruit juice reduces the plasma concentrations of several β-adrenoceptor blockers, likely by inhibiting OATP2B1-mediated intestinal absorption. The aim of this study was to investigate the effects of apple juice on the pharmacokinetics of atenolol. METHODS Twelve healthy Korean volunteers with genotypes of SLCO2B1 c.1457C> T (*1/*1 (n = 6) and *3/*3 (n = 6)) were enrolled in this study. In a three-phase, one-sequence crossover study, the pharmacokinetics (PK) of atenolol was evaluated after administration of 50 mg atenolol. Subjects received atenolol with either 300 ml water, 1200 ml apple juice or 600 ml apple juice. RESULTS Apple juice markedly reduced the systemic exposure to atenolol. The geometric mean ratios (95% confidence intervals) of apple juice : water were 0.18 (0.13, 0.25, 1200 ml) and 0.42 (0.30, 0.59, 600 ml) for the AUC(0,t(last)). In this study, the PK parameters of atenolol responded in a dose-dependent manner to apple juice. CONCLUSIONS Apple juice markedly reduced systemic exposure to atenolol. The genetic variation of SLCO2B1 c.1457C>T had a minimal effect on the pharmacokinetics of atenolol when the drug was administered with water or apple juice.
Collapse
Affiliation(s)
- Hyewon Jeon
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Multiple single nucleotide polymorphism analysis using penalized regression in nonlinear mixed-effect pharmacokinetic models. Pharmacogenet Genomics 2013; 23:167-74. [DOI: 10.1097/fpc.0b013e32835dd22c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
21
|
Lala A, Berger JS, Sharma G, Hochman JS, Scott Braithwaite R, Ladapo JA. Genetic testing in patients with acute coronary syndrome undergoing percutaneous coronary intervention: a cost-effectiveness analysis. J Thromb Haemost 2013; 11:81-91. [PMID: 23137413 DOI: 10.1111/jth.12059] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
BACKGROUND The CYP2C19 genotype is a predictor of adverse cardiovascular events in acute coronary syndrome (ACS) patients undergoing percutaneous coronary intervention (PCI) treated with clopidogrel. OBJECTIVES We aimed to evaluate the cost-effectiveness of a CYP2C19*2 genotype-guided strategy of antiplatelet therapy in ACS patients undergoing PCI, compared with two 'no testing' strategies (empiric clopidogrel or prasugrel). METHODS We developed a Markov model to compare three strategies. The model captured adverse cardiovascular events and antiplatelet-related complications. Costs were expressed in 2010 US dollars and estimated using diagnosis-related group codes and Medicare reimbursement rates. The net wholesale price for prasugrel was estimated as $5.45 per day. A generic estimate for clopidogrel of $1.00 per day was used and genetic testing was assumed to cost $500. RESULTS Base case analyses demonstrated little difference between treatment strategies. The genetic testing-guided strategy yielded the most QALYs and was the least costly. Over 15 months, total costs were $18 lower with a gain of 0.004 QALY in the genotype-guided strategy compared with empiric clopidogrel, and $899 lower with a gain of 0.0005 QALY compared with empiric prasugrel. The strongest predictor of the preferred strategy was the relative risk of thrombotic events in carriers compared with wild-type individuals treated with clopidogrel. Above a 47% increased risk, a genotype-guided strategy was the dominant strategy. Above a clopidogrel cost of $3.96 per day, genetic testing was no longer dominant but remained cost-effective. CONCLUSIONS Among ACS patients undergoing PCI, a genotype-guided strategy yields similar outcomes to empiric approaches to treatment, but is marginally less costly and more effective.
Collapse
Affiliation(s)
- A Lala
- Department of Medicine, Division of Cardiovascular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | | | | | | | | | | |
Collapse
|
22
|
Wang Y, Cottman M, Schiffman JD. Molecular inversion probes: a novel microarray technology and its application in cancer research. Cancer Genet 2012; 205:341-55. [PMID: 22867995 DOI: 10.1016/j.cancergen.2012.06.005] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/09/2012] [Accepted: 06/11/2012] [Indexed: 11/18/2022]
Abstract
The molecular inversion probe (MIP) assay technology was originally developed for single nucleotide polymorphism (SNP) genotyping, but has subsequently been used for identifying other types of genetic variation including focal insertions and deletions, larger copy number alterations (CNAs), loss of heterozygosity (LOH), and most recently, for somatic mutation detection. The assay requires as little as 75 ng of genomic DNA and has been shown to perform well with highly degraded DNA, such as that from formalin-fixed paraffin-embedded (FFPE)-preserved samples from 20 years ago or older. Central to the MIP assay technology are the padlock probes that hybridize to the DNA target of interest before polymerase chain reaction amplification, leading to high assay specificity. As outlined in this review, the MIP assay has enabled new discoveries and a deeper understanding of the molecular basis of cancer and its various disease subtypes. The use of novel genomic technology such as MIPs on clinically archived FFPE samples has the potential to lead to more accurate disease diagnosis, prognosis, and novel therapeutic intervention. This review describes the initial history of MIP technology, details of the MIP assay, its current analysis techniques, and recent publications related to this novel platform.
Collapse
Affiliation(s)
- Yuker Wang
- Assay Development and Bioinformatics Department, Affymetrix, Inc., Santa Clara, CA, USA
| | | | | |
Collapse
|
23
|
Concordance of DMET plus genotyping results with those of orthogonal genotyping methods. Clin Pharmacol Ther 2012; 92:360-5. [PMID: 22871999 DOI: 10.1038/clpt.2012.95] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
There are several hurdles to the clinical implementation of pharmacogenetics. One approach is to employ pre-prescription genotyping, involving interrogation of multiple pharmacogenetic variants using a high-throughput platform. We compared the performance of the Drug Metabolizing Enzymes and Transporters (DMET) Plus array (1,931 variants in 225 genes) with that of orthogonal genotyping methods in 220 pediatric patients. A total of 1,692 variants had call rates >98% and were in Hardy-Weinberg equilibrium. Of these, 259 were genotyped by at least one independent method, and a total of 19,942 single-nucleotide polymorphism (SNP)-patient sample pairs were evaluated. The concordance rate was 99.9%, with only 28 genotype discordances observed. For the genes deemed most likely to be clinically relevant (TPMT, CYP2D6, CYP2C19, CYP2C9, VKORC1, DPYD, UGT1A1, and SLCO1B1), a total of 3,799 SNP-patient sample pairs were evaluable and had a concordance rate of 99.96%. We conclude that the DMET Plus array performs well with primary patient samples, with the results in good concordance with those of several lower-throughput genotyping methods.
Collapse
|
24
|
Hu Y, Ehli EA, Nelson K, Bohlen K, Lynch C, Huizenga P, Kittlelsrud J, Soundy TJ, Davies GE. Genotyping performance between saliva and blood-derived genomic DNAs on the DMET array: a comparison. PLoS One 2012; 7:e33968. [PMID: 22448283 PMCID: PMC3309006 DOI: 10.1371/journal.pone.0033968] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/22/2012] [Indexed: 12/16/2022] Open
Abstract
The Affymetrix Drug Metabolism Enzymes and Transporters (DMET) microarray is the first assay to offer a large representation of SNPs conferring genetic diversity across known pharmacokinetic markers. As a convenient and painless alternative to blood, saliva samples have been reported to work well for genotyping on the high density SNP arrays, but no reports to date have examined this application for saliva-derived DNA on the DMET platform. Genomic DNA extractions from saliva samples produced an ample quantity of genomic DNA for DMET arrays, however when human amplifiable DNA was measured, it was determined that a large percentage of this DNA was from bacteria or fungi. A mean of 37.3% human amplifiable DNA was determined for saliva-derived DNAs, which results in a significant decrease in the genotyping call rate (88.8%) when compared with blood-derived DNAs (99.1%). More interestingly, the percentage of human amplifiable DNA correlated with a higher genotyping call rate, and almost all samples with more than 31.3% human DNA produced a genotyping call rate of at least 96%. SNP genotyping results for saliva derived DNA (n = 39) illustrated a 98.7% concordance when compared with blood DNA. In conclusion, when compared with blood DNA and tested on the DMET array, saliva-derived DNA provided adequate genotyping quality with a significant lower number of SNP calls. Saliva-derived DNA does perform very well if it contains greater than 31.3% human amplifiable DNA.
Collapse
Affiliation(s)
- Yueshan Hu
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
- Department of Psychiatry, University of South Dakota, Sioux Falls, South Dakota, United States of America
| | - Kelly Nelson
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Krista Bohlen
- Avera Research Institute, Sioux Falls, South Dakota, United States of America
- Avera Cancer Institute, Sioux Falls, South Dakota, United States of America
| | - Christophina Lynch
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota, United States of America
| | - Patty Huizenga
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
| | - Julie Kittlelsrud
- Avera Research Institute, Sioux Falls, South Dakota, United States of America
| | - Timothy J. Soundy
- Department of Psychiatry, University of South Dakota, Sioux Falls, South Dakota, United States of America
| | - Gareth E. Davies
- Avera Institute for Human Genetics, Sioux Falls, South Dakota, United States of America
- Department of Psychiatry, University of South Dakota, Sioux Falls, South Dakota, United States of America
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota, United States of America
- * E-mail:
| |
Collapse
|
25
|
Abstract
Thienopyridines are platelet adenosine diphosphate receptor antagonists used in the treatment and prevention of thrombotic events in patients with acute coronary syndrome. The pharmacokinetic profile of the thienopyridine clopidogrel has resulted in highly variable pharmacokinetics and efficacy responses. The purpose of this review is to provide a brief overview of the pharmacokinetics of prasugrel and clopidogrel and discuss factors that would influence the metabolism of those drugs. Clinical studies have shown that the coadministration of prasugrel with other drugs is less likely to result in clinically relevant pharmacokinetic drug interactions compared with clopidogrel. The lack of effect of variant genotypes on the efficacy of prasugrel suggests that more patients will receive adequate platelet inhibition after administration of prasugrel. The efficient generation of the active metabolite of prasugrel results in greater and more rapid inhibition of P2Y(12) receptor-mediated platelet aggregation.
Collapse
Affiliation(s)
- Suraj Achar
- Department of Family and Preventive Medicine, UCSD School of Medicine, San Diego, CA 92121, USA.
| |
Collapse
|
26
|
Li J, Zhang L, Zhou H, Stoneking M, Tang K. Global patterns of genetic diversity and signals of natural selection for human ADME genes. Hum Mol Genet 2010; 20:528-40. [DOI: 10.1093/hmg/ddq498] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
27
|
Extending and evaluating a warfarin dosing algorithm that includes CYP4F2 and pooled rare variants of CYP2C9. Pharmacogenet Genomics 2010; 20:407-13. [PMID: 20442691 DOI: 10.1097/fpc.0b013e328338bac2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Warfarin dosing remains challenging because of its narrow therapeutic window and large variability in dose response. We sought to analyze new factors involved in its dosing and to evaluate eight dosing algorithms, including two developed by the International Warfarin Pharmacogenetics Consortium (IWPC). METHODS we enrolled 108 patients on chronic warfarin therapy and obtained complete clinical and pharmacy records; we genotyped single nucleotide polymorphisms relevant to the VKORC1, CYP2C9, and CYP4F2 genes using integrated fluidic circuits made by Fluidigm. RESULTS When applying the IWPC pharmacogenetic algorithm to our cohort of patients, the percentage of patients within 1 mg/d of the therapeutic warfarin dose increases from 54% to 63% using clinical factors only, or from 38% using a fixed-dose approach. CYP4F2 adds 4% to the fraction of the variability in dose (R) explained by the IWPC pharmacogenetic algorithm (P<0.05). Importantly, we show that pooling rare variants substantially increases the R for CYP2C9 (rare variants: P=0.0065, R=6%; common variants: P=0.0034, R=7%; rare and common variants: P=0.00018; R=12%), indicating that relatively rare variants not genotyped in genome-wide association studies may be important. In addition, the IWPC pharmacogenetic algorithm and the Gage (2008) algorithm perform best (IWPC: R=50%; Gage: R=49%), and all pharmacogenetic algorithms outperform the IWPC clinical equation (R=22%). VKORC1 and CYP2C9 genotypes did not affect long-term variability in dose. Finally, the Fluidigm platform, a novel warfarin genotyping method, showed 99.65% concordance between different operators and instruments. CONCLUSION CYP4F2 and pooled rare variants of CYP2C9 significantly improve the ability to estimate warfarin dose.
Collapse
|
28
|
Srinivasan BS, Evans EA, Flannick J, Patterson AS, Chang CC, Pham T, Young S, Kaushal A, Lee J, Jacobson JL, Patrizio P. A universal carrier test for the long tail of Mendelian disease. Reprod Biomed Online 2010; 21:537-51. [PMID: 20729146 DOI: 10.1016/j.rbmo.2010.05.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/22/2010] [Accepted: 05/24/2010] [Indexed: 01/03/2023]
Abstract
Mendelian disorders are individually rare but collectively common, forming a 'long tail' of genetic disease. A single highly accurate assay for this long tail would allow the scaling up of the Jewish community's successful campaign of population screening for Tay-Sachs disease to the general population, thereby improving millions of lives, greatly benefiting minority health and saving billions of dollars. This need has been addressed by designing a universal carrier test: a non-invasive, saliva-based assay for more than 100 Mendelian diseases across all major population groups. The test has been exhaustively validated with a median of 147 positive and 525 negative samples per variant, demonstrating a multiplex assay whose performance compares favourably with the previous standard of care, namely blood-based single-gene carrier tests. Because the test represents a dramatic reduction in the cost and complexity of large-scale population screening, an end to many preventable genetic diseases is now in sight. Moreover, given that the assay is inexpensive and requires only a saliva sample, it is now increasingly feasible to make carrier testing a routine part of preconception care.
Collapse
|
29
|
Sorich MJ, Vitry A, Ward MB, Horowitz JD, McKinnon RA. Prasugrel vs. clopidogrel for cytochrome P450 2C19-genotyped subgroups: integration of the TRITON-TIMI 38 trial data. J Thromb Haemost 2010; 8:1678-84. [PMID: 20492467 DOI: 10.1111/j.1538-7836.2010.03923.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Prasugrel is a newly marketed antiplatelet drug with improved cardiac outcomes as compared with clopidogrel for acute coronary syndromes involving percutaneous coronary intervention (PCI). Analysis of a subset of the TRITON-TIMI 38 trial demonstrated that cytochrome P450 2C19 (CYP2C19) reduced-function genotypes are associated with differential clinical responses to clopidogrel, but not prasugrel. Whether the CYP2C19 genotype has the potential to influence clinical choice of these drugs prior to PCI for individuals with unstable angina or non-ST segment elevation myocardial infarction is currently uncertain. METHODS AND RESULTS An exploratory, secondary analysis was undertaken to estimate the clinical benefit of prasugrel over clopidogrel in subgroups defined by CYP2C19 genotype, by integrating the published results of the genetic substudy and the overall TRITON-TIMI 38 trial. Individuals with a CYP2C19 reduced-metabolizer genotype were estimated to have a substantial reduction in the risk of the composite primary outcome (cardiovascular death, myocardial infarction, or stroke) with prasugrel as compared with clopidogrel [relative risk (RR) 0.57; 95% confidence interval (CI) 0.39-0.83]. For CYP2C19 extensive metabolizers (∼70% of the population), however, the composite outcome risks with prasugrel and clopidogrel were not substantially different (RR 0.98; 95% CI 0.80-1.20). CONCLUSIONS Integration of the TRITON-TIMI 38 data suggests that the CYP2C19 genotype can discriminate between individuals who receive extensive benefit from using prasugrel instead of clopidogrel, and individuals with comparable clinical outcomes with prasugrel and clopidorel. Thus, CYP2C19 genotyping has the potential to guide the choice of antiplatelet therapy, and further research is warranted to validate this estimate.
Collapse
Affiliation(s)
- M J Sorich
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia.
| | | | | | | | | |
Collapse
|
30
|
Goodsaid FM, Amur S, Aubrecht J, Burczynski ME, Carl K, Catalano J, Charlab R, Close S, Cornu-Artis C, Essioux L, Fornace AJ, Hinman L, Hong H, Hunt I, Jacobson-Kram D, Jawaid A, Laurie D, Lesko L, Li HH, Lindpaintner K, Mayne J, Morrow P, Papaluca-Amati M, Robison TW, Roth J, Schuppe-Koistinen I, Shi L, Spleiss O, Tong W, Truter SL, Vonderscher J, Westelinck A, Zhang L, Zineh I. Voluntary exploratory data submissions to the US FDA and the EMA: experience and impact. Nat Rev Drug Discov 2010; 9:435-45. [DOI: 10.1038/nrd3116] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
31
|
Man M, Farmen M, Dumaual C, Teng CH, Moser B, Irie S, Noh GJ, Njau R, Close S, Wise S, Hockett R. Genetic variation in metabolizing enzyme and transporter genes: comprehensive assessment in 3 major East Asian subpopulations with comparison to Caucasians and Africans. J Clin Pharmacol 2010; 50:929-40. [PMID: 20173083 DOI: 10.1177/0091270009355161] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The advent of high-throughput technologies has proven valuable in the assessment of genetic differences and their effects on drug activation, metabolism, disposition, and transport. However, most studies to date have focused on a small number of genes or few alleles, some of which are rare and therefore observed infrequently or lacked rigorous ethnic characterization, thus reducing the ability to extrapolate within and among populations. In this study, the authors comprehensively assessed the allele frequencies of 165 variants comprising 27 drug-metabolizing enzyme and transporter (DMET) genes from 2188 participants across 3 major ethnic populations: Caucasians, Africans, and East Asians. This sample size was sufficiently large to demonstrate genetic differences among these major ethnic groups while concomitantly confirming similarities among East Asian subpopulations (Korean, Han Chinese, and Japanese). A comprehensive presentation of allele and genotype frequencies is included in the online supplement, and 3 of the most widely studied cytochrome P450 (CYP) genes, CYP2D6, CYP2C19, and CYP2C9; 2 non-CYP enzymes, NAT1 and TMPT; and 2 transporter genes, SLCO1B1 and SLCO2B1, are presented herein according to ethnic classification.
Collapse
Affiliation(s)
- Michael Man
- Discovery and Development Statistics, Eli Lilly and Company, Lilly Corporate Center DC 2026, Indianapolis, IN 46285, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Cuyàs E, Olano-Martín E, Khymenets O, Hernández L, Jofre-Monseny L, Grandoso L, Tejedor D, Martínez A, Farré M, de la Torre R. Errors and reproducibility of DNA array-based detection of allelic variants in ADME genes: PHARMAchip™. Pharmacogenomics 2010; 11:257-66. [DOI: 10.2217/pgs.09.165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aims: Differences in adverse drug reactions can be explained by genetic variations, especially if they determine the expression of certain protein effectors and/or drug-metabolizing enzymes. Over the last decade, several tests screening for the most frequent polymorphisms in drug-metabolizing enzymes have been marketed for research and diagnostic purposes. The aim of this study was to assess the suitability of PHARMAchip™ for the genotyping of polymorphisms of genes associated with drug metabolism and response as an alternative to Jurilab Ltd’s DrugMEt® Test. Materials & methods: In this observational study, performed using 100 previously genotyped DNA samples, we report on common genes included in the two different tests examined: the former DrugMEt test and the recently introduced PHARMAchip test. Results & conclusion: Although these tests are based on different methodological approaches, we have found a high concordance of results between both methods. Some of the discrepancies between tests were related to allelic variants not monitored in a particular microarray and the quality of the genomic DNA used.
Collapse
Affiliation(s)
- Elisabet Cuyàs
- Human Pharmacology & Clinical Neurosciences Research Group of the Neuropsychopharmacology Program, Institut Municipal d’Investigació Mèdica (IMIM-Hospital del Mar), Parc de Recerca Biomèdica de Barcelona, c/ Dr. Aiguader 88/08003 Barcelona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Olha Khymenets
- Human Pharmacology & Clinical Neurosciences Research Group of the Neuropsychopharmacology Program, Institut Municipal d’Investigació Mèdica (IMIM-Hospital del Mar), Parc de Recerca Biomèdica de Barcelona, c/ Dr. Aiguader 88/08003 Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | | | | | | | - Magí Farré
- Human Pharmacology & Clinical Neurosciences Research Group of the Neuropsychopharmacology Program, Institut Municipal d’Investigació Mèdica (IMIM-Hospital del Mar), Parc de Recerca Biomèdica de Barcelona, c/ Dr. Aiguader 88/08003 Barcelona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael de la Torre
- Human Pharmacology & Clinical Neurosciences Research Group of the Neuropsychopharmacology Program, Institut Municipal d’Investigació Mèdica (IMIM-Hospital del Mar), Parc de Recerca Biomèdica de Barcelona, c/ Dr. Aiguader 88/08003 Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| |
Collapse
|
33
|
Burmester JK, Sedova M, Shapero MH, Mansfield E. DMET microarray technology for pharmacogenomics-based personalized medicine. Methods Mol Biol 2010; 632:99-124. [PMID: 20217574 DOI: 10.1007/978-1-60761-663-4_7] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Human genome sequence variation in the form of single nucleotide polymorphisms (SNPs) as well as more complex structural variation such as insertions, duplications, and deletions underlies each individual's response to drugs and thus the likelihood of experiencing an adverse drug reaction. The ongoing challenge of the field of pharmacogenetics is to further understand the relationship between genetic variation and differential drug responses, with the overarching goal being that this will lead to improvements in both the safety and efficacy of drugs. The Affymetrix DMET Plus Premier Pack (DMET stands for Drug Metabolizing Enzymes and Transporters) enables highly multiplexed genotyping of known polymorphisms in Absorption, Distribution, Metabolism, and Elimination (ADME)-related genes on a single array. The DMET Plus Panel interrogates markers in 225 genes that have documented functional significance in phase I and phase II drug metabolism enzymes as well as drug transporters. The power of the DMET Assay has previously been demonstrated with regard to several different drugs including warfarin and clopidogrel. In a research study using an earlier four-color version of the assay, it was demonstrated that warfarin dosing can be influenced by a cytochrome P450 (CYP) 4F2 variant. Additionally, the assay has been used to demonstrate that CYP2C19 variants with decreased enzyme activity led to lower levels of the active clopidogrel metabolite, resulting in a decreased inhibition of platelets and a higher rate of cardiovascular events when compared to noncarriers of the DNA variant. Thus, highly multiplexed SNP genotyping focused on ADME-related polymorphisms should enable research into development of safer drugs with greater efficacy.
Collapse
Affiliation(s)
- James K Burmester
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA.
| | | | | | | |
Collapse
|
34
|
Abstract
While pharmacogenetics - the correlation of genotype and response to medicines - currently has a small but measurable impact on the prescribing practice of clinicians, the advent of the ;personal genome' is likely to change this significantly. Advances in high-throughput technologies aimed at characterizing human genetic variation, including chip-based genotyping and next-generation sequencing, are poised to provide a flood of information that will affect both pharmacogenetic discovery and pharmacogenetic application in clinical practice. In order for this flood of information to not overwhelm both researchers and clinicians alike, a variety of new and expanded information management tools will be needed, including electronic medical records, bioinformatic algorithms for analyzing sequence data, information management systems for storing, retrieving and interpreting whole-genome sequence data, and pharmacogenetic decision tools for prescribers.
Collapse
Affiliation(s)
- Michael J Wagner
- Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-27361, USA
| |
Collapse
|
35
|
Varenhorst C, James S, Erlinge D, Brandt JT, Braun OO, Man M, Siegbahn A, Walker J, Wallentin L, Winters KJ, Close SL. Genetic variation of CYP2C19 affects both pharmacokinetic and pharmacodynamic responses to clopidogrel but not prasugrel in aspirin-treated patients with coronary artery disease. Eur Heart J 2009; 30:1744-52. [PMID: 19429918 PMCID: PMC2709885 DOI: 10.1093/eurheartj/ehp157] [Citation(s) in RCA: 196] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
AIMS The metabolic pathways leading to the formation of prasugrel and clopidogrel active metabolites differ. We hypothesized that decreased CYP2C19 activity affects the pharmacokinetic and pharmacodynamic response to clopidogrel but not prasugrel. METHODS AND RESULTS Ninety-eight patients with coronary artery disease (CAD) taking either clopidogrel 600 mg loading dose (LD)/75 mg maintenance dose (MD) or prasugrel 60 mg LD/10 mg MD were genotyped for variation in six CYP genes. Based on CYP genotype, patients were segregated into two groups: normal function (extensive) metabolizers (EM) and reduced function metabolizers (RM). Plasma active metabolite concentrations were measured at 30 min, 1, 2, 4, and 6 h post-LD and during the MD period on Day 2, Day 14, and Day 29 at 30 min, 1, 2, and 4 h. Vasodilator-stimulated phosphoprotein (VASP) and VerifyNow P2Y12 were measured predose, 2, and 24 +/- 4 h post-LD and predose during the MD period on Day 14 +/- 3 and Day 29 +/- 3. For clopidogrel, active metabolite exposure was significantly lower (P = 0.0015) and VASP platelet reactivity index (PRI, %) and VerifyNow P2Y(12) reaction unit (PRU) values were significantly higher (P < 0.05) in the CYP2C19 RM compared with the EM group. For prasugrel, there was no statistically significant difference in active metabolite exposure or pharmacodynamic response between CYP2C19 EM and RM. Variation in the other five genes demonstrated no statistically significant differences in pharmacokinetic or pharmacodynamic responses. CONCLUSION Variation in the gene encoding CYP2C19 in patients with stable CAD contributes to reduced exposure to clopidogrel's active metabolite and a corresponding reduction in P2Y(12) inhibition, but has no significant influence on the response to prasugrel.
Collapse
Affiliation(s)
- Christoph Varenhorst
- Uppsala Clinical Research Center and Department of Medical Sciences, Cardiology, Uppsala University, Uppsala, Sweden.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Kim KK, Won HH, Cho SS, Park JH, Kim MJ, Kim S, Kim JW. Comparison of identical single nucleotide polymorphisms genotyped by the GeneChip Targeted Genotyping 25K, Affymetrix 500K and Illumina 550K platforms. Genomics 2009; 94:89-93. [PMID: 19394417 DOI: 10.1016/j.ygeno.2009.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 04/16/2009] [Accepted: 04/17/2009] [Indexed: 11/15/2022]
Abstract
Comparisons of targeted genotyping chips to ready-made chips are important because targeted chips are suitable for fine-scale association mapping with a reasonable cost. Genotypes produced by the Affymetrix Targeted Genotyping (TG) 25K, Affymetrix 500K, and Illumina 550K arrays for regions on chromosomes 2 and 7 of 90 individuals were assessed to investigate genotype accordance between the platforms. The common SNPs in TG the Affymetrix and Illumina arrays showed similar genotype accordance. The consistency rate of the Illumina array to consensus genotypes, i.e., identically called by more than two platforms, was the highest, and that of the Affymetrix array was the lowest. The TG array data showed high accordance and reasonable consistency between platforms.
Collapse
Affiliation(s)
- Ka-Kyung Kim
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, South Korea.
| | | | | | | | | | | | | |
Collapse
|
37
|
Burczynski M. Pharmacogenomic approaches in clinical studies to identify biomarkers of safety and efficacy. Toxicol Lett 2009; 186:18-21. [DOI: 10.1016/j.toxlet.2008.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 09/29/2008] [Accepted: 10/02/2008] [Indexed: 01/19/2023]
|
38
|
Mega JL, Close SL, Wiviott SD, Shen L, Hockett RD, Brandt JT, Walker JR, Antman EM, Macias W, Braunwald E, Sabatine MS. Cytochrome p-450 polymorphisms and response to clopidogrel. N Engl J Med 2009; 360:354-62. [PMID: 19106084 DOI: 10.1056/nejmoa0809171] [Citation(s) in RCA: 1720] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Clopidogrel requires transformation into an active metabolite by cytochrome P-450 (CYP) enzymes for its antiplatelet effect. The genes encoding CYP enzymes are polymorphic, with common alleles conferring reduced function. METHODS We tested the association between functional genetic variants in CYP genes, plasma concentrations of active drug metabolite, and platelet inhibition in response to clopidogrel in 162 healthy subjects. We then examined the association between these genetic variants and cardiovascular outcomes in a separate cohort of 1477 subjects with acute coronary syndromes who were treated with clopidogrel in the Trial to Assess Improvement in Therapeutic Outcomes by Optimizing Platelet Inhibition with Prasugrel-Thrombolysis in Myocardial Infarction (TRITON-TIMI) 38. RESULTS In healthy subjects who were treated with clopidogrel, carriers of at least one CYP2C19 reduced-function allele (approximately 30% of the study population) had a relative reduction of 32.4% in plasma exposure to the active metabolite of clopidogrel, as compared with noncarriers (P<0.001). Carriers also had an absolute reduction in maximal platelet aggregation in response to clopidogrel that was 9 percentage points less than that seen in noncarriers (P<0.001). Among clopidogrel-treated subjects in TRITON-TIMI 38, carriers had a relative increase of 53% in the composite primary efficacy outcome of the risk of death from cardiovascular causes, myocardial infarction, or stroke, as compared with noncarriers (12.1% vs. 8.0%; hazard ratio for carriers, 1.53; 95% confidence interval [CI], 1.07 to 2.19; P=0.01) and an increase by a factor of 3 in the risk of stent thrombosis (2.6% vs. 0.8%; hazard ratio, 3.09; 95% CI, 1.19 to 8.00; P=0.02). CONCLUSIONS Among persons treated with clopidogrel, carriers of a reduced-function CYP2C19 allele had significantly lower levels of the active metabolite of clopidogrel, diminished platelet inhibition, and a higher rate of major adverse cardiovascular events, including stent thrombosis, than did noncarriers.
Collapse
Affiliation(s)
- Jessica L Mega
- Thrombolysis in Myocardial Infarction Study Group, Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
Warfarin is an effective, commonly prescribed anticoagulant used to treat and prevent thrombotic events. Because of historically high rates of drug-associated adverse events, warfarin remains underprescribed. Further, interindividual variability in therapeutic dose mandates frequent monitoring until target anticoagulation is achieved. Genetic polymorphisms involved in warfarin metabolism and sensitivity have been implicated in variability of dose. Here, we describe a novel variant that influences warfarin requirements. To identify additional genetic variants that contribute to warfarin requirements, screening of DNA variants in additional genes that code for drug-metabolizing enzymes and drug transport proteins was undertaken using the Affymetrix drug-metabolizing enzymes and transporters panel. A DNA variant (rs2108622; V433M) in cytochrome P450 4F2 (CYP4F2) was associated with warfarin dose in 3 independent white cohorts of patients stabilized on warfarin representing diverse geographic regions in the United States and accounted for a difference in warfarin dose of approximately 1 mg/day between CC and TT subjects. Genetic variation of CYP4F2 was associated with a clinically relevant effect on warfarin requirement.
Collapse
|
40
|
von Ahsen N, Oellerich M. Chip-based genotyping: translation of pharmacogenetic research to clinical practice. Clin Chem 2007; 53:1186-7. [PMID: 17582149 DOI: 10.1373/clinchem.2007.088005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|