51
|
Macías Y, García-Menaya JM, Martí M, Cordobés C, Jurado-Escobar R, Cornejo-García JA, Torres MJ, Blanca-López N, Canto G, Blanca M, Laguna JJ, Bartra J, Rosado A, Fernández J, García-Martín E, Agúndez JAG. Lack of Major Involvement of Common CYP2C Gene Polymorphisms in the Risk of Developing Cross-Hypersensitivity to NSAIDs. Front Pharmacol 2021; 12:648262. [PMID: 34621165 PMCID: PMC8490926 DOI: 10.3389/fphar.2021.648262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cross-hypersensitivity to non-steroidal anti-inflammatory drugs (NSAIDs) is a relatively common, non-allergic, adverse drug event triggered by two or more chemically unrelated NSAIDs. Current evidence point to COX-1 inhibition as one of the main factors in its etiopathogenesis. Evidence also suggests that the risk is dose-dependent. Therefore it could be speculated that individuals with impaired NSAID biodisposition might be at increased risk of developing cross-hypersensitivity to NSAIDs. We analyzed common functional gene variants for CYP2C8, CYP2C9, and CYP2C19 in a large cohort composed of 499 patients with cross-hypersensitivity to NSAIDs and 624 healthy individuals who tolerated NSAIDs. Patients were analyzed as a whole group and subdivided in three groups according to the main enzymes involved in the metabolism of the culprit drugs as follows: CYP2C9, aceclofenac, indomethacin, naproxen, piroxicam, meloxicam, lornoxicam, and celecoxib; CYP2C8 plus CYP2C9, ibuprofen and diclofenac; CYP2C19 plus CYP2C9, metamizole. Genotype calls ranged from 94 to 99%. No statistically significant differences between patients and controls were identified in this study, either for allele frequencies, diplotypes, or inferred phenotypes. After patient stratification according to the enzymes involved in the metabolism of the culprit drugs, or according to the clinical presentation of the hypersensitivity reaction, we identified weak significant associations of a lower frequency (as compared to that of control subjects) of CYP2C8*3/*3 genotypes in patients receiving NSAIDs that are predominantly CYP2C9 substrates, and in patients with NSAIDs-exacerbated cutaneous disease. However, these associations lost significance after False Discovery Rate correction for multiple comparisons. Taking together these findings and the statistical power of this cohort, we conclude that there is no evidence of a major implication of the major functional CYP2C polymorphisms analyzed in this study and the risk of developing cross-hypersensitivity to NSAIDs. This argues against the hypothesis of a dose-dependent COX-1 inhibition as the main underlying mechanism for this adverse drug event and suggests that pre-emptive genotyping aiming at drug selection should have a low practical utility for cross-hypersensitivity to NSAIDs.
Collapse
Affiliation(s)
- Yolanda Macías
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres, Spain.,ARADyAL Instituto de Salud Carlos III, Cáceres, Spain
| | - Jesús M García-Menaya
- Allergy Service, Badajoz University Hospital, Badajoz, Spain.,ARADyAL Instituto de Salud Carlos III, Badajoz, Spain
| | - Manuel Martí
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres, Spain.,ARADyAL Instituto de Salud Carlos III, Cáceres, Spain
| | - Concepción Cordobés
- Allergy Service, Badajoz University Hospital, Badajoz, Spain.,ARADyAL Instituto de Salud Carlos III, Badajoz, Spain
| | - Raquel Jurado-Escobar
- Research Laboratory, IBIMA, Regional University Hospital of Málaga, UMA, Málaga, Spain.,ARADyAL Instituto de Salud Carlos III, Málaga, Spain
| | - José A Cornejo-García
- Research Laboratory, IBIMA, Regional University Hospital of Málaga, UMA, Málaga, Spain.,ARADyAL Instituto de Salud Carlos III, Málaga, Spain
| | - María J Torres
- ARADyAL Instituto de Salud Carlos III, Málaga, Spain.,Allergy Unit, IBIMA, Regional University Hospital of Málaga, UMA, Málaga, Spain
| | - Natalia Blanca-López
- Allergy Service, Infanta Leonor University Hospital, Madrid, Spain.,ARADyAL Instituto de Salud Carlos III, Madrid, Spain
| | - Gabriela Canto
- Allergy Service, Infanta Leonor University Hospital, Madrid, Spain.,ARADyAL Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel Blanca
- Allergy Service, Infanta Leonor University Hospital, Madrid, Spain.,ARADyAL Instituto de Salud Carlos III, Madrid, Spain
| | - José J Laguna
- ARADyAL Instituto de Salud Carlos III, Madrid, Spain.,Allergy Unit and Allergy-Anaesthesia Unit, Hospital Central Cruz Roja, Faculty of Medicine, Alfonso X El Sabio University, Madrid, Spain
| | - Joan Bartra
- Allergy Section, Pneumology Department, Hospital Clinic, ARADyAL, Universitat de Barcelona, Barcelona, Spain.,ARADyAL Instituto de Salud Carlos III, Barcelona, Spain
| | - Ana Rosado
- Allergy Service, Alcorcón Hospital, Madrid, Spain
| | - Javier Fernández
- Allergy Unit, Regional University Hospital, Alicante, Spain.,ARADyAL Instituto de Salud Carlos III, Alicante, Spain
| | - Elena García-Martín
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres, Spain.,ARADyAL Instituto de Salud Carlos III, Cáceres, Spain
| | - José A G Agúndez
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres, Spain.,ARADyAL Instituto de Salud Carlos III, Cáceres, Spain
| |
Collapse
|
52
|
Parikh SJ, Kamat S, Phillips M, Boyson SP, Yarbrough T, Davie D, Zhang Q, Glass KC, Shah MB. Insights into the Genetic Variations of Human Cytochrome P450 2C9: Structural Analysis, Characterization and Comparison. Int J Mol Sci 2021; 22:10206. [PMID: 34638547 PMCID: PMC8508694 DOI: 10.3390/ijms221910206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023] Open
Abstract
Cytochromes P450 (CYP) are one of the major xenobiotic metabolizing enzymes with increasing importance in pharmacogenetics. The CYP2C9 enzyme is responsible for the metabolism of a wide range of clinical drugs. More than sixty genetic variations have been identified in CYP2C9 with many demonstrating reduced activity compared to the wild-type (WT) enzyme. The CYP2C9*8 allele is predominantly found in persons of African ancestry and results in altered clearance of several drug substrates of CYP2C9. The X-ray crystal structure of CYP2C9*8, which represents an amino acid variation from arginine to histidine at position 150 (R150H), was solved in complex with losartan. The overall conformation of the CYP2C9*8-losartan complex was similar to the previously solved complex with wild type (WT) protein, but it differs in the occupancy of losartan. One molecule of losartan was bound in the active site and another on the surface in an identical orientation to that observed in the WT complex. However, unlike the WT structure, the losartan in the access channel was not observed in the *8 complex. Furthermore, isothermal titration calorimetry studies illustrated weaker binding of losartan to *8 compared to WT. Interestingly, the CYP2C9*8 interaction with losartan was not as weak as the CYP2C9*3 variant, which showed up to three-fold weaker average dissociation constant compared to the WT. Taken together, the structural and solution characterization yields insights into the similarities and differences of losartan binding to CYP2C9 variants and provides a useful framework for probing the role of amino acid substitution and substrate dependent activity.
Collapse
Affiliation(s)
- Sonia J. Parikh
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA; (S.J.P.); (S.K.); (M.P.); (S.P.B.); (T.Y.); (D.D.); (K.C.G.)
| | - Sumit Kamat
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA; (S.J.P.); (S.K.); (M.P.); (S.P.B.); (T.Y.); (D.D.); (K.C.G.)
| | - Margaret Phillips
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA; (S.J.P.); (S.K.); (M.P.); (S.P.B.); (T.Y.); (D.D.); (K.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA; (S.J.P.); (S.K.); (M.P.); (S.P.B.); (T.Y.); (D.D.); (K.C.G.)
| | - Thomas Yarbrough
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA; (S.J.P.); (S.K.); (M.P.); (S.P.B.); (T.Y.); (D.D.); (K.C.G.)
| | - Dylan Davie
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA; (S.J.P.); (S.K.); (M.P.); (S.P.B.); (T.Y.); (D.D.); (K.C.G.)
| | - Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA;
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA; (S.J.P.); (S.K.); (M.P.); (S.P.B.); (T.Y.); (D.D.); (K.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Manish B. Shah
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, 106 New Scotland Avenue, Albany, NY 12208, USA; (S.J.P.); (S.K.); (M.P.); (S.P.B.); (T.Y.); (D.D.); (K.C.G.)
| |
Collapse
|
53
|
Sangkuhl K, Claudio-Campos K, Cavallari LH, Agundez JAG, Whirl-Carrillo M, Duconge J, Del Tredici AL, Wadelius M, Rodrigues Botton M, Woodahl EL, Scott SA, Klein TE, Pratt VM, Daly AK, Gaedigk A. PharmVar GeneFocus: CYP2C9. Clin Pharmacol Ther 2021; 110:662-676. [PMID: 34109627 PMCID: PMC8607432 DOI: 10.1002/cpt.2333] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C9 gene. Genetic variation within the CYP2C9 gene locus impacts the metabolism or bioactivation of many clinically important drugs, including nonsteroidal anti-inflammatory drugs, phenytoin, antidiabetic agents, and angiotensin receptor blockers. Variable CYP2C9 activity is of particular importance regarding efficacy and safety of warfarin and siponimod as indicated in their package inserts. This GeneFocus provides a comprehensive overview and summary of CYP2C9 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium.
Collapse
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
| |
Collapse
|
54
|
Fekete F, Mangó K, Déri M, Incze E, Minus A, Monostory K. Impact of genetic and non-genetic factors on hepatic CYP2C9 expression and activity in Hungarian subjects. Sci Rep 2021; 11:17081. [PMID: 34429480 PMCID: PMC8384867 DOI: 10.1038/s41598-021-96590-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/11/2021] [Indexed: 12/20/2022] Open
Abstract
CYP2C9, one of the most abundant hepatic cytochrome P450 enzymes, is involved in metabolism of 15–20% of clinically important drugs (warfarin, sulfonylureas, phenytoin, non-steroid anti-inflammatory drugs). To avoid adverse events and/or impaired drug-response, CYP2C9 pharmacogenetic testing is recommended. The impact of CYP2C9 polymorphic alleles (CYP2C9*2, CYP2C9*3) and phenoconverting non-genetic factors on CYP2C9 function and expression was investigated in liver tissues from Caucasian subjects (N = 164). The presence of CYP2C9*3 allele was associated with CYP2C9 functional impairment, and CYP2C9*2 influenced tolbutamide 4′-hydroxylase activity only in subjects with two polymorphic alleles, whereas the contribution of CYP2C8*3 was not confirmed. In addition to CYP2C9 genetic polymorphisms, non-genetic factors (co-medication with CYP2C9-specific inhibitors/inducers and non-specific factors including amoxicillin + clavulanic acid therapy or chronic alcohol consumption) contributed to the prediction of hepatic CYP2C9 activity; however, a CYP2C9 genotype–phenotype mismatch still existed in 32.6% of the subjects. Substantial variability in CYP2C9 mRNA levels, irrespective of CYP2C9 genotype, was demonstrated; however, CYP2C9 induction and non-specific non-genetic factors potentially resulting in liver injury appeared to modify CYP2C9 expression. In conclusion, complex implementation of CYP2C9 genotype and non-genetic factors for the most accurate estimation of hepatic CYP2C9 activity may improve efficiency and safety of medication with CYP2C9 substrate drugs in clinical practice.
Collapse
Affiliation(s)
- Ferenc Fekete
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Katalin Mangó
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Máté Déri
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Evelyn Incze
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Annamária Minus
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary
| | - Katalin Monostory
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok 2, Budapest, 1117, Hungary.
| |
Collapse
|
55
|
Dorfman R, London Z, Metias M, Kabakchiev B, Mukerjee G, Moser A. Individualized Medication Management in Ontario Long-Term Care Clinical Impact on Management of Depression, Pain, and Dementia. J Am Med Dir Assoc 2021; 21:823-829.e5. [PMID: 32536434 DOI: 10.1016/j.jamda.2020.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/20/2020] [Accepted: 04/08/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Assess the potential benefits of identifying drug-gene interactions in nursing home (NH) residents on multiple medications. Reduce the use of high-risk medications for residents with reduced drug metabolism. DESIGN Open-label, nonrandomized, mixed methods study. SETTING Four NHs in Ontario. MEASUREMENTS Potential drug therapy problems (DTPs) for study cohort were identified during a medication review by a pharmacist using pharmacogenetic (PGx) clinical decision support to identify medication change opportunities. The number of DTPs identified during a standard medication review was compared with the number of DTPs identified with a PGx clinical decision support. Analysis of medication dispensing data at enrollment compared with dispensing in a 60-day window following medication review were compared for the PGx-tested study cohort with controls. RESULTS Prescription patterns of 90 study participants were compared with 895 controls for the same time period. Study participants were on 7 to 47 drugs, of which drugs with PGx indications ranged from 1 to 17 medications. The average medication load was 4.6 medications with PGx indications per person, whereas the controls were on 3.5 PGx drugs. Furthermore, 94% of cases and 84% of controls were on 2 or more drugs with PGx indication during the study period. Pharmacogenetic analysis identified 114 distinct DTPs in the 90 study participants, of which 29 were classified as serious. In this study, over 35% of residents were treated with antidepressants; of these, 64% have altered CYP2C19 or CYP2D6 metabolism and could benefit from drug dose adjustment or from a switch to alternative antidepressants. Twenty percent of residents were treated with hydromorphone, of which 30% have reduced response to opioids because of variations in the OPRM1 gene. CONCLUSIONS AND IMPLICATIONS This study demonstrated the clinical potential of PGx-based medication optimization for NH residents, impacting the management of depression, chronic pain, heart disease, and gastrointestinal symptoms.
Collapse
Affiliation(s)
- Ruslan Dorfman
- GeneYouIn Inc, Toronto, Ontario, Canada; Department of Anesthesia, McMaster University Hamilton, Ontario, Canada
| | | | | | | | | | - Andrea Moser
- Baycrest Center for Geriatric Care, Toronto, Ontario, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
56
|
Interactions between cardiology and oncology drugs in precision cardio-oncology. Clin Sci (Lond) 2021; 135:1333-1351. [PMID: 34076246 DOI: 10.1042/cs20200309] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022]
Abstract
Recent advances in treatment have transformed the management of cancer. Despite these advances, cardiovascular disease remains a leading cause of death in cancer survivors. Cardio-oncology has recently evolved as a subspecialty to prevent, diagnose, and manage cardiovascular side effects of antineoplastic therapy. An emphasis on optimal management of comorbidities and close attention to drug interactions are important in cardio-oncologic care. With interdisciplinary collaboration among oncologists, cardiologists, and pharmacists, there is potential to prevent and reduce drug-related toxicities of treatments. The cytochrome P450 (CYP450) family of enzymes and the P-glycoprotein (P-g) transporter play a crucial role in drug metabolism and drug resistance. Here we discuss the role of CYP450 and P-g in drug interactions in the field of cardio-oncology, provide an overview of the cardiotoxicity of a spectrum of cancer agents, highlight the role of precision medicine, and encourage a multidisciplinary treatment approach for patients with cancer.
Collapse
|
57
|
Sukprasong R, Chuwongwattana S, Koomdee N, Jantararoungtong T, Prommas S, Jinda P, Rachanakul J, Nuntharadthanaphong N, Jongjitsook N, Puangpetch A, Sukasem C. Allele frequencies of single nucleotide polymorphisms of clinically important drug-metabolizing enzymes CYP2C9, CYP2C19, and CYP3A4 in a Thai population. Sci Rep 2021; 11:12343. [PMID: 34117307 PMCID: PMC8195986 DOI: 10.1038/s41598-021-90969-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Prior knowledge of allele frequencies of cytochrome P450 polymorphisms in a population is crucial for the revision and optimization of existing medication choices and doses. In the current study, the frequency of the CYP2C9*2, CYP2C9*3, CYP2C19*2, CYP2C19*3, CYP2C19*6, CYP2C19*17, and CYP3A4 (rs4646437) alleles in a Thai population across different regions of Thailand was examined. Tests for polymorphisms of CYP2C9 and CYP3A4 were performed using TaqMan SNP genotyping assay and CYP2C19 was performed using two different methods; TaqMan SNP genotyping assay and Luminex x Tag V3. The blood samples were collected from 1205 unrelated healthy individuals across different regions within Thailand. Polymorphisms of CYP2C9 and CYP2C19 were transformed into phenotypes, which included normal metabolizer (NM), intermediate metabolizer (IM), poor metabolizer (PM), and rapid metabolizers (RM). The CYP2C9 allele frequencies among the Thai population were 0.08% and 5.27% for the CYP2C9*2 and CYP2C9*3 alleles, respectively. The CYP2C19 allele frequencies among the Thai population were 25.60%, 2.50%, 0.10%, and 1.80% for the CYP2C19*2, CYP2C19*3, CYP2C19*6, and CYP2C19*17 alleles, respectively. The allele frequency of the CYP3A4 (rs4646437) variant allele was 28.50% in the Thai population. The frequency of the CYP2C9*3 allele was significantly lower among the Northern Thai population (P < 0.001). The frequency of the CYP2C19*17 allele was significantly higher in the Southern Thai population (P < 0.001). Our results may provide an understanding of the ethnic differences in drug responses and support for the utilization of pharmacogenomics testing in clinical practice.
Collapse
Affiliation(s)
- Rattanaporn Sukprasong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Sumonrat Chuwongwattana
- Faculty of Medical Technology, Huachiew Chalermprakiet University, Bang Phli District, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Thawinee Jantararoungtong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Santirhat Prommas
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Pimonpan Jinda
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Jiratha Rachanakul
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Nutthan Nuntharadthanaphong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Nutcha Jongjitsook
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Apichaya Puangpetch
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.
| |
Collapse
|
58
|
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: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
59
|
Pratt VM, Turner A, Broeckel U, Dawson DB, Gaedigk A, Lynnes TC, Medeiros EB, Moyer AM, Requesens D, Vetrini F, Kalman LV. Characterization of Reference Materials with an Association for Molecular Pathology Pharmacogenetics Working Group Tier 2 Status: CYP2C9, CYP2C19, VKORC1, CYP2C Cluster Variant, and GGCX: A GeT-RM Collaborative Project. J Mol Diagn 2021; 23:952-958. [PMID: 34020041 DOI: 10.1016/j.jmoldx.2021.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/26/2021] [Accepted: 04/29/2021] [Indexed: 10/21/2022] Open
Abstract
Pharmacogenetic testing is increasingly available from clinical and research laboratories. However, only a limited number of quality control and other reference materials are currently available for many of the variants that are tested. The Association for Molecular Pathology Pharmacogenetic Work Group has published a series of papers recommending alleles for inclusion in clinical testing. Several of the alleles were not considered for tier 1 because of a lack of reference materials. To address this need, the Division of Laboratory Systems, Centers for Disease Control and Prevention-based Genetic Testing Reference Material (GeT-RM) program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Institute for Medical Research, has characterized 18 DNA samples derived from Coriell cell lines. DNA samples were distributed to five volunteer testing laboratories for genotyping using three commercially available and laboratory developed tests. Several tier 2 variants, including CYP2C9∗13, CYP2C19∗35, the CYP2C cluster variant (rs12777823), two variants in VKORC1 (rs61742245 and rs72547529) related to warfarin resistance, and two variants in GGCX (rs12714145 and rs11676382) related to clotting factor activation, were identified among these samples. These publicly available materials complement the pharmacogenetic reference materials previously characterized by the GeT-RM program and will support the quality assurance and quality control programs of clinical laboratories that perform pharmacogenetic testing.
Collapse
Affiliation(s)
- Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amy Turner
- RPRD Diagnostics, Milwaukee, Wisconsin; Department of Pediatrics, Section on Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ulrich Broeckel
- RPRD Diagnostics, Milwaukee, Wisconsin; Department of Pediatrics, Section on Genomic Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - D Brian Dawson
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio; Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Ty C Lynnes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Elizabeth B Medeiros
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lisa V Kalman
- Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia.
| |
Collapse
|
60
|
Descriptors of Cytochrome Inhibitors and Useful Machine Learning Based Methods for the Design of Safer Drugs. Pharmaceuticals (Basel) 2021; 14:ph14050472. [PMID: 34067565 PMCID: PMC8156202 DOI: 10.3390/ph14050472] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/16/2022] Open
Abstract
Roughly 2.8% of annual hospitalizations are a result of adverse drug interactions in the United States, representing more than 245,000 hospitalizations. Drug-drug interactions commonly arise from major cytochrome P450 (CYP) inhibition. Various approaches are routinely employed in order to reduce the incidence of adverse interactions, such as altering drug dosing schemes and/or minimizing the number of drugs prescribed; however, often, a reduction in the number of medications cannot be achieved without impacting therapeutic outcomes. Nearly 80% of drugs fail in development due to pharmacokinetic issues, outlining the importance of examining cytochrome interactions during preclinical drug design. In this review, we examined the physiochemical and structural properties of small molecule inhibitors of CYPs 3A4, 2D6, 2C19, 2C9, and 1A2. Although CYP inhibitors tend to have distinct physiochemical properties and structural features, these descriptors alone are insufficient to predict major cytochrome inhibition probability and affinity. Machine learning based in silico approaches may be employed as a more robust and accurate way of predicting CYP inhibition. These various approaches are highlighted in the review.
Collapse
|
61
|
Gammal RS, Smith DM, Wiisanen KW, Cusimano JM, Pettit RS, Stephens JW, Walko CM, Yang RH, Dunnenberger HM. The pharmacist's responsibility to ensure appropriate use of direct‐to‐consumer genetic testing. JOURNAL OF THE AMERICAN COLLEGE OF CLINICAL PHARMACY 2021. [DOI: 10.1002/jac5.1437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - D. Max Smith
- American College of Clinical Pharmacy Lenexa Kansas USA
| | | | | | | | | | | | | | | |
Collapse
|
62
|
Fredrikson KM, Fasolino T. Pharmacogenetic testing: Clinical integration and application for chronic pain management. Nurse Pract 2021; 46:12-19. [PMID: 33739321 DOI: 10.1097/01.npr.0000737180.73290.1f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT NPs commonly prescribe pharmaceutical therapies such as opiates, antidepressants, and/or other analgesics to improve the health and well-being of patients experiencing chronic pain. This article provides NPs with pharmacogenetic testing knowledge, such as readiness for clinical implementation, considerations for choosing a testing service, and testing costs for chronic pain management.
Collapse
|
63
|
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: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [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).
Collapse
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
| |
Collapse
|
64
|
Caraballo PJ, Sutton JA, Giri J, Wright JA, Nicholson WT, Kullo IJ, Parkulo MA, Bielinski SJ, Moyer AM. Integrating pharmacogenomics into the electronic health record by implementing genomic indicators. J Am Med Inform Assoc 2021; 27:154-158. [PMID: 31591640 DOI: 10.1093/jamia/ocz177] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/19/2019] [Accepted: 09/11/2019] [Indexed: 12/27/2022] Open
Abstract
Pharmacogenomics (PGx) clinical decision support integrated into the electronic health record (EHR) has the potential to provide relevant knowledge to clinicians to enable individualized care. However, past experience implementing PGx clinical decision support into multiple EHR platforms has identified important clinical, procedural, and technical challenges. Commercial EHRs have been widely criticized for the lack of readiness to implement precision medicine. Herein, we share our experiences and lessons learned implementing new EHR functionality charting PGx phenotypes in a unique repository, genomic indicators, instead of using the problem or allergy list. The Gen-Ind has additional features including a brief description of the clinical impact, a hyperlink to the original laboratory report, and links to additional educational resources. The automatic generation of genomic indicators from interfaced PGx test results facilitates implementation and long-term maintenance of PGx data in the EHR and can be used as criteria for synchronous and asynchronous CDS.
Collapse
Affiliation(s)
- Pedro J Caraballo
- Division of General Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, Minnesota, USA
| | - Joseph A Sutton
- Department of Information Technology, Mayo Clinic, Rochester, Minnesota
| | - Jyothsna Giri
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jessica A Wright
- Department of Pharmacy Services, Mayo Clinic, Rochester, Minnesota, USA
| | - Wayne T Nicholson
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark A Parkulo
- Center for the Science of Health Care Delivery, Mayo Clinic, Rochester, Minnesota, USA
- Division of Community Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Suzette J Bielinski
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
65
|
García-Martín E, García-Menaya JM, Esguevillas G, Cornejo-García JA, Doña I, Jurado-Escobar R, Torres MJ, Blanca-López N, Canto G, Blanca M, Laguna JJ, Bartra J, Rosado A, Fernández J, Cordobés C, Agúndez JAG. Deep sequencing of prostaglandin-endoperoxide synthase (PTGE) genes reveals genetic susceptibility for cross-reactive hypersensitivity to NSAID. Br J Pharmacol 2021; 178:1218-1233. [PMID: 33450044 DOI: 10.1111/bph.15366] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/30/2020] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND AND PURPOSE Cross-reactive hypersensitivity to nonsteroidal anti-inflammatory drugs (NSAIDs) is a relatively common adverse drug event caused by two or more chemically unrelated drugs and that is attributed to inhibition of the COX activity, particularly COX-1. Several studies investigated variations in the genes coding for COX enzymes as potential risk factors. However, these studies only interrogated a few single nucleotide variations (SNVs), leaving untested most of the gene sequence. EXPERIMENTAL APPROACH In this study, we analysed the whole sequence of the prostaglandin-endoperoxide synthase genes, PTGS1 and PTGS2, including all exons, exon-intron boundaries and both the 5' and 3' flanking regions in patients with cross-reactive hypersensitivity to NSAIDs and healthy controls. After sequencing analysis in 100 case-control pairs, we replicated the findings in 540 case-control pairs. Also, we analysed copy number variations for both PTGS genes. KEY RESULTS The most salient finding was the presence of two PTGS1 single nucleotide variations, which are significantly more frequent in patients than in control subjects. Patients carrying these single nucleotide variations displayed a significantly and markedly lower COX-1 activity as compared to non-carriers for both heterozygous and homozygous patients. CONCLUSION AND IMPLICATIONS Although the risk single nucleotide variations are present in a small proportion of patients, the strong association observed and the functional effect of these single nucleotide variations raise the hypothesis of genetic susceptibility to develop cross-reactive NSAID hypersensitivity in individuals with an impairment in COX-1 enzyme activity.
Collapse
Affiliation(s)
- Elena García-Martín
- University Institute of Molecular Pathology Biomarkers, University of Extremadura. ARADyAL Instituto de Salud Carlos III, Cáceres, Spain
| | - Jesús M García-Menaya
- Allergy Service, Badajoz University Hospital. ARADyAL Instituto de Salud Carlos III, Badajoz, Spain
| | - Gara Esguevillas
- University Institute of Molecular Pathology Biomarkers, University of Extremadura. ARADyAL Instituto de Salud Carlos III, Cáceres, Spain
| | - José A Cornejo-García
- Research Laboratory, IBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMA, Málaga, Spain
| | - Inmaculada Doña
- Allergy Unit, IBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMA, Málaga, Spain
| | - Raquel Jurado-Escobar
- Research Laboratory, IBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMA, Málaga, Spain
| | - María J Torres
- Allergy Unit, IBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMA, Málaga, Spain
| | - Natalia Blanca-López
- Allergy Service, ARADyAL Instituto de Salud Carlos III, Infanta Leonor University Hospital, Madrid, Spain
| | - Gabriela Canto
- Allergy Service, ARADyAL Instituto de Salud Carlos III, Infanta Leonor University Hospital, Madrid, Spain
| | - Miguel Blanca
- Allergy Service, ARADyAL Instituto de Salud Carlos III, Infanta Leonor University Hospital, Madrid, Spain
| | - José J Laguna
- Allergy Unit and Allergy-Anaesthesia Unit, ARADyAL Instituto de Salud Carlos III, Hospital Central Cruz Roja, Madrid, Spain
| | - Joan Bartra
- Allergy Section, Pneumology Department, Hospital Clinic, ARADyAL Instituto de Salud Carlos III, Universitat de Barcelona, Barcelona, Spain
| | - Ana Rosado
- Allergy Service, Alcorcón Hospital, Madrid, Spain
| | - Javier Fernández
- Allergy Unit, ARADyAL Instituto de Salud Carlos III, Regional University Hospital, Alicante, Spain
| | - Concepción Cordobés
- Allergy Service, Badajoz University Hospital. ARADyAL Instituto de Salud Carlos III, Badajoz, Spain
| | - José A G Agúndez
- University Institute of Molecular Pathology Biomarkers, University of Extremadura. ARADyAL Instituto de Salud Carlos III, Cáceres, Spain
| |
Collapse
|
66
|
Liu J, Chen H, Wang S, Zhou Q, Geng P, Zhou Y, Wu H, Shi H, Wang F, Yang J, Cai J, Dai D. Functional characterization of the defective CYP2C9 variant CYP2C9*18. Pharmacol Res Perspect 2021; 9:e00718. [PMID: 33508175 PMCID: PMC7842875 DOI: 10.1002/prp2.718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/23/2020] [Indexed: 11/10/2022] Open
Abstract
Cytochrome P450 2C9 (CYP2C9) is one of the most important drugs metabolizing enzymes and accounts for the metabolism of about 13%-17% of clinical drugs. Like other members in CYP2 family, CYP2C9 gene exhibits great genetic polymorphism among different races and individuals. CYP2C9*18 is one CYP2C9 allelic variant identified in a Southeast Asian population and is estimated to cause the amino acid substitutions of I359L and D397A in CYP2C9 enzyme simultaneously. Limited by the low expression level in bacteria and COS-7 cells, no valuable enzyme kinetics have been reported on this CYP2C9 variant. In this study, the baculovirus-based system was used for the high expression of recombinant CYP2C9 s in insect cells. As a result, together with I359L substitution, D397A could significantly decrease the protein expression of CYP2C9.18 in insect cells, although substitution of D397A alone had no effect on the expression of CYP2C9 in vitro. As compared with that of wild-type enzyme, both CYP2C9.18 variant and D397A variant could decrease more than 80% of the catalytic activity of CYP2C9 enzyme toward three probe substrates, suggesting that caution should be exercised when patients carrying CYP2C9*18 taking medicines metabolized by CYP2C9 enzyme with a narrow therapeutic window.
Collapse
Affiliation(s)
- Jian Liu
- The Key laboratory of GeriatricsBeijing Institute of GeriatricsBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingP. R. China
| | - Hao Chen
- Cardiovascular DepartmentBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingP. R. China
| | - Shuang‐Hu Wang
- Laboratory of Clinical PharmacyThe Sixth Affiliated Hospital of Wenzhou Medical UniversityThe People's Hospital of LishuiLishuiP.R. China
| | - Quan Zhou
- Laboratory of Clinical PharmacyThe Sixth Affiliated Hospital of Wenzhou Medical UniversityThe People's Hospital of LishuiLishuiP.R. China
| | - Pei‐Wu Geng
- Laboratory of Clinical PharmacyThe Sixth Affiliated Hospital of Wenzhou Medical UniversityThe People's Hospital of LishuiLishuiP.R. China
| | - Yun‐Fang Zhou
- Laboratory of Clinical PharmacyThe Sixth Affiliated Hospital of Wenzhou Medical UniversityThe People's Hospital of LishuiLishuiP.R. China
| | - Hua‐Lan Wu
- Cardiovascular DepartmentBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingP. R. China
| | - Hai‐Feng Shi
- Cardiovascular DepartmentBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingP. R. China
| | - Fang Wang
- Cardiovascular DepartmentBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingP. R. China
| | - Jie‐Fu Yang
- Cardiovascular DepartmentBeijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingP. R. China
| | - Jian‐Ping Cai
- The Key laboratory of GeriatricsBeijing Institute of GeriatricsBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingP. R. China
| | - Da‐Peng Dai
- The Key laboratory of GeriatricsBeijing Institute of GeriatricsBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingP. R. China
| |
Collapse
|
67
|
Lin YS, Thummel KE, Thompson BD, Totah RA, Cho CW. Sources of Interindividual Variability. Methods Mol Biol 2021; 2342:481-550. [PMID: 34272705 DOI: 10.1007/978-1-0716-1554-6_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The efficacy, safety, and tolerability of drugs are dependent on numerous factors that influence their disposition. A dose that is efficacious and safe for one individual may result in sub-therapeutic or toxic blood concentrations in others. A significant source of this variability in drug response is drug metabolism, where differences in presystemic and systemic biotransformation efficiency result in variable degrees of systemic exposure (e.g., AUC, Cmax, and/or Cmin) following administration of a fixed dose.Interindividual differences in drug biotransformation have been studied extensively. It is recognized that both intrinsic factors (e.g., genetics, age, sex, and disease states) and extrinsic factors (e.g., diet , chemical exposures from the environment, and the microbiome) play a significant role. For drug-metabolizing enzymes, genetic variation can result in the complete absence or enhanced expression of a functional enzyme. In addition, upregulation and downregulation of gene expression, in response to an altered cellular environment, can achieve the same range of metabolic function (phenotype), but often in a less predictable and time-dependent manner. Understanding the mechanistic basis for variability in drug disposition and response is essential if we are to move beyond the era of empirical, trial-and-error dose selection and into an age of personalized medicine that will improve outcomes in maintaining health and treating disease.
Collapse
Affiliation(s)
- Yvonne S Lin
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA.
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Brice D Thompson
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Rheem A Totah
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Christi W Cho
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| |
Collapse
|
68
|
Nicholson WT, Formea CM, Matey ET, Wright JA, Giri J, Moyer AM. Considerations When Applying Pharmacogenomics to Your Practice. Mayo Clin Proc 2021; 96:218-230. [PMID: 33308868 DOI: 10.1016/j.mayocp.2020.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/24/2020] [Accepted: 03/17/2020] [Indexed: 10/22/2022]
Abstract
Many practitioners who have not had pharmacogenomic education are required to apply pharmacogenomics to their practices. Although many aspects of pharmacogenomics are similar to traditional concepts of drug-drug interactions, there are some differences. We searched PubMed with the search terms pharmacogenomics and pharmacogenetics (January 1, 2005, through December 31, 2019) and selected articles that supported the application of pharmacogenomics to practice. For inclusion, we gave preference to national and international consortium guidelines for implementation of pharmacogenomics. We discuss special considerations important in the application of pharmacogenomics to assist clinicians with ordering, interpreting, and applying pharmacogenomics in their practices.
Collapse
Affiliation(s)
- Wayne T Nicholson
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN.
| | - Christine M Formea
- Intermountain Healthcare Department of Pharmacy Services Pharmacy Services, Salt Lake City, UT; Intermountain Precision Genomics, Intermountain Healthcare, St George, UT
| | - Eric T Matey
- Department of Pharmacy, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN
| | - Jessica A Wright
- Department of Pharmacy, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN
| | - Jyothsna Giri
- Mayo Clinic Center for Individualized Medicine, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, MN
| |
Collapse
|
69
|
Bousman CA, Bengesser SA, Aitchison KJ, Amare AT, Aschauer H, Baune BT, Asl BB, Bishop JR, Burmeister M, Chaumette B, Chen LS, Cordner ZA, Deckert J, Degenhardt F, DeLisi LE, Folkersen L, Kennedy JL, Klein TE, McClay JL, McMahon FJ, Musil R, Saccone NL, Sangkuhl K, Stowe RM, Tan EC, Tiwari AK, Zai CC, Zai G, Zhang J, Gaedigk A, Müller DJ. Review and Consensus on Pharmacogenomic Testing in
Psychiatry. PHARMACOPSYCHIATRY 2020; 54:5-17. [DOI: 10.1055/a-1288-1061] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AbstractThe implementation of pharmacogenomic (PGx) testing in psychiatry remains modest,
in part due to divergent perceptions of the quality and completeness of the
evidence base and diverse perspectives on the clinical utility of PGx testing
among psychiatrists and other healthcare providers. Recognizing the current lack
of consensus within the field, the International Society of Psychiatric Genetics
assembled a group of experts to conduct a narrative synthesis of the PGx
literature, prescribing guidelines, and product labels related to psychotropic
medications as well as the key considerations and limitations related to the use
of PGx testing in psychiatry. The group concluded that to inform medication
selection and dosing of several commonly-used antidepressant and antipsychotic
medications, current published evidence, prescribing guidelines, and product
labels support the use of PGx testing for 2 cytochrome P450 genes (CYP2D6,
CYP2C19). In addition, the evidence supports testing for human leukocyte
antigen genes when using the mood stabilizers carbamazepine (HLA-A and
HLA-B), oxcarbazepine (HLA-B), and phenytoin (CYP2C9, HLA-B). For
valproate, screening for variants in certain genes (POLG, OTC, CSP1) is
recommended when a mitochondrial disorder or a urea cycle disorder is suspected.
Although barriers to implementing PGx testing remain to be fully resolved, the
current trajectory of discovery and innovation in the field suggests these
barriers will be overcome and testing will become an important tool in
psychiatry.
Collapse
Affiliation(s)
- Chad A. Bousman
- Departments of Medical Genetics, Psychiatry, Physiology &
Pharmacology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of
Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Calgary, AB,
Canada
- Department of Psychiatry, Melbourne Medical School, The University of
Melbourne, Melbourne, VIC, Australia
| | - Susanne A. Bengesser
- Department of Psychiatry and Psychotherapeutic Medicine, Medical
University of Graz, Austria
| | - Katherine J. Aitchison
- Departments of Psychiatry, Medical Genetics and the Neuroscience and
Mental Health Institute, University of Alberta, Edmonton, AB,
Canada
| | - Azmeraw T. Amare
- Discipline of Psychiatry, School of Medicine, University of Adelaide,
Adelaide, SA, Australia
- South Australian Health and Medical Research Institute (SAHMRI),
Adelaide, SA, Australia
| | - Harald Aschauer
- Biopsychosocial Corporation (BioPsyC), non-profit association, Vienna,
Austria
| | - Bernhard T. Baune
- Department of Psychiatry and Psychotherapy, University of
Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of
Melbourne, Melbourne, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University
of Melbourne, Parkville, VIC, Australia
| | - Bahareh Behroozi Asl
- Departments of Psychiatry, Medical Genetics and the Neuroscience and
Mental Health Institute, University of Alberta, Edmonton, AB,
Canada
| | - Jeffrey R. Bishop
- Department of Experimental and Clinical Pharmacology, University of
Minnesota College of Pharmacy and Department of Psychiatry, University of
Minnesota Medical School, Minneapolis, MN, USA
| | - Margit Burmeister
- Michigan Neuroscience Institute and Departments of Computational
Medicine & Bioinformatics, Human Genetics and Psychiatry, The University
of Michigan, Ann Arbor MI, USA
| | - Boris Chaumette
- Institute of Psychiatry and Neuroscience of Paris, GHU Paris
Psychiatrie & Neurosciences, University of Paris, Paris,
France
- Department of Psychiatry, McGill University, Montreal,
Canada
| | - Li-Shiun Chen
- Departments of Psychiatry and Genetics, Washington University School of
Medicine in St. Louis, USA
| | - Zachary A. Cordner
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins
University School of Medicine, Baltimore, MD, USA
| | - Jürgen Deckert
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of
Mental Health, Würzburg, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, School of Medicine
& University Hospital Bonn, Bonn, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy, University Hospital Essen, University of Duisburg-Essen,
Duisburg, Germany
| | - Lynn E. DeLisi
- Department of Psychiatry, Harvard Medical School, Cambridge Health
Alliance, Cambridge, Massachusetts, USA
| | - Lasse Folkersen
- Institute of Biological Psychiatry, Capital Region Hospitals,
Copenhagen, Denmark
| | - James L. Kennedy
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford,
California, USA
| | - Joseph L. McClay
- Department of Pharmacotherapy and Outcome Science, Virginia
Commonwealth University School of Pharmacy, Richmond, VA, USA
| | - Francis J. McMahon
- Human Genetics Branch, National Institute of Mental Health, Bethesda,
MD, USA
| | - Richard Musil
- Department of Psychiatry and Psychotherapy,
Ludwig-Maximilians-University, Munich, Germany
| | - Nancy L. Saccone
- Departments of Psychiatry and Genetics, Washington University School of
Medicine in St. Louis, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford,
California, USA
| | - Robert M. Stowe
- Departments of Psychiatry and Neurology (Medicine), University of
British Columbia, USA
| | - Ene-Choo Tan
- KK Research Centre, KK Women’s and Children’s Hospital,
Singapore, Singapore
| | - Arun K. Tiwari
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| | - Clement C. Zai
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| | - Gwyneth Zai
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| | - Jianping Zhang
- Department of Psychiatry, Weill Cornell Medical College, New
York-Presbyterian Westchester Division, White Plains, NY, USA
| | - 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, MO, USA
| | - Daniel J Müller
- Department of Psychiatry, University of Toronto, Toronto, Ontario,
Canada
- Centre for Addiction and Mental Health, University of Toronto, Toronto,
Ontario, Canada
| |
Collapse
|
70
|
Ustare LAT, Reyes KG, Lasac MAG, Brodit SE, Baclig MO. Single nucleotide polymorphisms on CYP2C9 gene among Filipinos and its association with post-operative pain relief via COX-2 inhibitors. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2020; 11:31-38. [PMID: 33240461 PMCID: PMC7677506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
CYP2C9 gene encodes an enzyme involved in the metabolism of a wide variety of drugs which include celecoxib. This study investigated the frequencies of the alleles and genotypes of CYP2C9*1, CYP2C9*2, and CYP2C9*3 among Filipinos who underwent surgery, and to determine the association of CYP2C9 polymorphisms with post-operative pain relief via COX-2 inhibitors. Response to celecoxib was determined using the numerical rating scale (0-10) on the 24th and 48th hour of surgery. The CYP2C9 alleles were detected by real-time PCR. For CYP2C9*1 and CYP2C9*3, the allele frequencies among Filipinos were 99% and 1% respectively, which is similar with other East Asians. CYP2C9*2 alleles were not detected. The frequencies of CYP2C9*1/*1 and CYP2C9*1/*3 genotypes were 98% and 2% respectively. At 24 hours post-surgery, the average pain score was 2.57 ± 1.03, while on 48 hours post-surgery, the average pain score was 0.67 ± 0.61 among those who have the wild-type CYP2C9*1 allele. The average pain score on the 24th and 48th hour post-operatively was observed to be 2.5 ± 0.71 and 0.5 ± 0.71 respectively among two patients classified as intermediate metabolizer carrying the CYP2C9*1/*3 genotype. Low frequencies of CYP2C9 polymorphisms were observed in the present study, this pattern was similar with other Asians except Indians, and considerably lower than Caucasians. Our results suggest that CYP2C9 genotyping is not routinely needed for Filipinos but must be considered among mixed races. Consequently, a more personalized therapeutic strategy was derived from these data, resulting in good clinical outcomes and less adverse drug effects.
Collapse
Affiliation(s)
- Leland Arden T Ustare
- Department of Anesthesiology, St. Luke’s Medical Center279 E. Rodriguez Sr. Blvd., Quezon 1112, Philippines
| | - Karen G Reyes
- Research and Biotechnology, St. Luke’s Medical Center279 E. Rodriguez Sr. Blvd., Quezon 1112, Philippines
| | - Marie Angelica G Lasac
- Department of Anesthesiology, St. Luke’s Medical Center279 E. Rodriguez Sr. Blvd., Quezon 1112, Philippines
| | - Salvador E Brodit
- Department of Anesthesiology, St. Luke’s Medical Center279 E. Rodriguez Sr. Blvd., Quezon 1112, Philippines
- Pain Management Center, St. Luke’s Medical Center279 E. Rodriguez Sr. Blvd., Quezon 1112, Philippines
| | - Michael O Baclig
- Research and Biotechnology, St. Luke’s Medical Center279 E. Rodriguez Sr. Blvd., Quezon 1112, Philippines
- St. Luke’s Medical Center College of Medicine-William H. Quasha Memorial, Cathedral Heights ComplexE. Rodriguez Sr. Blvd., Quezon, 1112, Philippines
| |
Collapse
|
71
|
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.
Collapse
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)
| |
Collapse
|
72
|
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.
Collapse
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
| |
Collapse
|
73
|
Hoffman JM, Flynn AJ, Juskewitch JE, Freimuth RR. Biomedical Data Science and Informatics Challenges to Implementing Pharmacogenomics with Electronic Health Records. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-020320-093614] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pharmacogenomic information must be incorporated into electronic health records (EHRs) with clinical decision support in order to fully realize its potential to improve drug therapy. Supported by various clinical knowledge resources, pharmacogenomic workflows have been implemented in several healthcare systems. Little standardization exists across these efforts, however, which limits scalability both within and across clinical sites. Limitations in information standards, knowledge management, and the capabilities of modern EHRs remain challenges for the widespread use of pharmacogenomics in the clinic, but ongoing efforts are addressing these challenges. Although much work remains to use pharmacogenomic information more effectively within clinical systems, the experiences of pioneering sites and lessons learned from those programs may be instructive for other clinical areas beyond genomics. We present a vision of what can be achieved as informatics and data science converge to enable further adoption of pharmacogenomics in the clinic.
Collapse
Affiliation(s)
- James M. Hoffman
- Department of Pharmaceutical Sciences and the Office of Quality and Patient Care, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Allen J. Flynn
- Department of Learning Health Sciences, Medical School, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Justin E. Juskewitch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Robert R. Freimuth
- Division of Digital Health Sciences, Department of Health Sciences Research, Center for Individualized Medicine, and Information and Knowledge Management, Mayo Clinic, Rochester, Minnesota 55905, USA
| |
Collapse
|
74
|
Marrero RJ, Cicali EJ, Arwood MJ, Eddy E, DeRemer D, Ramnaraign BH, Daily KC, Jones D, Cook KJ, Cavallari LH, Wiisanen Weitzel K, Langaee T, Newsom KJ, Starostik P, Clare-Salzer MJ, Johnson JA, George TJ, Cooper-DeHoff RM. How to Transition from Single-Gene Pharmacogenetic Testing to Preemptive Panel-Based Testing: A Tutorial. Clin Pharmacol Ther 2020; 108:557-565. [PMID: 32460360 DOI: 10.1002/cpt.1912] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/08/2020] [Indexed: 12/14/2022]
Abstract
There have been significant advancements in precision medicine and approaches to medication selection based on pharmacogenetic results. With the availability of direct-to-consumer genetic testing and growing awareness of genetic interindividual variability, patient demand for more precise, individually tailored drug regimens is increasing. The University of Florida (UF) Health Precision Medicine Program (PMP) was established in 2011 to improve integration of genomic data into clinical practice. In the ensuing years, the UF Health PMP has successfully implemented several single-gene tests to optimize the precision of medication prescribing across a variety of clinical settings. Most recently, the UF Health PMP launched a custom-designed pharmacogenetic panel, including pharmacogenes relevant to supportive care medications commonly prescribed to patients undergoing chemotherapy treatment, referred to as "GatorPGx." This tutorial provides guidance and information to institutions on how to transition from the implementation of single-gene pharmacogenetic testing to a preemptive panel-based testing approach. Here, we demonstrate application of the preemptive panel in the setting of an adult solid tumor oncology clinic. Importantly, the information included herein can be applied to other clinical practice settings.
Collapse
Affiliation(s)
- Richard J Marrero
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Emily J Cicali
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Meghan J Arwood
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Elizabeth Eddy
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - David DeRemer
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | | | - Karen C Daily
- University of Florida Health Cancer Center, Gainesville, Florida, USA
| | - Dennie Jones
- University of Florida Health Cancer Center, Gainesville, Florida, USA
| | - Kelsey J Cook
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Kristin Wiisanen Weitzel
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Taimour Langaee
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Kimberly J Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Michael J Clare-Salzer
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| | - Thomas J George
- University of Florida Health Cancer Center, Gainesville, Florida, USA
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, Florida, USA.,Center for Pharmacogenomics and Precision Medicine, University of Florida College of Pharmacy, Gainesville, Florida, USA
| |
Collapse
|
75
|
Asiimwe IG, Zhang EJ, Osanlou R, Krause A, Dillon C, Suarez-Kurtz G, Zhang H, Perini JA, Renta JY, Duconge J, Cavallari LH, Marcatto LR, Beasly MT, Perera MA, Limdi NA, Santos PCJL, Kimmel SE, Lubitz SA, Scott SA, Kawai VK, Jorgensen AL, Pirmohamed M. Genetic Factors Influencing Warfarin Dose in Black-African Patients: A Systematic Review and Meta-Analysis. Clin Pharmacol Ther 2020; 107:1420-1433. [PMID: 31869433 PMCID: PMC7217737 DOI: 10.1002/cpt.1755] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022]
Abstract
Warfarin is the most commonly used oral anticoagulant in sub-Saharan Africa. Dosing is challenging due to a narrow therapeutic index and high interindividual variability in dose requirements. To evaluate the genetic factors affecting warfarin dosing in black-Africans, we performed a meta-analysis of 48 studies (2,336 patients). Significant predictors for CYP2C9 and stable dose included rs1799853 (CYP2C9*2), rs1057910 (CYP2C9*3), rs28371686 (CYP2C9*5), rs9332131 (CYP2C9*6), and rs28371685 (CYP2C9*11) reducing dose by 6.8, 12.5, 13.4, 8.1, and 5.3 mg/week, respectively. VKORC1 variants rs9923231 (-1639G>A), rs9934438 (1173C>T), rs2359612 (2255C>T), rs8050894 (1542G>C), and rs2884737 (497T>G) decreased dose by 18.1, 21.6, 17.3, 11.7, and 19.6 mg/week, respectively, whereas rs7294 (3730G>A) increased dose by 6.9 mg/week. Finally, rs12777823 (CYP2C gene cluster) was associated with a dose reduction of 12.7 mg/week. Few studies were conducted in Africa, and patient numbers were small, highlighting the need for further work in black-Africans to evaluate genetic factors determining warfarin response.
Collapse
Affiliation(s)
- Innocent G. Asiimwe
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Eunice J. Zhang
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Rostam Osanlou
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, Johannesburg, South Africa
| | - Chrisly Dillon
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | | | - Honghong Zhang
- Department of Pharmacology, Center for Pharmacogenomics, Northwestern University, Chicago IL
| | - Jamila A Perini
- Research Laboratory of Pharmaceutical Sciences, West Zone State University-UEZO, Rio de Janeiro, Brazil
| | - Jessicca Y. Renta
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067
| | - Jorge Duconge
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067
| | - Larisa H Cavallari
- Center for Pharmacogenomics, Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA
| | - Leiliane R. Marcatto
- Laboratory of Genetics and Molecular Cardiology, Faculdade de Medicina FMUSP, Heart Institute (InCor), Universidade de São Paulo, São Paulo, Brazil
| | - Mark T. Beasly
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | - Minoli A Perera
- Department of Pharmacology, Center for Pharmacogenomics, Northwestern University, Chicago IL
| | - Nita A. Limdi
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | - Paulo C. J. L. Santos
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-Unifesp, São Paulo, Brazil
| | - Stephen E. Kimmel
- Perelman School of Medicine at the University of Pennsylvania, Department of Biostatistics, Epidemiology, and Informatics
| | - Steven A. Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Vivian K. Kawai
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrea L. Jorgensen
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool
- These authors contributed equally: Andrea Jorgensen and Munir Pirmohamed
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
- These authors contributed equally: Andrea Jorgensen and Munir Pirmohamed
| |
Collapse
|
76
|
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: 37] [Impact Index Per Article: 9.3] [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.
Collapse
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
| |
Collapse
|
77
|
Shah RR. Genotype‐guided warfarin therapy: Still of only questionable value two decades on. J Clin Pharm Ther 2020; 45:547-560. [DOI: 10.1111/jcpt.13127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 02/07/2020] [Indexed: 12/20/2022]
|
78
|
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 2020; 107:154-170. [PMID: 31544239 PMCID: PMC6925641 DOI: 10.1002/cpt.1643] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [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).
Collapse
Affiliation(s)
| | - 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
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | - José A. G. Agúndez
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres; ARADyAL Instituto de Salud Carlos III. Spain
| | - John L. Black
- Personalized Genomics Laboratory, Division of Laboratory Genetics and Genomics, Mayo Clinic laboratories, Mayo Clinic, Rochester MN (200 1st Street SW, Rochester MN 55902)
| | - Henry M. Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanton, IL, USA
| | - Gualberto Ruano
- Institute of Living at Hartford Hospital, Genomas Laboratory of Personalized Health, Hartford, Connecticut (67 Jefferson Street, Hartford, Connecticut 06106)
| | - Martin A. Kennedy
- Department of Pathology and Biomedical Science, University Otago, Christchurch, New Zealand
| | - Michael S. Phillips
- Sequence Bioinformatics Inc., 139 Water Street, 2 Floor, St. John’s NL, A1C 1B2, Canada
| | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - 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, MO, USA
| |
Collapse
|
79
|
Liu M, Obeng AO. Siponimod and CYP2C9 Allele Prevalence Among Blacks. J Clin Pharmacol 2019; 60:429-431. [DOI: 10.1002/jcph.1546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/16/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Michelle Liu
- Department of Pharmaceutical ServicesVanderbilt University Medical Center Nashville Tennessee USA
| | - Aniwaa Owusu Obeng
- The Charles Bronfman Institute for Personalized MedicineIcahn School of Medicine at Mount Sinai New York New York USA
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount Sinai New York New York USA
- Pharmacy DepartmentThe Mount Sinai Hospital New York New York USA
| |
Collapse
|
80
|
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: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
81
|
Giri J, Moyer AM, Bielinski SJ, Caraballo PJ. Concepts Driving Pharmacogenomics Implementation Into Everyday Healthcare. Pharmgenomics Pers Med 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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
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.
Collapse
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
| |
Collapse
|
82
|
Haga SB. Managing Increased Accessibility to Pharmacogenomic Data. Clin Pharmacol Ther 2019; 106:922-924. [PMID: 31482575 DOI: 10.1002/cpt.1602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/12/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| |
Collapse
|
83
|
Challenges in clinical implementation of CYP2D6 genotyping: choice of variants to test affects phenotype determination. Genet Med 2019; 22:232-233. [PMID: 31341243 DOI: 10.1038/s41436-019-0614-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022] Open
|