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Xu X, Zhang J, Xing H, Han L, Li X, Wu P, Tang J, Jing L, Luo J, Luo J, Liu L. Identification of metabolism-related key genes as potential biomarkers for pathogenesis of immune thrombocytopenia. Sci Rep 2024; 14:9040. [PMID: 38641637 PMCID: PMC11031595 DOI: 10.1038/s41598-024-59493-7] [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] [Received: 01/03/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024] Open
Abstract
Immune thrombocytopenia (ITP), an acquired autoimmune disease, is characterized by immune-mediated platelet destruction. A biomarker is a biological entity that contributes to disease pathogenesis and reflects disease activity. Metabolic alterations are reported to be associated with the occurrence of various diseases. As metabolic biomarkers for ITP have not been identified. This study aimed to identify metabolism-related differentially expressed genes as potential biomarkers for pathogenesis of ITP using bioinformatic analyses.The microarray expression data of the peripheral blood mononuclear cells were downloaded from the Gene Expression Omnibus database (GSE112278 download link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112278 ). Key module genes were intersected with metabolism-related genes to obtain the metabolism-related key candidate genes. The hub genes were screened based on the degree function in the coytoscape sofware. The key ITP-related genes were subjected to functional enrichment analysis. Immune infiltration analysis was performed using a single-sample gene set enrichment analysis algorithm to evaluate the differential infiltration levels of immune cell types between ITP patient and control. Molecular subtypes were identified based on the expression of hub genes. The expression of hub genes in the ITP patients was validated using quantitative real-time polymerase chain reaction analysis. This study identified five hub genes (ADH4, CYP7A1, CYP1A2, CYP8B1, and NR1H4), which were be associated with the pathogenesis of ITP, and two molecular subtypes of ITP. Among these hub genes, CYP7A1 and CYP8B1 involved in cholesterol metabolism,were further verified in clinical samples.
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Affiliation(s)
- Xiangmei Xu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
- Department of Oncology and Hematology, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Jiamin Zhang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Hongyun Xing
- Department of Hematology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Liying Han
- Department of Hematology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Xiaoming Li
- Department of Hematology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Pengqiang Wu
- Department of Hematology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Jirui Tang
- Department of Hematology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Li Jing
- Department of Hematology, The Affiliated Hospital, Southwest Medical University, Luzhou, China
| | - Jie Luo
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Jing Luo
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Lin Liu
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China.
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2
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Kennedy A, Ma G, Manshaei R, Jobling RK, Kim RH, Lewis T, Cohn I. A call for increased inclusivity and global representation in pharmacogenetic testing. NPJ Genom Med 2024; 9:13. [PMID: 38388691 PMCID: PMC10883987 DOI: 10.1038/s41525-024-00403-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Commercial pharmacogenetic testing panels capture a fraction of the genetic variation underlying medication metabolism and predisposition to adverse reactions. In this study we compared variation in six pharmacogenes detected by whole genome sequencing (WGS) to a targeted commercial panel in a cohort of 308 individuals with family history of pediatric heart disease. In 1% of the cohort, WGS identified rare variants that altered the interpretation of metabolizer status and would thus prevent potential errors in gene-based dosing.
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Affiliation(s)
- April Kennedy
- Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Gabriel Ma
- University of Toronto, Toronto, ON, Canada
| | - Roozbeh Manshaei
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rebekah K Jobling
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Raymond H Kim
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tamorah Lewis
- Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Neonatology, Department of Paediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, ON, Canada.
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON, Canada.
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3
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Booyse RP, Twesigomwe D, Hazelhurst S. Characterization of CYP2C19 pharmacogenetic variation in African populations and comparison with other global populations. Pharmacogenomics 2023; 24:845-857. [PMID: 37929326 PMCID: PMC10694788 DOI: 10.2217/pgs-2023-0166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023] Open
Abstract
Background: CYP2C19 is important in the metabolism of clopidogrel and several antidepressants. This study aimed to characterize the distribution of CYP2C19 star alleles (haplotypes) across diverse African populations compared with global populations. Methods: CYP2C19 star alleles and diplotypes were called from high coverage genomes using the StellarPGx pipeline. Results: CYP2C19*1 (51%), *2 (17%) and *17 (22%) were the most common star alleles across African populations in this study. It was observed that 3% of African participants had potentially novel CYP2C19 haplotypes. Conclusion: This study supports the necessity for CYP2C19 pharmacogenetic testing in African and global clinical settings, as well as the importance of comprehensive star allele characterization in the African context.
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Affiliation(s)
- Ross P Booyse
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - David Twesigomwe
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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4
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Giorgetti A, Amurri S, Fazio G, Bini C, Anniballi L, Pirani F, Pelletti G, Pelotti S. The Evaluation of CYP2D6, CYP2C9, CYP2C19, and CYP2B6 Phenoconversion in Post-Mortem Casework: The Challenge of Forensic Toxicogenetics. Metabolites 2023; 13:metabo13050661. [PMID: 37233702 DOI: 10.3390/metabo13050661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/27/2023] Open
Abstract
In toxicogenetics, an integrative approach including the prediction of phenotype based on post-mortem genotyping of drug-metabolising enzymes might help explain the cause of death (CoD) and manner of death (MoD). The use of concomitant drugs, however, might lead to phenoconversion, a mismatch between the phenotype based on the genotype and the metabolic profile actually observed after phenoconversion. The aim of our study was to evaluate the phenoconversion of CYP2D6, CYP2C9, CYP2C19, and CYP2B6 drug-metabolising enzymes in a series of autopsy cases tested positive for drugs that are substrates, inducers, or inhibitors of these enzymes. Our results showed a high rate of phenoconversion for all enzymes and a statistically significant higher frequency of poor and intermediate metabolisers for CYP2D6, CYP2C9, and CYP2C19 after phenoconversion. No association was found between phenotypes and CoD or MoD, suggesting that, although phenoconversion might be useful for a forensic toxicogenetics approach, more research is needed to overcome the challenges arising from the post-mortem setting.
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Affiliation(s)
- Arianna Giorgetti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Sara Amurri
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Giulia Fazio
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Carla Bini
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Laura Anniballi
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Filippo Pirani
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Guido Pelletti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Susi Pelotti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
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Vu NP, Nguyen TD, Nguyen BH, Nguyen DT, Nong HV, Nguyen HH. Copy number variations of cytochrome P450 genes in Kinh Vietnamese. ASIAN BIOMED 2023; 17:84-92. [PMID: 37719322 PMCID: PMC10505059 DOI: 10.2478/abm-2023-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Background The cytochrome P450 (CYP450) family is well known as a major group of drug metabolizing enzymes. The polymorphism of CYP450 genes is the main factor having an impact on the interindividual difference in drug response, including drug efficacy and drug safety. The single nucleotide polymorphism (SNPs) of Vietnamese Kinh has been widely studied, but information about the copy number variations (CNVs) of other CYP450 genes is still unknown. Objective To identify the CNV variability of CYP450 in 154 healthy unrelated Kinh Vietnamese, except eCYP2D6, which was previously reported. Methods Multiplex Ligation-Dependent Probe Amplification (MLPA) was applied for determination of copy number of 10 CYP450 genes. Later, PCR or quantitative PCR (qPCR) was used to confirm the detected CNVs in randomly chosen subjects. Results Of the 154 subjects, along with CYP2D6, 4 other CYP450 genes showed CNVs including duplications (CYP1B1), deletions (CYP2A6 and CYP2C9), and both duplications and deletions (CYP2E1). Among these, CYP2A6 exhibited the greatest frequency of CNVs compared with other CYP450, in which CYP2A6Del accounted for 11%. Meanwhile, allele CYP2E1Del showed the lowest frequency with only 0.3%. Conclusions The present study provides new insight into CYP450 CNVs in the Kinh Vietnamese cohort. Our data have contributed to genetic profiling of CYP450 CNVs in Vietnam, which would be helpful for facilitating implementation of pharmacogenetics in drug dosing adjustment in Vietnam.
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Affiliation(s)
- Nhung Phuong Vu
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
| | - Ton Dang Nguyen
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
| | - Binh Huy Nguyen
- Department of Physiology, Hanoi Medical University, Dong Da, Hanoi100000, Vietnam
| | - Duong Thuy Nguyen
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
| | - Hai Van Nong
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
| | - Ha Hai Nguyen
- Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
- Genome Analysis Laboratory, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi100000, Vietnam
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6
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Lee CR, Luzum JA, Sangkuhl K, Gammal RS, Sabatine MS, Stein CM, Kisor DF, Limdi NA, Lee YM, Scott SA, Hulot JS, Roden DM, Gaedigk A, Caudle KE, Klein TE, Johnson JA, Shuldiner AR. Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2C19 Genotype and Clopidogrel Therapy: 2022 Update. Clin Pharmacol Ther 2022; 112:959-967. [PMID: 35034351 PMCID: PMC9287492 DOI: 10.1002/cpt.2526] [Citation(s) in RCA: 154] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/22/2021] [Indexed: 11/06/2022]
Abstract
CYP2C19 catalyzes the bioactivation of the antiplatelet prodrug clopidogrel, and CYP2C19 genotype impacts clopidogrel active metabolite formation. CYP2C19 intermediate and poor metabolizers who receive clopidogrel experience reduced platelet inhibition and increased risk for major adverse cardiovascular and cerebrovascular events. This guideline is an update to the 2013 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for the use of clopidogrel based on CYP2C19 genotype and includes expanded indications for CYP2C19 genotype-guided antiplatelet therapy, increased strength of recommendation for CYP2C19 intermediate metabolizers, updated CYP2C19 genotype to phenotype translation, and evidence from an expanded literature review (updates at www.cpicpgx.org).
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Affiliation(s)
- Craig R. Lee
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Jasmine A. Luzum
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Roseann S. Gammal
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Marc S. Sabatine
- Thrombolysis in Myocardial Infarction Study Group, Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - C. Michael Stein
- Division of Clinical Pharmacology, Departments of Medicine and Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David F. Kisor
- Department of Pharmaceutical Sciences, Manchester University, Fort Wayne, IN, USA
| | - Nita A Limdi
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yee Ming Lee
- Department of Clinical Pharmacy, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
| | - Stuart A. Scott
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, CA, USA
| | - Jean-Sébastien Hulot
- Université de Paris, CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, F-75015, Paris, France
| | - Dan M. Roden
- Departments of Medicine and Pharmacology, Office of Personalized Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Kelly E. Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Alan R. Shuldiner
- Department of Medicine, and Program for Genomic and Personalized Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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7
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Kirac D, Yaman AE, Doran T, Mihmanli M, Keles EC. COX-1, COX-2 and CYP2C19 variations may be related to cardiovascular events due to acetylsalicylic acid resistance. Mol Biol Rep 2022; 49:3007-3014. [PMID: 35000048 DOI: 10.1007/s11033-022-07124-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/04/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND In some stent implanted patients, cardiovascular events (CE) may occur. Acetylsalicylic acid (ASA) is routinely administered to these patients in order to prevent the occurrence of CE. CE may be related to gene variations which cause ASA resistance (AR). Therefore, it was aimed to investigate the relationship between COX-1, COX-2, CYP2C9 and CYP2C19 variations with CE due to AR. MATERIALS AND RESULTS Seventy-four stent implanted patients, using 100 mg of ASA per day during five years were enrolled into the study. Following stent implantation, thirty-eight patients who had a CE within five years due to AR and 36 patients without CE were enrolled in patient and control group, respectively. AR was confirmed by platelet aggregation testing. After DNA isolation from blood; COX-1, COX-2, CYP2C19 and CYP2C9 variations were investigated with real-time polymerase chain reaction. At the end of this study, heterozygous genotype of COX-1 was found statistically high in patients whereas heterozygous genotype of CYP2C19*17 was found statistically high in controls. The presence of C and G allele in COX-1 and COX-2 were found statistically high in patients, respectively. The presence of T allele in CYP2C19*17 was found statistically high in controls. Heterozygous genotype of COX-1 variation was found statistically high in patients who have AR. Additionally heterozygous genotype of CYP2C19*17 was found statistically high in patients who have low thrombosis risk. CONCLUSIONS COX-1 and COX-2 gene mutations may increase the risk of CE due to AR whereas CYP2C19*17 may have a protective effect in this process.
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Affiliation(s)
- Deniz Kirac
- Department of Medical Biology, Faculty of Medicine, Yeditepe University, Istanbul, Turkey.
| | - Aysun Erdem Yaman
- Department of Cardiology, Istanbul Dr. Siyami Ersek Thoracic and Cardiovascular Surgery Training and Research Hospital, Istanbul, Turkey
| | - Tansu Doran
- Department of Medical Biology, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Mujgan Mihmanli
- Department of Biochemistry, Istanbul Dr. Siyami Ersek Thoracic and Cardiovascular Surgery Training and Research Hospital, Istanbul, Turkey
| | - Elif Cigdem Keles
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
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Carvalho Henriques B, Buchner A, Hu X, Wang Y, Yavorskyy V, Wallace K, Dong R, Martens K, Carr MS, Behroozi Asl B, Hague J, Sivapalan S, Maier W, Dernovsek MZ, Henigsberg N, Hauser J, Souery D, Cattaneo A, Mors O, Rietschel M, Pfeffer G, Hume S, Aitchison KJ. Methodology for clinical genotyping of CYP2D6 and CYP2C19. Transl Psychiatry 2021; 11:596. [PMID: 34811360 PMCID: PMC8608805 DOI: 10.1038/s41398-021-01717-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 10/28/2021] [Indexed: 01/10/2023] Open
Abstract
Many antidepressants, atomoxetine, and several antipsychotics are metabolized by the cytochrome P450 enzymes CYP2D6 and CYP2C19, and guidelines for prescribers based on genetic variants exist. Although some laboratories offer such testing, there is no consensus regarding validated methodology for clinical genotyping of CYP2D6 and CYP2C19. The aim of this paper was to cross-validate multiple technologies for genotyping CYP2D6 and CYP2C19 against each other, and to contribute to feasibility for clinical implementation by providing an enhanced range of assay options, customizable automated translation of data into haplotypes, and a workflow algorithm. AmpliChip CYP450 and some TaqMan single nucleotide variant (SNV) and copy number variant (CNV) data in the Genome-based therapeutic drugs for depression (GENDEP) study were used to select 95 samples (out of 853) to represent as broad a range of CYP2D6 and CYP2C19 genotypes as possible. These 95 included a larger range of CYP2D6 hybrid configurations than have previously been reported using inter-technology data. Genotyping techniques employed were: further TaqMan CNV and SNV assays, xTAGv3 Luminex CYP2D6 and CYP2C19, PharmacoScan, the Ion AmpliSeq Pharmacogenomics Panel, and, for samples with CYP2D6 hybrid configurations, long-range polymerase chain reactions (L-PCRs) with Sanger sequencing and Luminex. Agena MassARRAY was also used for CYP2C19. This study has led to the development of a broader range of TaqMan SNV assays, haplotype phasing methodology with TaqMan adaptable for other technologies, a multiplex genotyping method for efficient identification of some hybrid haplotypes, a customizable automated translation of SNV and CNV data into haplotypes, and a clinical workflow algorithm.
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Affiliation(s)
| | - Avery Buchner
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XNeuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Xiuying Hu
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada
| | - Yabing Wang
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada
| | - Vasyl Yavorskyy
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Keanna Wallace
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada
| | - Rachael Dong
- grid.17089.370000 0001 2190 316XNeuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Kristina Martens
- grid.22072.350000 0004 1936 7697Department of Clinical Neurosciences, Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Michael S. Carr
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XDepartment of Pharmacology, University of Alberta, Edmonton, Canada
| | - Bahareh Behroozi Asl
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XNeuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Joshua Hague
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XDepartment of Medical Genetics, University of Alberta, Edmonton, Canada
| | - Sudhakar Sivapalan
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada
| | - Wolfgang Maier
- grid.10388.320000 0001 2240 3300Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | | | - Neven Henigsberg
- grid.4808.40000 0001 0657 4636Croatian Institute for Brain Research, Centre for Excellence for Basic, Clinical and Translational Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Joanna Hauser
- grid.22254.330000 0001 2205 0971Departnent of Psychiatry, Poznan University of Medical Sciences, Poznań, Poland
| | - Daniel Souery
- grid.4989.c0000 0001 2348 0746Laboratoire de Psychologie Médicale, Université Libre de Bruxelles and Psy Pluriel, Centre Européen de Psychologie Médicale, Brussels, Belgium
| | - Annamaria Cattaneo
- grid.419422.8Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy ,grid.4708.b0000 0004 1757 2822Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, 20133 Milan, Italy
| | - Ole Mors
- grid.154185.c0000 0004 0512 597XPsychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Marcella Rietschel
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
| | - Gerald Pfeffer
- grid.22072.350000 0004 1936 7697Department of Clinical Neurosciences, Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, Canada ,grid.22072.350000 0004 1936 7697Alberta Child Health Research Institute & Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Stacey Hume
- grid.17089.370000 0001 2190 316XDepartment of Medical Genetics, University of Alberta, Edmonton, Canada ,Alberta Precision Laboratories, Edmonton, Canada
| | - Katherine J. Aitchison
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XNeuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XDepartment of Medical Genetics, University of Alberta, Edmonton, Canada ,grid.413574.00000 0001 0693 8815Alberta Health Services, Edmonton, Canada ,grid.13097.3c0000 0001 2322 6764King’s College London, London, UK
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Sangkuhl K, Claudio-Campos K, Cavallari LH, Agundez JAG, Whirl-Carrillo M, Duconge J, Del Tredici AL, Wadelius M, Rodrigues Botton M, Woodahl EL, Scott SA, Klein TE, Pratt VM, Daly AK, Gaedigk A. PharmVar GeneFocus: CYP2C9. Clin Pharmacol Ther 2021; 110:662-676. [PMID: 34109627 PMCID: PMC8607432 DOI: 10.1002/cpt.2333] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C9 gene. Genetic variation within the CYP2C9 gene locus impacts the metabolism or bioactivation of many clinically important drugs, including nonsteroidal anti-inflammatory drugs, phenytoin, antidiabetic agents, and angiotensin receptor blockers. Variable CYP2C9 activity is of particular importance regarding efficacy and safety of warfarin and siponimod as indicated in their package inserts. This GeneFocus provides a comprehensive overview and summary of CYP2C9 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium.
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Affiliation(s)
- Katrin Sangkuhl
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Karla Claudio-Campos
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Jose A G Agundez
- University Institute of Molecular Pathology Biomarkers, University of Extremadura, Asthma, Adverse Drug Reactions and Allergy (ARADyAL) Institute de Salud Carlos III, Cáceres, Spain
| | - Michelle Whirl-Carrillo
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Jorge Duconge
- School of Pharmacy, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, USA
| | | | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, California, USA
- Stanford Health Care Clinical Genomics Laboratory, Palo Alto, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ann K Daly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri - Kansas City, Kansas City, Missouri, USA
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10
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Singh R, Cohen ASA, Poulton C, Hjortshøj TD, Akahira-Azuma M, Mendiratta G, Khan WA, Azmanov DN, Woodward KJ, Kirchhoff M, Shi L, Edelmann L, Baynam G, Scott SA, Jabs EW. Deletion of ERF and CIC causes abnormal skull morphology and global developmental delay. Cold Spring Harb Mol Case Stud 2021; 7:a005991. [PMID: 34117072 PMCID: PMC8208047 DOI: 10.1101/mcs.a005991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
The ETS2 repressor factor (ERF) is a transcription factor in the RAS-MEK-ERK signal transduction cascade that regulates cell proliferation and differentiation, and pathogenic sequence variants in the ERF gene cause variable craniosynostosis inherited in an autosomal dominant pattern. The reported ERF variants are largely loss-of-function, implying haploinsufficiency as a primary disease mechanism; however, ERF gene deletions have not been reported previously. Here we describe three probands with macrocephaly, craniofacial dysmorphology, and global developmental delay. Clinical genetic testing for fragile X and other relevant sequencing panels were negative; however, chromosomal microarray identified heterozygous deletions (63.7-583.2 kb) on Chromosome 19q13.2 in each proband that together included five genes associated with Mendelian diseases (ATP1A3, ERF, CIC, MEGF8, and LIPE). Parental testing indicated that the aberrations were apparently de novo in two of the probands and were inherited in the one proband with the smallest deletion. Deletion of ERF is consistent with the reported loss-of-function ERF variants, prompting clinical copy-number-variant classifications of likely pathogenic. Moreover, the recent characterization of heterozygous loss-of-function CIC sequence variants as a cause of intellectual disability and neurodevelopmental disorders inherited in an autosomal dominant pattern is also consistent with the developmental delays and intellectual disabilities identified among the two probands with CIC deletions. Taken together, this case series adds to the previously reported patients with ERF and/or CIC sequence variants and supports haploinsufficiency of both genes as a mechanism for a variable syndromic cranial phenotype with developmental delays and intellectual disability inherited in an autosomal dominant pattern.
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Affiliation(s)
- Ram Singh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Sema4, Stamford, Connecticut 06902, USA
| | - Ana S A Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Sema4, Stamford, Connecticut 06902, USA
| | - Cathryn Poulton
- Genetic Service of Western Australia, King Edward Memorial Hospital, Perth, Western Australia 6008, Australia
| | - Tina Duelund Hjortshøj
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Moe Akahira-Azuma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Geetu Mendiratta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Sema4, Stamford, Connecticut 06902, USA
| | - Wahab A Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Sema4, Stamford, Connecticut 06902, USA
| | - Dimitar N Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Pathology and Laboratory Medicine, Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Karen J Woodward
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Pathology and Laboratory Medicine, Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Maria Kirchhoff
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Sema4, Stamford, Connecticut 06902, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Sema4, Stamford, Connecticut 06902, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia 6008, Australia
- Faculty of Health and Medical Sciences, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia 6008, Australia
- Faculty of Medicine, University of Notre Dame, Australia, Perth, Western Australia 6160, Australia
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Sema4, Stamford, Connecticut 06902, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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11
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Botton MR, Whirl-Carrillo M, Del Tredici AL, Sangkuhl K, Cavallari LH, Agúndez JAG, Duconge J, Lee MTM, Woodahl EL, Claudio-Campos K, Daly AK, Klein TE, Pratt VM, Scott SA, Gaedigk A. PharmVar GeneFocus: CYP2C19. Clin Pharmacol Ther 2021; 109:352-366. [PMID: 32602114 PMCID: PMC7769975 DOI: 10.1002/cpt.1973] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the metabolism of many drugs and has been associated with both efficacy and safety issues for several commonly prescribed medications. This GeneFocus provides a comprehensive overview and summary of CYP2C19 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | | | | | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - José A G Agúndez
- UNEx, ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Jorge Duconge
- School of Pharmacy, University of Puerto Rico, San Juan, Puerto Rico
| | | | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | | | - Ann K Daly
- Newcastle University, Newcastle upon Tyne, UK
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy, Kansas City, Missouri, USA
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12
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Chernikova NA, Kamynina LL, Ametov AS, Sychev DA, Grishina EA, Ryzhikova KA. [The pharmacogenetics of hypoglycemia and the glycemic variability at the patients ith type 2 diabetes mellitus]. TERAPEVT ARKH 2020; 92:54-62. [PMID: 33346480 DOI: 10.26442/00403660.2020.10.000530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 11/22/2022]
Abstract
AIM To investigate the link between the hypoglycemia (registrated accurately by the professional Continuous Glucose Monitoring CGM; severe hypoglycemia at home) and the hetero-/homozygote carriage of single nucleotide polymorphisms (SNP) of cytochrome systems geneCYP2C9(rs1799853CYP2C9*2 иrs1057910CYP2C9*3) at the patients with Type 2 Diabetes Mellitus (T2DM) used sulphonylurea (SU). MATERIALS AND METHODS In Study Case-Control 120 T2DM-SU-patients genotyped by SNPs of geneCYP2C9(using PCR-RT) had been done the professional CGM (System iPro2, Medtronic) recorded Time in Range of Hypoglycemia (TIR-HYPO), level of Minimal CGM-hypoglycemia (MinGl) and standard CGM-parameters of Glycemic Variability. Severe hypoglycemia at home was recorded from visit to visit. The odds ratio (OR) of metabolic disturbances had been assessed for carriage SNPs in comparison with wide alleles. RESULTS The Study established that carriage of SNPsrs1799853andrs1057910geneCYP2C9at T2DM-SU-patients associated with rising of Glycemic Variability and frequency of CGM-hypoglycemia (MinGl decreasing, increasing of TIR-HYPO and number of Glycemia Excursion 4 mmol/L/h), as well as increasing severe hypoglycemia at home (p0.05). Thus, OR at the carriage ofrs1799853andrs1057910respectively equaled: for CGM-hypoglycemia 7.78 (3.0220.01) and 5.80 (0.23145.87); number of Glycemia Excursion 4 mmol/L/h 5.76 (2.2914.43) and 4.44 (1.4313.76); MinGl3.9 mmol/L 4.39 (1.7910.75) and 6.26 (1.8421.30); CV40% (vs30%) 3.63 (1.0412.62) and 15.22 (0.59393.94);p0.05. CONCLUSION At the real clinical practice the assessment of carriage of SNPs of geneCYP2C9before inclusion of SU to glucose-lowering scheme of T2DM-therapy it necessary to carry out for the detecting patients with a higher risk of hypoglycemia and rising of Glycemic Variability.
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Affiliation(s)
- N A Chernikova
- Russian Medical Academy of Continuous Professional Education
| | - L L Kamynina
- Russian Medical Academy of Continuous Professional Education
| | - A S Ametov
- Russian Medical Academy of Continuous Professional Education
| | - D A Sychev
- Russian Medical Academy of Continuous Professional Education
| | - E A Grishina
- Russian Medical Academy of Continuous Professional Education
| | - K A Ryzhikova
- Russian Medical Academy of Continuous Professional Education
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13
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Lima JJ, Thomas CD, Barbarino J, Desta Z, Van Driest SL, El Rouby N, Johnson JA, Cavallari LH, Shakhnovich V, Thacker DL, Scott SA, Schwab M, Uppugunduri CRS, Formea CM, Franciosi JP, Sangkuhl K, Gaedigk A, Klein TE, Gammal RS, Furuta T. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2C19 and Proton Pump Inhibitor Dosing. Clin Pharmacol Ther 2020; 109:1417-1423. [PMID: 32770672 DOI: 10.1002/cpt.2015] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/15/2020] [Indexed: 12/27/2022]
Abstract
Proton pump inhibitors (PPIs) are widely used for acid suppression in the treatment and prevention of many conditions, including gastroesophageal reflux disease, gastric and duodenal ulcers, erosive esophagitis, Helicobacter pylori infection, and pathological hypersecretory conditions. Most PPIs are metabolized primarily by cytochrome P450 2C19 (CYP2C19) into inactive metabolites, and CYP2C19 genotype has been linked to PPI exposure, efficacy, and adverse effects. We summarize the evidence from the literature and provide therapeutic recommendations for PPI prescribing based on CYP2C19 genotype (updates at www.cpicpgx.org). The potential benefits of using CYP2C19 genotype data to guide PPI therapy include (i) identifying patients with genotypes predictive of lower plasma exposure and prescribing them a higher dose that will increase the likelihood of efficacy, and (ii) identifying patients on chronic therapy with genotypes predictive of higher plasma exposure and prescribing them a decreased dose to minimize the risk of toxicity that is associated with long-term PPI use, particularly at higher plasma concentrations.
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Affiliation(s)
- John J Lima
- Center for Pharmacogenomics and Translational Research, Nemours Children's Health, Jacksonville, Florida, USA
| | - Cameron D Thomas
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Julia Barbarino
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Zeruesenay Desta
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sara L Van Driest
- Departments of Pediatrics and Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Nihal El Rouby
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Division of Pharmacy Practice & Administrative Sciences, University of Cincinnati James Winkle College of Pharmacy, Cincinnati, Ohio, USA
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, and Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Valentina Shakhnovich
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, Missouri, USA.,Division of Gastroenterology, Hepatology, and Nutrition, Children's Mercy Kansas City, Kansas City, Missouri, USA.,Center for Children's Healthy Lifestyles & Nutrition, Kansas City, Missouri, USA
| | - David L Thacker
- Department of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Translational Software, Bellevue, Washington, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital, Tuebingen, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Chakradhara Rao S Uppugunduri
- CANSEARCH Research Laboratory, Department of Pediatrics, Gynecology, and Obstetrics, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Oncology-Hematology Unit, Department of Pediatrics, Gynecology, and Obstetrics, Geneva University Hospital, Geneva, Switzerland
| | - Christine M Formea
- Department of Pharmacy Services and Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - James P Franciosi
- Division of Gastroenterology, Hepatology, and Nutrition, Nemours Children's Hospital, Orlando, Florida, USA.,Department of Pediatrics, University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Roseann S Gammal
- Department of Pharmacy Practice, MCPHS University School of Pharmacy, Boston, Massachusetts, USA.,Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Takahisa Furuta
- Center for Clinical Research, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
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14
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Scott SA, Scott ER, Seki Y, Chen AJ, Wallsten R, Owusu Obeng A, Botton MR, Cody N, Shi H, Zhao G, Brake P, Nicoletti P, Yang Y, Delio M, Shi L, Kornreich R, Schadt EE, Edelmann L. Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi-Ethnic Allele and Copy Number Variant Detection. Clin Transl Sci 2020; 14:204-213. [PMID: 32931151 PMCID: PMC7877843 DOI: 10.1111/cts.12844] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022] Open
Abstract
To develop a novel pharmacogenetic genotyping panel, a multidisciplinary team evaluated available evidence and selected 29 genes implicated in interindividual drug response variability, including 130 sequence variants and additional copy number variants (CNVs). Of the 29 genes, 11 had guidelines published by the Clinical Pharmacogenetics Implementation Consortium. Targeted genotyping and CNV interrogation were accomplished by multiplex single‐base extension using the MassARRAY platform (Agena Biosciences) and multiplex ligation‐dependent probe amplification (MRC Holland), respectively. Analytical validation of the panel was accomplished by a strategic combination of > 500 independent tests performed on 170 unique reference material DNA samples, which included sequence variant and CNV accuracy, reproducibility, and specimen (blood, saliva, and buccal swab) controls. Among the accuracy controls were 32 samples from the 1000 Genomes Project that were selected based on their enrichment of sequence variants included in the pharmacogenetic panel (VarCover.org). Coupled with publicly available samples from the Genetic Testing Reference Materials Coordination Program (GeT‐RM), accuracy validation material was available for the majority (77%) of interrogated sequence variants (100% with average allele frequencies > 0.1%), as well as additional structural alleles with unique copy number signatures (e.g., CYP2D6*5, *13, *36, *68; CYP2B6*29; and CYP2C19*36). Accuracy and reproducibility for both genotyping and copy number were > 99.9%, indicating that the optimized panel platforms were precise and robust. Importantly, multi‐ethnic allele frequencies of the interrogated variants indicate that the vast majority of the general population carries at least one of these clinically relevant pharmacogenetic variants, supporting the implementation of this panel for pharmacogenetic research and/or clinical implementation programs.
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Affiliation(s)
- Stuart A Scott
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erick R Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Aniwaa Owusu Obeng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariana R Botton
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Neal Cody
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Paola Nicoletti
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Lisong Shi
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruth Kornreich
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Edelmann
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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