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Wang WY, Lin L, Boone EC, Stevens J, Gaedigk A. CYP2D6 copy number determination using digital PCR. Front Pharmacol 2024; 15:1429286. [PMID: 39206265 PMCID: PMC11349684 DOI: 10.3389/fphar.2024.1429286] [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] [Received: 05/07/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Background CYP2D6 testing is increasingly used to guide drug therapy and thus, reliable methods are needed to test this complex and polymorphic gene locus. A particular challenge arises from the detection and interpretation of structural variants (SVs) including gene deletions, duplications, and hybrids with the CYP2D7 pseudogene. This study validated the Absolute Q™ platform for digital PCR-based CYP2D6 copy number variation (CNV) determination by comparing results to those obtained with a previously established method using the QX200 platform. In addition, protocols for streamlining CYP2D6 CNV testing were established and validated including the "One-pot" single-step restriction enzyme digestion and a multiplex assay simultaneously targeting the CYP2D6 5'UTR, intron 6, and exon 9 regions. Methods Genomic DNA (gDNA) samples from Coriell (n = 13) and from blood, saliva, and liver tissue (n = 17) representing 0-6 copies were tested on the Absolute Q and QX200 platforms. Custom TaqMan™ copy number (CN) assays targeting CYP2D6 the 5'UTR, intron 6, and exon 9 regions and a reference gene assay (TERT or RNaseP) were combined for multiplexing by optical channel. In addition, two digestion methods (One-pot digestion and traditional) were assessed. Inconclusive CN values on the Absolute Q were resolved using an alternate reference gene and/or diluting gDNA. Results Overall, results between the two platforms and digestions methods were consistent. The "One-pot" digestion method and optically multiplexing up to three CYP2D6 regions yielded consistent result across DNA sample types and diverse SVs, reliably detecting up to 6 gene copies. Rare variation in reference genes were found to interfere with results and interpretation, which were resolved by using a different reference. Conclusion The Absolute Q produced accurate and reliable CYP2D6 copy number results allowing for a streamlined and economical protocol using One-pot digestion and multiplexing three target regions. Protocols are currently being expanded to other pharmacogenes presenting with SVs/CNVs.
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Affiliation(s)
- Wendy Y. Wang
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy Research Institute (CMRI), Kansas City, MO, United States
| | - Lancy Lin
- Genetic Sciences Division, Thermo Fisher Scientific, Waltham, CA, United States
| | - Erin C. Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy Research Institute (CMRI), Kansas City, MO, United States
| | - Junko Stevens
- Genetic Sciences Division, Thermo Fisher Scientific, Waltham, CA, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy Research Institute (CMRI), Kansas City, MO, United States
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
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Duarte JD, Thomas CD, Lee CR, Huddart R, Agundez JAG, Baye JF, Gaedigk A, Klein TE, Lanfear DE, Monte AA, Nagy M, Schwab M, Stein CM, Uppugunduri CRS, van Schaik RHN, Donnelly RS, Caudle KE, Luzum JA. Clinical Pharmacogenetics Implementation Consortium Guideline (CPIC) for CYP2D6, ADRB1, ADRB2, ADRA2C, GRK4, and GRK5 Genotypes and Beta-Blocker Therapy. Clin Pharmacol Ther 2024. [PMID: 38951961 DOI: 10.1002/cpt.3351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/30/2024] [Indexed: 07/03/2024]
Abstract
Beta-blockers are widely used medications for a variety of indications, including heart failure, myocardial infarction, cardiac arrhythmias, and hypertension. Genetic variability in pharmacokinetic (e.g., CYP2D6) and pharmacodynamic (e.g., ADRB1, ADRB2, ADRA2C, GRK4, GRK5) genes have been studied in relation to beta-blocker exposure and response. We searched and summarized the strength of the evidence linking beta-blocker exposure and response with the six genes listed above. The level of evidence was high for associations between CYP2D6 genetic variation and both metoprolol exposure and heart rate response. Evidence indicates that CYP2D6 poor metabolizers experience clinically significant greater exposure and lower heart rate in response to metoprolol compared with those who are not poor metabolizers. Therefore, we provide therapeutic recommendations regarding genetically predicted CYP2D6 metabolizer status and metoprolol therapy. However, there was insufficient evidence to make therapeutic recommendations for CYP2D6 and other beta-blockers or for any beta-blocker and the other five genes evaluated (updates at www.cpicpgx.org).
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Affiliation(s)
- Julio D Duarte
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Cameron D Thomas
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Craig R Lee
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Jose A G Agundez
- Institute of Molecular Pathology Biomarkers, University of Extremadura, Cáceres, Spain
| | - Jordan F Baye
- Department of Pharmacy Practice, South Dakota State University College of Pharmacy & Allied Health Professions, Brookings, South Dakota, USA
- Sanford Imagenetics, Sioux Falls, South Dakota, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Research Institute and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - David E Lanfear
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Hospital, Detroit, Michigan, USA
- Heart and Vascular Institute, Henry Ford Health, Detroit, Michigan, USA
| | - Andrew A Monte
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Mohamed Nagy
- Department of Pharmaceutical Services, Children's Cancer Hospital Egypt 57357, Cairo, Egypt
- Personalized Medication Management Unit, Children's Cancer Hospital Egypt 57357, Cairo, Egypt
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- Department of Clinical Pharmacology, University Hospital Tuebingen, Tuebingen, Germany
- Department of Biochemistry and Pharmacy, University Tuebingen, Tuebingen, Germany
| | - C Michael Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Chakradhara Rao S Uppugunduri
- Division of Pediatric Oncology and Hematology, Department of Women, Child and Adolescent, University Geneva Hospitals, Geneva, Switzerland
- Department of Pediatrics, Gynecology and Obstetrics, Cansearch Research Platform for Pediatric Oncology and Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Roseann S Donnelly
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences, Boston, Massachusetts, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kelly E Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jasmine A Luzum
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Hospital, Detroit, Michigan, USA
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
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de Brabander E, Kleine Schaars K, van Amelsvoort T, van Westrhenen R. Influence of CYP2C19 and CYP2D6 on side effects of aripiprazole and risperidone: A systematic review. J Psychiatr Res 2024; 174:137-152. [PMID: 38631139 DOI: 10.1016/j.jpsychires.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/25/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Variability in hepatic cytochrome P450 (CYP) enzymes such as 2C19 and 2D6 may influence side-effect and efficacy outcomes for antipsychotics. Aripiprazole and risperidone are two commonly prescribed antipsychotics, metabolized primarily through CYP2D6. Here, we aimed to provide an overview of the effect of CYP2C19 and CYP2D6 on side-effects of aripiprazole and risperidone, and expand on existing literature by critically examining methodological issues associated with pharmacogenetic studies. A PRISMA compliant search of six electronic databases (Pubmed, PsychInfo, Embase, Central, Web of Science, and Google Scholar) identified pharmacogenetic studies on aripiprazole and risperidone. 2007 publications were first identified, of which 34 were included. Quality of literature was estimated using Newcastle-Ottowa Quality Assessment Scale (NOS) and revised Cochrane Risk of Bias tool. The average NOS score was 5.8 (range: 3-8) for risperidone literature and 5 for aripiprazole (range: 4-6). All RCTs on aripiprazole were rated as high risk of bias, and four out of six for risperidone literature. Study populations ranged from healthy volunteers to inpatient individuals in psychiatric units and included adult and pediatric samples. All n = 34 studies examined CYP2D6. Only one study genotyped for CYP2C19 and found a positive association with neurological side-effects of risperidone. Most studies did not report any relationship between CYP2D6 and any side-effect outcome. Heterogeneity between and within studies limited the ability to synthesize data and draw definitive conclusions. Studies lacked statistical power due to small sample size, selective genotyping methods, and study design. Large-scale randomized trials with multiple measurements, providing robust evidence on this topic, are suggested.
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Affiliation(s)
- Emma de Brabander
- Mental Health and Neuroscience Research Institute, Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, the Netherlands.
| | | | - Therese van Amelsvoort
- Mental Health and Neuroscience Research Institute, Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, the Netherlands
| | - Roos van Westrhenen
- Department of Psychiatry, Parnassia Groep BV, the Netherlands; Institute of Psychiatry, Psychology & Neurosciences, King's College London, United Kingdom
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Abad-Santos F, Aliño SF, Borobia AM, García-Martín E, Gassó P, Maroñas O, Agúndez JAG. Developments in pharmacogenetics, pharmacogenomics, and personalized medicine. Pharmacol Res 2024; 200:107061. [PMID: 38199278 DOI: 10.1016/j.phrs.2024.107061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
The development of Pharmacogenetics and Pharmacogenomics in Western Europe is highly relevant in the worldwide scenario. Despite the usually low institutional support, many research groups, composed of basic and clinical researchers, have been actively working for decades in this field. Their contributions made an international impact and paved the way for further studies and pharmacogenomics implementation in clinical practice. In this manuscript, that makes part of the Special Issue entitled Spanish Pharmacology, we present an analysis of the state of the art of Pharmacogenetics and Pharmacogenomics research in Europe, we compare it with the developments in Spain, and we summarize the most salient contributions since 1988 to the present, as well as recent developments in the clinical application of pharmacogenomics knowledge. Finally, we present some considerations on how we could improve translation to clinical practice in this specific scenario.
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Affiliation(s)
- Francisco Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Universidad Autónoma de Madrid (UAM), CIBEREHD, Instituto de Investigación Sanitaria La Princesa (IP), Madrid, Spain.
| | - Salvador F Aliño
- Gene Therapy and Pharmacogenomics Group, Department of Pharmacology, Faculty of Medicine, Universitat de València, Av. Blasco Ibáñez 15, 46010 Valencia, Spain
| | - Alberto M Borobia
- Clinical Pharmacology Department, La Paz University Hospital, School of Medicine, Universidad Autónoma de Madrid (UAM), IdiPAZ, Madrid, Spain
| | - Elena García-Martín
- Department of Pharmacology, Universidad de Extremadura, Avda de la Universidad s/n, 10071 Cáceres, Spain
| | - Patricia Gassó
- Basic Clinical Practice Department, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona Clínic Schizophrenia Unit (BCSU), IDIBAPS, CIBERSAM, Barcelona, Spain
| | - Olalla Maroñas
- Public Foundation of Genomic Medicine, Santiago University Hospital, Genomic Medicine group, Pharmacogenetics and Drug Discovery (GenDeM), CIBERER, Santiago Health Research Institute (IDIS), Galicia, Spain
| | - José A G Agúndez
- Universidad de Extremadura. University Institute of Molecular Pathology Biomarkers, Avda de las Ciencias s/n, 10071 Cáceres, Spain.
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