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Parikh SJ, Edara S, Deodhar S, Singh AK, Maekawa K, Zhang Q, Glass KC, Shah MB. Structural and biophysical analysis of cytochrome P450 2C9*14 and *27 variants in complex with losartan. J Inorg Biochem 2024; 258:112622. [PMID: 38852293 PMCID: PMC11285081 DOI: 10.1016/j.jinorgbio.2024.112622] [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: 03/17/2024] [Revised: 05/20/2024] [Accepted: 05/26/2024] [Indexed: 06/11/2024]
Abstract
The human cytochrome P450 (CYP) 1, 2 and 3 families of enzymes are responsible for the biotransformation of a majority of the currently available pharmaceutical drugs. The highly polymorphic CYP2C9 predominantly metabolizes many drugs including anticoagulant S-warfarin, anti-hypertensive losartan, anti-diabetic tolbutamide, analgesic ibuprofen, etc. There are >80 single nucleotide changes identified in CYP2C9, many of which significantly alter the clearance of important drugs. Here we report the structural and biophysical analysis of two polymorphic variants, CYP2C9*14 (Arg125His) and CYP2C9*27 (Arg150Leu) complexed with losartan. The X-ray crystal structures of the CYP2C9*14 and *27 illustrate the binding of two losartan molecules, one in the active site near heme and another on the periphery. Both losartan molecules are bound in an identical conformation to that observed in the previously solved CYP2C9 wild-type complex, however, the number of losartan differs from the wild-type structure, which showed binding of three molecules. Additionally, isothermal titration calorimetry experiments reveal a lower binding affinity of losartan with *14 and *27 variants when compared to the wild-type. Overall, the results provide new insights into the effects of these genetic polymorphisms and suggests a possible mechanism contributing to reduced metabolic activity in patients carrying these alleles.
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Affiliation(s)
- Sonia J Parikh
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA
| | - Sreeja Edara
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA
| | - Shruti Deodhar
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA
| | - Ajit K Singh
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Keiko Maekawa
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kodo, Kyotanabe, Kyoto 610-0395, Japan
| | - Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Karen C Glass
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Manish B Shah
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA.
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2
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Russell LE, Claw KG, Aagaard KM, Glass SM, Dasgupta K, Nez FL, Haimbaugh A, Maldonato BJ, Yadav J. Insights into pharmacogenetics, drug-gene interactions, and drug-drug-gene interactions. Drug Metab Rev 2024:1-19. [PMID: 39154360 DOI: 10.1080/03602532.2024.2385928] [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: 02/13/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024]
Abstract
This review explores genetic contributors to drug interactions, known as drug-gene and drug-drug-gene interactions (DGI and DDGI, respectively). This article is part of a mini-review issue led by the International Society for the Study of Xenobiotics (ISSX) New Investigators Group. Pharmacogenetics (PGx) is the study of the impact of genetic variation on pharmacokinetics (PK), pharmacodynamics (PD), and adverse drug reactions. Genetic variation in pharmacogenes, including drug metabolizing enzymes and drug transporters, is common and can increase the risk of adverse drug events or contribute to reduced efficacy. In this review, we summarize clinically actionable genetic variants, and touch on methodologies such as genotyping patient DNA to identify genetic variation in targeted genes, and deep mutational scanning as a high-throughput in vitro approach to study the impact of genetic variation on protein function and/or expression in vitro. We highlight the utility of physiologically based pharmacokinetic (PBPK) models to integrate genetic and chemical inhibitor and inducer data for more accurate human PK simulations. Additionally, we analyze the limitations of historical ethnic descriptors in pharmacogenomics research. Altogether, the work herein underscores the importance of identifying and understanding complex DGI and DDGIs with the intention to provide better treatment outcomes for patients. We also highlight current barriers to wide-scale implementation of PGx-guided dosing as standard or care in clinical settings.
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Affiliation(s)
- Laura E Russell
- Drug Metabolism and Pharmacokinetics, AbbVie Inc, North Chicago, IL, USA
| | - Katrina G Claw
- Division of Biomedical Informatics and Personalized Medicine, CO Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kaja M Aagaard
- Division of Biomedical Informatics and Personalized Medicine, CO Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sarah M Glass
- Preclinical Sciences and Translational Safety, Janssen Research &Development, San Diego, CA, USA
| | - Kuheli Dasgupta
- Department of Molecular Genetics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - F Leah Nez
- Division of Biomedical Informatics and Personalized Medicine, CO Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alex Haimbaugh
- Division of Biomedical Informatics and Personalized Medicine, CO Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Benjamin J Maldonato
- Department of Nonclinical Development and Clinical Pharmacology, Revolution Medicines, Inc, Redwood City, CA, USA
| | - Jaydeep Yadav
- Department of Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, Merck & Co., Inc, Boston, MA, USA
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3
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Kong BL, Donnelly RS, Abubakar A, Dunnenberger HM, Jones JS, Rogers SL, Kisor D. STRIPE partners in precision medicine series: pharmacist perspective. THE PHARMACOGENOMICS JOURNAL 2024; 24:26. [PMID: 39138184 DOI: 10.1038/s41397-024-00347-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Affiliation(s)
- Ben L Kong
- Oregon Health & Science University, Knight Cancer Institute, Portland, OR, USA.
| | - Roseann S Donnelly
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
| | | | - Henry M Dunnenberger
- Pharmacogenomics, Mark R. Neaman Center for Personalized Medicine, NorthShore University Health System, 2650 Ridge Avenue, Evanston, IL, 60201, USA
| | - J Shawn Jones
- Department of Pharmaceutical Sciences, Texas Tech University Health Sciences Center Jerry H. Hodge School of Pharmacy, Dallas, TX, USA
| | - Sara L Rogers
- Department of Pharmacy Practice, Irma Lerma Rangel School of Pharmacy, Texas A&M University, Kingsville, TX, USA
- Department of Translational Medical Sciences, School of Medicine, Texas A&M University, Bryan, TX, USA
- Center for Genomic and Precision Medicine, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
- American Society of Pharmacovigilance, Houston, TX, USA
| | - David Kisor
- Department of Pharmaceutical Sciences, Manchester University, Fort Wayne, IN, USA
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4
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Manson LEN, Nijenhuis M, Soree B, de Boer-Veger NJ, Buunk AM, Houwink EJF, Risselada A, Rongen GAPJM, van Schaik RHN, Swen JJ, Touw DJ, van Westrhenen R, Deneer VHM, Guchelaar HJ. Dutch Pharmacogenetics Working Group (DPWG) guideline for the gene-drug interaction of CYP2C9, HLA-A and HLA-B with anti-epileptic drugs. Eur J Hum Genet 2024; 32:903-911. [PMID: 38570725 PMCID: PMC11291682 DOI: 10.1038/s41431-024-01572-4] [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: 08/11/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 04/05/2024] Open
Abstract
By developing evidence-based pharmacogenetics guidelines to optimize pharmacotherapy, the Dutch Pharmacogenetics Working Group (DPWG) aims to advance the implementation of pharmacogenetics (PGx). This guideline outlines the gene-drug interaction of CYP2C9 and HLA-B with phenytoin, HLA-A and HLA-B with carbamazepine and HLA-B with oxcarbazepine and lamotrigine. A systematic review was performed and pharmacotherapeutic recommendations were developed. For CYP2C9 intermediate and poor metabolisers, the DPWG recommends lowering the daily dose of phenytoin and adjust based on effect and serum concentration after 7-10 days. For HLA-B*15:02 carriers, the risk of severe cutaneous adverse events associated with phenytoin, carbamazepine, oxcarbazepine, and lamotrigine is strongly increased. For carbamazepine, this risk is also increased in HLA-B*15:11 and HLA-A*31:01 carriers. For HLA-B*15:02, HLA-B*15:11 and HLA-A*31:01 positive patients, the DPWG recommends choosing an alternative anti-epileptic drug. If not possible, it is recommended to advise the patient to report any rash while using carbamazepine, lamotrigine, oxcarbazepine or phenytoin immediately. Carbamazepine should not be used in an HLA-B*15:02 positive patient. DPWG considers CYP2C9 genotyping before the start of phenytoin "essential" for toxicity prevention. For patients with an ancestry in which the abovementioned HLA-alleles are prevalent, the DPWG considers HLA-B*15:02 genotyping before the start of carbamazepine, phenytoin, oxcarbazepine, and lamotrigine "beneficial", as well as genotyping for HLA-B*15:11 and HLA-A*31:01 before initiating carbamazepine.
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Affiliation(s)
- Lisanne E N Manson
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marga Nijenhuis
- Royal Dutch Pharmacists Association (KNMP), The Hague, The Netherlands.
| | - Bianca Soree
- Royal Dutch Pharmacists Association (KNMP), The Hague, The Netherlands
| | | | | | | | - Arne Risselada
- Department of Clinical Pharmacy, Wilhelmina Hospital, Assen, The Netherlands
| | - Gerard A P J M Rongen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jesse J Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daan J Touw
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pharmaceutical Analysis, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Roos van Westrhenen
- Department of Psychiatry, Parnassia Group, Amsterdam, The Netherlands
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Vera H M Deneer
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Department of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
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5
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Shilbayeh SAR, Adeen IS, Alhazmi AS, Ibrahim SF, Al Enazi FAR, Ghanem EH, Binduraihem AM. The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism. Biochem Genet 2024; 62:2907-2932. [PMID: 38041757 DOI: 10.1007/s10528-023-10580-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 10/28/2023] [Indexed: 12/03/2023]
Abstract
Data on the role of CYP2D6 and CYP3A4/5 polymorphisms in relation to risperidone (RIS) pharmacokinetics (PK) in children are relatively limited and inconsistent. This is partially attributable to the limited coverage of CYP2D6 and CYP3A4/5 metabolizer phenotypes, particularly those of poor and ultrarapid metabolizers (PMs and UMs), which has led to calls for studies of populations with a non-European background that may carry variants that are less frequent in Europeans. Children ≤ 18 years old with at least 8 weeks of a RIS-based regimen were recruited from three autism centers in Riyadh, Saudi Arabia. The primary outcomes measured were plasma concentrations of RIS and 9-hydroxyrisperidone (9-OH-RIS) and their dose-adjusted (C/D) ratios as a function of phenotypes and activity score (AS). For accurate DNA genotyping, targeted pharmacogenomic testing with the Axiom PharmacoFocus Array was performed via examination of a broad collection of probesets targeting CYP2D6 and CYP3A4/5 variants. The frequency of genotypes/phenotypes and the impact of their allele translation and phenoconversion-predicted enzyme activity were examined. The final cohort included 83 individuals. The most common CYP2D6 phenotype in our population was normal metabolizers (NMs, 66.3%). Inconsistent with some previous studies, the three phenotypes of intermediate metabolizers (IMs), NMs, and UMs were significantly different in terms of RIS concentration, the RIS/9-OH-RIS ratio, the RIS C/D ratio and the 9-OH-RIS C/D ratio. According to AS analyses, there were statistically significant differences in the RIS concentration (P = 0.013), RIS/9-OH-RIS ratio (P < 0.001) and RIS C/D ratio (P = 0.030) when patients were categorized into AS ≤ 1 vs. AS > 1. None of the CYP3A4/5 star allele translated phenotypes revealed a significant influence on any of the RIS PK parameters. Notably, neither CYP2D6 nor CYP3A4/5 phenotyping demonstrated a significant impact on the total active moiety, suggesting that other gene variants could modulate RIS PK. The study confirmed the previously reported partial impact of the CYP2D6 gene on RIS PK. However, future studies using contemporary genotyping techniques targeting a wide range of variants in other candidate genes must be conducted to further examine their interactive effects on RIS PK and the clinical response.
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Affiliation(s)
- Sireen Abdul Rahim Shilbayeh
- Department of Pharmacy Practice, College of Pharmacy, Princess Nourah bint Abdulrahman University (PNU), P.O. Box 84428, 11671, Riyadh, Saudi Arabia.
| | - Iman Sharaf Adeen
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ayman Shawqi Alhazmi
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Saud Medical City, Riyadh, Saudi Arabia
| | - Samah Fathy Ibrahim
- College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fawwaz Abdul Razaq Al Enazi
- Department of Pediatric Behavior and Development and Adolescent Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ezzeldeen Hasan Ghanem
- Pharmaceutical Analysis Section, King Abdullah International Medical Research Center (KAIMRC), King Abdulaziz Medical City, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia
| | - Adel Mohammed Binduraihem
- Health Sciences Research Center, King Abdullah Bin Abdulaziz University Hospital, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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6
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Pratt VM, Cavallari LH, Fulmer ML, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, Turner AJ, van Schaik RHN, Whirl-Carrillo M, Weck KE. DPYD Genotyping Recommendations: A Joint Consensus Recommendation of the Association for Molecular Pathology, American College of Medical Genetics and Genomics, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, Pharmacogenomics Knowledgebase, and Pharmacogene Variation Consortium. J Mol Diagn 2024:S1525-1578(24)00154-5. [PMID: 39032821 DOI: 10.1016/j.jmoldx.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/09/2024] [Accepted: 05/21/2024] [Indexed: 07/23/2024] Open
Abstract
The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations for a minimum set of variant alleles (tier 1) and an extended list of variant alleles (tier 2) that will aid clinical laboratories when designing assays for PGx testing. The Association for Molecular Pathology PGx Working Group considered the functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, and other technical considerations for PGx testing when developing these recommendations. The goal of this Working Group is to promote standardization of PGx testing across clinical laboratories. This document will focus on clinical DPYD PGx testing that may be applied to all dihydropyrimidine dehydrogenase-related medications. These recommendations are not to be interpreted as prescriptive but to provide a reference guide.
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Affiliation(s)
- Victoria M Pratt
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana; Agena Bioscience, San Diego, California.
| | - Larisa H Cavallari
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida
| | - Makenzie L Fulmer
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Gaedigk
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Houda Hachad
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Operations, AccessDx, Houston, Texas
| | - Yuan Ji
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lisa V Kalman
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Systems, CDC, Atlanta, Georgia
| | - Reynold C Ly
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stuart A Scott
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Laboratory, Stanford Medicine, Palo Alto, California
| | - Amy J Turner
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pediatrics, Children's Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin; RPRD Diagnostics LLC, Wauwatosa, Wisconsin
| | - Ron H N van Schaik
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Chemistry/International Federation of Clinical Chemistry and Laboratory Medicine Expert Center Pharmacogenetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Michelle Whirl-Carrillo
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Karen E Weck
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina; Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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7
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Gaedigk A, Turner AJ, Moyer AM, Zubiaur P, Boone EC, Wang WY, Broeckel U, Kalman LV. Characterization of Reference Materials for DPYD: A GeT-RM Collaborative Project. J Mol Diagn 2024:S1525-1578(24)00155-7. [PMID: 39032822 DOI: 10.1016/j.jmoldx.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/24/2024] [Accepted: 06/28/2024] [Indexed: 07/23/2024] Open
Abstract
The DPYD gene encodes dihydropyrimidine dehydrogenase (DPD), which is involved in the catalysis of uracil and thymine, as well as 5-fluorouracil (5-FU), which is used to treat solid tumors. Patients with decreased DPD activity are at risk of serious, sometimes fatal, adverse drug reactions to this important cancer drug. Pharmacogenetic testing for DPYD is increasingly provided by clinical and research laboratories; however, only a limited number of quality control and reference materials are currently available for clinical DPYD testing. To address this need, the Division of Laboratory Systems, Centers for Disease Control and Prevention-based Genetic Testing Reference Materials Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Institute for Medical Research, has characterized 33 DNA samples derived from Coriell cell lines for DPYD. Samples were distributed to four volunteer laboratories for genetic testing using a variety of commercially available and laboratory-developed tests. Sanger sequencing was used by one laboratory and publicly available whole-genome sequence data from the 1000 Genomes Project were used by another to inform genotype. Thirty-three distinct DPYD variants were identified among the 33 samples characterized. These publicly available and well-characterized materials can be used to support the quality assurance and quality control programs of clinical laboratories performing clinical pharmacogenetic testing.
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Affiliation(s)
- Andrea Gaedigk
- Children's Mercy Research Institute, Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, and University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Amy J Turner
- RPRD Diagnostics and Medical College of Wisconsin, Department of Pediatrics, Section on Genomic Pediatrics, Milwaukee, Wisconsin
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Pablo Zubiaur
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Instituto de Investigación Sanitaria de La Princesa, Madrid, Spain
| | - Erin C Boone
- Children's Mercy Research Institute, Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, and University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Wendy Y Wang
- Children's Mercy Research Institute, Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, and University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Ulrich Broeckel
- RPRD Diagnostics and Medical College of Wisconsin, Department of Pediatrics, Section on Genomic Pediatrics, Milwaukee, Wisconsin
| | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
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8
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Bao S, Yang S, Hua Z, Li J, Zang Y, Li X. Ziprasidone population pharmacokinetics and co-medication effects in Chinese patients. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03244-y. [PMID: 38918237 DOI: 10.1007/s00210-024-03244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
Ziprasidone is widely used in the treatment of psychiatric disorders. Despite its prevalence, there is a notable lack of population pharmacokinetics (PPK) studies on ziprasidone in serum, both domestically and internationally. This study aimed to comprehensively investigate the various factors influencing the PPK characteristics of Ziprasidone, thereby providing a scientific basis for personalized treatment strategies in clinical settings. This is a retrospective study. A non-linear mixed-effects modeling method was used for data analysis, with the ziprasidone PPK model established using the Phoenix NLME 8.1 software. Model evaluation employed goodness-of-fit plots, visual predictive checks, and Bootstrap methods to ensure reliability and accuracy. To further validate the model's applicability, data from an additional 30 patients meeting the same inclusion criteria but not included in the final model were collected for external validation. Simulations were performed to explore the personalized dosage regimens. This retrospective analysis collected 547 drug concentration data points from 185 psychiatric disorder patients, along with related medical records. The data included detailed demographic information (such as age, gender, weight), dosing regimens, laboratory test results, and concomitant medication details. In the final model, Ka was fixed at 0.5 h-1 based on literature, and the population typical values for ziprasidone clearance (CL) and volume of distribution (V) were 18.74 L/h and 110.24 L, respectively. Co-administration of lorazepam and valproic acid significantly influenced the clearance of ziprasidone. Moreover, the model evaluation indicated good stability and predictive accuracy. A simple to use dosage regimen table was derived based on the results of simulations. This study successfully established and validated a PPK model for ziprasidone in Chinese patients with psychiatric disorders. The model provides a scientific reference for individualized dosing of ziprasidone and holds the potential to optimize treatment strategies, thereby enhancing therapeutic efficacy and safety.
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Affiliation(s)
- Shuang Bao
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, No. 95 Yongan Road, Xicheng District, Beijing, 100050, China
- Department of Pharmacy, Beijing Anding Hospital, Capital Medical University, No. 5 Ankang Hutong, Xicheng District, Beijing, 100088, China
| | - Siyu Yang
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, No. 95 Yongan Road, Xicheng District, Beijing, 100050, China
| | - Zixin Hua
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, No. 95 Yongan Road, Xicheng District, Beijing, 100050, China
| | - Jiqian Li
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, No. 95 Yongan Road, Xicheng District, Beijing, 100050, China
| | - Yannan Zang
- Department of Pharmacy, Beijing Anding Hospital, Capital Medical University, No. 5 Ankang Hutong, Xicheng District, Beijing, 100088, China
| | - Xingang Li
- Department of Pharmacy, Beijing Friendship Hospital, Capital Medical University, No. 95 Yongan Road, Xicheng District, Beijing, 100050, China.
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9
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Lenz C, Narang A, Bousman CA. Pharmacogenomic allele coverage of genome-wide genotyping arrays: a comparative analysis. Pharmacogenet Genomics 2024; 34:130-134. [PMID: 38359167 DOI: 10.1097/fpc.0000000000000523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The use of genome-wide genotyping arrays in pharmacogenomics (PGx) research and clinical implementation applications is increasing but it is unclear which arrays are best suited for these applications. Here, we conduct a comparative coverage analysis of PGx alleles included on genome-wide genotyping arrays, with an emphasis on alleles in genes with PGx-based prescribing guidelines. Genomic manifest files for seven arrays including the Axiom Precision Medicine Diversity Array (PMDA), Axiom PMDA Plus, Axiom PangenomiX, Axiom PangenomiX Plus, Infinium Global Screening Array, Infinium Global Diversity Array (GDA) and Infinium GDA with enhanced PGx (GDA-PGx) Array, were evaluated for coverage of 523 star alleles across 19 pharmacogenes included in prescribing guidelines developed by the Clinical Pharmacogenetic Implementation Consortium and Dutch Pharmacogenomics Working Group. Specific attention was given to coverage of the Association of Molecular Pathology's Tier 1 and Tier 2 allele sets for CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, NUDT15, TPMT and VKORC1 . Coverage of the examined PGx alleles was highest for the Infinium GDA-PGx (88%), Axiom PangenomiX Plus (77%), Axiom PangenomiX (72%) and Axiom PMDA Plus (70%). Three arrays (Infinium GDA-PGx, Axiom PangenomiX Plus and Axiom PMDA Plus) fully covered the Tier 1 alleles and the Axiom PangenomiX array provided full coverage of Tier 2 alleles. In conclusion, PGx allele coverage varied by gene and array. A superior array for all PGx applications was not identified. Future comparative analyses of genotype data produced by these arrays are needed to determine the robustness of the reported coverage estimates.
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Affiliation(s)
| | | | - Chad A Bousman
- Alberta Children's Hospital Research Institute
- Department of Medical Genetics
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine
- Departments of Psychiatry
- Physiology and Pharmacology
- Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
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10
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Denisenko NP, Zhiryakova AS, Sychev IV, Kryukov AV, Tuchkova SN, Vakulenko OY, Averkov OV, Vechorko VI, Mirzaev KB, Sychev DA. Clinical and pharmacogenetic features of patients with upper gastrointestinal lesions at a multidisciplinary hospital: the role of nonsteroidal anti-inflammatory drugs. Drug Metab Pers Ther 2024; 39:69-79. [PMID: 38996813 DOI: 10.1515/dmpt-2024-0040] [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: 05/17/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024]
Abstract
OBJECTIVES Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most commonly prescribed medications, but their use can be associated with a number of adverse reactions, including upper gastrointestinal lesions. The aim of the study was to identify clinical and pharmacogenetic factors associated with upper gastrointestinal lesions, including those linked to NSAIDs, in patients at a multidisciplinary hospital. METHODS The study included 92 patients (mean age 59.4±16.5 years; 47 women), who underwent esophagogastroduodenoscopy during inpatient treatment. Patients' intake of NSAIDs and gastroprotectors during the year before hospitalization was considered. Demographic, clinical, laboratory data of patients were compared between groups, including genotyping for CYP2C9*2 rs179985, CYP2C9*3 rs1057910, CYP2C8*3 rs11572080, CYP2C8*3 rs10509681, PTGS-1 rs10306135, PTGS-1 rs12353214, and PTGS-2 rs20417 using real-time PCR. RESULTS In NSAIDs+ patients, PTGS1 rs10306135 AT+TT genotypes increased the chance of developing gastrointestinal complications by 5.4 times (95 % CI=1.30-22.27). In total sample, smoking (OR=3.12, 95 % CI=1.15-8.46), and alcohol intake (OR=4.09, 95 % CI=1.05-15.87) increased odds of gastrointestinal damage. In NSAIDs+ patients omeprazole, famotidine and both famotidine and omeprazole during the last year were as ineffective as not taking gastroprotectors; in total sample famotidine (OR=0.19, 95 % CI=0.04-0.93) and two gastroprotectors (OR=0.13, 95 % CI=0.02-0.75) reduced the chance of upper gastrointestinal lesions. CONCLUSIONS Pharmacogenetic features of patients may significantly contribute to the development NSAIDs-induced upper gastrointestinal injuries.
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Affiliation(s)
- Natalia P Denisenko
- Research Institute of Molecular and Personalized Medicine, 442138 Russian Medical Academy of Continuous Professional Education , Moscow, Russian Federation
| | - Anna S Zhiryakova
- Department of Clinical Pharmacology and Therapeutics named after Academician B.E. Votchal, Russian Medical Academy of Continuous Professional Education, Moscow, Russian Federation
- Department of Clinical pharmacology, Municipal Clinical Hospital No. 15 named after O.M. Filatov, Moscow, Russian Federation
| | - Ivan V Sychev
- Research Institute of Molecular and Personalized Medicine, 442138 Russian Medical Academy of Continuous Professional Education , Moscow, Russian Federation
| | - Alexander V Kryukov
- Department of Clinical Pharmacology and Therapeutics named after Academician B.E. Votchal, Russian Medical Academy of Continuous Professional Education, Moscow, Russian Federation
- Department of Clinical pharmacology, Municipal Clinical Hospital No. 15 named after O.M. Filatov, Moscow, Russian Federation
| | - Svetlana N Tuchkova
- Research Institute of Molecular and Personalized Medicine, 442138 Russian Medical Academy of Continuous Professional Education , Moscow, Russian Federation
| | - Olga Y Vakulenko
- Clinical Diagnostic Department, Municipal Clinical Hospital No. 15 named after O.M. Filatov, Moscow, Russian Federation
| | - Oleg V Averkov
- The Regional Vascular Center, Municipal Clinical Hospital No. 15 named after O.M. Filatov, Moscow, Russian Federation
| | - Valery I Vechorko
- Municipal Clinical Hospital No. 15 named after O.M. Filatov, Moscow, Russian Federation
| | - Karin B Mirzaev
- Research Institute of Molecular and Personalized Medicine, 442138 Russian Medical Academy of Continuous Professional Education , Moscow, Russian Federation
| | - Dmitry A Sychev
- Department of Clinical Pharmacology and Therapeutics named after Academician B.E. Votchal, Russian Medical Academy of Continuous Professional Education, Moscow, Russian Federation
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11
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Gan P, Hajis MIB, Yumna M, Haruman J, Matoha HK, Wahyudi DT, Silalahi S, Oktariani DR, Dela F, Annisa T, Pitaloka TDA, Adhiwijaya PK, Pauzi RY, Hertanto R, Kumaheri MA, Sani L, Irwanto A, Pradipta A, Chomchopbun K, Gonzalez-Porta M. Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip. Front Pharmacol 2024; 15:1349203. [PMID: 38529185 PMCID: PMC10961362 DOI: 10.3389/fphar.2024.1349203] [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: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/27/2024] Open
Abstract
Background: Microarrays are a well-established and widely adopted technology capable of interrogating hundreds of thousands of loci across the human genome. Combined with imputation to cover common variants not included in the chip design, they offer a cost-effective solution for large-scale genetic studies. Beyond research applications, this technology can be applied for testing pharmacogenomics, nutrigenetics, and complex disease risk prediction. However, establishing clinical reporting workflows requires a thorough evaluation of the assay's performance, which is achieved through validation studies. In this study, we performed pre-clinical validation of a genetic testing workflow based on the Illumina Global Screening Array for 25 pharmacogenomic-related genes. Methods: To evaluate the accuracy of our workflow, we conducted multiple pre-clinical validation studies. Here, we present the results of accuracy and precision assessments, involving a total of 73 cell lines. These assessments encompass reference materials from the Genome-In-A-Bottle (GIAB), the Genetic Testing Reference Material Coordination Program (GeT-RM) projects, as well as additional samples from the 1000 Genomes project (1KGP). We conducted an accuracy assessment of genotype calls for target loci in each indication against established truth sets. Results: In our per-sample analysis, we observed a mean analytical sensitivity of 99.39% and specificity 99.98%. We further assessed the accuracy of star-allele calls by relying on established diplotypes in the GeT-RM catalogue or calls made based on 1KGP genotyping. On average, we detected a diplotype concordance rate of 96.47% across 14 pharmacogenomic-related genes with star allele-calls. Lastly, we evaluated the reproducibility of our findings across replicates and observed 99.48% diplotype and 100% phenotype inter-run concordance. Conclusion: Our comprehensive validation study demonstrates the robustness and reliability of the developed workflow, supporting its readiness for further development for applied testing.
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Affiliation(s)
- Pamela Gan
- Nalagenetics Pte Ltd., Singapore, Singapore
| | | | | | | | | | | | | | | | - Fitria Dela
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
| | - Tazkia Annisa
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
| | | | | | | | | | | | | | | | - Ariel Pradipta
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
- Department Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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12
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Shriver SP, Adams D, McKelvey BA, McCune JS, Miles D, Pratt VM, Ashcraft K, McLeod HL, Williams H, Fleury ME. Overcoming Barriers to Discovery and Implementation of Equitable Pharmacogenomic Testing in Oncology. J Clin Oncol 2024:JCO2301748. [PMID: 38386947 DOI: 10.1200/jco.23.01748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/08/2023] [Accepted: 12/12/2023] [Indexed: 02/24/2024] Open
Abstract
Pharmacogenomics (PGx), the study of inherited genomic variation and drug response or safety, is a vital tool in precision medicine. In oncology, testing to identify PGx variants offers patients the opportunity for customized treatments that can minimize adverse effects and maximize the therapeutic benefits of drugs used for cancer treatment and supportive care. Because individuals of shared ancestry share specific genetic variants, PGx factors may contribute to outcome disparities across racial and ethnic categories when genetic ancestry is not taken into account or mischaracterized in PGx research, discovery, and application. Here, we examine how the current scientific understanding of the role of PGx in differential oncology safety and outcomes may be biased toward a greater understanding and more complete clinical implementation of PGx for individuals of European descent compared with other genetic ancestry groups. We discuss the implications of this bias for PGx discovery, access to care, drug labeling, and patient and provider understanding and use of PGx approaches. Testing for somatic genetic variants is now the standard of care in treatment of many solid tumors, but the integration of PGx into oncology care is still lacking despite demonstrated actionable findings from PGx testing, reduction in avoidable toxicity and death, and return on investment from testing. As the field of oncology is poised to expand and integrate germline genetic variant testing, it is vital that PGx discovery and application are equitable for all populations. Recommendations are introduced to address barriers to facilitate effective and equitable PGx application in cancer care.
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Affiliation(s)
| | | | | | - Jeannine S McCune
- City of Hope/Beckman Research Institute Department of Hematologic Malignancies Translational Sciences, Duarte, CA
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13
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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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14
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Choi D, Becker M, Ivanov M, Bhat S. Etrasimod: A Sphingosine-1-Phosphate Receptor Modulator for the Treatment of Ulcerative Colitis. Ann Pharmacother 2024:10600280231225770. [PMID: 38258760 DOI: 10.1177/10600280231225770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
OBJECTIVE To review the pharmacologic and clinical profile of etrasimod in the treatment of ulcerative colitis (UC). DATA SOURCES A PubMed search was conducted from inception to November 2023 using the keywords etrasimod, ulcerative colitis, and sphingosine-1-phosphate receptor modulator. Information was also obtained from published abstracts and package insert. STUDY SELECTION AND DATA EXTRACTION Phase 2 and 3 studies plus relevant literature on etrasimod pharmacologic and clinical profile were reviewed. DATA SYNTHESIS Per ELEVATE, 2 phase 3 studies, a higher proportion of patients with moderately to severely active UC achieved clinical remission in the induction and maintenance phase with etrasimod compared with placebo. In addition, a higher proportion of patients achieved secondary endpoints of clinical response, endoscopic improvement-histologic remission, corticosteroid-free remission, and endoscopic improvement with etrasimod vs placebo. Common adverse events include anemia and headache. RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE IN COMPARISON WITH EXISTING DRUGS Etrasimod is now the second orally administered sphingosine-1-phosphate modulator approved for UC, providing patients with additional treatment options. Efficacy rates of this treatment are in line with other UC medication options. Similar to other sphingosine-1-phosphate receptor modulators, various assessments are required at baseline and during treatment to ensure safe and appropriate use. CONCLUSION Etrasimod is another possibility in the armamentarium of UC treatment, providing patients with more oral medication options. Prior to treatment initiation, several assessments relating to safety, drug interactions, and pharmacogenomics factors are advised.
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Affiliation(s)
- David Choi
- University of Chicago Medicine Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - Michelle Becker
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Marina Ivanov
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, AZ, USA
| | - Shubha Bhat
- Department of Pharmacy and Digestive Disease Institute, Cleveland Clinic, Cleveland, OH, USA
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15
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Ji Y, Shaaban S. Interrogating Pharmacogenetics Using Next-Generation Sequencing. J Appl Lab Med 2024; 9:50-60. [PMID: 38167765 DOI: 10.1093/jalm/jfad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/18/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Pharmacogenetics or pharmacogenomics (PGx) is the study of the role of inherited or acquired sequence change in drug response. With the rapid evolution of molecular techniques, bioinformatic tools, and increased throughput of functional genomic studies, the discovery of PGx associations and clinical implementation of PGx test results have now moved beyond a handful variants in single pharmacogenes and multi-gene panels that interrogate a few pharmacogenes to whole-exome and whole-genome scales. Although some laboratories have adopted next-generation sequencing (NGS) as a testing platform for PGx and other molecular tests, most clinical laboratories that offer PGx tests still use targeted genotyping approaches. CONTENT This article discusses primarily the technical considerations for clinical laboratories to develop NGS-based PGx tests including whole-genome and whole-exome sequencing analyses and highlights the challenges and opportunities in test design, content selection, bioinformatic pipeline for PGx allele and diplotype assignment, rare variant classification, reporting, and briefly touches a few additional areas that are important for successful clinical implementation of PGx results. SUMMARY The accelerated speed of technology development associated with continuous cost reduction and enhanced ability to interrogate complex genome regions makes it inevitable for most, if not all, clinical laboratories to transition PGx testing to an NGS-based platform in the near future. It is important for laboratories and relevant professional societies to recognize both the potential and limitations of NGS-based PGx profiling, and to work together to develop a standard and consistent practice to maximize the variant or allele detection rate and utility of PGx testing.
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Affiliation(s)
- Yuan Ji
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
- Molecular Genetics and Genomics, ARUP Laboratories, Salt Lake City, UT, United States
| | - Sherin Shaaban
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
- Molecular Genetics and Genomics, ARUP Laboratories, Salt Lake City, UT, United States
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16
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Paetznick C, Okoro O. The Intersection between Pharmacogenomics and Health Equity: A Case Example. PHARMACY 2023; 11:186. [PMID: 38133461 PMCID: PMC10747429 DOI: 10.3390/pharmacy11060186] [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: 09/01/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
Pharmacogenomics (PGx) and the study of precision medicine has substantial power to either uplift health equity efforts or further widen the gap of our already existing health disparities. In either occurrence, the medication experience plays an integral role within this intersection on an individual and population level. Examples of this intertwined web are highlighted through a case discussion. With these perspectives in mind, several recommendations for the research and clinical communities are highlighted to promote equitable healthcare with PGx integrated.
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Affiliation(s)
| | - Olihe Okoro
- Department of Pharmacy Practice and Pharmaceutical Sciences, College of Pharmacy, University of Minnesota, Duluth, MN 55812, USA
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17
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Van Heukelom J, Morgan J, Massmann A, Jacobsen K, Petry NJ, Baye JF, Frear S, Schultz A. Evolution of pharmacogenomic services and implementation of a multi-state pharmacogenomics clinic across a large rural healthcare system. Front Pharmacol 2023; 14:1274165. [PMID: 38035031 PMCID: PMC10682150 DOI: 10.3389/fphar.2023.1274165] [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: 08/07/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: Pharmacogenomics (PGx) aims to maximize drug benefits while minimizing risk of toxicity. Although PGx has proven beneficial in many settings, clinical uptake lags. Lack of clinician confidence and limited availability of PGx testing can deter patients from completing PGx testing. A few novel PGx clinic models have been described as a way to incorporate PGx testing into the standard of care. Background: A PGx clinic was implemented to fill an identified gap in provider availability, confidence, and utilization of PGx across our health system. Through a joint pharmacist and Advanced Practice Provider (APP) collaborative clinic, patients received counseling and PGx medication recommendations both before and after PGx testing. The clinic serves patients both in-person and virtually across four states in the upper Midwest. Results: The majority of patients seen in the PGx clinic during the early months were clinician referred (77%, n = 102) with the remainder being self-referred. Patients were, on average, taking two medications with Clinical Pharmacogenetics Implementation Consortium guidelines. Visits were split almost equally between in-person and virtual visits. Conclusion: Herein, we describe the successful implementation of an interdisciplinary PGx clinic to further enhance our PGx program. Throughout the implementation of the PGx clinic we have learned valuable lessons that may be of interest to other implementors. Clinicians were actively engaged in clinic referrals and early adoption of telemedicine was key to the clinic's early successes.
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Affiliation(s)
- Joel Van Heukelom
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, United States
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, United States
| | - Jennifer Morgan
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, United States
- Department of Medical Genetics, Sanford Health, Sioux Falls, SD, United States
| | - Amanda Massmann
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, United States
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, United States
| | - Kristen Jacobsen
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, United States
| | - Natasha J. Petry
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, United States
- Department of Pharmacy Practice, North Dakota State University, Fargo, ND, United States
| | - Jordan F. Baye
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, United States
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, United States
- Department of Pharmacy Practice, South Dakota State University College of Pharmacy and Allied Health Professions, Brookings, SD, United States
| | - Samantha Frear
- Translational Software, Inc., Mercer Island, WA, United States
| | - April Schultz
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD, United States
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, United States
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18
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Hertz DL, Smith DM, Scott SA, Patel JN, Hicks JK. Response to the FDA Decision Regarding DPYD Testing Prior to Fluoropyrimidine Chemotherapy. Clin Pharmacol Ther 2023; 114:768-779. [PMID: 37350752 DOI: 10.1002/cpt.2978] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/31/2023] [Indexed: 06/24/2023]
Abstract
Fluoropyrimidine (FP) chemotherapy is associated with severe, life-threatening toxicities, particularly among patients who carry deleterious germline variants in the DPYD gene. Pretreatment DPYD testing is standard of care throughout most of Europe; however, it has not been recommended in clinical practice guidelines in the United States. Due to increased risk of severe toxicity, a Citizen's Petition asked the US Food and Drug Administration (FDA) to update language in FP drug labels to recommend DPYD testing as part of a boxed warning and recommend FP dose reduction in patients carrying deleterious germline variants. In response, the FDA updated the capecitabine package insert to inform patients about the toxicity risk and test availability and consider DPYD testing. However, the FDA did not include a testing recommendation or requirement, or a boxed warning. Additionally, the FDA did not recommend FP dose adjustment in DPYD variant carriers. This review provides a critical assessment of the DPYD-FP pharmacogenetic association using the FDA's previously published Pharmacogenetic Pyramid, demonstrating that the evidence is compelling for recommending DPYD testing prior to FP treatment. Additionally, the FDA's stated concerns about recommending DPYD testing and DPYD-guided FP dose adjustment are addressed and discussed in the context of the FDA's other genetic testing and dose adjustment recommendations. We call on the FDA to follow our European counterparts in recommending DPYD testing and genotype-based dose adjustment to ensure patients with cancer receive safe and effective FP chemotherapy.
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Affiliation(s)
- Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
| | - D Max Smith
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
- MedStar Health, Columbia, Maryland, USA
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, California, USA
- Clinical Genomics Laboratory, Stanford Medicine, Palo Alto, California, USA
| | - Jai N Patel
- Department of Cancer Pharmacology and Pharmacogenomics, Levine Cancer Institute, Atrium Health, Charlotte, North Carolina, USA
| | - J Kevin Hicks
- Department of Individualized Cancer Management, Moffitt Cancer Center, Tampa, Florida, USA
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Pratt VM, Cavallari LH, Fulmer ML, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, van Schaik RHN, Whirl-Carrillo M, Weck KE. CYP3A4 and CYP3A5 Genotyping Recommendations: A Joint Consensus Recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn 2023; 25:619-629. [PMID: 37419245 PMCID: PMC10565868 DOI: 10.1016/j.jmoldx.2023.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/17/2023] [Accepted: 06/01/2023] [Indexed: 07/09/2023] Open
Abstract
The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations for a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clinical laboratories when designing assays for PGx testing. The Association for Molecular Pathology PGx Working Group considered functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, and other technical considerations for PGx testing when developing these recommendations. The goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This document will focus on clinical CYP3A4 and CYP3A5 PGx testing that may be applied to all CYP3A4- and CYP3A5-related medications. These recommendations are not to be interpreted as prescriptive but to provide a reference guide.
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Affiliation(s)
- Victoria M Pratt
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Larisa H Cavallari
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida
| | - Makenzie L Fulmer
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Gaedigk
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Houda Hachad
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Operations, AccessDx, Houston, Texas
| | - Yuan Ji
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lisa V Kalman
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Reynold C Ly
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stuart A Scott
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Laboratory, Stanford Medicine, Palo Alto, California
| | - Ron H N van Schaik
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Chemistry/International Federation of Clinical Chemistry and Laboratory Medicine Expert Center Pharmacogenetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Michelle Whirl-Carrillo
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Karen E Weck
- Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina; Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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20
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Gaedigk A, Boone EC, Turner AJ, van Schaik RHN, Chernova D, Wang WY, Broeckel U, Granfield CA, Hodge JC, Ly RC, Lynnes TC, Mitchell MW, Moyer AM, Oliva J, Kalman LV. Characterization of Reference Materials for CYP3A4 and CYP3A5: A (GeT-RM) Collaborative Project. J Mol Diagn 2023; 25:655-664. [PMID: 37354993 PMCID: PMC11284628 DOI: 10.1016/j.jmoldx.2023.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/26/2023] Open
Abstract
Pharmacogenetic testing for CYP3A4 is increasingly provided by clinical and research laboratories; however, only a limited number of quality control and reference materials are currently available for many of the CYP3A4 variants included in clinical tests. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program (GeT-RM), in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Institute for Medical Research, has characterized 30 DNA samples derived from Coriell cell lines for CYP3A4. Samples were distributed to five volunteer laboratories for genotyping using a variety of commercially available and laboratory-developed tests. Sanger and next-generation sequencing were also utilized by some of the laboratories. Whole-genome sequencing data from the 1000 Genomes Projects were utilized to inform genotype. Twenty CYP3A4 alleles were identified in the 30 samples characterized for CYP3A4: CYP3A4∗4, ∗5, ∗6, ∗7, ∗8, ∗9, ∗10, ∗11, ∗12, ∗15, ∗16, ∗18, ∗19, ∗20, ∗21, ∗22, ∗23, ∗24, ∗35, and a novel allele, CYP3A4∗38. Nineteen additional samples with preexisting data for CYP3A4 or CYP3A5 were re-analyzed to generate comprehensive reference material panels for these genes. These publicly available and well-characterized materials can be used to support the quality assurance and quality control programs of clinical laboratories performing clinical pharmacogenetic testing.
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Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri
| | - Amy J Turner
- RPRD Diagnostics, Milwaukee, Wisconsin; Section on Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ron H N van Schaik
- Department of Clinical Chemistry/International Federation of Clinical Chemistry and Laboratory Medicine Expert Center Pharmacogenetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Dilyara Chernova
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri
| | - Wendy Y Wang
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, Missouri
| | - Ulrich Broeckel
- RPRD Diagnostics, Milwaukee, Wisconsin; Section on Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Caitlin A Granfield
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Reynold C Ly
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ty C Lynnes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
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21
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Alsultan A, Alalwan AA, Alshehri B, Jeraisy MA, Alghamdi J, Alqahtani S, Albassam AA. Interethnic differences in drug response: projected impact of genetic variations in the Saudi population. Pharmacogenomics 2023; 24:685-696. [PMID: 37610881 DOI: 10.2217/pgs-2023-0105] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
Ethnicity is known to have an impact on drug responses. This is particularly important for drugs that have a narrow therapeutic window, nonlinearity in pharmacokinetics and are metabolized by enzymes that demonstrate genetic polymorphisms. However, most clinical trials are conducted among Caucasians, which might limit the usefulness of the findings of such studies for other ethnicities. The representation of participants from Saudi Arabia in global clinical trials is low. Therefore, there is a paucity of evidence to assess the impact of ethnic variability in the Saudi population on drug response. In this article, the authors assess the projected impact of genetic polymorphisms in drug-metabolizing enzymes and drug targets on drug response in the Saudi population.
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Affiliation(s)
- Abdullah Alsultan
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah A Alalwan
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Bashayer Alshehri
- Pharmaceutical Care Department, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Majed Al Jeraisy
- Pharmaceutical Care Department, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Jahad Alghamdi
- Saudi Food and Drug Authority, Drug Sector, Riyadh, Saudi Arabia
| | - Saeed Alqahtani
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed A Albassam
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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22
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Shugg T, Ly RC, Osei W, Rowe EJ, Granfield CA, Lynnes TC, Medeiros EB, Hodge JC, Breman AM, Schneider BP, Sahinalp SC, Numanagić I, Salisbury BA, Bray SM, Ratcliff R, Skaar TC. Computational pharmacogenotype extraction from clinical next-generation sequencing. Front Oncol 2023; 13:1199741. [PMID: 37469403 PMCID: PMC10352904 DOI: 10.3389/fonc.2023.1199741] [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: 04/03/2023] [Accepted: 05/22/2023] [Indexed: 07/21/2023] Open
Abstract
Background Next-generation sequencing (NGS), including whole genome sequencing (WGS) and whole exome sequencing (WES), is increasingly being used for clinic care. While NGS data have the potential to be repurposed to support clinical pharmacogenomics (PGx), current computational approaches have not been widely validated using clinical data. In this study, we assessed the accuracy of the Aldy computational method to extract PGx genotypes from WGS and WES data for 14 and 13 major pharmacogenes, respectively. Methods Germline DNA was isolated from whole blood samples collected for 264 patients seen at our institutional molecular solid tumor board. DNA was used for panel-based genotyping within our institutional Clinical Laboratory Improvement Amendments- (CLIA-) certified PGx laboratory. DNA was also sent to other CLIA-certified commercial laboratories for clinical WGS or WES. Aldy v3.3 and v4.4 were used to extract PGx genotypes from these NGS data, and results were compared to the panel-based genotyping reference standard that contained 45 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, TPMT, and VKORC1. Results Mean WGS read depth was >30x for all variant regions except for G6PD (average read depth was 29 reads), and mean WES read depth was >30x for all variant regions. For 94 patients with WGS, Aldy v3.3 diplotype calls were concordant with those from the genotyping reference standard in 99.5% of cases when excluding diplotypes with additional major star alleles not tested by targeted genotyping, ambiguous phasing, and CYP2D6 hybrid alleles. Aldy v3.3 identified 15 additional clinically actionable star alleles not covered by genotyping within CYP2B6, CYP2C19, DPYD, SLCO1B1, and NUDT15. Within the WGS cohort, Aldy v4.4 diplotype calls were concordant with those from genotyping in 99.7% of cases. When excluding patients with CYP2D6 copy number variation, all Aldy v4.4 diplotype calls except for one CYP3A4 diplotype call were concordant with genotyping for 161 patients in the WES cohort. Conclusion Aldy v3.3 and v4.4 called diplotypes for major pharmacogenes from clinical WES and WGS data with >99% accuracy. These findings support the use of Aldy to repurpose clinical NGS data to inform clinical PGx.
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Affiliation(s)
- Tyler Shugg
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Reynold C. Ly
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Wilberforce Osei
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elizabeth J. Rowe
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Caitlin A. Granfield
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ty C. Lynnes
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elizabeth B. Medeiros
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jennelle C. Hodge
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Amy M. Breman
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bryan P. Schneider
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - S. Cenk Sahinalp
- Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Ibrahim Numanagić
- Department of Computer Science, University of Victoria, Victoria, BC, Canada
| | | | | | | | - Todd C. Skaar
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
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23
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Batinic A, Sutlović D, Kuret S, Matana A, Kumric M, Bozic J, Dujic Z. Trial of a Novel Oral Cannabinoid Formulation in Patients with Hypertension: A Double-Blind, Placebo-Controlled Pharmacogenetic Study. Pharmaceuticals (Basel) 2023; 16:ph16050645. [PMID: 37242428 DOI: 10.3390/ph16050645] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
Cannabidiol (CBD) is a non-psychoactive cannabinoid, and available evidence suggests potential efficacy in the treatment of many disorders. DehydraTECH™2.0 CBD is a patented capsule formulation that improves the bioabsorption of CBD. We sought to compare the effects of CBD and DehydraTECH™2.0 CBD based on polymorphisms in CYP P450 genes and investigate the effects of a single CBD dose on blood pressure. In a randomized and double-blinded order, 12 females and 12 males with reported hypertension were given either placebo capsules or DehydraTECH™2.0 CBD (300 mg of CBD, each). Blood pressure and heart rate were measured during 3 h, and blood and urine samples were collected. In the first 20 min following the dose, there was a greater reduction in diastolic blood pressure (p = 0.025) and mean arterial pressure MAP (p = 0.056) with DehydraTECH™2.0 CBD, which was probably due to its greater CBD bioavailability. In the CYP2C9*2*3 enzyme, subjects with the poor metabolizer (PM) phenotype had higher plasma CBD concentrations. Both CYP2C19*2 (p = 0.037) and CYP2C19*17 (p = 0.022) were negatively associated with urinary CBD levels (beta = -0.489 for CYP2C19*2 and beta = -0.494 for CYP2C19*17). Further research is required to establish the impact of CYP P450 enzymes and the identification of metabolizer phenotype for the optimization of CBD formulations.
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Affiliation(s)
- Ana Batinic
- Pharmacy of Split-Dalmatia County, 21000 Split, Croatia
| | - Davorka Sutlović
- University Department of Health Studies, University of Split, 21000 Split, Croatia
- Department of Toxicology and Pharmacogenetics, School of Medicine, University of Split, 21000 Split, Croatia
| | - Sendi Kuret
- University Department of Health Studies, University of Split, 21000 Split, Croatia
| | - Antonela Matana
- University Department of Health Studies, University of Split, 21000 Split, Croatia
| | - Marko Kumric
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia
| | - Josko Bozic
- Department of Pathophysiology, University of Split School of Medicine, 21000 Split, Croatia
| | - Zeljko Dujic
- Department of Integrative Physiology, School of Medicine, University of Split, 21000 Split, Croatia
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24
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Ramsey LB, Gong L, Lee SB, Wagner JB, Zhou X, Sangkuhl K, Adams SM, Straka RJ, Empey PE, Boone EC, Klein TE, Niemi M, Gaedigk A. PharmVar GeneFocus: SLCO1B1. Clin Pharmacol Ther 2023; 113:782-793. [PMID: 35797228 PMCID: PMC10900141 DOI: 10.1002/cpt.2705] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/24/2022] [Indexed: 11/06/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) is now providing star (*) allele nomenclature for the highly polymorphic human SLCO1B1 gene encoding the organic anion transporting polypeptide 1B1 (OATP1B1) drug transporter. Genetic variation within the SLCO1B1 gene locus impacts drug transport, which can lead to altered pharmacokinetic profiles of several commonly prescribed drugs. Variable OATP1B1 function is of particular importance regarding hepatic uptake of statins and the risk of statin-associated musculoskeletal symptoms. To introduce this important drug transporter gene into the PharmVar database and serve as a unified reference of haplotype variation moving forward, an international group of gene experts has performed an extensive review of all published SLCO1B1 star alleles. Previously published star alleles were self-assigned by authors and only loosely followed the star nomenclature system that was first developed for cytochrome P450 genes. This nomenclature system has been standardized by PharmVar and is now applied to other important pharmacogenes such as SLCO1B1. In addition, data from the 1000 Genomes Project and investigator-submitted data were utilized to confirm existing haplotypes, fill knowledge gaps, and/or define novel star alleles. The PharmVar-developed SLCO1B1 nomenclature has been incorporated by the Clinical Pharmacogenetics Implementation Consortium (CPIC) 2022 guideline on statin-associated musculoskeletal symptoms.
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Affiliation(s)
- Laura B Ramsey
- Divisions of Clinical Pharmacology and Research in Patient Services, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Seung-Been Lee
- Precision Medicine Institute, Macrogen Inc., Seoul, Korea
| | - Jonathan B Wagner
- 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
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Solomon M Adams
- School of Pharmacy, Shenandoah University, Fairfax, Virginia, USA
| | - Robert J Straka
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Philip E Empey
- School of Pharmacy and Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Medicine (BMIR), Stanford University, Stanford, California, USA
| | - Mikko Niemi
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - 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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25
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Smith DM, Figg WD. Evidence Regarding Pharmacogenetics in Pain Management and Cancer. Oncologist 2023; 28:189-192. [PMID: 36718020 PMCID: PMC10020807 DOI: 10.1093/oncolo/oyac277] [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: 10/10/2022] [Accepted: 12/15/2022] [Indexed: 02/01/2023] Open
Abstract
Patients experience interindividual variation in response to analgesics, which may be partially explained by genetics. This commentary discusses a recently published trial on COMT genotype and opioid dose requirements and describes the potential role for COMT and other genes (eg, CYP2D6) on opioid therapy and the current evidence for germline pharmacogenetics and resources for opioid pharmacogenetics.
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Affiliation(s)
- D Max Smith
- Corresponding author: D. Max Smith, PharmD, MedStar Health, 3007 Tilden Street NW, Suite 7L, Washington, DC 20008, USA.
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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26
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Williams GR, Tsongalis GJ, Lewis LD, Barney RE, Cook LJ, Geno KA, Nerenz RD. Potential Impact of Pharmacogenomic Single Nucleotide Variants in a Rural Caucasian Population. J Appl Lab Med 2023; 8:251-263. [PMID: 36611001 PMCID: PMC10539040 DOI: 10.1093/jalm/jfac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/15/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND In the US adverse drug reactions (ADRs) are estimated to cause 100 000 fatalities and cost over $136 billion annually. A patient's genes play a significant role in their response to a drug. Pharmacogenomics aims to optimize drug choice and dose for individual patients by characterizing patients' pharmacologically relevant genes to identify variants of known impact. METHODS DNA was extracted from randomly selected remnant whole blood samples from Caucasian patients with previously performed complete blood counts. Samples were genotyped by mass spectrometry using a customized pharmacogenomics panel. A third-party result interpretation service used genotypic results to predict likely individual responses to frequently prescribed drugs. RESULTS Complete genotypic and phenotypic calls for all tested Cytochrome P450 isoenzymes and other genes were obtained from 152 DNA samples. Of these 152 unique genomic DNA samples, 140 had genetic variants suggesting dose adjustment for at least one drug. Cardiovascular and psychiatry drugs had the highest number of recommendations, which included United States Food and Drug Administration warnings for highly prescribed drugs metabolized by CYP2C19, CYP2C9, CYP2D6, HLA-A, and VKORC1. CONCLUSIONS Risk for each drug:gene pairing primarily depends upon the degree of predicted enzyme impairment or activation, width of the therapeutic window, and whether parent compound or metabolite is pharmacologically active. The resulting metabolic variations range from risk of toxicity to therapeutic failure. Pharmacogenomic profiling likely reduces ADR potential by allowing up front drug/dose selection to fit a patient's unique drug-response profile.
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Affiliation(s)
- Grace R. Williams
- Department of Pathology, Virginia Commonwealth University Health System, Richmond, VA, USA
| | - Gregory J. Tsongalis
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Lionel D. Lewis
- Department of Medicine, The Geisel School of Medicine at Dartmouth and Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Rachael E. Barney
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Leanne J. Cook
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - K. Aaron Geno
- Department of Pathology, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Robert D. Nerenz
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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27
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Calleja S, Zubiaur P, Ochoa D, Villapalos-García G, Mejia-Abril G, Soria-Chacartegui P, Navares-Gómez M, de Miguel A, Román M, Martín-Vílchez S, Abad-Santos F. Impact of polymorphisms in CYP and UGT enzymes and ABC and SLCO1B1 transporters on the pharmacokinetics and safety of desvenlafaxine. Front Pharmacol 2023; 14:1110460. [PMID: 36817149 PMCID: PMC9934922 DOI: 10.3389/fphar.2023.1110460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Venlafaxine pharmacokinetic variability and pharmacotherapy outcomes are well known to be related to CYP2D6 pharmacogenetic phenotype. In contrast, scarce pharmacogenetic information is available nowadays concerning desvenlafaxine, its active metabolite first marketed in 2012. The aim of this study was to evaluate the impact of 29 alleles in 12 candidate genes (e.g., CYP enzymes like CYP2D6, CYP3A4, or CYP2C19; ABC transporters like ABCB1; SLCO1B1; and UGT enzymes like UGT1A1) on desvenlafaxine pharmacokinetic variability and tolerability. Pharmacokinetic parameters and adverse drug reaction (ADR) incidence obtained from six bioequivalence clinical trials (n = 98) evaluating desvenlafaxine formulations (five with single dose administration and one with multiple-dose administration) were analyzed. No genetic polymorphism was related to pharmacokinetic variability or ADR incidence. Volunteers enrolled in the multiple-dose clinical trial also showed a higher incidence of ADRs, e.g., xerostomia or appetite disorders. Volunteers experiencing any ADR showed a significantly higher area under the time-concentration curve (AUC) than those not experiencing any ADR (5115.35 vs. 4279.04 ng*h/mL, respectively, p = 0.034). In conclusion, the strong dose-dependent relationship with the occurrence of ADRs confirms that the mechanism of action of desvenlafaxine is essentially dose-dependent.
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Affiliation(s)
- Sofía Calleja
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Pablo Zubiaur
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy Research Institute, Kansas City, MO, United States
| | - Dolores Ochoa
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Gonzalo Villapalos-García
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Gina Mejia-Abril
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Paula Soria-Chacartegui
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Marcos Navares-Gómez
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Alejandro de Miguel
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Manuel Román
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Samuel Martín-Vílchez
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Francisco Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Instituto Teófilo Hernando, Instituto de Investigación Sanitaria La Princesa (IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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28
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LILLEY CULLENM, DELILLE MINERVE, MIRZA KAMRANM, PARILLA MEGAN. Toward a More Just System of Care in Molecular Pathology. Milbank Q 2022; 100:1192-1242. [PMID: 36454130 PMCID: PMC9836258 DOI: 10.1111/1468-0009.12587] [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: 02/02/2022] [Revised: 05/09/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
Policy Points American health care policy must be critically assessed to establish the role it plays in sustaining and alleviating the health disparities that currently exist in molecular genetic testing. It is critical to understand the economic and sociocultural influences that drive patients to undergo or forgo molecular testing, especially in marginalized patient populations. A multipronged solution with actions necessary from multiple stakeholders is required to reduce the cost of health care, rebalance regional disparities, encourage physician engagement, reduce data bias, and earn patients' trust. CONTEXT The health status of a population is greatly influenced by both biological processes and external factors. For years, minority and low socioeconomic patient populations have faced worse outcomes and poorer health in the United States. Experts have worked extensively to understand the issues and find solutions to alleviate this disproportionate burden of disease. As a result, there have been some improvements and successes, but wide gaps still exist. Diagnostic molecular genetic testing and so-called personalized medicine are just now being integrated into the current American health care system. The way in which these tests are integrated can either exacerbate or reduce health disparities. METHODS We provide case scenarios-loosely based on real-life patients-so that nonexperts can see the impacts of complex policy decisions and unintentional biases in technology without needing to understand all the intricacies. We use data to explain these findings from an extensive literature search examining both peer-reviewed and gray literature. FINDINGS Access to diagnostic molecular genetic testing is not equitable or sufficient, owing to at least five major factors: (1) cost to the patient, (2) location, (3) lack of provider buy-in, (4) data-set bias, and (5) lack of public trust. CONCLUSIONS Molecular genetic pathology can be made more equitable with the concerted efforts of multiple stakeholders. Confronting the five major factors identified here may help us usher in a new era of precision medicine without its discriminatory counterpart.
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Affiliation(s)
| | | | - KAMRAN M. MIRZA
- Loyola University Chicago, Strich School of Medicine
- Loyola Medical Center
| | - MEGAN PARILLA
- Loyola University Chicago, Strich School of Medicine
- Loyola Medical Center
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Rodriguez-Antona C, Savieo JL, Lauschke VM, Sangkuhl K, Drögemöller BI, Wang D, van Schaik RHN, Gilep AA, Peter AP, Boone EC, Ramey BE, Klein TE, Whirl-Carrillo M, Pratt VM, Gaedigk A. PharmVar GeneFocus: CYP3A5. Clin Pharmacol Ther 2022; 112:1159-1171. [PMID: 35202484 PMCID: PMC9399309 DOI: 10.1002/cpt.2563] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 01/31/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP3A5 gene. Genetic variation within the CYP3A5 gene locus impacts the metabolism of several clinically important drugs, including the immunosuppressants tacrolimus, sirolimus, cyclosporine, and the benzodiazepine midazolam. Variable CYP3A5 activity is of clinical importance regarding tacrolimus metabolism. This GeneFocus provides a CYP3A5 gene summary with a focus on aspects regarding standardized nomenclature. In addition, this review also summarizes recent changes and updates, including the retirement of several allelic variants and provides an overview of how PharmVar CYP3A5 star allele nomenclature is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
- Cristina Rodriguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | | | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, Florida, USA
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrei A Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Arul P Peter
- Coriell Life Sciences, Philadelphia, Pennsylvania, USA
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | | | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - 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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A Theory-Informed Systematic Review of Barriers and Enablers to Implementing Multi-Drug Pharmacogenomic Testing. J Pers Med 2022; 12:jpm12111821. [PMID: 36579514 PMCID: PMC9696651 DOI: 10.3390/jpm12111821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
PGx testing requires a complex set of activities undertaken by practitioners and patients, resulting in varying implementation success. This systematic review aimed (PROSPERO: CRD42019150940) to identify barriers and enablers to practitioners and patients implementing pharmacogenomic testing. We followed PRISMA guidelines to conduct and report this review. Medline, EMBASE, CINAHL, PsycINFO, and PubMed Central were systematically searched from inception to June 2022. The theoretical domain framework (TDF) guided the organisation and reporting of barriers or enablers relating to pharmacogenomic testing activities. From the twenty-five eligible reports, eleven activities were described relating to four implementation stages: ordering, facilitating, interpreting, and applying pharmacogenomic testing. Four themes were identified across the implementation stages: IT infrastructure, effort, rewards, and unknown territory. Barriers were most consistently mapped to TDF domains: memory, attention and decision-making processes, environmental context and resources, and belief about consequences.
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Cicali EJ, Lemke L, Al Alshaykh H, Nguyen K, Cavallari LH, Wiisanen K. How to Implement a Pharmacogenetics Service at your Institution. JOURNAL OF THE AMERICAN COLLEGE OF CLINICAL PHARMACY 2022; 5:1161-1175. [PMID: 36589694 PMCID: PMC9799247 DOI: 10.1002/jac5.1699] [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: 01/31/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023]
Abstract
The vast majority of patients possess one or more pharmacogenetic variants that can influence optimal medication use. When pharmacogenetic data are used to guide drug choice and dosing, evidence points to improved disease outcomes, fewer adverse effects, and lower healthcare spending. Although its science is well established, clinical use of pharmacogenetic data to guide drug therapy is still in its infancy. Pharmacogenetics essentially involves the intersection of an individual's genetic data with their medications, which makes pharmacists uniquely qualified to provide clinical support and education in this field. In fact, most pharmacogenetics implementations, to date, have been led by pharmacists as leaders or members of a multidisciplinary team or as individual practitioners. A successful large-scale pharmacogenetics implementation requires coordination and synergy among administrators, clinicians, informatics teams, laboratories, and patients. Because clinical implementation of pharmacogenetics is in its early stages, there is an urgent need for guidance and dissemination of shared experiences to provide a framework for clinicians. Many early adopters of pharmacogenetics have explored various strategies among diverse practice settings. This article relies on the experiences of early adopters to provide guidance for critical steps along the pathway to implementation, including strategies to engage stakeholders; evaluate pharmacogenetic evidence; coordinate laboratory testing, results interpretation and their integration into the electronic health record; identify reimbursement avenues; educate providers and patients; and maintain a successful program. Learning from early adopters' published experiences and strategies can allow clinicians leading a new pharmacogenetics implementation to avoid pitfalls and adapt and apply lessons learned by others to their own practice.
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Affiliation(s)
- Emily J Cicali
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
| | - Lauren Lemke
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
| | - Hana Al Alshaykh
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
| | - Khoa Nguyen
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
| | - Kristin Wiisanen
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
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Aldiban W, Altawil Y, Hussein S, Aljamali M, Youssef LA. Hyper-responsiveness to warfarin in a young patient with the VKORC1 -1639GA/CYP2C9*1*46 genotype: a case report. Thromb J 2022; 20:65. [PMID: 36303140 PMCID: PMC9608913 DOI: 10.1186/s12959-022-00425-8] [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: 07/12/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Warfarin is the most widely used oral anticoagulant; nevertheless, dosing of warfarin is problematic for clinicians worldwide. Inter-individual variability in response to warfarin is attributed to genetic as well as non-genetic factors. Pharmacogenomics studies have identified variants in CYP2C9 and VKORC1 genes as significant predictors of warfarin dose, however, phenotypes of rare variants are not well characterized. CASE PRESENTATION We report a case of hyper-responsiveness to warfarin in a 22-year-old outpatient with Crohn's disease who presented with a swollen, red, and painful left calf. Deep venous thrombosis (DVT) in the left lower extremity was confirmed via ultrasonography, and hence, anticoagulation therapy of heparin and concomitant warfarin was initiated. Warfarin dose of 7.5 mg/day was estimated by the physician based on clinical factors. Higher than the expected international normalized ratio (INR) value of 4.5 necessitated the reduction of the warfarin dose to 5 and eventually to 2.5 mg/day to reach a therapeutic INR value of 2.6. Pharmacogenetic profiling of the VKORC1 -1639G > A and CYP2C9 *2, *3, *4, *5, *8, *14, *20, *24, *26, *33, *40, *41, *42, *43, *45, *46, *55, *62, *63, *66, *68, *72, *73 and *78 revealed a VKORC1-1639GA/CYP2C9*1*46 genotype. The lower catalytic activity of the CYP2C9*46 (A149T) variant was previously reported in in vitro settings. CONCLUSIONS This is the first report on a case of warfarin hyper-responsive phenotype of a patient with the heterozygous CYP2C9*1*46 polymorphism.
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Affiliation(s)
- Weam Aldiban
- grid.8192.20000 0001 2353 3326Program of Clinical and Hospital Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Damascus University, Damascus, Syrian Arab Republic ,grid.461272.40000 0004 0417 813XFaculty of Pharmacy, International University for Science and Technology (IUST), Daraa, Syrian Arab Republic
| | - Yara Altawil
- grid.8192.20000 0001 2353 3326Program of Clinical and Hospital Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Damascus University, Damascus, Syrian Arab Republic
| | | | - Majd Aljamali
- grid.8192.20000 0001 2353 3326Department of Biochemistry and Microbiology, Faculty of Pharmacy, Damascus University, Damascus, Syrian Arab Republic ,National Commission for Biotechnology, Damascus, Syrian Arab Republic
| | - Lama A. Youssef
- grid.8192.20000 0001 2353 3326Program of Clinical and Hospital Pharmacy, Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Damascus University, Damascus, Syrian Arab Republic ,grid.461272.40000 0004 0417 813XFaculty of Pharmacy, International University for Science and Technology (IUST), Daraa, Syrian Arab Republic ,National Commission for Biotechnology, Damascus, Syrian Arab Republic
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Pratt VM, Cavallari LH, Fulmer ML, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, van Schaik RHN, Whirl-Carrillo M, Weck KE. TPMT and NUDT15 Genotyping Recommendations: A Joint Consensus Recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn 2022; 24:1051-1063. [PMID: 35931343 PMCID: PMC9808500 DOI: 10.1016/j.jmoldx.2022.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 06/14/2022] [Indexed: 02/06/2023] Open
Abstract
The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This article provides recommendations for a minimum panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories when designing assays for PGx testing. The Association for Molecular Pathology PGx Working Group considered the functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations for PGx testing when developing these recommendations. The ultimate goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This article focuses on clinical TPMT and NUDT15 PGx testing, which may be applied to all thiopurine S-methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15)-related medications. These recommendations are not to be interpreted as prescriptive, but to provide a reference guide.
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Affiliation(s)
- Victoria M Pratt
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Larisa H Cavallari
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Center for Pharmacogenomics and Precision Medicine, Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, Florida
| | - Makenzie L Fulmer
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Gaedigk
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Houda Hachad
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Clinical Operations, AccessDx, Houston, Texas
| | - Yuan Ji
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lisa V Kalman
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Reynold C Ly
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stuart A Scott
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, California
| | - R H N van Schaik
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Clinical Chemistry/International Federation of Clinical Chemistry and Laboratory Medicine Expert Center Pharmacogenetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands; European Society of Pharmacogenomics and Personalized Therapy (ESPT), Milan, Italy; Dutch Pharmacogenetics Working Group (DPWG), The Hague, the Netherlands
| | - Michelle Whirl-Carrillo
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Karen E Weck
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina; Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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Pratt VM, Wang WY, Boone EC, Broeckel U, Cody N, Edelmann L, Gaedigk A, Lynnes TC, Medeiros EB, Moyer AM, Mitchell MW, Scott SA, Starostik P, Turner A, Kalman LV. Characterization of Reference Materials for TPMT and NUDT15: A GeT-RM Collaborative Project. J Mol Diagn 2022; 24:1079-1088. [PMID: 35931342 PMCID: PMC9554816 DOI: 10.1016/j.jmoldx.2022.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 06/22/2022] [Indexed: 02/09/2023] Open
Abstract
Pharmacogenetic testing is increasingly provided by clinical and research laboratories; however, only a limited number of quality control and reference materials are currently available for many of the TPMT and NUDT15 variants included in clinical tests. To address this need, the Division of Laboratory Systems, Centers for Disease Control and Prevention-based Genetic Testing Reference Material (GeT-RM) coordination program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Institute for Medical Research, has characterized 19 DNA samples derived from Coriell cell lines. DNA samples were distributed to four volunteer testing laboratories for genotyping using a variety of commercially available and laboratory developed tests and/or Sanger sequencing. Of the 12 samples characterized for TPMT, newly identified variants include TPMT∗2, ∗6, ∗12, ∗16, ∗21, ∗24, ∗32, ∗33, and ∗40; for the 7 NUDT15 reference material samples, newly identified variants are NUDT15∗2, ∗3, ∗4, ∗5, ∗6, and ∗9. In addition, a novel haplotype, TPMT∗46, was identified in this study. Preexisting data on an additional 11 Coriell samples, as well as some supplemental testing, were used to create comprehensive reference material panels for TPMT and NUDT15. These publicly available and well-characterized materials can be used to support the quality assurance and quality control programs of clinical laboratories performing clinical pharmacogenetic testing.
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Affiliation(s)
- Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Wendy Y Wang
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri
| | - Ulrich Broeckel
- RPRD Diagnostics, Milwaukee, Wisconsin; Department of Pediatrics, Section on Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Neal Cody
- Sema4, Stamford, Connecticut; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lisa Edelmann
- Sema4, Stamford, Connecticut; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri; Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Ty C Lynnes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Elizabeth B Medeiros
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Laboratory, Stanford Healthcare, Palo Alto, California
| | - Petr Starostik
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida
| | - Amy Turner
- RPRD Diagnostics, Milwaukee, Wisconsin; Department of Pediatrics, Section on Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
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Bartos MN, Scott SA, Jabs EW, Naik H. Attitudes on pharmacogenomic results as secondary findings among medical geneticists. Pharmacogenet Genomics 2022; 32:273-280. [PMID: 35916546 DOI: 10.1097/fpc.0000000000000479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
OBJECTIVES As evidence mounts supporting the utility of pharmacogenomic-guided medication management, incorporating pharmacogenomic genes into secondary finding results from sequencing panels is increasingly under consideration. We studied medical geneticists' attitudes on receiving pharmacogenomic results as secondary finding. METHODS Four focus groups with 16 medical geneticists total were conducted followed by thematic analysis. RESULTS All participants ordered genetic sequencing tests; however, the majority had rarely or never ordered pharmacogenomic tests (10/16) or prescribed medications with established response variability (11/16). In total 81.3% expressed low comfort interpreting pharmacogenomic results without appropriate clinical resources (13/16). The positives of receiving pharmacogenomic results as secondary finding included prevention of adverse drug reactions in adults, grateful information-seeking patients, the ability to rapidly prescribe more effective treatments and appreciation of the recent advances in both pharmacogenomic knowledge and available guidelines. Negatives included laboratory reporting issues, exclusivity of pharmacogenomic results to certain populations, lengthy reports concealing pharmacogenomic results in patient charts and laboratories marketing to individuals without prior pharmacogenomic knowledge or targeting inappropriate populations. The most desirable pharmacogenomic resources included a universal electronic health record clinical decision support tool to assist identifying and implementing pharmacogenomic results, a specialized pharmacist as part of the care team, additional pharmacogenomic training during medical/graduate school, and a succinct interpretation of pharmacogenomic results included on laboratory reports. CONCLUSIONS The majority of participants agreed that adding certain actionable pharmacogenomic genes to the American College of Medical Genetics and Genomics SF list is reasonable; however, this was qualified with a need for additional resources to support implementation.
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Affiliation(s)
- Meghan N Bartos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
- Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
- Department of Pathology, Stanford University, Stanford
- Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, California, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
| | - Hetanshi Naik
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
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Asiimwe IG, Blockman M, Cohen K, Cupido C, Hutchinson C, Jacobson B, Lamorde M, Morgan J, Mouton JP, Nakagaayi D, Okello E, Schapkaitz E, Sekaggya-Wiltshire C, Semakula JR, Waitt C, Zhang EJ, Jorgensen AL, Pirmohamed M. A genome-wide association study of plasma concentrations of warfarin enantiomers and metabolites in sub-Saharan black-African patients. Front Pharmacol 2022; 13:967082. [PMID: 36210801 PMCID: PMC9537548 DOI: 10.3389/fphar.2022.967082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
Diversity in pharmacogenomic studies is poor, especially in relation to the inclusion of black African patients. Lack of funding and difficulties in recruitment, together with the requirement for large sample sizes because of the extensive genetic diversity in Africa, are amongst the factors which have hampered pharmacogenomic studies in Africa. Warfarin is widely used in sub-Saharan Africa, but as in other populations, dosing is highly variable due to genetic and non-genetic factors. In order to identify genetic factors determining warfarin response variability, we have conducted a genome-wide association study (GWAS) of plasma concentrations of warfarin enantiomers/metabolites in sub-Saharan black-Africans. This overcomes the issue of non-adherence and may have greater sensitivity at genome-wide level, to identify pharmacokinetic gene variants than focusing on mean weekly dose, the usual end-point used in previous studies. Participants recruited at 12 outpatient sites in Uganda and South Africa on stable warfarin dose were genotyped using the Illumina Infinium H3Africa Consortium Array v2. Imputation was conducted using the 1,000 Genomes Project phase III reference panel. Warfarin/metabolite plasma concentrations were determined by high-performance liquid chromatography with tandem mass spectrometry. Multivariable linear regression was undertaken, with adjustment made for five non-genetic covariates and ten principal components of genetic ancestry. After quality control procedures, 548 participants and 17,268,054 SNPs were retained. CYP2C9*8, CYP2C9*9, CYP2C9*11, and the CYP2C cluster SNP rs12777823 passed the Bonferroni-adjusted replication significance threshold (p < 3.21E-04) for warfarin/metabolite ratios. In an exploratory GWAS analysis, 373 unique SNPs in 13 genes, including CYP2C9*8, passed the Bonferroni-adjusted genome-wide significance threshold (p < 3.846E-9), with 325 (87%, all located on chromosome 10) SNPs being associated with the S-warfarin/R-warfarin outcome (top SNP rs11188082, CYP2C19 intron variant, p = 1.55E-17). Approximately 69% of these SNPs were in linkage disequilibrium (r2 > 0.8) with CYP2C9*8 (n = 216) and rs12777823 (n = 8). Using a pharmacokinetic approach, we have shown that variants other than CYP2C9*2 and CYP2C9*3 are more important in sub-Saharan black-Africans, mainly due to the allele frequencies. In exploratory work, we conducted the first warfarin pharmacokinetics-related GWAS in sub-Saharan Africans and identified novel SNPs that will require external replication and functional characterization before they can be considered for inclusion in warfarin dosing algorithms.
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Affiliation(s)
- Innocent G. Asiimwe
- The Wolfson Centre for Personalized Medicine, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Innocent G. Asiimwe, ; Munir Pirmohamed,
| | - Marc Blockman
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Karen Cohen
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Clint Cupido
- Victoria Hospital Internal Medicine Research Initiative, Victoria Hospital Wynberg and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Claire Hutchinson
- The Wolfson Centre for Personalized Medicine, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Barry Jacobson
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohammed Lamorde
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Jennie Morgan
- Metro District Health Services, Western Cape Department of Health, Cape Town, South Africa
| | - Johannes P. Mouton
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Elise Schapkaitz
- Department of Molecular Medicine and Hematology, Charlotte Maxeke Johannesburg Academic Hospital National Health Laboratory System Complex and University of Witwatersrand, Johannesburg, South Africa
| | | | - Jerome R. Semakula
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Catriona Waitt
- The Wolfson Centre for Personalized Medicine, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Eunice J. Zhang
- The Wolfson Centre for Personalized Medicine, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrea L. Jorgensen
- Department of Health Data Science, Institute of Population Health Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Innocent G. Asiimwe, ; Munir Pirmohamed,
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Grimsrud KN, Davis RR, Tepper CG, Palmieri TL. Pharmacogenetic Gene-Drug Associations in Pediatric Burn and Surgery Patients. J Burn Care Res 2022; 43:987-996. [PMID: 35639664 PMCID: PMC9435482 DOI: 10.1093/jbcr/irac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Management of critically ill patients requires simultaneous administration of many medications. Treatment for patient comorbidities may lead to drug-drug interactions which decrease drug efficacy or increase adverse reactions. Current practices rely on a one-size-fits-all dosing approach. Pharmacogenetic testing is generally reserved for addressing problems rather than used proactively to optimize care. We hypothesized that burn and surgery patients will have one or more genetic variants in drug metabolizing pathways used by one or more medications administered during the patient's hospitalization. The aim of this study was to determine the frequency of variants with abnormal function in the primary drug pathways and identify which medications may be impacted. Genetic (19 whole exome and 11 whole genome) and medication data from 30 pediatric burn and surgery patients were analyzed to identify pharmacogene-drug associations. Nineteen patients were identified with predicted altered function in one or more of the following genes: CYP2C9, CYP2C19, CYP2D6, and CYP3A4. The majority had decreased function, except for several patients with CYP2C19 rapid or ultrarapid variants. Some drugs administered during hospitalization that rely on these pathways include hydrocodone, oxycodone, methadone, ibuprofen, ketorolac, celecoxib, diazepam, famotidine, diphenhydramine, and glycopyrrolate. Approximately one-third of the patients tested had functionally impactful genotypes in each of the primary drug metabolizing pathways. This study suggests that genetic variants may in part explain the vast variability in drug efficacy and suggests that future pharmacogenetics research may optimize dosing regimens.
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Affiliation(s)
- Kristin N Grimsrud
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, USA
| | - Ryan R Davis
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California, Davis, USA
| | - Clifford G Tepper
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, USA
| | - Tina L Palmieri
- Department of Surgery, School of Medicine, University of California, Davis, USA
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38
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Maruf AA, Bousman CA. Approaches and hurdles of implementing pharmacogenetic testing in the psychiatric clinic. PCN REPORTS : PSYCHIATRY AND CLINICAL NEUROSCIENCES 2022; 1:e26. [PMID: 38868642 PMCID: PMC11114389 DOI: 10.1002/pcn5.26] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 06/14/2024]
Abstract
Pharmacogenetic (PGx) testing has emerged as a tool for predicting a person's ability to process and react to drugs. Despite the growing evidence-base, enthusiasm, and successful efforts to implement PGx testing in psychiatry, a consensus on how best to implement PGx testing into practice has not been established and numerous hurdles to widespread adoption remain to be overcome. In this article, we summarize the most used approaches and commonly encountered hurdles when implementing PGx testing into routine psychiatric care. We also highlight effective strategies that have been used to overcome hurdles. These strategies include the development of user-friendly clinical workflows for test ordering, use, and communication of results, establishment of test standardization and reimbursement policies, and development of tailored curriculums for educating health-care providers and the public. Although knowledge and awareness of these approaches and strategies to overcome hurdles alone may not be sufficient for successful implementation, they are necessary to ensure the effective spread, scale, and sustainability of PGx testing in psychiatry and other areas of medicine.
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Affiliation(s)
- Abdullah Al Maruf
- Rady Faculty of Health Sciences, College of PharmacyUniversity of ManitobaWinnipegManitobaCanada
- Children's Hospital Research Institute of ManitobaWinnipegManitobaCanada
- Centre on AgingUniversity of ManitobaWinnipegManitobaCanada
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain InstituteUniversity of CalgaryCalgaryAlbertaCanada
- Departments of Psychiatry and Physiology & PharmacologyUniversity of CalgaryCalgaryAlbertaCanada
| | - Chad A. Bousman
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain InstituteUniversity of CalgaryCalgaryAlbertaCanada
- Departments of Psychiatry and Physiology & PharmacologyUniversity of CalgaryCalgaryAlbertaCanada
- Department of Medical GeneticsUniversity of CalgaryCalgaryAlbertaCanada
- Department of Community Health SciencesUniversity of CalgaryCalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryCalgaryAlbertaCanada
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Asiimwe IG, Pirmohamed M. Ethnic Diversity and Warfarin Pharmacogenomics. Front Pharmacol 2022; 13:866058. [PMID: 35444556 PMCID: PMC9014219 DOI: 10.3389/fphar.2022.866058] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/14/2022] [Indexed: 12/23/2022] Open
Abstract
Warfarin has remained the most commonly prescribed vitamin K oral anticoagulant worldwide since its approval in 1954. Dosing challenges including having a narrow therapeutic window and a wide interpatient variability in dosing requirements have contributed to making it the most studied drug in terms of genotype-phenotype relationships. However, most of these studies have been conducted in Whites or Asians which means the current pharmacogenomics evidence-base does not reflect ethnic diversity. Due to differences in minor allele frequencies of key genetic variants, studies conducted in Whites/Asians may not be applicable to underrepresented populations such as Blacks, Hispanics/Latinos, American Indians/Alaska Natives and Native Hawaiians/other Pacific Islanders. This may exacerbate health inequalities when Whites/Asians have better anticoagulation profiles due to the existence of validated pharmacogenomic dosing algorithms which fail to perform similarly in the underrepresented populations. To examine the extent to which individual races/ethnicities are represented in the existing body of pharmacogenomic evidence, we review evidence pertaining to published pharmacogenomic dosing algorithms, including clinical utility studies, cost-effectiveness studies and clinical implementation guidelines that have been published in the warfarin field.
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Affiliation(s)
- Innocent G Asiimwe
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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40
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Wen YF, Gaedigk A, Boone EC, Wang WY, Straka RJ. The Identification of Novel CYP2D6 Variants in US Hmong: Results From Genome Sequencing and Clinical Genotyping. Front Pharmacol 2022; 13:867331. [PMID: 35387332 PMCID: PMC8979107 DOI: 10.3389/fphar.2022.867331] [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: 02/01/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Hmong individuals represent a unique East Asian subpopulation in whom limited information concerning pharmacogenetic variation exists. The objectives of this study were to comprehensively characterize the highly polymorphic CYP2D6 gene in Hmong, estimate allele and phenotype frequencies and to compare results between two testing platforms. Methods: DNA from 48 self-identified Hmong participants were sequenced using a targeted next-generation sequencing (NGS) panel. Star allele calls were made using Astrolabe, manual inspection of NGS variant calls and confirmatory Sanger sequencing. Structural variation was determined by long-range (XL)-PCR and digital droplet PCR (ddPCR). The consensus diplotypes were subsequently translated into phenotype utilizing the activity score system. Clinical grade pharmacogenetic testing was obtained for 12 of the 48 samples enabling an assessment of concordance between the consensus calls and those determined by clinical testing platforms. Results: A total of 13 CYP2D6 alleles were identified. The most common alleles were CYP2D6*10 and its structural arrangements (37.5%, 36/96) and the *5 gene deletion (13.5%, 13/96). Three novel suballeles (*10.007, *36.004, and *75.002) were also identified. Phenotype frequencies were as follows: ultrarapid metabolizers (4.2%, 2/48), normal metabolizers (41.7%, 20/48) and intermediate metabolizers (52.1%, 25/48); none of the 48 participants were predicted to be poor metabolizers. Concordance of diplotype and phenotype calls between the consensus and clinical testing were 66.7 and 50%, respectively. Conclusion: Our study to explore CYP2D6 genotypes in the Hmong population suggests that this subpopulation is unique regarding CYP2D6 allelic variants; also, a higher portion of Hmong participants (50%) are predicted to have an intermediate metabolizer phenotype for CYP2D6 compared to other East Asians which range between 27 and 44%. Results from different testing methods varied considerably. These preliminary findings underscore the importance of thoroughly interrogating unique subpopulations to accurately predict a patient's CYP2D6 metabolizer status.
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Affiliation(s)
- Ya Feng Wen
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Twin Cities, MN, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, MO, United States.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, MO, United States
| | - Wendy Y Wang
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, MO, United States
| | - Robert J Straka
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Twin Cities, MN, United States
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41
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Tayeh MK, Gaedigk A, Goetz MP, Klein TE, Lyon E, McMillin GA, Rentas S, Shinawi M, Pratt VM, Scott SA. Clinical pharmacogenomic testing and reporting: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:759-768. [PMID: 35177334 DOI: 10.1016/j.gim.2021.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/14/2022] Open
Abstract
Pharmacogenomic testing interrogates germline sequence variants implicated in interindividual drug response variability to infer a drug response phenotype and to guide medication management for certain drugs. Specifically, discrete aspects of pharmacokinetics, such as drug metabolism, and pharmacodynamics, as well as drug sensitivity, can be predicted by genes that code for proteins involved in these pathways. Pharmacogenomics is unique and differs from inherited disease genetics because the drug response phenotype can be drug-dependent and is often unrecognized until an unexpected drug reaction occurs or a patient fails to respond to a medication. Genes and variants with sufficiently high levels of evidence and consensus may be included in a clinical pharmacogenomic test; however, result interpretation and phenotype prediction can be challenging for some genes and medications. This document provides a resource for laboratories to develop and implement clinical pharmacogenomic testing by summarizing publicly available resources and detailing best practices for pharmacogenomic nomenclature, testing, result interpretation, and reporting.
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Affiliation(s)
- Marwan K Tayeh
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO; Department of Pediatrics, UMKC School of Medicine, University of Missouri-Kansas City, Kansas City, MO
| | - Matthew P Goetz
- Department of Pharmacology and Oncology, Mayo Clinic, Rochester, MN
| | - Teri E Klein
- Department of Biomedical Data Science and Department of Medicine, Stanford University, Stanford, CA
| | - Elaine Lyon
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | - Stefan Rentas
- Department of Pathology, Duke University School of Medicine, Durham, NC
| | - Marwan Shinawi
- Division of Genetics & Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, CA; Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, CA
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Klanderman BJ, Koch C, Machini K, Parpattedar SS, Bandyadka S, Lin CF, Hynes E, Lebo MS, Amr SS. Automated Pharmacogenomic Reports for Clinical Genome Sequencing. J Mol Diagn 2022; 24:205-218. [PMID: 35041930 DOI: 10.1016/j.jmoldx.2021.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/09/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022] Open
Abstract
Clinical laboratories offering genome sequencing have the opportunity to return pharmacogenomic findings to patients, providing the added benefit of preemptive testing that could help inform medication selection or dosing throughout the lifespan. Implementation of pharmacogenomic reporting must address several challenges, including inherent limitations in short-read genome sequencing methods, gene and variant selection, standardization of genotype and phenotype nomenclature, and choice of guidelines and drugs to report. An automated pipeline, lmPGX, was developed as an end-to-end solution that produces two versions of a pharmacogenomic report, presenting either Clinical Pharmacogenetics Implementation Consortium or US Food and Drug Administration guidelines for 12 genes. The pipeline was validated for performance using reference samples and pharmacogenetic data from the Genetic Testing Reference Materials Coordination Program. To determine performance and limitations, lmPGX was compared with three additional publicly available pharmacogenomic pipelines. The lmPGX pipeline offers clinical laboratories an opportunity for seamless integration of pharmacogenomic results with genome reporting.
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Affiliation(s)
- Barbara J Klanderman
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Kalotina Machini
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Shruti S Parpattedar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Shruthi Bandyadka
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Chiao-Feng Lin
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
| | - Sami S Amr
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts.
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43
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Lopes JL, Harris K, Karow MB, Peterson SE, Kluge ML, Kotzer KE, Lopes GS, Larson NB, Bielinski SJ, Scherer SE, Wang L, Weinshilboum RM, Black JL, Moyer AM. Targeted Genotyping in Clinical Pharmacogenomics: What Is Missing? J Mol Diagn 2022; 24:253-261. [PMID: 35041929 PMCID: PMC8961466 DOI: 10.1016/j.jmoldx.2021.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/09/2021] [Accepted: 11/29/2021] [Indexed: 01/01/2023] Open
Abstract
Clinical pharmacogenomic testing typically uses targeted genotyping, which only detects variants included in the test design and may vary among laboratories. To evaluate the potential patient impact of genotyping compared with sequencing, which can detect common and rare variants, an in silico targeted genotyping panel was developed based on the variants most commonly included in clinical tests and applied to a cohort of 10,030 participants who underwent sequencing for CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4, CYP3A5, DPYD, SLCO1B1, TPMT, UGT1A1, and VKORC1. The results of in silico targeted genotyping were compared with the clinically reported sequencing results. Of the 10,030 participants, 2780 (28%) had at least one potentially clinically relevant variant/allele identified by sequencing that would not have been detected in a standard targeted genotyping panel. The genes with the largest number of participants with variants only detected by sequencing were SLCO1B1, DPYD, and CYP2D6, which affected 13%, 6.3%, and 3.5% of participants, respectively. DPYD (112 variants) and CYP2D6 (103 variants) had the largest number of unique variants detected only by sequencing. Although targeted genotyping detects most clinically significant pharmacogenomic variants, sequencing-based approaches are necessary to detect rare variants that collectively affect many patients. However, efforts to establish pharmacogenomic variant classification systems and nomenclature to accommodate rare variants will be required to adopt sequencing-based pharmacogenomics.
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Affiliation(s)
- Jaime L. Lopes
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kimberley Harris
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mary Beth Karow
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sandra E. Peterson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Michelle L. Kluge
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Katrina E. Kotzer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Guilherme S. Lopes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Nicholas B. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | | | - Steven E. Scherer
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Richard M. Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - John L. Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ann M. Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota,Address correspondence to Ann M. Moyer, M.D., Ph.D., Mayo Clinic, 200 First St SW, Rochester, MN 55905.
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Zhu GD, Whitley P, LaRue L, Adkins B, Dawson E, Huskey A, Capparelli EV, Del Tredici AL. Impact of genetic variation in CYP2C19, CYP2D6, and CYP3A4 on oxycodone and its metabolites in a large database of clinical urine drug tests. THE PHARMACOGENOMICS JOURNAL 2022; 22:25-32. [PMID: 34480108 DOI: 10.1038/s41397-021-00253-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023]
Abstract
Urine drug testing (UDT) is a tool for monitoring drug use, including oxycodone. While variation in cytochrome P450 (CYP) genes is known to alter oxycodone metabolism, its impact on UDT results of oxycodone and its metabolites has not been well-studied. Here, multivariate analysis was performed on retrospective UDT results of 90,379 specimens collected from 14,684 genotyped patients prescribed oxycodone. Genetic variation in CYP2D6 and CYP2C19 had a significant impact on oxymorphone/oxycodone ratios, with a 6.9-fold difference between CYP2D6 ultrarapid metabolizers (UMs) and poor metabolizers (PMs; p < 10-300) and a 1.6-fold difference between CYP2C19 UMs and PMs (p = 1.50 × 10-4). CYP2D6 variation also significantly impacted noroxycodone/oxycodone ratios (p = 6.95 × 10-38). Oxycodone-positive specimens from CYP2D6 PMs were ~5-fold more likely to be oxymorphone-negative compared to normal metabolizers. These findings indicate that multivariate analysis of UDT data may be used to reveal the real-world impact of genetic and non-genetic factors on drug metabolism.
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Affiliation(s)
| | | | - Leah LaRue
- Millennium Health, LLC, San Diego, CA, USA
| | | | | | | | - Edmund V Capparelli
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
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45
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Bousman CA, Mukerjee G, Men X, Dorfman R, Müller DJ, Thomas RE. Encountering Pharmacogenetic Test Results in the Psychiatric Clinic. CANADIAN JOURNAL OF PSYCHIATRY. REVUE CANADIENNE DE PSYCHIATRIE 2022; 67:95-100. [PMID: 34783587 PMCID: PMC8892046 DOI: 10.1177/07067437211058847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chad A Bousman
- Departments of Medical Genetics, Psychiatry, Physiology & Pharmacology, and Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada.,Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Xiaoyu Men
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada
| | - Ruslan Dorfman
- GeneYouIn Inc, Toronto, Ontario, Canada.,Department of Anesthesia, McMaster University, Hamilton, Ontario, Canada
| | - Daniel J Müller
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Roger E Thomas
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
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46
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Nine-gene pharmacogenomics profile service: The Mayo Clinic experience. THE PHARMACOGENOMICS JOURNAL 2022; 22:69-74. [PMID: 34671112 DOI: 10.1038/s41397-021-00258-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]
Abstract
PURPOSE The Pharmacogenomics (PGx) Profile Service was a proof-of-concept project to implement PGx in patient care at Mayo Clinic. METHODS Eighty-two healthy individuals aged 18 and older underwent genotyping of CYP1A2, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, SLCO1B1, HLA-B*58:01, and VKORC1. A PGx pharmacist was involved in ordering, meeting with patients, interpreting, reviewing, and documenting results. RESULTS Ninety three percent were CYP1A2 rapid metabolizers, 92% CYP3A4 normal metabolizers, and 88% CYP3A5 poor metabolizers; phenotype frequencies for CYP2C19 and CYP2D6 varied. Seventy-three percent had normal functioning SLCO1B1 transporter, 4% carried the HLA-B*58:01 risk variant, and 35% carried VKORC1 and CYP2C9 variants that increased warfarin sensitivity. CONCLUSION Pre-emptive PGx testing offered medication improvement opportunity in 56% of participants for commonly used medications. A collaborative approach involving a PGx pharmacist integrated within a clinical practice with regards to utility of PGx results allowed for implementation of the PGx Profile Service. KEY POINTS The Mayo Clinic PGx (PGx) Profile Service was a proof-of-concept project to utilize PGx testing as another clinical tool to enhance medication selection and decrease serious adverse reactions or medication failures. Over one-half of participants in the pilot using the PGx Profile Service were predicted to benefit from pre-emptive PGx testing to guide pharmacotherapy. PGx pharmacists played a crucial role in the PGx Profile Service by educating participants, identifying medication-gene interactions, and providing evidence-based (CPIC and DPWG) PGx recommendations for past, current, and future medication us.
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47
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Mroz P, Michel S, Allen JD, Meyer T, McGonagle EJ, Carpentier R, Vecchia A, Schlichte A, Bishop JR, Dunnenberger HM, Yohe S, Thyagarajan B, Jacobson PA, Johnson SG. Development and Implementation of In-House Pharmacogenomic Testing Program at a Major Academic Health System. Front Genet 2021; 12:712602. [PMID: 34745204 PMCID: PMC8564018 DOI: 10.3389/fgene.2021.712602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/16/2021] [Indexed: 12/26/2022] Open
Abstract
Pharmacogenomics (PGx) studies how a person's genes affect the response to medications and is quickly becoming a significant part of precision medicine. The clinical application of PGx principles has consistently been cited as a major opportunity for improving therapeutic outcomes. Several recent studies have demonstrated that most individuals (> 90%) harbor PGx variants that would be clinically actionable if prescribed a medication relevant to that gene. In multiple well-conducted studies, the results of PGx testing have been shown to guide therapy choice and dosing modifications which improve treatment efficacy and reduce the incidence of adverse drug reactions (ADRs). Although the value of PGx testing is evident, its successful implementation in a clinical setting presents a number of challenges to molecular diagnostic laboratories, healthcare systems, providers and patients. Different molecular methods can be applied to identify PGx variants and the design of the assay is therefore extremely important. Once the genotyping results are available the biggest technical challenge lies in turning this complex genetic information into phenotypes and actionable recommendations that a busy clinician can effectively utilize to provide better medical care, in a cost-effective, efficient and reliable manner. In this paper we describe a successful and highly collaborative implementation of the PGx testing program at the University of Minnesota and MHealth Fairview Molecular Diagnostic Laboratory and selected Pharmacies and Clinics. We offer detailed descriptions of the necessary components of the pharmacogenomic testing implementation, the development and technical validation of the in-house SNP based multiplex PCR based assay targeting 20 genes and 48 SNPs as well as a separate CYP2D6 copy number assay along with the process of PGx report design, results of the provider and pharmacists usability studies, and the development of the software tool for genotype-phenotype translation and gene-phenotype-drug CPIC-based recommendations. Finally, we outline the process of developing the clinical workflow that connects the providers with the PGx experts within the Molecular Diagnostic Laboratory and the Pharmacy.
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Affiliation(s)
- Pawel Mroz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Stephen Michel
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Josiah D Allen
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN, United States
| | - Tim Meyer
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, United States
| | - Erin J McGonagle
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN, United States
| | | | | | | | - Jeffrey R Bishop
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN, United States.,Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Henry M Dunnenberger
- Mark R Neaman Center for Personalized Medicine Center, NorthShore University HealthSystem, Evanston, IL, United States
| | - Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Pamala A Jacobson
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN, United States
| | - Steven G Johnson
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, United States
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48
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Sayer M, Duche A, Nguyen TJT, Le M, Patel K, Vu J, Pham D, Vernick B, Beuttler R, Roosan D, Roosan MR. Clinical Implications of Combinatorial Pharmacogenomic Tests Based on Cytochrome P450 Variant Selection. Front Genet 2021; 12:719671. [PMID: 34650593 PMCID: PMC8506148 DOI: 10.3389/fgene.2021.719671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Despite the potential to improve patient outcomes, the application of pharmacogenomics (PGx) is yet to be routine. A growing number of PGx implementers are leaning toward using combinatorial PGx (CPGx) tests (i.e., multigene tests) that are reusable over patients’ lifetimes. However, selecting a single best available CPGx test is challenging owing to many patient- and population-specific factors, including variant frequency differences across ethnic groups. The primary objective of this study was to evaluate the detection rate of currently available CPGx tests based on the cytochrome P450 (CYP) gene variants they target. The detection rate was defined as the percentage of a given population with an “altered metabolizer” genotype predicted phenotype, where a CPGx test targeted both gene variants a prospective diplotypes. A potential genotype predicted phenotype was considered an altered metabolizer when it resulted in medication therapy modification based on Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. Targeted variant CPGx tests found in the Genetic Testing Registry (GTR), gene selection information, and diplotype frequency data from the Pharmacogenomics Knowledge Base (PharmGKB) were used to determine the detection rate of each CPGx test. Our results indicated that the detection rate of CPGx tests covering CYP2C19, CYP2C9, CYP2D6, and CYP2B6 show significant variation across ethnic groups. Specifically, the Sub-Saharan Africans have 63.9% and 77.9% average detection rates for CYP2B6 and CYP2C19 assays analyzed, respectively. In addition, East Asians (EAs) have an average detection rate of 55.1% for CYP2C9 assays. Therefore, the patient’s ethnic background should be carefully considered in selecting CPGx tests.
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Affiliation(s)
- Michael Sayer
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Ashley Duche
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Trang Jenny Tran Nguyen
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Michelle Le
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Kunj Patel
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Jacqueline Vu
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Danny Pham
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Brianne Vernick
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Richard Beuttler
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Don Roosan
- College of Pharmacy, Western University of Health Sciences, Pomona, CA, United States
| | - Moom R Roosan
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA, United States
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49
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Camuto C, Guglielmelli A, De-Giorgio F, de la Torre X, Mazzarino M, Marti M, Botrè F. In vitro metabolic profile of mexedrone, a mephedrone analog, studied by high- and low-resolution mass spectrometry. Drug Test Anal 2021; 14:269-276. [PMID: 34652887 PMCID: PMC9298855 DOI: 10.1002/dta.3179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/24/2022]
Abstract
Mexedrone is a synthetic cathinone structurally related to mephedrone, which belongs to the class of N‐alkyl cathinone derivatives, whose metabolic profile has not been fully clarified yet. This study considers the in vitro phase I metabolism of mexedrone, to pre‐select the most appropriate marker(s) of intake. Mexedrone was incubated in the presence of either human liver microsomes or single recombinant CYP450 isoforms. The metabolic profile was outlined by ultra‐high‐performance liquid chromatography coupled to both high‐ and low‐resolution mass spectrometry. In detail, the phase I metabolic profile of mexedrone was initially defined by a time‐of‐flight analyzer, while the chemical structures of the detected metabolites and the potential presence of minor metabolites were subsequently studied by tandem mass spectrometry, using a triple quadrupole analyzer. The main phase I metabolic reactions were hydroxylation and N‐ and O‐dealkylation. The CYP450 isoforms most involved were CYP2C19, responsible for the formation of both hydroxylated and dealkylated metabolites, followed by CYP2D6 and CYP1A2, involved in the hydroxylation reactions only. Finally, a significant fraction of mexedrone unchanged was also detected. Based on this evidence, the most appropriate markers of intake are mexedrone unchanged and the hydroxylated metabolites.
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Affiliation(s)
| | | | - Fabio De-Giorgio
- Department of Health Care Surveillance and Bioethics, Section of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | | | - Matteo Marti
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy.,Collaborative Center for the Italian National Early Warning System, Department of Anti-Drug Policies, Presidency of the Council of Ministers, Rome, Italy
| | - Francesco Botrè
- Laboratorio Antidoping, FMSI, Rome, Italy.,REDs-Research and Expertise in anti-Doping Sciences, ISSUL-Institute of Sport Sciences, University of Lausanne, Lausanne, Switzerland
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50
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Jameson A, Fylan B, Bristow GC, Sagoo GS, Dalton C, Cardno A, Sohal J, McLean SL. What Are the Barriers and Enablers to the Implementation of Pharmacogenetic Testing in Mental Health Care Settings? Front Genet 2021; 12:740216. [PMID: 34630531 PMCID: PMC8493030 DOI: 10.3389/fgene.2021.740216] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/30/2021] [Indexed: 01/29/2023] Open
Abstract
In psychiatry, the selection of antipsychotics and antidepressants is generally led by a trial-and-error approach. The prescribing of these medications is complicated by sub-optimal efficacy and high rates of adverse drug reactions (ADRs). These both contribute to poor levels of adherence. Pharmacogenetics (PGx) considers how genetic variation can influence an individual’s response to a drug. Pharmacogenetic testing is a tool that could aid clinicians when selecting psychotropic medications, as part of a more personalized approach to prescribing. This may improve the use of and adherence to these medications. Yet to date, the implementation of PGx in mental health environments in the United Kingdom has been slow. This review aims to identify the current barriers and enablers to the implementation of PGx in psychiatry and determine how this can be applied to the uptake of PGx by NHS mental health providers. A systematic searching strategy was developed, and searches were carried out on the PsychInfo, EmBase, and PubMed databases, yielding 11 appropriate papers. Common barriers to the implementation of PGx included cost, concerns over incorporation into current workflow and a lack of knowledge about PGx; whilst frequent enablers included optimism that PGx could lead to precision medicine, reduce ADRs and become a more routine part of psychiatric clinical care. The uptake of PGx in psychiatric care settings in the NHS should consider and overcome these barriers, while looking to capitalize on the enablers identified in this review.
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Affiliation(s)
- Adam Jameson
- Bradford District Care NHS Foundation Trust, Bradford, United Kingdom.,School of Pharmacy and Medical Sciences, University of Bradford, Bradford, United Kingdom.,Wolfson Centre for Applied Health Research, Bradford, United Kingdom
| | - Beth Fylan
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford, United Kingdom.,Wolfson Centre for Applied Health Research, Bradford, United Kingdom.,Bradford Institute of Health Research, NIHR Yorkshire and Humber Patient Safety Translational Research Centre, Bradford, United Kingdom
| | - Greg C Bristow
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford, United Kingdom
| | - Gurdeep S Sagoo
- Academic Unit of Health Economics, Leeds Institute of Health Sciences, University of Leeds, Leeds, United Kingdom.,National Institute for Health Research Leeds in vitro Diagnostics Co-operative, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Caroline Dalton
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, United Kingdom
| | - Alastair Cardno
- Leeds Institute of Health Sciences, Faculty of Medicine and Health, University of Leeds, Leeds, United Kingdom
| | - Jaspreet Sohal
- Bradford District Care NHS Foundation Trust, Bradford, United Kingdom
| | - Samantha L McLean
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford, United Kingdom.,Wolfson Centre for Applied Health Research, Bradford, United Kingdom
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