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Moyer AM, McMillin GA, Long TA, Gandhi MJ, Mao R, Smock KJ, Halley JG, Weck KE. Genotype and Phenotype Concordance for Pharmacogenetic Tests Through Proficiency Survey Testing. Arch Pathol Lab Med 2020; 144:1057-1066. [PMID: 32150456 DOI: 10.5858/arpa.2019-0478-cp] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— As pharmacogenetic testing is incorporated into routine care, it is essential for laboratories to provide accurate and consistent results. Certified laboratories must successfully complete proficiency testing. OBJECTIVES.— To understand and examine trends in participation and performance of laboratories participating in the College of American Pathologists pharmacogenetic proficiency testing surveys. DESIGN.— Results from College of American Pathologists pharmacogenetic proficiency testing challenges from 2012 through 2017 were reviewed for concordance with expected genotype and phenotype for each sample (intended responses). RESULTS.— Laboratories correctly reported results for 96.7% to 100% of samples with no variants. Excluding CYP2D6, laboratories correctly detected and reported variant alleles for each gene (93.7%-99.2% correct). CYP2D6 showed lower concordance, with 83.1% of laboratories reporting the intended genotype across all samples; however, in many cases, the laboratories that did not report a variant allele did not test for that allele. Among laboratories reporting the intended genotype, most successfully reported the intended phenotype (85.9%-99.0%). CONCLUSIONS.— Although laboratories are generally performing well, there is room for additional improvement, particularly for challenging genes, such as CYP2D6. Efforts in the field of pharmacogenomics to recommend alleles that should be included in clinical tests, identify reference materials, and standardize translation from genotype to phenotype may address some of the remaining variability in results.
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Affiliation(s)
- Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Moyer, Gandhi)
| | - Gwendolyn A McMillin
- Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City (McMillin, Mao, Smock)
| | - Thomas A Long
- Biostatistics (Long), College of American Pathologists, Northfield, Illinois
| | - Manish J Gandhi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Moyer, Gandhi)
| | - Rong Mao
- Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City (McMillin, Mao, Smock)
| | - Kristi J Smock
- Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City (McMillin, Mao, Smock)
| | - Jaimie G Halley
- Proficiency Testing (Halley), College of American Pathologists, Northfield, Illinois
| | - Karen E Weck
- Department of Pathology and Laboratory Medicine and Department of Genetics, University of North Carolina, Chapel Hill (Weck)
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Scott SA, Scott ER, Seki Y, Chen AJ, Wallsten R, Owusu Obeng A, Botton MR, Cody N, Shi H, Zhao G, Brake P, Nicoletti P, Yang Y, Delio M, Shi L, Kornreich R, Schadt EE, Edelmann L. Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi-Ethnic Allele and Copy Number Variant Detection. Clin Transl Sci 2020; 14:204-213. [PMID: 32931151 PMCID: PMC7877843 DOI: 10.1111/cts.12844] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022] Open
Abstract
To develop a novel pharmacogenetic genotyping panel, a multidisciplinary team evaluated available evidence and selected 29 genes implicated in interindividual drug response variability, including 130 sequence variants and additional copy number variants (CNVs). Of the 29 genes, 11 had guidelines published by the Clinical Pharmacogenetics Implementation Consortium. Targeted genotyping and CNV interrogation were accomplished by multiplex single‐base extension using the MassARRAY platform (Agena Biosciences) and multiplex ligation‐dependent probe amplification (MRC Holland), respectively. Analytical validation of the panel was accomplished by a strategic combination of > 500 independent tests performed on 170 unique reference material DNA samples, which included sequence variant and CNV accuracy, reproducibility, and specimen (blood, saliva, and buccal swab) controls. Among the accuracy controls were 32 samples from the 1000 Genomes Project that were selected based on their enrichment of sequence variants included in the pharmacogenetic panel (VarCover.org). Coupled with publicly available samples from the Genetic Testing Reference Materials Coordination Program (GeT‐RM), accuracy validation material was available for the majority (77%) of interrogated sequence variants (100% with average allele frequencies > 0.1%), as well as additional structural alleles with unique copy number signatures (e.g., CYP2D6*5, *13, *36, *68; CYP2B6*29; and CYP2C19*36). Accuracy and reproducibility for both genotyping and copy number were > 99.9%, indicating that the optimized panel platforms were precise and robust. Importantly, multi‐ethnic allele frequencies of the interrogated variants indicate that the vast majority of the general population carries at least one of these clinically relevant pharmacogenetic variants, supporting the implementation of this panel for pharmacogenetic research and/or clinical implementation programs.
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Affiliation(s)
- Stuart A Scott
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erick R Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Aniwaa Owusu Obeng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariana R Botton
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Neal Cody
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Paola Nicoletti
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Lisong Shi
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruth Kornreich
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Edelmann
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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3
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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] [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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4
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Giri J, Moyer AM, Bielinski SJ, Caraballo PJ. Concepts Driving Pharmacogenomics Implementation Into Everyday Healthcare. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2019; 12:305-318. [PMID: 31802928 PMCID: PMC6826176 DOI: 10.2147/pgpm.s193185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022]
Abstract
Pharmacogenomics (PGx) is often promoted as the domain of precision medicine with the greatest potential to readily impact everyday healthcare. Rapid advances in PGx knowledge derived from extensive basic and clinical research along with decreasing costs of laboratory testing have led to an increased interest in PGx and expectations of imminent clinical translation with substantial clinical impact. However, the implementation of PGx into clinical workflows is neither simple nor straightforward, and comprehensive processes and multidisciplinary collaboration are required. Several national and international institutions have pioneered models for implementing clinical PGx, and these initial models have led to a better understanding of unresolved challenges. In this review, we have categorized and explored the most relevant of these challenges to highlight potential gaps and present possible solutions. We describe the ongoing need for basic and clinical research to drive further developments in evidence-based medicine. Integration into daily clinical workflows introduces new challenges requiring innovative solutions; specifically those related to the electronic health record and embedded clinical decision support. We describe advances in PGx testing and result reporting and describe the critical need for increased standardization in these areas across laboratories. We also explore the complexity of the PGx knowledge required for clinical practice and the need for educational strategies to ensure adequate understanding among members of current and future healthcare teams. Finally, we evaluate knowledge obtained from previous implementation efforts and discuss how to best apply these learnings to future projects. Despite these challenges, the future of precision medicine appears promising due to the rapidity of recent advances in the field and current multidisciplinary efforts to effectively translate PGx to everyday clinical practice.
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Affiliation(s)
- Jyothsna Giri
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Pedro J Caraballo
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA.,Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, MN, USA
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5
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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: 325] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [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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6
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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] [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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Chambliss AB, Marzinke MA. Clinical Pharmacogenetics for Precision Medicine: Successes and Setbacks. J Appl Lab Med 2018; 3:474-486. [PMID: 33636912 DOI: 10.1373/jalm.2017.023127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/05/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Pharmacogenetics is a key component in the delivery of therapeutics to maximize pharmacologic efficacy and minimize toxicity. There are numerous identified gene-drug pairs that demonstrate the utility of pharmacogenetics testing for drug or dose selection. Although some of these pairs have translated into clinical use, pharmacogenetic testing has not yet made its way into routine clinical practice at many institutions. CONTENT This review provides an overview of clinically actionable pharmacogenetics in precision medicine. Examples of successfully implemented gene-drug pairs, along with common testing methodologies and guidelines for application, are discussed. Remaining barriers to widespread clinical implementation are also examined. SUMMARY There is a recognized role for genotyping in the guidance of therapeutic drug regimens and the prevention of adverse drug reactions. Evidence-based guidelines are available to aid in the selection of treatment upon pharmacogenetics testing for established gene-drug pairs. Multidisciplinary clinical collaboration and clinical decision support tools will be critical for widespread adoption, and financial reimbursement barriers remain.
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Affiliation(s)
- Allison B Chambliss
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - Mark A Marzinke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
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Moyer AM, Caraballo PJ. The challenges of implementing pharmacogenomic testing in the clinic. Expert Rev Pharmacoecon Outcomes Res 2017; 17:567-577. [PMID: 28949250 DOI: 10.1080/14737167.2017.1385395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Pharmacogenomic testing has the potential to greatly benefit patients by enabling personalization of medication management, ensuring better efficacy and decreasing the risk of side effects. However, to fully realize the potential of pharmacogenomic testing, there are several important issues that must be addressed. Areas covered: In this expert review we discuss current challenges impacting the implementation of pharmacogenomic testing in the clinical practice. We emphasize issues related to testing methods, reporting of the results, test selection, clinical interpretation of the results, cost-effectiveness, and the long-term use of pharmacogenomic results in clinical practice. We identify opportunities and future directions to facilitate clinical implementation. Expert commentary: Several key elements are necessary to optimally integrate pharmacogenomic testing into clinical practice. Collaborative efforts among laboratories are needed to improve standardization of testing and reporting of the results. Clinicians need educational opportunities to improve understanding of which test to order and how to interpret the results. The electronic health records and other clinical systems need to improve their storage of the pharmacogenomics test results and interoperability to facilitate the use of clinically actionable results to improve patient care.
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Affiliation(s)
- Ann M Moyer
- a Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA
| | - Pedro J Caraballo
- b Department of Medicine , Mayo Clinic , Rochester , MN , USA.,c Center for Translational Informatics and Knowledge Management, Mayo Clinic , Rochester , MN , USA
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9
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Lin G, Zhang K, Han Y, Li J. Quality control materials for pharmacogenomic testing in the clinic. Clin Chem Lab Med 2017; 55:926-933. [PMID: 27845879 DOI: 10.1515/cclm-2016-0755] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/05/2016] [Indexed: 12/27/2022]
Abstract
Pharmacogenomics has significantly added to our understanding of drug responses in clinical pharmacology, changing the paradigm of treatment decisions. Interrogations of both inherited and somatic variations for therapeutic purposes are increasingly being adopted in clinics, where quality control (QC) materials are required. However, for many pharmacogenomic tests, the acquisition of well-characterized QC materials is often difficult or impossible. In this review, several sources of appropriate QC materials for therapy-associated genetic testing are discussed. Among them, the novel methods for producing renewable controls that resemble patient samples are highlighted. Owing to technological complexity, more efforts are needed to develop proper controls for next-generation sequencing-based assay.
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10
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Yang Y, Botton MR, Scott ER, Scott SA. Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing. Pharmacogenomics 2017; 18:673-685. [PMID: 28470112 DOI: 10.2217/pgs-2017-0033] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
CYP2D6 is one of the most studied enzymes in the field of pharmacogenetics. The CYP2D6 gene is highly polymorphic with over 100 catalogued star (*) alleles, and clinical CYP2D6 testing is increasingly accessible and supported by practice guidelines. However, the degree of variation at the CYP2D6 locus and homology with its pseudogenes make interrogating CYP2D6 by short-read sequencing challenging. Moreover, accurate prediction of CYP2D6 metabolizer status necessitates analysis of duplicated alleles when an increased copy number is detected. These challenges have recently been overcome by long-read CYP2D6 sequencing; however, such platforms are not widely available. This review highlights the genomic complexities of CYP2D6, current sequencing methods and the evolution of CYP2D6 from allele discovery to clinical pharmacogenetic testing.
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Affiliation(s)
- Yao Yang
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics & Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mariana R Botton
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erick R Scott
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics & Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stuart A Scott
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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11
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Lin G, Zhang K, Han Y, Xie J, Li J. External quality assessment for laboratory testing of HLA-B*15:02 allele in relation to carbamazepine therapy. J Clin Lab Anal 2017; 32. [PMID: 28440597 DOI: 10.1002/jcla.22242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/25/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Due to the significant risk of developing Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN), the use of carbamazepine is not recommended in patients carrying the human leukocyte antigen B (HLA-B) *15:02 allele. In an effort to guarantee reliable community-based HLA-B*15:02 testing throughout China, a HLA-B*15:02 genotyping external quality assessment (EQA) program was set up. METHODS In 2016, 10 genomic DNA samples with known HLA-B*15:02 allele status were sent to 37 laboratories from 16 provinces with a request for routine HLA-B*15:02 screening. The samples were validated using Sanger sequencing by a reference laboratory. Both genotyping results and clinical written reports were evaluated. RESULTS Thirty-six of the participating laboratories correctly identified the HLA-B*15:02 allele status for all EQA samples. However, one lab failed to identify any positive challenges. The overall analytical sensitivity was 97.3% (180/185 challenges; 95% confidence interval: 93.8%-99.1%) and the analytic specificity was 100% (185/185; 95% confidence interval: 98.0%-100%). A review of the written reports showed that the clinical reporting for HLA-B*15:02 detection should be improved. Some essential information was missing, most notably laboratory information/contact, therapeutic recommendations, and methodology. CONCLUSION External quality assessment is valuable in assessing and improving the quality of laboratory testing of HLA-B*15:02 allele.
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Affiliation(s)
- Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
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12
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Lin G, Zhang K, Yi L, Han Y, Xie J, Li J. National Prociency Testing Result of CYP2D6*10 Genotyping for Adjuvant Tamoxifen Therapy in China. PLoS One 2016; 11:e0162361. [PMID: 27603206 PMCID: PMC5015788 DOI: 10.1371/journal.pone.0162361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/22/2016] [Indexed: 01/13/2023] Open
Abstract
Tamoxifen has been successfully used for treating breast cancer and preventing cancer recurrence. Cytochrome P450 2D6 (CYP2D6) plays a key role in the process of metabolizing tamoxifen to its active moiety, endoxifen. Patients with variants of the CYP2D6 gene may not receive the full benefit of tamoxifen treatment. The CYP2D6*10 variant (the most common variant in Asians) was analyzed to optimize the prescription of tamoxifen in China. To ensure referring clinicians have accurate information for genotype-guided tamoxifen treatment, the Chinese National Center for Clinical Laboratories (NCCL) organized a national proficiency testing (PT) to evaluate the performance of laboratories providing CYP2D6*10 genotyping. Ten genomic DNA samples with CYP2D6 wild-type or CYP2D6*10 variants were validated by PCR-sequencing and sent to 28 participant laboratories. The genotyping results and pharmacogenomic test reports were submitted and evaluated by NCCL experts. Additional information regarding the number of samples tested, the accreditation/certification status, and detecting technology was also requested. Thirty-one data sets were received, with a corresponding analytical sensitivity of 98.2% (548/558 challenges; 95% confidence interval: 96.7–99.1%) and an analytic specificity of 96.5% (675/682; 95% confidence interval: 97.9–99.5%). Overall, 25/28 participants correctly identified CYP2D6*10 status in 10 samples; however, two laboratories made serious genotyping errors. Most of the essential information was included in the 20 submitted CYP2D6*10 test reports. The majority of Chinese laboratories are reliable for detecting the CYP2D6*10 variant; however, several issues revealed in this study underline the importance of PT schemes in continued external assessment and provision of guidelines.
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Affiliation(s)
- Guigao Lin
- Beijing Hospital, National Center of Gerontology, Beijing, China
- Beijing Hospital, National Center for Clinical Laboratories, Beijing, China
- Beijing Hospital, Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
| | - Kuo Zhang
- Beijing Hospital, National Center of Gerontology, Beijing, China
- Beijing Hospital, National Center for Clinical Laboratories, Beijing, China
- Beijing Hospital, Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
| | - Lang Yi
- Beijing Hospital, National Center for Clinical Laboratories, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanxi Han
- Beijing Hospital, National Center of Gerontology, Beijing, China
- Beijing Hospital, National Center for Clinical Laboratories, Beijing, China
- Beijing Hospital, Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
| | - Jiehong Xie
- Beijing Hospital, National Center of Gerontology, Beijing, China
- Beijing Hospital, National Center for Clinical Laboratories, Beijing, China
- Beijing Hospital, Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
| | - Jinming Li
- Beijing Hospital, National Center of Gerontology, Beijing, China
- Beijing Hospital, National Center for Clinical Laboratories, Beijing, China
- Beijing Hospital, Beijing Engineering Research Center of Laboratory Medicine, Beijing, China
- * E-mail:
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13
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Improvements in CYP2C9 Genotyping Accuracy Are Needed: A Report of the First Proficiency Testing for Warfarin-related CYP2C9 and VKORC1 Genotyping in China. J Cardiovasc Pharmacol 2016; 66:129-34. [PMID: 25815675 DOI: 10.1097/fjc.0000000000000254] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Warfarin is the most commonly used oral anticoagulant in clinical practice. The cytochrome P450 2C9 (CYP2C9) and vitamin K epoxide reductase complex 1 (VKORC1) genotypes have been confirmed to be associated with warfarin dose requirements. Accurate genotyping results are of particular importance for obtaining reliable genotype-guided warfarin dosing information. This study aims to determine analytic performance of laboratories offering CYP2C9 and VKORC1 testing in China. A proficiency panel of 15 validated cell samples covering common CYP2C9 and VKORC1 genetic polymorphisms was provided to 31 participating laboratories, and their genotyping results were evaluated. Fourteen data sets (45.2%) performed well with the entire panel of samples, and 17 data sets (54.8%) reported at least one genotyping error. For VKORC1 (-1639G>A), participating laboratories were 100% successful in detecting genotypes of GG, GA, and AA. For CYP2C9, participants were greater than 90% successful in detecting genotypes of *1/*1, *1/*2, *1/*3, *2/*3, and *3/*3. However, 15 laboratories failed to detect rarely encountered variant genotype *2/*2. The poor performance of CYP2C9 genotyping may be because of the limitation of methodologies used for detecting CYP2C9*2 allele. The proficiency testing survey highlighted the need for improving genotyping accuracy for some laboratories in this field.
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14
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Highly accurate molecular genetic testing for HFE hereditary hemochromatosis: results from 10 years of blinded proficiency surveys by the College of American Pathologists. Genet Med 2016; 18:1206-1213. [PMID: 27124787 DOI: 10.1038/gim.2016.34] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/26/2016] [Indexed: 01/26/2023] Open
Abstract
PURPOSE The College of American Pathologists offers blinded proficiency testing (PT) for laboratories performing HFE genetic tests for hereditary hemochromatosis (common C282Y and H63D variants). This study used 10 years of PT data to determine laboratory performance for HFE analytical genotyping and clinical interpretation. METHODS Laboratories were graded for accuracy of genotype determination (six possible C282Y/H63D genotypes) and clinical interpretation regarding whether the genotype was likely to have contributed to iron overload in a hypothetical patient. RESULTS The analytical genotyping error rate was low (0.73%) in 7,663 results (from 257 unique laboratories). Genotyping errors were significantly higher in C282Y heterozygous, H63D homozygous, and C282Y homozygous samples, in non-American laboratories, and in laboratories with lower testing volume. Analytical sensitivity and specificity were >98.5 and >99.5%. The interpretive error rate (4.3%) was higher than the genotyping error rate, with two problematic genotypes (C282Y heterozygous and H63D homozygous) accounting for 77% of total interpretive errors. There was a time-dependent improvement in the interpretation of the clinical significance of HFE genotypes. CONCLUSIONS HFE molecular genetic testing, performed by non-US Food and Drug Administration-approved laboratory-developed tests, demonstrated excellent accuracy, sensitivity, and specificity. Clinical interpretations were more heterogeneous, probably owing to the low clinical penetrance of some common HFE genotypes.Genet Med 18 12, 1206-1213.
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15
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Ruaño G, Kocherla M, Graydon JS, Holford TR, Makowski GS, Goethe JW. Practical interpretation of CYP2D6 haplotypes: Comparison and integration of automated and expert calling. Clin Chim Acta 2016; 456:7-14. [PMID: 26908082 DOI: 10.1016/j.cca.2016.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/23/2015] [Accepted: 02/16/2016] [Indexed: 01/16/2023]
Abstract
We describe a population genetic approach to compare samples interpreted with expert calling (EC) versus automated calling (AC) for CYP2D6 haplotyping. The analysis represents 4812 haplotype calls based on signal data generated by the Luminex xMap analyzers from 2406 patients referred to a high-complexity molecular diagnostics laboratory for CYP450 testing. DNA was extracted from buccal swabs. We compared the results of expert calls (EC) and automated calls (AC) with regard to haplotype number and frequency. The ratio of EC to AC was 1:3. Haplotype frequencies from EC and AC samples were convergent across haplotypes, and their distribution was not statistically different between the groups. Most duplications required EC, as only expansions with homozygous or hemizygous haplotypes could be automatedly called. High-complexity laboratories can offer equivalent interpretation to automated calling for non-expanded CYP2D6 loci, and superior interpretation for duplications. We have validated scientific expert calling specified by scoring rules as standard operating procedure integrated with an automated calling algorithm. The integration of EC with AC is a practical strategy for CYP2D6 clinical haplotyping.
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Affiliation(s)
- Gualberto Ruaño
- Laboratory of Personalized Health, Genomas Inc, United States.
| | - Mohan Kocherla
- Laboratory of Personalized Health, Genomas Inc, United States
| | - James S Graydon
- Laboratory of Personalized Health, Genomas Inc, United States
| | | | | | - John W Goethe
- Institute of Living, Hartford Hospital, United States
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16
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Kalman LV, Agúndez JA, Appell ML, Black JL, Bell GC, Boukouvala S, Bruckner C, Bruford E, Bruckner C, Caudle K, Coulthard S, Daly AK, Del Tredici AL, den Dunnen JT, Drozda K, Everts R, Flockhart D, Freimuth R, Gaedigk A, Hachad H, Hartshorne T, Ingelman-Sundberg M, Klein TE, Lauschke VM, Maglott DR, McLeod HL, McMillin GA, Meyer UA, Müller DJ, Nickerson DA, Oetting WS, Pacanowski M, Pratt VM, Relling MV, Roberts A, Rubinstein WS, Sangkuhl K, Schwab M, Scott SA, Sim SC, Thirumaran RK, Toji LH, Tyndale R, van Schaik RHN, Whirl-Carrillo M, Yeo KTJ, Zanger UM. Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting. Clin Pharmacol Ther 2016; 99:172-85. [PMID: 26479518 PMCID: PMC4724253 DOI: 10.1002/cpt.280] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 12/21/2022]
Abstract
This article provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.
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Affiliation(s)
- Lisa V. Kalman
- Centers for Disease, Control and Prevention, 1600 Clifton Rd, MSG23, Atlanta GA 30333, 404 498-2707, 404 498-2231
| | - José A.G. Agúndez
- Dept. Pharmacology, University of Extremadura, Avda de la, Universidad s/n., 10071 Cáceres, SPAIN, +34924289458, +34927257000
| | - Malin Lindqvist Appell
- Department of Medical and Health sciences, Faculty of Medicine and Health Sciences, Linköping University, Division of Drug Research, Linköping University, SE-581 83, LINKÖPING, +4613286880
| | | | - Gillian C. Bell
- Moffitt Cancer Center, 12902 Magnolia Dr Tampa, FL 33612, 813-745-6525, 813-745-3882
| | - Sotiria Boukouvala
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Building 10, University Campus, Alexandroupolis 68100, Greece, +30-25510-30613, +30-25510-30632
| | - Carsten Bruckner
- Affymetrix, 3420 Central Expy, Santa Clara, CA 95051, USA, 1-408-731-5879
| | - Elspeth Bruford
- HUGO Gene, Nomenclature, Committee (HGNC), EMBL-EBI, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK, +44-1223-494468, +44-1223-492624
| | - Carsten Bruckner
- Affymetrix, 3420 Central Expy, Santa Clara, CA 95051, USA, 1-408-731-5879
| | - Kelly Caudle
- St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS 313 Memphis, TN 38105, 901-595-3125, 901-595-3994
| | - Sally Coulthard
- Newcastle University, Institute for Cellular Medicine, William Leech Building, Newcastle Medical School, Framlington Place, Newcastle University NE2 4HH UK, +44 1912080723, +44 1912085232
| | - Ann K. Daly
- Newcastle University, Institute of Cellular Medicine, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK, None, 44-191-208-7031
| | - Andria L. Del Tredici
- Millennium Health, LLC, 16981 Via Tazon, San Diego, CA 92127, none, (858) 451-3535 x1682
| | - Johan T den Dunnen
- Leiden University Medical Center, Human Genetics and Clinical Genetics, PO Box 9600, 2300RC Leiden, Nederland, none, +31-71-5269501
| | - Katarzyna Drozda
- Food and Drug Administration, 10903 New Hampshire Ave. Silver Spring, MD 20993, 240 402-0422
| | - Robin Everts
- Agena Bioscience, 3565 General Atomics Court, San Diego, CA 92121, None, +1 858-882-2655
| | - David Flockhart
- Indiana University, 950 W. Walnut St., room 402, Indianaplis, IN 46202, 317-274-2810
| | - Robert Freimuth
- Mayo Clinic, 200 First Street SW Rochester, MN 55905, 507-284-0753
| | - Andrea Gaedigk
- Division of Clinical Pharmacology & Therapeutic Innovation, Children’s Mercy Kansas City and School of Medicine, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, 816-234-1958, 816-234-3941
| | - Houda Hachad
- Translational Software, 12410 SE 32 Street Suite 150, Bellevue, WA 98005, 206-777-4132
| | - Toinette Hartshorne
- Genetic Analysis, Thermo Fisher Scientific, 180 Oyster Point Blvd. South San Francisco, CA 94080, 650-244-1669, 650-246-4080
| | - Magnus Ingelman-Sundberg
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz väg 2, 17177 Stockholm, SwedenSE, +468337327, +46852487735+
| | - Teri E. Klein
- Department of Genetics, Stanford University, 443 Via Ortega Avenue, Stanford, CA 94305, 650-725-3863, 650-736-0156
| | - Volker M. Lauschke
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz väg 2, 17177 Stockholm, Sweden, +46 8-337327, +46 8-5248-7711
| | - Donna R. Maglott
- National Institutes of Health / National Library of Medicine / National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20894, 301 435-4895
| | - Howard L. McLeod
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa FL 33612, 813-745-3347
| | - Gwendolyn A. McMillin
- University of Utah and ARUP Laboratories, 500 Chipeta Way, Salt Lake City UT 84108, 801-584-5207, 801-583-2787
| | - Urs A. Meyer
- University of Basel, Biozentrum, Klingelbergstrasse 50/70, CH 4056, Basel, Switzerland, +41612672208, +41 61 267 2220
| | - Daniel J. Müller
- Dept. of Psychiatry, University of Toronto, CAMH, 250 College ST., R132, 416 979 4666, 416 535 8501 (x. 36851)
| | - Deborah A. Nickerson
- University of Washington, Department of Genome Sciences, Box 355065, Seattle, WA, 98195-5065, 206-221-6498, 206-685-7387
| | - William S. Oetting
- Experimental and Clinical Pharmacology, University of Minnesota, 7-115 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, 612-624-6645, 612-624-1139
| | - Michael Pacanowski
- U.S. Food and Drug Administration, 10903 New Hampshire Ave., WO Building 51, Rm 2132, HFD870, Silver Spring, MD 20993, 301-847-8720, 301-796-3919
| | - Victoria M. Pratt
- Indiana University School of Medicine, 975 W. Walnut St., IB-130, Indianapolis IN 46202, 317-274-2293, 317-274-8322
| | - Mary V. Relling
- Chair, Pharmaceutical Dept., St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Room I-5112 Memphis, TN 38105, ph 901 595 2348, fax 901 595 8869
| | - Ali Roberts
- Aegis Science Corporation, 515 Great Circle Road, Nashville, TN 37228, 615-255-3030, 615-477-9429
| | - Wendy S. Rubinstein
- National Institutes of Health / National Library of Medicine / National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20894, 301.480.4023, 301.435.5991
| | - Katrin Sangkuhl
- Stanford University, 443 Via Ortega, Room 213, MC4245, Stanford CA 94305, 650-725-3863, 650-725-0659
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch- Institute of Clinical Pharmacology, Stuttgart and Department of Clinical Pharmacology, University Hospital, Tuebingen, Germany, Auerbachstrasse 112, 70378 Stuttgart, +49 711 859295, +49 711 8101 3700
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1487, 212-241-0139, 212-241-3780
| | - Sarah C Sim
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz Väg 2, 171 77 Stockholm, Sweden, +468337327, +46852487735
| | - Ranjit K Thirumaran
- Genelex Corporation, 3101 Western Ave., Suite 100, Seattle, WA 98121., 206 219-4000, 206 826-1926
| | - Lorraine H. Toji
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ 08103, 856 757-9719
| | - Rachel Tyndale
- CAMH and Departments of Psychiatry, Pharmacology and Toxicology, University of Toronto, Rm 4326, Department of Pharmacology, 1 King’s College Circle, Toronto, Canada, M5S 1A8., 416 978-6395, 416 978-6374
| | - Ron HN van Schaik
- 1Dept Clinical Chemistry, Erasmus MC Rotterdam; 2IFCC Task Force Pharmacogenetics, Room Na-415; Wytemaweg 80, 3015CN Rotterdam, The Netherlands, +31-10-7033119
| | - Michelle Whirl-Carrillo
- Department of Genetics, Stanford University, 443 Via Ortega, Rm 213 Stanford, CA 94305, 650-725-3863, 650-725-0659
| | - Kiang-Teck J Yeo
- Department of Pathology, The University of Chicago, 5841 S Maryland Ave, MC 0004, TW010, Chicago, IL 60637, 773-702-6268, 773-702-1318
| | - Ulrich M. Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, Stuttgart, 70376, Germany, +49-711-859295, +49-711-81013704
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17
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Yi L, Lin G, Zhang K, Wang L, Zhang R, Xie J, Li J. Molecular Genetics External Quality Assessment Pilot Scheme for Irinotecan-Related UGT1A1 Genotyping in China. PLoS One 2016; 11:e0148081. [PMID: 26820647 PMCID: PMC4731084 DOI: 10.1371/journal.pone.0148081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 01/12/2016] [Indexed: 12/27/2022] Open
Abstract
Irinotecan is widely used in the treatment of solid tumors, especially in colorectal cancer and lung cancer. Molecular testing for UGT1A1 genotyping is increasingly required in China for optimum irinotecan administration. In order to determine the performance of laboratories with regard to the whole testing process for UGT1A1 to ensure the consistency and accuracy of the test results, the National Center for Clinical Laboratories conducted an external quality assessment program for UGT1A1*28 genotyping in 2015. The panel, which comprised of four known mutational samples and six wild-type samples, was distributed to 45 laboratories that test for the presence of UGT1A1*28 polymorphisms. Participating laboratories were allowed to perform polymorphism analysis by using their routine methods. The accuracy of the genotyping and reporting of results was analyzed. Other information from the individual laboratories, including the number of samples tested each month, accreditation/certification status, and test methodology, was reviewed. Forty-four of the 45 participants reported the correct results for all samples. There was only one genotyping error, with a corresponding analytical sensitivity of 99.44% (179/180 challenges; 95% confidence interval: 96.94-99.99%) and an analytical specificity of 100% (270/270 challenges; 95% confidence interval: 98.64-100%). Both commercial kits and laboratory development tests were commonly used by the laboratories, and pyrosequencing was the main methodology used (n = 26, 57.8%). The style of the written reports showed large variation, and many reports showed a shortage of information. In summary, the first UGT1A1 genotyping external quality assessment result demonstrated that UGT1A1 genotype analysis of good quality was performed in the majority of pharmacogenetic testing centers that were investigated. However, greater education on the reporting of UGT1A1 genetic testing results is needed.
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Affiliation(s)
- Lang Yi
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, P R China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, P R China
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18
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Pratt VM, Everts RE, Aggarwal P, Beyer BN, Broeckel U, Epstein-Baak R, Hujsak P, Kornreich R, Liao J, Lorier R, Scott SA, Smith CH, Toji LH, Turner A, Kalman LV. Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes: A GeT-RM Collaborative Project. J Mol Diagn 2015; 18:109-23. [PMID: 26621101 DOI: 10.1016/j.jmoldx.2015.08.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/24/2015] [Accepted: 08/13/2015] [Indexed: 10/22/2022] Open
Abstract
Pharmacogenetic testing is increasingly available from clinical laboratories. However, only a limited number of quality control and other reference materials are currently available to support clinical testing. To address this need, the Centers for Disease Control and Prevention-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing community and the Coriell Cell Repositories, has characterized 137 genomic DNA samples for 28 genes commonly genotyped by pharmacogenetic testing assays (CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, CYP3A5, CYP4F2, DPYD, GSTM1, GSTP1, GSTT1, NAT1, NAT2, SLC15A2, SLC22A2, SLCO1B1, SLCO2B1, TPMT, UGT1A1, UGT2B7, UGT2B15, UGT2B17, and VKORC1). One hundred thirty-seven Coriell cell lines were selected based on ethnic diversity and partial genotype characterization from earlier testing. DNA samples were coded and distributed to volunteer testing laboratories for targeted genotyping using a number of commercially available and laboratory developed tests. Through consensus verification, we confirmed the presence of at least 108 variant pharmacogenetic alleles. These samples are also being characterized by other pharmacogenetic assays, including next-generation sequencing, which will be reported separately. Genotyping results were consistent among laboratories, with most differences in allele assignments attributed to assay design and variability in reported allele nomenclature, particularly for CYP2D6, UGT1A1, and VKORC1. These publicly available samples will help ensure the accuracy of pharmacogenetic testing.
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Affiliation(s)
- Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Praful Aggarwal
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brittany N Beyer
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Paul Hujsak
- Department of Research & Development, Autogenomics Inc., Vista, California
| | - Ruth Kornreich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Liao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rachel Lorier
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Lorraine H Toji
- Coriell Cell Repositories, Coriell Institute for Medical Research, Camden, New Jersey
| | - Amy Turner
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
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19
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Lin G, Yi L, Zhang K, Wang L, Zhang R, Xie J, Li J. Implementation of Cell Samples as Controls in National Proficiency Testing for Clopidogrel Therapy-Related CYP2C19 Genotyping in China: A Novel Approach. PLoS One 2015. [PMID: 26218263 PMCID: PMC4517881 DOI: 10.1371/journal.pone.0134174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Laboratories are increasingly requested to perform CYP2C19 genetic testing when managing clopidogrel therapy, especially in patients with acute coronary syndrome undergoing percutaneous coronary intervention. To ensure high quality molecular testing and ascertain that the referring clinician has the correct information for CYP2C19 genotype–directed antiplatelet therapy, a proficiency testing scheme was set up to evaluate the laboratory performance for the entire testing process. Proficiency panels of 10 cell samples encompassing the common CYP2C19 genetic polymorphisms were distributed to 62 participating laboratories for routine molecular testing and the responses were analyzed for accuracy of genotyping and the reporting of results. Data including the number of samples tested, the accreditation/certification status, and test methodology of each individual laboratory were also reviewed. Fifty-seven of the 62 participants correctly identified the CYP2C19 variants in all samples. There were six genotyping errors, with a corresponding analytical sensitivity of 98.5% (333/338 challenges; 95% confidence interval: 96.5–99.5%) and an analytic specificity of 99.6% (281/282; 95% confidence interval: 98.0–99.9%). Reports of the CYP2C19 genotyping results often lacked essential information. In conclusion, clinical laboratories demonstrated good analytical sensitivity and specificity; however, the pharmacogenetic testing community requires additional education regarding the correct reporting of CYP2C19 genetic test results.
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Affiliation(s)
- Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Lang Yi
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, P R China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing 100730, P R China
- * E-mail:
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20
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Abul-Husn NS, Owusu Obeng A, Sanderson SC, Gottesman O, Scott SA. Implementation and utilization of genetic testing in personalized medicine. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2014; 7:227-40. [PMID: 25206309 PMCID: PMC4157398 DOI: 10.2147/pgpm.s48887] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Clinical genetic testing began over 30 years ago with the availability of mutation detection for sickle cell disease diagnosis. Since then, the field has dramatically transformed to include gene sequencing, high-throughput targeted genotyping, prenatal mutation detection, preimplantation genetic diagnosis, population-based carrier screening, and now genome-wide analyses using microarrays and next-generation sequencing. Despite these significant advances in molecular technologies and testing capabilities, clinical genetics laboratories historically have been centered on mutation detection for Mendelian disorders. However, the ongoing identification of deoxyribonucleic acid (DNA) sequence variants associated with common diseases prompted the availability of testing for personal disease risk estimation, and created commercial opportunities for direct-to-consumer genetic testing companies that assay these variants. This germline genetic risk, in conjunction with other clinical, family, and demographic variables, are the key components of the personalized medicine paradigm, which aims to apply personal genomic and other relevant data into a patient’s clinical assessment to more precisely guide medical management. However, genetic testing for disease risk estimation is an ongoing topic of debate, largely due to inconsistencies in the results, concerns over clinical validity and utility, and the variable mode of delivery when returning genetic results to patients in the absence of traditional counseling. A related class of genetic testing with analogous issues of clinical utility and acceptance is pharmacogenetic testing, which interrogates sequence variants implicated in interindividual drug response variability. Although clinical pharmacogenetic testing has not previously been widely adopted, advances in rapid turnaround time genetic testing technology and the recent implementation of preemptive genotyping programs at selected medical centers suggest that personalized medicine through pharmacogenetics is now a reality. This review aims to summarize the current state of implementing genetic testing for personalized medicine, with an emphasis on clinical pharmacogenetic testing.
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Affiliation(s)
- Noura S Abul-Husn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aniwaa Owusu Obeng
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA ; Department of Pharmacy, Mount Sinai Hospital, New York, NY, USA
| | - Saskia C Sanderson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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