1
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Turner AJ, Nofziger C, Ramey BE, Ly RC, Bousman CA, Agúndez JAG, Sangkuhl K, Whirl-Carrillo M, Vanoni S, Dunnenberger HM, Ruano G, Kennedy MA, Phillips MS, Hachad H, Klein TE, Moyer AM, Gaedigk A. PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting. Clin Pharmacol Ther 2023; 114:1220-1237. [PMID: 37669183 PMCID: PMC10840842 DOI: 10.1002/cpt.3044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus and a comprehensive summary of structural variation. CYP2D6 contributes to the metabolism of numerous drugs and, thus, genetic variation in its gene impacts drug efficacy and safety. To accurately predict a patient's CYP2D6 phenotype, testing must include structural variants including gene deletions, duplications, hybrid genes, and combinations thereof. This tutorial offers a comprehensive overview of CYP2D6 structural variation, terms, and definitions, a review of methods suitable for their detection and characterization, and practical examples to address the lack of standards to describe CYP2D6 structural variants or any other pharmacogene. This PharmVar tutorial offers practical guidance on how to detect the many, often complex, structural variants, as well as recommends terms and definitions for clinical and research reporting. Uniform reporting is not only essential for electronic health record-keeping but also for accurate translation of a patient's genotype into phenotype which is typically utilized to guide drug therapy.
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Affiliation(s)
- Amy J Turner
- Department of Pediatrics, Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | | | | | - Reynold C Ly
- Department of Medical and Molecular Genetics, Division of Diagnostic Genomics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Chad A Bousman
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - José AG Agúndez
- University of Extremadura, Cáceres, Spain
- Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | | | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University Health System, Evanston, Illinois, USA
| | - Gualberto Ruano
- Institute of Living, Hartford Hospital (Hartford CT) and Department of Psychiatry, University of Connecticut School of Medicine (Farmington CT), USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Houda Hachad
- Houda Hachad, Department of Clinical Operations, AccessDx Laboratories, Houston, Texas, USA
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California, USA
| | - Ann M Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrea Gaedigk
- Children’s Mercy Research Institute (CMRI), Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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2
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Gonzalez-Suarez AD, Thorn CF, Whirl-Carrillo M, Klein TE. PharmGKB summary: disulfiram pathway. Pharmacogenet Genomics 2023; 33:207-216. [PMID: 37728645 PMCID: PMC10627108 DOI: 10.1097/fpc.0000000000000509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Affiliation(s)
| | | | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford, CA 94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
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3
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Li B, Sangkuhl K, Whaley R, Woon M, Keat K, Whirl-Carrillo M, Ritchie MD, Klein TE. Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank. Am J Hum Genet 2023; 110:1628-1647. [PMID: 37757824 PMCID: PMC10577080 DOI: 10.1016/j.ajhg.2023.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Pharmacogenomics (PGx) is an integral part of precision medicine and contributes to the maximization of drug efficacy and reduction of adverse drug event risk. Accurate information on PGx allele frequencies improves the implementation of PGx. Nonetheless, curating such information from published allele data is time and resource intensive. The limited number of allelic variants in most studies leads to an underestimation of certain alleles. We applied the Pharmacogenomics Clinical Annotation Tool (PharmCAT) on an integrated 200K UK Biobank genetic dataset (N = 200,044). Based on PharmCAT results, we estimated PGx frequencies (alleles, diplotypes, phenotypes, and activity scores) for 17 pharmacogenes in five biogeographic groups: European, Central/South Asian, East Asian, Afro-Caribbean, and Sub-Saharan African. PGx frequencies were distinct for each biogeographic group. Even biogeographic groups with similar proportions of phenotypes were driven by different sets of dominant PGx alleles. PharmCAT also identified "no-function" alleles that were rare or seldom tested in certain groups by previous studies, e.g., SLCO1B1∗31 in the Afro-Caribbean (3.0%) and Sub-Saharan African (3.9%) groups. Estimated PGx frequencies are disseminated via the PharmGKB (The Pharmacogenomics Knowledgebase: www.pharmgkb.org). We demonstrate that genetic biobanks such as the UK Biobank are a robust resource for estimating PGx frequencies. Improving our understanding of PGx allele and phenotype frequencies provides guidance for future PGx studies and clinical genetic test panel design, and better serves individuals from wider biogeographic backgrounds.
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Affiliation(s)
- Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ryan Whaley
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Karl Keat
- Genomics and Computational Biology PhD Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Genetics (by courtesy), Stanford University, Stanford, CA 94305, USA; Department of Medicine (BMIR), Stanford University, Stanford, CA 94305, USA.
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4
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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: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Oni-Orisan A, Tuteja S, Hoffecker G, Smith DM, Castrichini M, Crews KR, Murphy WA, Nguyen NHK, Huang Y, Lteif C, Friede KA, Tantisira K, Aminkeng F, Voora D, Cavallari LH, Whirl-Carrillo M, Duarte JD, Luzum JA. An Introductory Tutorial on Cardiovascular Pharmacogenetics for Healthcare Providers. Clin Pharmacol Ther 2023; 114:275-287. [PMID: 37303270 PMCID: PMC10406163 DOI: 10.1002/cpt.2957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/17/2023] [Indexed: 06/13/2023]
Abstract
Pharmacogenetics can improve clinical outcomes by reducing adverse drug effects and enhancing therapeutic efficacy for commonly used drugs that treat a wide range of cardiovascular diseases. One of the major barriers to the clinical implementation of cardiovascular pharmacogenetics is limited education on this field for current healthcare providers and students. The abundance of pharmacogenetic literature underscores its promise, but it can also be challenging to learn such a wealth of information. Moreover, current clinical recommendations for cardiovascular pharmacogenetics can be confusing because they are outdated, incomplete, or inconsistent. A myriad of misconceptions about the promise and feasibility of cardiovascular pharmacogenetics among healthcare providers also has halted clinical implementation. Therefore, the main goal of this tutorial is to provide introductory education on the use of cardiovascular pharmacogenetics in clinical practice. The target audience is any healthcare provider (or student) with patients that use or have indications for cardiovascular drugs. This tutorial is organized into the following 6 steps: (1) understand basic concepts in pharmacogenetics; (2) gain foundational knowledge of cardiovascular pharmacogenetics; (3) learn the different organizations that release cardiovascular pharmacogenetic guidelines and recommendations; (4) know the current cardiovascular drugs/drug classes to focus on clinically and the supporting evidence; (5) discuss an example patient case of cardiovascular pharmacogenetics; and (6) develop an appreciation for emerging areas in cardiovascular pharmacogenetics. Ultimately, improved education among healthcare providers on cardiovascular pharmacogenetics will lead to a greater understanding for its potential in improving outcomes for a leading cause of morbidity and mortality.
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Affiliation(s)
- Akinyemi Oni-Orisan
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, California, USA
| | - Sony Tuteja
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Glenda Hoffecker
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - D. Max Smith
- MedStar Health, Columbia, Maryland, USA
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Matteo Castrichini
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Kristine R. Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - William A. Murphy
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nam H. K. Nguyen
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Yimei Huang
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Christelle Lteif
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Kevin A. Friede
- Division of Cardiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelan Tantisira
- Division of Respiratory Medicine, Department of Pediatrics, University of California San Diego, San Diego, California, USA
| | - Folefac Aminkeng
- Departments of Medicine and Biomedical Informatics (DBMI), Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
- Centre for Precision Health (CPH), National University Health System (NUHS), Singapore City, Singapore
| | - Deepak Voora
- Precision Medicine Program, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Larisa H. Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | | | - Julio D. Duarte
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Jasmine A. Luzum
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, Michigan, USA
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6
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Gammal RS, Pirmohamed M, Somogyi AA, Morris SA, Formea CM, Elchynski AL, Oshikoya KA, McLeod HL, Haidar CE, Whirl-Carrillo M, Klein TE, Caudle KE, Relling MV. Expanded Clinical Pharmacogenetics Implementation Consortium Guideline for Medication Use in the Context of G6PD Genotype. Clin Pharmacol Ther 2023; 113:973-985. [PMID: 36049896 PMCID: PMC10281211 DOI: 10.1002/cpt.2735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/26/2022] [Indexed: 11/06/2022]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is associated with development of acute hemolytic anemia in the setting of oxidative stress, which can be caused by medication exposure. Regulatory agencies worldwide warn against the use of certain medications in persons with G6PD deficiency, but in many cases, this information is conflicting, and the clinical evidence is sparse. This guideline provides information on using G6PD genotype as part of the diagnosis of G6PD deficiency and classifies medications that have been previously implicated as unsafe in individuals with G6PD deficiency by one or more sources. We classify these medications as high, medium, or low to no risk based on a systematic review of the published evidence of the gene-drug associations and regulatory warnings. In patients with G6PD deficiency, high-risk medications should be avoided, medium-risk medications should be used with caution, and low-to-no risk medications can be used with standard precautions, without regard to G6PD phenotype. This new document replaces the prior Clinical Pharmacogenetics Implementation Consortium guideline for rasburicase therapy in the context of G6PD genotype (updates at: www.cpicpgx.org).
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Affiliation(s)
- Roseann S. Gammal
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Munir Pirmohamed
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew A. Somogyi
- Discipline of Pharmacology, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Sarah A. Morris
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Cancer Pharmacology and Pharmacogenomics, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Christine M. Formea
- Department of Pharmacy and Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, UT, USA
| | | | - Kazeem A. Oshikoya
- Department of Pharmacology, Therapeutics and Toxicology, College of Medicine, Lagos State University, Ikeja, Lagos, Nigeria
| | - Howard L. McLeod
- Intermountain Precision Genomics, Intermountain Healthcare, St George, UT, USA
| | - Cyrine E. Haidar
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kelly E. Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mary V. Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA
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7
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Li B, Sangkuhl K, Keat K, Whaley RM, Woon M, Verma S, Dudek S, Tuteja S, Verma A, Whirl-Carrillo M, Ritchie MD, Klein TE. How to Run the Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clin Pharmacol Ther 2023; 113:1036-1047. [PMID: 36350094 PMCID: PMC10121724 DOI: 10.1002/cpt.2790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022]
Abstract
Pharmacogenomics (PGx) investigates the genetic influence on drug response and is an integral part of precision medicine. While PGx testing is becoming more common in clinical practice and may be reimbursed by Medicare/Medicaid and commercial insurance, interpreting PGx testing results for clinical decision support is still a challenge. The Pharmacogenomics Clinical Annotation Tool (PharmCAT) has been designed to tackle the need for transparent, automatic interpretations of patient genetic data. PharmCAT incorporates a patient's genotypes, annotates PGx information (allele, genotype, and phenotype), and generates a report with PGx guideline recommendations from the Clinical Pharmacogenetics Implementation Consortium (CPIC) and/or the Dutch Pharmacogenetics Working Group (DPWG). PharmCAT has introduced new features in the last 2 years, including a variant call format (VCF) Preprocessor, the inclusion of DPWG guidelines, and functionalities for PGx research. For example, researchers can use the VCF Preprocessor to prepare biobank-scale data for PharmCAT. In addition, PharmCAT enables the assessment of novel partial and combination alleles that are composed of known PGx variants and can call CYP2D6 genotypes based on single and deletions in the input VCF file. This tutorial provides materials and detailed step-by-step instructions for how to use PharmCAT in a versatile way that can be tailored to users' individual needs.
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Affiliation(s)
- Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Karl Keat
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan M. Whaley
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Shefali Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, PA, USA
| | - Scott Dudek
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sony Tuteja
- Department of Medicine, University of Pennsylvania, PA, USA
| | - Anurag Verma
- Department of Medicine, University of Pennsylvania, PA, USA
| | | | - Marylyn D. Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Medicine (BMIR), Stanford University, Stanford, CA, USA
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8
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Verma SS, Keat K, Li B, Hoffecker G, Risman M, Sangkuhl K, Whirl-Carrillo M, Dudek S, Verma A, Klein TE, Ritchie MD, Tuteja S. Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population. J Transl Med 2022; 20:550. [PMID: 36443877 PMCID: PMC9703665 DOI: 10.1186/s12967-022-03745-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/30/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pharmacogenomics (PGx) aims to utilize a patient's genetic data to enable safer and more effective prescribing of medications. The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides guidelines with strong evidence for 24 genes that affect 72 medications. Despite strong evidence linking PGx alleles to drug response, there is a large gap in the implementation and return of actionable pharmacogenetic findings to patients in standard clinical practice. In this study, we evaluated opportunities for genetically guided medication prescribing in a diverse health system and determined the frequencies of actionable PGx alleles in an ancestrally diverse biobank population. METHODS A retrospective analysis of the Penn Medicine electronic health records (EHRs), which includes ~ 3.3 million patients between 2012 and 2020, provides a snapshot of the trends in prescriptions for drugs with genotype-based prescribing guidelines ('CPIC level A or B') in the Penn Medicine health system. The Penn Medicine BioBank (PMBB) consists of a diverse group of 43,359 participants whose EHRs are linked to genome-wide SNP array and whole exome sequencing (WES) data. We used the Pharmacogenomics Clinical Annotation Tool (PharmCAT), to annotate PGx alleles from PMBB variant call format (VCF) files and identify samples with actionable PGx alleles. RESULTS We identified ~ 316.000 unique patients that were prescribed at least 2 drugs with CPIC Level A or B guidelines. Genetic analysis in PMBB identified that 98.9% of participants carry one or more PGx actionable alleles where treatment modification would be recommended. After linking the genetic data with prescription data from the EHR, 14.2% of participants (n = 6157) were prescribed medications that could be impacted by their genotype (as indicated by their PharmCAT report). For example, 856 participants received clopidogrel who carried CYP2C19 reduced function alleles, placing them at increased risk for major adverse cardiovascular events. When we stratified by genetic ancestry, we found disparities in PGx allele frequencies and clinical burden. Clopidogrel users of Asian ancestry in PMBB had significantly higher rates of CYP2C19 actionable alleles than European ancestry users of clopidrogrel (p < 0.0001, OR = 3.68). CONCLUSIONS Clinically actionable PGx alleles are highly prevalent in our health system and many patients were prescribed medications that could be affected by PGx alleles. These results illustrate the potential utility of preemptive genotyping for tailoring of medications and implementation of PGx into routine clinical care.
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Affiliation(s)
- Shefali S. Verma
- grid.25879.310000 0004 1936 8972Department of Pathology & Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Karl Keat
- grid.25879.310000 0004 1936 8972Genomics & Computational Biology PhD Program, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Binglan Li
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Glenda Hoffecker
- grid.25879.310000 0004 1936 8972Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Marjorie Risman
- grid.25879.310000 0004 1936 8972Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | | | - Katrin Sangkuhl
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Michelle Whirl-Carrillo
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Scott Dudek
- grid.25879.310000 0004 1936 8972Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Anurag Verma
- grid.25879.310000 0004 1936 8972Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Teri E. Klein
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, CA USA
| | - Marylyn D. Ritchie
- grid.25879.310000 0004 1936 8972Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
| | - Sony Tuteja
- grid.25879.310000 0004 1936 8972Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA USA
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10
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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: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Maillard M, Gong L, Nishii R, Yang JJ, Whirl-Carrillo M, Klein TE. PharmGKB summary: acyclovir/ganciclovir pathway. Pharmacogenet Genomics 2022; 32:201-208. [PMID: 35665708 PMCID: PMC9179945 DOI: 10.1097/fpc.0000000000000474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Maud Maillard
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Li Gong
- Departments of Biomedical Data Science
| | - Rina Nishii
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Teri E Klein
- Departments of Biomedical Data Science
- Medicine (BMIR), Stanford University, Stanford, California, USA
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12
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Miller E, Norwood C, Giles JB, Huddart R, Karnes JH, Whirl-Carrillo M, Klein TE. PharmGKB summary: heparin-induced thrombocytopenia pathway, adverse drug reaction. Pharmacogenet Genomics 2022; 32:117-124. [PMID: 35102073 PMCID: PMC8988468 DOI: 10.1097/fpc.0000000000000465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Elise Miller
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Charles Norwood
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Jason B. Giles
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | - Jason H. Karnes
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA
- Department of Biomedical Informatics Research, Stanford University, Stanford, CA
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13
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McDermott JH, Wolf J, Hoshitsuki K, Huddart R, Caudle KE, Whirl-Carrillo M, Steyger PS, Smith RJH, Cody N, Rodriguez-Antona C, Klein TE, Newman WG. Clinical Pharmacogenetics Implementation Consortium Guideline for the Use of Aminoglycosides Based on MT-RNR1 Genotype. Clin Pharmacol Ther 2022; 111:366-372. [PMID: 34032273 PMCID: PMC8613315 DOI: 10.1002/cpt.2309] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/17/2021] [Indexed: 02/03/2023]
Abstract
Aminoglycosides are widely used antibiotics with notable side effects, such as nephrotoxicity, vestibulotoxicity, and sensorineural hearing loss (cochleotoxicity). MT-RNR1 is a gene that encodes the 12s rRNA subunit and is the mitochondrial homologue of the prokaryotic 16s rRNA. Some MT-RNR1 variants (i.e., m.1095T>C; m.1494C>T; m.1555A>G) more closely resemble the bacterial 16s rRNA subunit and result in increased risk of aminoglycoside-induced hearing loss. Use of aminoglycosides should be avoided in individuals with an MT-RNR1 variant associated with an increased risk of aminoglycoside-induced hearing loss unless the high risk of permanent hearing loss is outweighed by the severity of infection and safe or effective alternative therapies are not available. We summarize evidence from the literature supporting this association and provide therapeutic recommendations for the use of aminoglycosides based on MT-RNR1 genotype (updates at https://cpicpgx.org/guidelines/ and www.pharmgkb.org).
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Affiliation(s)
- John Henry McDermott
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Keito Hoshitsuki
- School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Kelly E. Caudle
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Peter S. Steyger
- Translational Hearing Center, Biomedical Sciences, Creighton University, National Center for Rehabilitative Auditory Research, VA Portland Health Care System, Portland, Oregon, USA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Internal Medicine (Nephrology), Pediatrics and Molecular Physiology & Biophysics, University of Iowa, Iowa City, Iowa, USA
| | - Neal Cody
- Department of Genetics and Genomic Sciences, Ichan School of Medicine at Mount Sinai, New York, New York, USA,Sema4, Stamford, Connecticut, USA
| | - Cristina Rodriguez-Antona
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA,Department of Medicine, Stanford University, Stanford, California, USA
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK,Correspondence: William Newman ()
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14
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Abstract
The Pharmacogenomics Knowledgebase (PharmGKB) is an integrated online knowledge resource for the understanding of how genetic variation contributes to variation in drug response. Our focus includes not only pharmacogenomic information useful for clinical implementation (e.g., drug dosing guidelines and annotated drug labels), but also information to catalyze scientific research and drug discovery (e.g., variant-drug annotations and drug-centered pathways). As of April 2021, the annotated content of PharmGKB spans 715 drugs, 1761 genes, 227 diseases, 165 clinical guidelines, and 784 drug labels. We have manually curated data from more than 9000 published papers to generate the content of PharmGKB. Recently, we have also implemented an automated natural language processing (NLP) tool to broaden our coverage of the pharmacogenomic literature. This article contains a basic protocol describing how to navigate the PharmGKB website to retrieve information on how genes and genetic variations affect drug efficacy and toxicity. It also includes a protocol on how to use PharmGKB to facilitate interpretation of findings for a pharmacogenomic variant genotype or metabolizer phenotype. PharmGKB is freely available at http://www.pharmgkb.org. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Navigating the homepage of PharmGKB and searching by drug Basic Protocol 2: Using PharmGKB to facilitate interpretation of pharmacogenomic variant genotypes or metabolizer phenotypes.
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Affiliation(s)
- Li Gong
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California
| | - Michelle Whirl-Carrillo
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California
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15
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Giacomini KM, Karnes JH, Crews KR, Monte AA, Murphy WA, Oni-Orisan A, Ramsey LB, Yang JJ, Whirl-Carrillo M. Advancing Precision Medicine Through the New Pharmacogenomics Global Research Network. Clin Pharmacol Ther 2021; 110:559-562. [PMID: 34318925 DOI: 10.1002/cpt.2340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/04/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Jason H Karnes
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona, USA
| | - Kristine R Crews
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Andrew A Monte
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - William A Murphy
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Akinyemi Oni-Orisan
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, California, USA
| | - Laura B Ramsey
- Division of Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Research in Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Michelle Whirl-Carrillo
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California, USA
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16
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Whirl-Carrillo M, Huddart R, Gong L, Sangkuhl K, Thorn CF, Whaley R, Klein TE. An Evidence-Based Framework for Evaluating Pharmacogenomics Knowledge for Personalized Medicine. Clin Pharmacol Ther 2021; 110:563-572. [PMID: 34216021 PMCID: PMC8457105 DOI: 10.1002/cpt.2350] [Citation(s) in RCA: 243] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/16/2021] [Indexed: 11/23/2022]
Abstract
Clinical annotations are one of the most popular resources available on the Pharmacogenomics Knowledgebase (PharmGKB). Each clinical annotation summarizes the association between variant‐drug pairs, shows relevant findings from the curated literature, and is assigned a level of evidence (LOE) to indicate the strength of support for that association. Evidence from the pharmacogenomic literature is curated into PharmGKB as variant annotations, which can be used to create new clinical annotations or added to existing clinical annotations. This means that the same clinical annotation can be worked on by multiple curators over time. As more evidence is curated into PharmGKB, the task of maintaining consistency when assessing all the available evidence and assigning an LOE becomes increasingly difficult. To remedy this, a scoring system has been developed to automate LOE assignment to clinical annotations. Variant annotations are scored according to certain attributes, including study size, reported P value, and whether the variant annotation supports or fails to find an association. Clinical guidelines or US Food and Drug Administration (FDA)‐approved drug labels which give variant‐specific prescribing guidance are also scored. The scores of all annotations attached to a clinical annotation are summed together to give a total score for the clinical annotation, which is used to calculate an LOE. Overall, the system increases transparency, consistency, and reproducibility in LOE assignment to clinical annotations. In combination with increased standardization of how clinical annotations are written, use of this scoring system helps to ensure that PharmGKB clinical annotations continue to be a robust source of pharmacogenomic information.
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Affiliation(s)
- Michelle Whirl-Carrillo
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Rachel Huddart
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Li Gong
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Caroline F Thorn
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Ryan Whaley
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science and Biomedical Informatics Research, School of Medicine, Stanford University, Stanford, California, USA
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17
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Gaedigk A, Casey ST, Whirl-Carrillo M, Miller NA, Klein TE. Pharmacogene Variation Consortium: A Global Resource and Repository for Pharmacogene Variation. Clin Pharmacol Ther 2021; 110:542-545. [PMID: 34091888 DOI: 10.1002/cpt.2321] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Affiliation(s)
- 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
| | - Scott T Casey
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | | | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
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18
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Sangkuhl K, Claudio-Campos K, Cavallari LH, Agundez JAG, Whirl-Carrillo M, Duconge J, Del Tredici AL, Wadelius M, Rodrigues Botton M, Woodahl EL, Scott SA, Klein TE, Pratt VM, Daly AK, Gaedigk A. PharmVar GeneFocus: CYP2C9. Clin Pharmacol Ther 2021; 110:662-676. [PMID: 34109627 DOI: 10.1002/cpt.2333] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C9 gene. Genetic variation within the CYP2C9 gene locus impacts the metabolism or bioactivation of many clinically important drugs, including nonsteroidal anti-inflammatory drugs, phenytoin, antidiabetic agents, and angiotensin receptor blockers. Variable CYP2C9 activity is of particular importance regarding efficacy and safety of warfarin and siponimod as indicated in their package inserts. This GeneFocus provides a comprehensive overview and summary of CYP2C9 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium.
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Affiliation(s)
- Katrin Sangkuhl
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Karla Claudio-Campos
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida, USA
| | - Jose A G Agundez
- University Institute of Molecular Pathology Biomarkers, University of Extremadura, Asthma, Adverse Drug Reactions and Allergy (ARADyAL) Institute de Salud Carlos III, Cáceres, Spain
| | - Michelle Whirl-Carrillo
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Jorge Duconge
- School of Pharmacy, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, USA
| | | | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, California, USA.,Stanford Health Care Clinical Genomics Laboratory, Palo Alto, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, USA
| | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ann K Daly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri - Kansas City, Kansas City, Missouri, USA
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19
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Pratt VM, Cavallari LH, Del Tredici AL, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, van Schaik RHN, Whirl-Carrillo M, Weck KE. Recommendations for Clinical CYP2D6 Genotyping Allele Selection: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, and the European Society for Pharmacogenomics and Personalized Therapy. J Mol Diagn 2021; 23:1047-1064. [PMID: 34118403 DOI: 10.1016/j.jmoldx.2021.05.013] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/11/2021] [Accepted: 05/25/2021] [Indexed: 01/14/2023] 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 to determine a minimal set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations on a minimal panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories in designing assays for PGx testing. When developing these recommendations, 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 with regard to PGx testing. The ultimate goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This document is focused on clinical CYP2D6 PGx testing that may be applied to all cytochrome P450 2D6-metabolized medications. These recommendations are not meant to be interpreted as prescriptive but to provide a reference guide for clinical laboratories that may be either implementing PGx testing or reviewing and updating their existing platform.
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Affiliation(s)
- Victoria M Pratt
- The 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.
| | - Larisa H Cavallari
- The 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
| | - Andria L Del Tredici
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Millennium Health, LLC, San Diego, California
| | - Andrea Gaedigk
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Houda Hachad
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; private precision medicine consultancy, Seattle, Washington
| | - Yuan Ji
- The 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
- The 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
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- The 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
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Program, Stanford Health Care, Palo Alto, California
| | - R H N van Schaik
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Chemistry/IFCC Expert center Pharmacogenetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands; European Society of Pharmacogenomics and Personalized Therapy
| | - Michelle Whirl-Carrillo
- The 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
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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20
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Desta Z, El-Boraie A, Gong L, Somogyi AA, Lauschke VM, Dandara C, Klein K, Miller NA, Klein TE, Tyndale RF, Whirl-Carrillo M, Gaedigk A. PharmVar GeneFocus: CYP2B6. Clin Pharmacol Ther 2021; 110:82-97. [PMID: 33448339 DOI: 10.1002/cpt.2166] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP2B6 gene. Genetic variation within the CYP2B6 gene locus impacts the metabolism or bioactivation of clinically important drugs. Of particular importance are efficacy and safety concerns regarding: efavirenz, which is used for the treatment of HIV type-1 infection; methadone, a mainstay in the treatment of opioid use disorder and as an analgesic; ketamine, used as an antidepressant and analgesic; and bupropion, which is prescribed to treat depression and for smoking cessation. This GeneFocus provides a comprehensive overview and summary of CYP2B6 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
- Zeruesenay Desta
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ahmed El-Boraie
- Centre for Addiction and Mental Health and Departments of Pharmacology & Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Andrew A Somogyi
- Discipline of Pharmacology, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology & Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Neil A Miller
- Genomic Medicine Center, Children's Mercy, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Rachel F Tyndale
- Centre for Addiction and Mental Health and Departments of Pharmacology & Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | | | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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21
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Jeiziner C, Suter K, Wernli U, Barbarino JM, Gong L, Whirl-Carrillo M, Klein TE, Szucs TD, Hersberger KE, Meyer zu Schwabedissen HE. Pharmacogenetic information in Swiss drug labels - a systematic analysis. Pharmacogenomics J 2021; 21:423-434. [PMID: 33070160 PMCID: PMC8292148 DOI: 10.1038/s41397-020-00195-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/18/2020] [Accepted: 10/05/2020] [Indexed: 01/31/2023]
Abstract
Implementation of pharmacogenetics (PGx) and individualization of drug therapy is supposed to obviate adverse drug reactions or therapy failure. Health care professionals (HCPs) use drug labels (DLs) as reliable information about drugs. We analyzed the Swiss DLs to give an overview on the currently available PGx instructions. We screened 4306 DLs applying natural language processing focusing on drug metabolism (pharmacokinetics) and we assigned PGx levels following the classification system of PharmGKB. From 5979 hits, 2564 were classified as PGx-relevant affecting 167 substances. 55% (n = 93) were classified as "actionable PGx". Frequently, PGx information appeared in the pharmacokinetics section and in DLs of the anatomic group "nervous system". Unstandardized wording, appearance of PGx information in different sections and unclear instructions challenge HCPs to identify and interpret PGx information and translate it into practice. HCPs need harmonization and standardization of PGx information in DLs to personalize drug therapies and tailor pharmaceutical care.
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Affiliation(s)
- C. Jeiziner
- grid.6612.30000 0004 1937 0642Pharmaceutical Care Research Group, Department of Pharmaceutical Sciences, University of Basel, Basel, 4001 Switzerland
| | - K. Suter
- grid.6612.30000 0004 1937 0642European Center of Pharmaceutical Medicine, Faculty of Medicine, University of Basel, Basel, 4056 Switzerland
| | - U. Wernli
- grid.6612.30000 0004 1937 0642Pharmaceutical Care Research Group, Department of Pharmaceutical Sciences, University of Basel, Basel, 4001 Switzerland
| | - J. M. Barbarino
- grid.168010.e0000000419368956Department of Biomedical Data Sciences, Stanford University, Stanford, CA 94305 USA
| | - L. Gong
- grid.168010.e0000000419368956Department of Biomedical Data Sciences, Stanford University, Stanford, CA 94305 USA
| | - M. Whirl-Carrillo
- grid.168010.e0000000419368956Department of Biomedical Data Sciences, Stanford University, Stanford, CA 94305 USA
| | - T. E. Klein
- grid.168010.e0000000419368956Department of Biomedical Data Sciences, Stanford University, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Stanford University, Stanford, CA 94305 USA
| | - T. D. Szucs
- grid.6612.30000 0004 1937 0642European Center of Pharmaceutical Medicine, Faculty of Medicine, University of Basel, Basel, 4056 Switzerland
| | - K. E. Hersberger
- grid.6612.30000 0004 1937 0642Pharmaceutical Care Research Group, Department of Pharmaceutical Sciences, University of Basel, Basel, 4001 Switzerland
| | - H. E. Meyer zu Schwabedissen
- grid.6612.30000 0004 1937 0642Biopharmacy, Department of Pharmaceutical Sciences, University of Basel, Basel, 4056 Switzerland
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22
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McInnes G, Lavertu A, Sangkuhl K, Klein TE, Whirl-Carrillo M, Altman RB. Pharmacogenetics at Scale: An Analysis of the UK Biobank. Clin Pharmacol Ther 2020; 109:1528-1537. [PMID: 33237584 DOI: 10.1002/cpt.2122] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/22/2020] [Indexed: 01/06/2023]
Abstract
Pharmacogenetics (PGx) studies the influence of genetic variation on drug response. Clinically actionable associations inform guidelines created by the Clinical Pharmacogenetics Implementation Consortium (CPIC), but the broad impact of genetic variation on entire populations is not well understood. We analyzed PGx allele and phenotype frequencies for 487,409 participants in the UK Biobank, the largest PGx study to date. For 14 CPIC pharmacogenes known to influence human drug response, we find that 99.5% of individuals may have an atypical response to at least 1 drug; on average they may have an atypical response to 10.3 drugs. Nearly 24% of participants have been prescribed a drug for which they are predicted to have an atypical response. Non-European populations carry a greater frequency of variants that are predicted to be functionally deleterious; many of these are not captured by current PGx allele definitions. Strategies for detecting and interpreting rare variation will be critical for enabling broad application of pharmacogenetics.
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Affiliation(s)
- Gregory McInnes
- Biomedical Informfatics Training Program, Stanford University, Stanford, California, USA
| | - Adam Lavertu
- Biomedical Informfatics Training Program, Stanford University, Stanford, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | | | - Russ B Altman
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Departments of Bioengineering, Genetics, and Medicine, Stanford University, Stanford, California, USA
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23
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McInnes G, Dalton R, Sangkuhl K, Whirl-Carrillo M, Lee SB, Tsao PS, Gaedigk A, Altman RB, Woodahl EL. Transfer learning enables prediction of CYP2D6 haplotype function. PLoS Comput Biol 2020; 16:e1008399. [PMID: 33137098 PMCID: PMC7660895 DOI: 10.1371/journal.pcbi.1008399] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 11/12/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene whose protein product metabolizes more than 20% of clinically used drugs. Genetic variations in CYP2D6 are responsible for interindividual heterogeneity in drug response that can lead to drug toxicity and ineffective treatment, making CYP2D6 one of the most important pharmacogenes. Prediction of CYP2D6 phenotype relies on curation of literature-derived functional studies to assign a functional status to CYP2D6 haplotypes. As the number of large-scale sequencing efforts grows, new haplotypes continue to be discovered, and assignment of function is challenging to maintain. To address this challenge, we have trained a convolutional neural network to predict functional status of CYP2D6 haplotypes, called Hubble.2D6. Hubble.2D6 predicts haplotype function from sequence data and was trained using two pre-training steps with a combination of real and simulated data. We find that Hubble.2D6 predicts CYP2D6 haplotype functional status with 88% accuracy in a held-out test set and explains 47.5% of the variance in in vitro functional data among star alleles with unknown function. Hubble.2D6 may be a useful tool for assigning function to haplotypes with uncurated function, and used for screening individuals who are at risk of being poor metabolizers.
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Affiliation(s)
- Gregory McInnes
- Biomedical Informatics Training Program, Stanford University, Stanford, California, United States of America
| | - Rachel Dalton
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, United States of America
- Department of Biomedical and Translational Research, University of Florida, Gainesville, Florida, United States of America
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Michelle Whirl-Carrillo
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | - Seung-been Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Philip S. Tsao
- VA Palo Alto Epidemiology Research and Information Center for Genomics, VAPAHCS, Palo Alto, California, United States of America
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, Missouri, United States of America
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
- Departments of Bioengineering, Genetics, and Medicine, Stanford University, Stanford, California, United States of America
| | - Erica L. Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, United States of America
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24
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Luvsantseren S, Whirl-Carrillo M, Sangkuhl K, Shin N, Wen A, Empey P, Alam B, David S, Dunnenberger HM, Orlando L, Altman R, Palaniappan L. Variant Interpretation in Current Pharmacogenetic Testing. J Pers Med 2020; 10:jpm10040204. [PMID: 33142667 PMCID: PMC7712137 DOI: 10.3390/jpm10040204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 11/17/2022] Open
Abstract
In the current marketplace, there are now more than a dozen commercial companies providing pharmacogenetic tests. Each company varies in the panel of genes they test and the variants they are able to screen for. The reports generated by these companies provide phenotypic interpretations of pharmacogenes and clinically actionable gene–drug interactions based on internally curated data and proprietary algorithms. The freedom to choose the types of evidence to include versus exclude in interpreting genomics has created reporting discrepancies in the industry. The case report presented here reveals the discordant phenotype analysis provided by two pharmacogenetic testing companies. The uncertainty and unnecessary distress experienced by the patient highlights the need for consensus in phenotype reporting within the industry.
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Affiliation(s)
- Sally Luvsantseren
- Department of Pharmacy, Stanford Health Care, Stanford, CA 94305, USA; (S.L.); (N.S.); (A.W.)
| | - Michelle Whirl-Carrillo
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; (M.W.-C.); (K.S.); (R.A.)
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; (M.W.-C.); (K.S.); (R.A.)
| | - Nancy Shin
- Department of Pharmacy, Stanford Health Care, Stanford, CA 94305, USA; (S.L.); (N.S.); (A.W.)
| | - Alice Wen
- Department of Pharmacy, Stanford Health Care, Stanford, CA 94305, USA; (S.L.); (N.S.); (A.W.)
| | - Philip Empey
- Department of Pharmacy and Therapeutics, Center for Clinical Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA;
| | - Benish Alam
- Department of Pharmacotherapy & Translational Research, University of Florida College of Pharmacy, Gainesville, FL 32610, USA;
| | - Sean David
- Department of Family Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA;
| | - Henry M. Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University Health System, Evanston, IL 60201, USA;
| | - Lori Orlando
- Department of Medicine and The Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27708, USA;
| | - Russ Altman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; (M.W.-C.); (K.S.); (R.A.)
| | - Latha Palaniappan
- Division of Primary Care and Population Health, School of Medicine, Stanford University, Stanford, CA 94305, USA
- Correspondence:
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25
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Huddart R, Whirl-Carrillo M, Altman RB, Klein TE. PharmGKB Tutorial for Pharmacogenomics of Drugs Potentially Used in the Context of COVID-19. Clin Pharmacol Ther 2020; 109:116-122. [PMID: 32978778 PMCID: PMC7537078 DOI: 10.1002/cpt.2067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/17/2020] [Indexed: 12/03/2022]
Abstract
Pharmacogenomics (PGx) is a key area of precision medicine, which is already being implemented in some health systems and may help guide clinicians toward effective therapies for individual patients. Over the last 2 decades, the Pharmacogenomics Knowledgebase (PharmGKB) has built a unique repository of PGx knowledge, including annotations of clinical guideline and regulator‐approved drug labels in addition to evidence‐based drug pathways and annotations of the scientific literature. All of this knowledge is freely accessible on the PharmGKB website. In the first of a series of PharmGKB tutorials, we introduce the PharmGKB coronavirus disease 2019 (COVID‐19) portal and, using examples of drugs found in the portal, demonstrate some of the main features of PharmGKB. This paper is intended as a resource to help users become quickly acquainted with the wealth of information stored in PharmGKB.
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Affiliation(s)
- Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Russ B Altman
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Biomedical Engineering, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
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26
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Karnes JH, Rettie AE, Somogyi AA, Huddart R, Fohner AE, Formea CM, Ta Michael Lee M, Llerena A, Whirl-Carrillo M, Klein TE, Phillips EJ, Mintzer S, Gaedigk A, Caudle KE, Callaghan JT. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2C9 and HLA-B Genotypes and Phenytoin Dosing: 2020 Update. Clin Pharmacol Ther 2020; 109:302-309. [PMID: 32779747 DOI: 10.1002/cpt.2008] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/25/2020] [Indexed: 12/19/2022]
Abstract
Phenytoin is an antiepileptic drug with a narrow therapeutic index and large interpatient pharmacokinetic variability, partly due to genetic variation in CYP2C9. Furthermore, the variant allele HLA-B*15:02 is associated with an increased risk of Stevens-Johnson syndrome and toxic epidermal necrolysis in response to phenytoin treatment. We summarize evidence from the published literature supporting these associations and provide therapeutic recommendations for the use of phenytoin based on CYP2C9 and/or HLA-B genotypes (updates on cpicpgx.org).
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Affiliation(s)
- Jason H Karnes
- Department of Pharmacy Practice & Science, University of Arizona College of Pharmacy, Tucson, Arizona, USA
- Sarver Heart Center, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington School of Pharmacy, Seattle, Washington, USA
| | - Andrew A Somogyi
- Discipline of Pharmacology, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Alison E Fohner
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Institute of Public Health Genetics, University of Washington, Seattle, Washington, USA
| | - Christine M Formea
- Department of Pharmacy and Intermountain Precision Genomics, Intermountain Healthcare, Salt Lake City, Utah, USA
| | - Ming Ta Michael Lee
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Adrian Llerena
- INUBE Extremadura University Biosanitary Research Institute and Medical School, Badajoz, Spain
| | | | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Medicine, Stanford University, Stanford, California, USA
| | - Elizabeth J Phillips
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Scott Mintzer
- Department of Neurology, Thomas Jefferson University Hospital Methodist Hospital Division of Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, 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
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John T Callaghan
- Department of Veteran Affairs and Departments of Medicine and Pharmacology/Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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27
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Huddart R, Gong L, Sangkuhl K, Thorn CF, Whirl-Carrillo M, Caudle KE, Relling MV, Klein TE. Response to: Unveiling the guidance heterogeneity for genome-informed drug treatment interventions among regulatory bodies and research consortia. Pharmacol Res 2020; 158:104838. [DOI: 10.1016/j.phrs.2020.104838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 12/17/2022]
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28
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Botton MR, Whirl-Carrillo M, Del Tredici AL, Sangkuhl K, Cavallari LH, Agúndez JAG, Duconge J, Lee MTM, Woodahl EL, Claudio-Campos K, Daly AK, Klein TE, Pratt VM, Scott SA, Gaedigk A. PharmVar GeneFocus: CYP2C19. Clin Pharmacol Ther 2020; 109:352-366. [PMID: 32602114 DOI: 10.1002/cpt.1973] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the metabolism of many drugs and has been associated with both efficacy and safety issues for several commonly prescribed medications. This GeneFocus provides a comprehensive overview and summary of CYP2C19 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | | | | | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - José A G Agúndez
- UNEx, ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Jorge Duconge
- School of Pharmacy, University of Puerto Rico, San Juan, Puerto Rico
| | | | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | | | - Ann K Daly
- Newcastle University, Newcastle upon Tyne, UK
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Victoria M Pratt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy, Kansas City, Missouri, USA
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29
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Pratt VM, Cavallari LH, Del Tredici AL, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, Whirl-Carrillo M, Weck KE. Recommendations for Clinical Warfarin Genotyping Allele Selection: A Report of the Association for Molecular Pathology and the College of American Pathologists. J Mol Diagn 2020; 22:847-859. [PMID: 32380173 DOI: 10.1016/j.jmoldx.2020.04.204] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/18/2020] [Accepted: 04/01/2020] [Indexed: 11/19/2022] Open
Abstract
The goal of the Association for Molecular Pathology (AMP) Clinical Practice Committee's AMP Pharmacogenomics (PGx) Working Group is to define the key attributes of PGx 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 AMP PGx Working Group considered functional impact of the variants, 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 is to promote standardization of PGx gene/allele testing across clinical laboratories. These recommendations are not to be interpreted as prescriptive but to provide a reference guide. Of note, a separate article with recommendations for CYP2C9 allele selection was previously developed by the PGx Working Group that can be applied broadly to CYP2C9-related medications. The warfarin allele recommendations in this report incorporate the previous CYP2C9 allele recommendations and additional genes and alleles that are specific to warfarin testing.
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Affiliation(s)
- Victoria M Pratt
- The 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.
| | - Larisa H Cavallari
- The 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
| | - Andria L Del Tredici
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Millennium Health, LLC, San Diego, California
| | - Houda Hachad
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Translational Software, Bellevue, Washington
| | - Yuan Ji
- The 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
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Reynold C Ly
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- The 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
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, a Mount Sinai venture, Stamford, Connecticut
| | - Michelle Whirl-Carrillo
- The 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
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Departments of Pathology and Laboratory Medicine and Genetics, University of North Carolina, Chapel Hill, North Carolina
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Gaedigk A, Whirl-Carrillo M, Pratt VM, Miller NA, Klein TE. PharmVar and the Landscape of Pharmacogenetic Resources. Clin Pharmacol Ther 2020; 107:43-46. [PMID: 31758698 PMCID: PMC6925620 DOI: 10.1002/cpt.1654] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 08/27/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | | | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
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31
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Nofziger C, Turner AJ, Sangkuhl K, Whirl-Carrillo M, Agúndez JAG, Black JL, Dunnenberger HM, Ruano G, Kennedy MA, Phillips MS, Hachad H, Klein TE, Gaedigk A. PharmVar GeneFocus: CYP2D6. Clin Pharmacol Ther 2019; 107:154-170. [PMID: 31544239 DOI: 10.1002/cpt.1643] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 01/13/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus. CYP2D6 genetic variation impacts the metabolism of numerous drugs and, thus, can impact drug efficacy and safety. This GeneFocus provides a comprehensive overview and summary of CYP2D6 genetic variation and describes how the information provided by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | - Amy J Turner
- Section of Genomic Pediatrics, Department of Pediatrics, Children's Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - José A G Agúndez
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres, Spain.,ARADyAL Instituto de Salud Carlos III, Madrid, Spain
| | - John L Black
- Division of Laboratory Genetics and Genomics, Personalized Genomics Laboratory, Mayo Clinic Laboratories, Mayo Clinic, Rochester, Minnesota, USA
| | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanton, Illinois, USA
| | - Gualberto Ruano
- Institute of Living at Hartford Hospital, Genomas Laboratory of Personalized Health, Hartford, Connecticut, USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University Otago, Christchurch, New Zealand
| | | | - Houda Hachad
- Translational Software, Bellevue, Washington, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, 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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32
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Relling MV, Klein TE, Gammal RS, Whirl-Carrillo M, Hoffman JM, Caudle KE. The Clinical Pharmacogenetics Implementation Consortium: 10 Years Later. Clin Pharmacol Ther 2019; 107:171-175. [PMID: 31562822 DOI: 10.1002/cpt.1651] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/04/2019] [Indexed: 01/07/2023]
Abstract
In 2009, the Clinical Pharmacogenetics Implementation Consortium (CPIC, www.cpicpgx.org), a shared project between Pharmacogenomics Knowledge Base (PharmGKB, http://www.pharmgkb.org) and the National Institutes of Health (NIH), was created to provide freely available, evidence-based, peer-reviewed, and updated pharmacogenetic clinical practice guidelines. To date, CPIC has published 23 guidelines (of which 11 have been updated), covering 19 genes and 46 drugs across several therapeutic areas. CPIC also now provides additional resources to facilitate the implementation of pharmacogenetics into routine clinical practice and the electronic health record. Furthermore, since its inception, CPIC's interactions with other resources, databases, websites, and genomic communities have grown. The purpose of this paper is to highlight the progress of CPIC over the past 10 years.
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Affiliation(s)
- Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Roseann S Gammal
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Pharmacy Practice, MCPHS University School of Pharmacy, Boston, Massachusetts, USA
| | | | - James M Hoffman
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Office of Quality & Patient Care, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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33
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Caudle KE, Sangkuhl K, Whirl-Carrillo M, Swen JJ, Haidar CE, Klein TE, Gammal RS, Relling MV, Scott SA, Hertz DL, Guchelaar HJ, Gaedigk A. Standardizing CYP2D6 Genotype to Phenotype Translation: Consensus Recommendations from the Clinical Pharmacogenetics Implementation Consortium and Dutch Pharmacogenetics Working Group. Clin Transl Sci 2019; 13:116-124. [PMID: 31647186 PMCID: PMC6951851 DOI: 10.1111/cts.12692] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 08/05/2019] [Indexed: 12/17/2022] Open
Abstract
Translating CYP2D6 genotype to metabolizer phenotype is not standardized across clinical laboratories offering pharmacogenetic (PGx) testing and PGx clinical practice guidelines, such as the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG). The genotype to phenotype translation discordance between laboratories and guidelines can cause discordant cytochrome P450 2D6 (CYP2D6) phenotype assignments and, thus lead to inconsistent therapeutic recommendations and confusion among patients and clinicians. A modified-Delphi method was used to obtain consensus for a uniform system for translating CYP2D6 genotype to phenotype among a panel of international CYP2D6 experts. Experts with diverse involvement in CYP2D6 interpretation (clinicians, researchers, genetic testing laboratorians, and PGx implementers; n = 37) participated in conference calls and surveys. After completion of 7 surveys, a consensus (> 70%) was reached with 82% of the CYP2D6 experts agreeing to the final CYP2D6 genotype to phenotype translation method. Broad adoption of the proposed CYP2D6 genotype to phenotype translation method by guideline developers, such as CPIC and DPWG, and clinical laboratories as well as researchers will result in more consistent interpretation of CYP2D6 genotype.
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Affiliation(s)
- Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Jesse J Swen
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Cyrine E Haidar
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Roseann S Gammal
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Pharmacy Practice, MCPHS University School of Pharmacy, Boston, Massachusetts, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, a Mount Sinai venture, Stamford, Connecticut, USA
| | - Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - 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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34
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Thorn CF, Whirl-Carrillo M, Hachad H, Johnson JA, McDonagh EM, Ratain MJ, Relling MV, Scott SA, Altman RB, Klein TE. Essential Characteristics of Pharmacogenomics Study Publications. Clin Pharmacol Ther 2019; 105:86-91. [PMID: 30406943 DOI: 10.1002/cpt.1279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/02/2018] [Indexed: 12/17/2022]
Abstract
Pharmacogenomics (PGx) can be seen as a model for biomedical studies: it includes all disease areas of interest and spans in vitro studies to clinical trials, while focusing on the relationships between genes and drugs and the resulting phenotypes. This review will examine different characteristics of PGx study publications and provide examples of excellence in framing PGx questions and reporting their resulting data in a way that maximizes the knowledge that can be built on them.
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Affiliation(s)
- Caroline F Thorn
- Department of Biomedical Data Sciences, Stanford University, Stanford, California, USA
| | | | - Houda Hachad
- Translational Software, Bellevue, Washington, USA
| | - Julie A Johnson
- College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | | | - Mark J Ratain
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Mary V Relling
- Pharmaceutical Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - Russ B Altman
- Department of Genetics, Department of Computer Science, Department of Biomedical Engineering, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Sciences, Stanford University, Stanford, California, USA
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35
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Sangkuhl K, Whirl-Carrillo M, Whaley RM, Woon M, Lavertu A, Altman RB, Carter L, Verma A, Ritchie MD, Klein TE. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clin Pharmacol Ther 2019; 107:203-210. [PMID: 31306493 PMCID: PMC6977333 DOI: 10.1002/cpt.1568] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/11/2019] [Indexed: 11/07/2022]
Abstract
Pharmacogenomics (PGx) decision support and return of results is an active area of precision medicine. One challenge of implementing PGx is extracting genomic variants and assigning haplotypes in order to apply prescribing recommendations and information from the Clinical Pharmacogenetics Implementation Consortium (CPIC), the US Food and Drug Administration (FDA), the Pharmacogenomics Knowledgebase (PharmGKB), etc. Pharmacogenomics Clinical Annotation Tool (PharmCAT) (i) extracts variants specified in guidelines from a genetic data set derived from sequencing or genotyping technologies, (ii) infers haplotypes and diplotypes, and (iii) generates a report containing genotype/diplotype-based annotations and guideline recommendations. We describe PharmCAT and a pilot validation project comparing results for 1000 Genomes Project sequences of Coriell samples with corresponding Genetic Testing Reference Materials Coordination Program (GeT-RM) sample characterization. PharmCAT was highly concordant with the GeT-RM data. PharmCAT is available in GitHub to evaluate, test, and report results back to the community. As precision medicine becomes more prevalent, our ability to consistently, accurately, and clearly define and report PGx annotations and prescribing recommendations is critical.
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Affiliation(s)
- Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | | | - Ryan M Whaley
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | - Adam Lavertu
- Biomedical Informatics Training Program, Stanford University, Palo Alto, California, USA
| | - Russ B Altman
- Departments of Biomedical Data Science, Biomedical Engineering, Genetics and Medicine, Stanford University, Palo Alto, California, USA
| | - Lester Carter
- formerly Department of Genetics, Stanford University, Palo Alto, California, USA
| | - Anurag Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Teri E Klein
- Department of Biomedical Data Science and Biomedical Informatics Research, School of Medicine, Stanford University, Palo Alto, California, USA
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36
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Pratt VM, Cavallari LH, Del Tredici AL, Hachad H, Ji Y, Moyer AM, Scott SA, Whirl-Carrillo M, Weck KE. Recommendations for Clinical CYP2C9 Genotyping Allele Selection: A Joint Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2019; 21:746-755. [PMID: 31075510 PMCID: PMC7057225 DOI: 10.1016/j.jmoldx.2019.04.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/03/2019] [Accepted: 04/22/2019] [Indexed: 01/17/2023] Open
Abstract
The goals of the Association for Molecular Pathology Pharmacogenomics (PGx) Working Group of the Association for Molecular Pathology Clinical Practice Committee are to define the key attributes of PGx alleles recommended for clinical testing and a minimum set of variants that should be included in clinical PGx genotyping assays. This document 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 CYP2C9 testing. The Working Group considered the functional impact of the variants, allele frequencies in different populations and ethnicities, the availability of reference materials, and other technical considerations for PGx testing when developing these recommendations. Our goal is to promote standardization of testing PGx genes and alleles across clinical laboratories. These recommendations are not to be interpreted as restrictive but to provide a reference guide. The current document will focus on CYP2C9 testing that can be applied to all CYP2C9-related medications. A separate recommendation on warfarin PGx testing is being developed to include recommendations on CYP2C9 alleles and additional warfarin sensitivity-associated genes and alleles.
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Affiliation(s)
- Victoria M Pratt
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, 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, Bethesda, Maryland; Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, Florida
| | - Andria L Del Tredici
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Millennium Health, LLC, San Diego, California
| | - Houda Hachad
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Translational Software, Bellevue, Washington
| | - Yuan Ji
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ann M Moyer
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, 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, Bethesda, Maryland; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, Stamford, Connecticut
| | - Michelle Whirl-Carrillo
- The Pharmacogenomics (PGx) Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, 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, Bethesda, Maryland; Department of Pathology and Laboratory Medicine and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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37
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Desta Z, Gammal RS, Gong L, Whirl-Carrillo M, Gaur AH, Sukasem C, Hockings J, Myers A, Swart M, Tyndale RF, Masimirembwa C, Iwuchukwu OF, Chirwa S, Lennox J, Gaedigk A, Klein TE, Haas DW. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2B6 and Efavirenz-Containing Antiretroviral Therapy. Clin Pharmacol Ther 2019; 106:726-733. [PMID: 31006110 DOI: 10.1002/cpt.1477] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/12/2019] [Indexed: 01/11/2023]
Abstract
The HIV type-1 nonnucleoside reverse transcriptase inhibitor, efavirenz, is widely used to treat HIV type-1 infection. Efavirenz is predominantly metabolized into inactive metabolites by cytochrome P450 (CYP)2B6, and patients with certain CYP2B6 genetic variants may be at increased risk for adverse effects, particularly central nervous system toxicity and treatment discontinuation. We summarize the evidence from the literature and provide therapeutic recommendations for efavirenz prescribing based on CYP2B6 genotypes.
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Affiliation(s)
- Zeruesenay Desta
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Roseann S Gammal
- Department of Pharmacy Practice, Massachusetts College of Pharmacy and Health Sciences University School of Pharmacy, Boston, Massachusetts, USA.,Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Aditya H Gaur
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Faculty of Medicine Ramathibodi Hospital, Department of Pathology, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Faculty of Medicine Ramathibodi Hospital, Somdech Phra Debaratana Medical Center, Bangkok, Thailand
| | - Jennifer Hockings
- Department of Pharmacy and Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Alan Myers
- Department of Diagnostic & Biomedical Sciences, The University of Texas Health Sciences Center School of Dentistry, Houston, Texas, USA
| | - Marelize Swart
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rachel F Tyndale
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada
| | - Collen Masimirembwa
- African Institute of Biomedical Science & Technology, Wilkins Hospital, Harare, Zimbabwe
| | - Otito F Iwuchukwu
- Division of Pharmaceutical Sciences, Fairleigh Dickinson University School of Pharmacy, Florham Park, New Jersey, USA
| | - Sanika Chirwa
- Department of Internal Medicine, Meharry Medical College School of Medicine, Nashville, Tennessee, USA
| | - Jeffrey Lennox
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrea Gaedigk
- 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
| | - David W Haas
- Department of Internal Medicine, Meharry Medical College School of Medicine, Nashville, Tennessee, USA.,Departments of Medicine, Pharmacology, Pathology, Microbiology, & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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Huddart R, Sangkuhl K, Whirl-Carrillo M, Klein TE. Are Randomized Controlled Trials Necessary to Establish the Value of Implementing Pharmacogenomics in the Clinic? Clin Pharmacol Ther 2019; 106:284-286. [PMID: 30977517 DOI: 10.1002/cpt.1420] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 02/22/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
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39
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Huddart R, Fohner AE, Whirl-Carrillo M, Wojcik GL, Gignoux CR, Popejoy AB, Bustamante CD, Altman RB, Klein TE. Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research. Clin Pharmacol Ther 2019; 105:1256-1262. [PMID: 30506572 DOI: 10.1002/cpt.1322] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022]
Abstract
The varying frequencies of pharmacogenetic alleles among populations have important implications for the impact of these alleles in different populations. Current population grouping methods to communicate these patterns are insufficient as they are inconsistent and fail to reflect the global distribution of genetic variability. To facilitate and standardize the reporting of variability in pharmacogenetic allele frequencies, we present seven geographically defined groups: American, Central/South Asian, East Asian, European, Near Eastern, Oceanian, and Sub-Saharan African, and two admixed groups: African American/Afro-Caribbean and Latino. These nine groups are defined by global autosomal genetic structure and based on data from large-scale sequencing initiatives. We recognize that broadly grouping global populations is an oversimplification of human diversity and does not capture complex social and cultural identity. However, these groups meet a key need in pharmacogenetics research by enabling consistent communication of the scale of variability in global allele frequencies and are now used by Pharmacogenomics Knowledgebase (PharmGKB).
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Affiliation(s)
- Rachel Huddart
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Alison E Fohner
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | | | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Christopher R Gignoux
- Department of Biostatistics, Division of Bioinformatics and Personalized Medicine, University of Colorado, Aurora, Colorado, USA
| | - Alice B Popejoy
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Stanford Center for Integration of Research on Genetics and Ethics, Stanford, California, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA
| | - Russ B Altman
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Genetics, Stanford University, Stanford, California, USA.,Department of Biomedical Engineering, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA.,Shriram Center for BioE & ChemE, Stanford, California, USA
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40
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Relling MV, Schwab M, Whirl-Carrillo M, Suarez-Kurtz G, Pui CH, Stein CM, Moyer AM, Evans WE, Klein TE, Antillon-Klussmann FG, Caudle KE, Kato M, Yeoh AEJ, Schmiegelow K, Yang JJ. Clinical Pharmacogenetics Implementation Consortium Guideline for Thiopurine Dosing Based on TPMT and NUDT15 Genotypes: 2018 Update. Clin Pharmacol Ther 2019; 105:1095-1105. [PMID: 30447069 DOI: 10.1002/cpt.1304] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/24/2018] [Indexed: 12/14/2022]
Abstract
Thiopurine methyltransferase (TPMT) activity exhibits a monogenic codominant inheritance and catabolizes thiopurines. TPMT variant alleles are associated with low enzyme activity and pronounced pharmacologic effects of thiopurines. Loss-of-function alleles in the NUDT15 gene are common in Asians and Hispanics and reduce the degradation of active thiopurine nucleotide metabolites, also predisposing to myelosuppression. We provide recommendations for adjusting starting doses of azathioprine, mercaptopurine, and thioguanine based on TPMT and NUDT15 genotypes (updates on www.cpicpgx.org).
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Affiliation(s)
- Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- Department of Clinical Pharmacology, Institute of Experimental and Clinical Pharmacology and Toxicology, University Hospital, Tuebingen, Germany
- Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | | | - Guilherme Suarez-Kurtz
- Instituto Nacional de Câncer, Rio de Janeiro, Brazil Pharmacogenomics Network, Rio de Janeiro, Brazil
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles M Stein
- Division of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - William E Evans
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teri E Klein
- Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | | | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development, Tokyo, Japan
| | - Allen E J Yeoh
- National University Health System, National University Cancer Institute, Singapore
- Viva University Children's Cancer Centre, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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41
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Whirl-Carrillo M. Bioinformatics: Accumulating and implementing pharmacogenomics information. Drug Metab Pharmacokinet 2019. [DOI: 10.1016/j.dmpk.2018.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Gaedigk A, Sangkuhl K, Whirl-Carrillo M, Twist GP, Klein TE, Miller NA. The Evolution of PharmVar. Clin Pharmacol Ther 2018; 105:29-32. [PMID: 30536702 PMCID: PMC6312487 DOI: 10.1002/cpt.1275] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/25/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | - Greyson P Twist
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Neil A Miller
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA
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43
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Yang JJ, Whirl-Carrillo M, Scott SA, Turner AJ, Schwab M, Tanaka Y, Suarez-Kurtz G, Schaeffeler E, Klein TE, Miller NA, Gaedigk A. Pharmacogene Variation Consortium Gene Introduction: NUDT15. Clin Pharmacol Ther 2018; 105:1091-1094. [PMID: 30515762 PMCID: PMC6465081 DOI: 10.1002/cpt.1268] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - Amy J Turner
- Department of Pediatrics, Section of Genomic Pediatrics and Children's Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
| | - Yoichi Tanaka
- Department of Clinical Pharmacy, School of Pharmacy, Kitasato University, Shirokane, Minato-ku, Tokyo, Japan
| | | | - Elke Schaeffeler
- RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA.,University of Tübingen, Tübingen, Germany
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Andrea Gaedigk
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
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44
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Caudle KE, Keeling NJ, Klein TE, Whirl-Carrillo M, Pratt VM, Hoffman JM. Standardization can accelerate the adoption of pharmacogenomics: current status and the path forward. Pharmacogenomics 2018; 19:847-860. [PMID: 29914287 DOI: 10.2217/pgs-2018-0028] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Successfully implementing pharmacogenomics into routine clinical practice requires an efficient process to order genetic tests and report the results to clinicians and patients. Lack of standardized approaches and terminology in clinical laboratory processes, ordering of the test and reporting of test results all impede this workflow. Expert groups such as the Association for Molecular Pathology and the Clinical Pharmacogenetics Implementation Consortium have published recommendations for standardizing laboratory genetic testing, reporting and terminology. Other resources such as PharmGKB, ClinVar, ClinGen and PharmVar have established databases of nomenclature for pharmacogenetic alleles and variants. Opportunities remain to develop new standards and further disseminate existing standards which will accelerate the implementation of pharmacogenomics.
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Affiliation(s)
- Kelly E Caudle
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nicholas J Keeling
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Pharmacy Administration, University of Mississippi School of Pharmacy, Oxford, MS 38655, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Victoria M Pratt
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - James M Hoffman
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN 38105, USA.,Office of Quality & Patient Care, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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45
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Lavertu A, McInnes G, Daneshjou R, Whirl-Carrillo M, Klein TE, Altman RB. Pharmacogenomics and big genomic data: from lab to clinic and back again. Hum Mol Genet 2018; 27:R72-R78. [PMID: 29635477 PMCID: PMC5946941 DOI: 10.1093/hmg/ddy116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 02/06/2023] Open
Abstract
The field of pharmacogenomics is an area of great potential for near-term human health impacts from the big genomic data revolution. Pharmacogenomics research momentum is building with numerous hypotheses currently being investigated through the integration of molecular profiles of different cell lines and large genomic data sets containing information on cellular and human responses to therapies. Additionally, the results of previous pharmacogenetic research efforts have been formulated into clinical guidelines that are beginning to impact how healthcare is conducted on the level of the individual patient. This trend will only continue with the recent release of new datasets containing linked genotype and electronic medical record data. This review discusses key resources available for pharmacogenomics and pharmacogenetics research and highlights recent work within the field.
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Affiliation(s)
- Adam Lavertu
- Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA
| | - Greg McInnes
- Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305, USA
| | - Roxana Daneshjou
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Russ B Altman
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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46
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Phillips EJ, Sukasem C, Whirl-Carrillo M, Müller DJ, Dunnenberger HM, Chantratita W, Goldspiel B, Chen YT, Carleton BC, George AL, Mushiroda T, Klein T, Gammal RS, Pirmohamed M. Clinical Pharmacogenetics Implementation Consortium Guideline for HLA Genotype and Use of Carbamazepine and Oxcarbazepine: 2017 Update. Clin Pharmacol Ther 2018; 103:574-581. [PMID: 29392710 DOI: 10.1002/cpt.1004] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022]
Abstract
The variant allele HLA-B*15:02 is strongly associated with greater risk of Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) in patients treated with carbamazepine or oxcarbazepine. The variant allele HLA-A*31:01 is associated with greater risk of maculopapular exanthema, drug reaction with eosinophilia and systemic symptoms, and SJS/TEN in patients treated with carbamazepine. We summarize evidence from the published literature supporting these associations and provide recommendations for carbamazepine and oxcarbazepine use based on HLA genotypes.
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Affiliation(s)
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center, Faculty of Medicine Ramathibodi Hospital, Bangkok, Thailand
| | | | - Daniel J Müller
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry and Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Henry M Dunnenberger
- Center for Molecular Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Wasun Chantratita
- Virology Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Center for Medical Genomics, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Barry Goldspiel
- Pharmacy Department, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Bruce C Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, and BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - Teri Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Roseann S Gammal
- Department of Pharmacy Practice, MCPHS University, Boston, Massachusetts, USA.,Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Munir Pirmohamed
- Department of Pharmacology, University of Liverpool, Liverpool, UK
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47
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Goetz MP, Sangkuhl K, Guchelaar HJ, Schwab M, Province M, Whirl-Carrillo M, Symmans WF, McLeod HL, Ratain MJ, Zembutsu H, Gaedigk A, van Schaik RH, Ingle JN, Caudle KE, Klein TE. Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2D6 and Tamoxifen Therapy. Clin Pharmacol Ther 2018; 103:770-777. [PMID: 29385237 DOI: 10.1002/cpt.1007] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/14/2017] [Accepted: 12/23/2017] [Indexed: 12/15/2022]
Abstract
Tamoxifen is biotransformed by CYP2D6 to 4-hydroxytamoxifen and 4-hydroxy N-desmethyl tamoxifen (endoxifen), both with greater antiestrogenic potency than the parent drug. Patients with certain CYP2D6 genetic polymorphisms and patients who receive strong CYP2D6 inhibitors exhibit lower endoxifen concentrations and a higher risk of disease recurrence in some studies of tamoxifen adjuvant therapy of early breast cancer. We summarize evidence from the literature and provide therapeutic recommendations for tamoxifen based on CYP2D6 genotype.
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Affiliation(s)
- Matthew P Goetz
- Department of Oncology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital, Tuebingen, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Michael Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - W Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Mark J Ratain
- Center for Personalized Therapeutics, University of Chicago, Chicago, Illinois, USA
| | - Hitoshi Zembutsu
- Division of Human Genetics, National Cancer Center, Research Institute, Tokyo, Japan
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City and Department of Pediatrics, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Ron H van Schaik
- International Expertcenter Pharmacogenetics, Dept Clinical Chemistry, Erasmus MC, Rotterdam, The Netherlands.,LKCH UMC Utrecht, The Netherlands
| | - James N Ingle
- Department of Oncology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Kelly E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
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48
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Bank PCD, Caudle KE, Swen JJ, Gammal RS, Whirl-Carrillo M, Klein TE, Relling MV, Guchelaar HJ. Comparison of the Guidelines of the Clinical Pharmacogenetics Implementation Consortium and the Dutch Pharmacogenetics Working Group. Clin Pharmacol Ther 2017; 103:599-618. [PMID: 28994452 DOI: 10.1002/cpt.762] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 05/24/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022]
Abstract
Both the Clinical Pharmacogenetics Implementation Consortium (CPIC) and Dutch Pharmacogenetics Working Group provide therapeutic recommendations for well-known gene-drug pairs. Published recommendations show a high rate of concordance. However, as a result of different guideline development methods used by these two consortia, differences between the published guidelines exist. The aim of this paper is to compare both initiatives and explore these differences, with the objective to achieve harmonization.
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Affiliation(s)
- P C D Bank
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Centre, Leiden, The Netherlands
| | - K E Caudle
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - J J Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Centre, Leiden, The Netherlands
| | - R S Gammal
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Pharmacy Practice, MCPHS University, Boston, Massachusetts, USA
| | - M Whirl-Carrillo
- Pharmacogenomics Knowledgebase (PharmGKB), Stanford University School of Medicine, Palo Alto, California, USA
| | - T E Klein
- Pharmacogenomics Knowledgebase (PharmGKB), Stanford University School of Medicine, Palo Alto, California, USA
| | - M V Relling
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - H-J Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Centre, Leiden, The Netherlands
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49
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Luzum JA, Pakyz RE, Elsey AR, Haidar CE, Peterson JF, Whirl-Carrillo M, Handelman SK, Palmer K, Pulley JM, Beller M, Schildcrout JS, Field JR, Weitzel KW, Cooper-DeHoff RM, Cavallari LH, O’Donnell PH, Altman RB, Pereira N, Ratain MJ, Roden DM, Embi PJ, Sadee W, Klein TE, Johnson JA, Relling MV, Wang L, Weinshilboum RM, Shuldiner AR, Freimuth RR. The Pharmacogenomics Research Network Translational Pharmacogenetics Program: Outcomes and Metrics of Pharmacogenetic Implementations Across Diverse Healthcare Systems. Clin Pharmacol Ther 2017; 102:502-510. [PMID: 28090649 PMCID: PMC5511786 DOI: 10.1002/cpt.630] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022]
Abstract
Numerous pharmacogenetic clinical guidelines and recommendations have been published, but barriers have hindered the clinical implementation of pharmacogenetics. The Translational Pharmacogenetics Program (TPP) of the National Institutes of Health (NIH) Pharmacogenomics Research Network was established in 2011 to catalog and contribute to the development of pharmacogenetic implementations at eight US healthcare systems, with the goal to disseminate real-world solutions for the barriers to clinical pharmacogenetic implementation. The TPP collected and normalized pharmacogenetic implementation metrics through June 2015, including gene-drug pairs implemented, interpretations of alleles and diplotypes, numbers of tests performed and actionable results, and workflow diagrams. TPP participant institutions developed diverse solutions to overcome many barriers, but the use of Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines provided some consistency among the institutions. The TPP also collected some pharmacogenetic implementation outcomes (scientific, educational, financial, and informatics), which may inform healthcare systems seeking to implement their own pharmacogenetic testing programs.
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Affiliation(s)
- Jasmine A. Luzum
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
- Center for Pharmacogenomics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Ruth E. Pakyz
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Amanda R. Elsey
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Cyrine E. Haidar
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Josh F. Peterson
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Samuel K. Handelman
- Center for Pharmacogenomics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Kathleen Palmer
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Jill M. Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Marc Beller
- Office of Research Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jonathan S. Schildcrout
- Department of Statistics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Julie R. Field
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kristin W. Weitzel
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Rhonda M. Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Larisa H. Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Peter H. O’Donnell
- Center for Personalized Therapeutics, University of Chicago, Chicago, IL, USA
| | - Russ B. Altman
- Stanford University School of Medicine, Palo Alto, California, USA
| | - Naveen Pereira
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Mark J. Ratain
- Center for Personalized Therapeutics, University of Chicago, Chicago, IL, USA
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Peter J. Embi
- Department of Biomedical Informatics, Ohio State University, Columbus, OH, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics, College of Medicine, Ohio State University, Columbus, OH, USA
- Department of Cancer Biology and Genetics, College of Medicine, Ohio State University, Columbus, OH, USA
| | - Teri E. Klein
- Stanford University School of Medicine, Palo Alto, California, USA
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL, USA
| | - Mary V. Relling
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Richard M. Weinshilboum
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Alan R. Shuldiner
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, MD, USA
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50
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Bell GC, Caudle KE, Whirl-Carrillo M, Gordon RJ, Hikino K, Prows CA, Gaedigk A, Agundez J, Sadhasivam S, Klein TE, Schwab M. Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6 genotype and use of ondansetron and tropisetron. Clin Pharmacol Ther 2017; 102:213-218. [PMID: 28002639 DOI: 10.1002/cpt.598] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/07/2016] [Indexed: 12/16/2022]
Affiliation(s)
- G C Bell
- Personalized Medicine Program, Mission Health, Asheville, North Carolina, USA
| | - K E Caudle
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - M Whirl-Carrillo
- Department of Genetics, Stanford University, Stanford, California, USA
| | - R J Gordon
- University of California, San Diego, Department of Anesthesiology, San Diego, California, USA
| | - K Hikino
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, USA
| | - C A Prows
- Division of Human Genetics, Division of Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - A Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - Jag Agundez
- Department of Pediatrics, University of Missouri-Kansas City, Kansas City, Missouri, USA.,Department of Pharmacology, University of Extremadura, Cáceres, Spain
| | - S Sadhasivam
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA.,Department of Anesthesia, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - T E Klein
- Department of Genetics, Stanford University, Stanford, California, USA
| | - M Schwab
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tübingen, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany.,Department of Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
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