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Gerlach S, Maruf AA, Shaheen SM, McCloud R, Heintz M, McAusland L, Arnold PD, Bousman CA. Effect of CYP2D6 genetic variation on patient-reported symptom improvement and side effects among children and adolescents treated with amphetamines. Pharmacogenet Genomics 2024; 34:149-153. [PMID: 38517706 DOI: 10.1097/fpc.0000000000000529] [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: 03/24/2024]
Abstract
OBJECTIVES Amphetamine-based medications are recommended as a first-line pharmacotherapy for the treatment of attention-deficit/hyperactivity disorder in children and adolescents. However, the efficacy and tolerability of these medications vary across individuals, which could be related to interindividual differences in amphetamine metabolism. This study examined if genotype-predicted phenotypes of the cytochrome P450 isozyme CYP2D6 were associated with self-reported side effects and symptom improvement in youth treated with amphetamines. METHODS Two hundred fourteen participants aged 6-24 who had a history of past or current amphetamine treatment were enrolled from Western Canada. Amphetamine dose and duration information was collected from the participants along with questions regarding adherence, concomitant medications, symptom improvement and side effects. DNA was extracted from saliva samples and genotyped for CYP2D6 . Binomial logistic regression models were used to determine the effect of CYP2D6 metabolizer phenotype with and without correction for phenoconversion on self-reported symptom improvement and side effects. RESULTS Genotype-predicted CYP2D6 poor metabolizers had significantly higher odds of reporting symptom improvement when compared to intermediate metabolizers (OR = 3.67, 95% CI = 1.15-11.7, P = 0.029) after correction for phenoconversion and adjusting for sex, age, dose, duration, and adherence. There was no association between CYP2D6 metabolizer phenotype and self-reported side effects. CONCLUSION Our findings indicate that phenoconverted and genotype-predicted CYP2D6 poor metabolizer phenotype is significantly associated with higher odds of symptom improvement in children and adolescents treated with amphetamine. If replicated, these results could inform the development of future dosing guidelines for amphetamine treatment in children and adolescents.
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Affiliation(s)
- Samuel Gerlach
- Cumming School of Medicine, University of Calgary, Calgary, AB
| | - Abdullah Al Maruf
- College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary
- Department of Psychiatry, University of Calgary
| | - Sarker M Shaheen
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary
- Department of Psychiatry, University of Calgary
| | - Ryden McCloud
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary
| | - Madison Heintz
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary
- Department of Medical Genetics, University of Calgary
| | - Laina McAusland
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary
- Department of Psychiatry, University of Calgary
- Department of Medical Genetics, University of Calgary
| | - Paul D Arnold
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary
- Department of Psychiatry, University of Calgary
- Department of Medical Genetics, University of Calgary
- Alberta Children's Hospital Research Institute, University of Calgary
| | - Chad A Bousman
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary
- Department of Psychiatry, University of Calgary
- Department of Medical Genetics, University of Calgary
- Department of Physiology and Pharmacology, University of Calgary
- Alberta Children's Hospital Research Institute, University of Calgary
- Department of Community Health Sciences, University of Calgary, Calgary, AB, Canada
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Abdel‐latif R, Badji R, Mohammed S, Al‐Muftah W, Mbarek H, Darwish D, Assaf D, Al‐Badriyeh D, Elewa H, Afifi N, Masoodi NA, Omar AS, Al Suwaidi J, Bujassoum S, Al Hail M, Ismail SI, Althani A. QPGx-CARES: Qatar pharmacogenetics clinical applications and research enhancement strategies. Clin Transl Sci 2024; 17:e13800. [PMID: 38818903 PMCID: PMC11140449 DOI: 10.1111/cts.13800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 06/01/2024] Open
Abstract
Pharmacogenetic (PGx)-informed medication prescription is a cutting-edge genomic application in contemporary medicine, offering the potential to overcome the conventional "trial-and-error" approach in drug prescription. The ability to use an individual's genetic profile to predict drug responses allows for personalized drug and dosage selection, thereby enhancing the safety and efficacy of treatments. However, despite significant scientific and clinical advancements in PGx, its integration into routine healthcare practices remains limited. To address this gap, the Qatar Genome Program (QGP) has embarked on an ambitious initiative known as QPGx-CARES (Qatar Pharmacogenetics Clinical Applications and Research Enhancement Strategies), which aims to set a roadmap for optimizing PGx research and clinical implementation on a national scale. The goal of QPGx-CARES initiative is to integrate PGx testing into clinical settings with the aim of improving patient health outcomes. In 2022, QGP initiated several implementation projects in various clinical settings. These projects aimed to evaluate the clinical utility of PGx testing, gather valuable insights into the effective dissemination of PGx data to healthcare professionals and patients, and identify the gaps and the challenges for wider adoption. QPGx-CARES strategy aimed to integrate evidence-based PGx findings into clinical practice, focusing on implementing PGx testing for cardiovascular medications, supported by robust scientific evidence. The current initiative sets a precedent for the nationwide implementation of precision medicine across diverse clinical domains.
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Affiliation(s)
- Rania Abdel‐latif
- Qatar Genome Program, Qatar Precision Health InstituteQatar FoundationDohaQatar
| | - Radja Badji
- Qatar Genome Program, Qatar Precision Health InstituteQatar FoundationDohaQatar
| | | | - Wadha Al‐Muftah
- Qatar Genome Program, Qatar Precision Health InstituteQatar FoundationDohaQatar
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Precision Health InstituteQatar FoundationDohaQatar
| | - Dima Darwish
- Qatar Genome Program, Qatar Precision Health InstituteQatar FoundationDohaQatar
| | - Duha Assaf
- Qatar Genome Program, Qatar Precision Health InstituteQatar FoundationDohaQatar
| | | | - Hazem Elewa
- College of Pharmacy, QU HealthQatar UniversityDohaQatar
| | - Nahla Afifi
- Qatar Biobank for Medical ResearchQatar Foundation for Education, Science, and CommunityDohaQatar
| | | | - Amr Salah Omar
- Cardiology and Cardiovascular SurgeryDepartment Hamad Medical CorporationDohaQatar
| | - Jassim Al Suwaidi
- Cardiology and Cardiovascular SurgeryDepartment Hamad Medical CorporationDohaQatar
| | - Salha Bujassoum
- Medical Oncology, National Center for Cancer Care and ResearchDepartment Hamad Medical CorporationDohaQatar
| | - Moza Al Hail
- Pharmacy DepartmentHamad Medical CorporationDohaQatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Precision Health InstituteQatar FoundationDohaQatar
| | - Asma Althani
- Biomedical Research CenterQatar UniversityDohaQatar
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Carini C, Seyhan AA. Tribulations and future opportunities for artificial intelligence in precision medicine. J Transl Med 2024; 22:411. [PMID: 38702711 PMCID: PMC11069149 DOI: 10.1186/s12967-024-05067-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 05/06/2024] Open
Abstract
Upon a diagnosis, the clinical team faces two main questions: what treatment, and at what dose? Clinical trials' results provide the basis for guidance and support for official protocols that clinicians use to base their decisions. However, individuals do not consistently demonstrate the reported response from relevant clinical trials. The decision complexity increases with combination treatments where drugs administered together can interact with each other, which is often the case. Additionally, the individual's response to the treatment varies with the changes in their condition. In practice, the drug and the dose selection depend significantly on the medical protocol and the medical team's experience. As such, the results are inherently varied and often suboptimal. Big data and Artificial Intelligence (AI) approaches have emerged as excellent decision-making tools, but multiple challenges limit their application. AI is a rapidly evolving and dynamic field with the potential to revolutionize various aspects of human life. AI has become increasingly crucial in drug discovery and development. AI enhances decision-making across different disciplines, such as medicinal chemistry, molecular and cell biology, pharmacology, pathology, and clinical practice. In addition to these, AI contributes to patient population selection and stratification. The need for AI in healthcare is evident as it aids in enhancing data accuracy and ensuring the quality care necessary for effective patient treatment. AI is pivotal in improving success rates in clinical practice. The increasing significance of AI in drug discovery, development, and clinical trials is underscored by many scientific publications. Despite the numerous advantages of AI, such as enhancing and advancing Precision Medicine (PM) and remote patient monitoring, unlocking its full potential in healthcare requires addressing fundamental concerns. These concerns include data quality, the lack of well-annotated large datasets, data privacy and safety issues, biases in AI algorithms, legal and ethical challenges, and obstacles related to cost and implementation. Nevertheless, integrating AI in clinical medicine will improve diagnostic accuracy and treatment outcomes, contribute to more efficient healthcare delivery, reduce costs, and facilitate better patient experiences, making healthcare more sustainable. This article reviews AI applications in drug development and clinical practice, making healthcare more sustainable, and highlights concerns and limitations in applying AI.
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Affiliation(s)
- Claudio Carini
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, New Hunt's House, King's College London, Guy's Campus, London, UK.
- Biomarkers Consortium, Foundation of the National Institute of Health, Bethesda, MD, USA.
| | - Attila A Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA.
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI, USA.
- Legorreta Cancer Center at Brown University, Providence, RI, USA.
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Gambari R, Waziri AD, Goonasekera H, Peprah E. Pharmacogenomics of Drugs Used in β-Thalassemia and Sickle-Cell Disease: From Basic Research to Clinical Applications. Int J Mol Sci 2024; 25:4263. [PMID: 38673849 PMCID: PMC11050010 DOI: 10.3390/ijms25084263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
In this short review we have presented and discussed studies on pharmacogenomics (also termed pharmacogenetics) of the drugs employed in the treatment of β-thalassemia or Sickle-cell disease (SCD). This field of investigation is relevant, since it is expected to help clinicians select the appropriate drug and the correct dosage for each patient. We first discussed the search for DNA polymorphisms associated with a high expression of γ-globin genes and identified this using GWAS studies and CRISPR-based gene editing approaches. We then presented validated DNA polymorphisms associated with a high HbF production (including, but not limited to the HBG2 XmnI polymorphism and those related to the BCL11A, MYB, KLF-1, and LYAR genes). The expression of microRNAs involved in the regulation of γ-globin genes was also presented in the context of pharmacomiRNomics. Then, the pharmacogenomics of validated fetal hemoglobin inducers (hydroxyurea, butyrate and butyrate analogues, thalidomide, and sirolimus), of iron chelators, and of analgesics in the pain management of SCD patients were considered. Finally, we discuss current clinical trials, as well as international research networks focusing on clinical issues related to pharmacogenomics in hematological diseases.
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Affiliation(s)
- Roberto Gambari
- Center “Chiara Gemmo and Elio Zago” for the Research on Thalassemia, Department of Life Sciences and Biotechnology, Ferrara University, 40124 Ferrara, Italy
| | - Aliyu Dahiru Waziri
- Department of Hematology and Blood Transfusion, Ahmadu Bello University Teaching Hospital Zaria, Kaduna 810001, Nigeria;
| | - Hemali Goonasekera
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo P.O. Box 271, Sri Lanka;
| | - Emmanuel Peprah
- Implementing Sustainable Evidence-Based Interventions through Engagement (ISEE) Lab, Department of Global and Environmental Health, School of Global Public Health, New York University, New York, NY 10003, USA;
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Calendo G, Kusic D, Madzo J, Gharani N, Scheinfeldt L. ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole-genome sequencing data. FRONTIERS IN BIOINFORMATICS 2024; 4:1351620. [PMID: 38533129 PMCID: PMC10963438 DOI: 10.3389/fbinf.2024.1351620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Long-read sequencing technologies offer new opportunities to generate high-confidence phased whole-genome sequencing data for robust pharmacogenetic annotation. Here, we describe a new user-friendly R package, ursaPGx, designed to accept multi-sample phased whole-genome sequencing data VCF input files and output star allele annotations for pharmacogenes annotated in PharmVar.
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Affiliation(s)
- Gennaro Calendo
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Dara Kusic
- Coriell Institute for Medical Research, Camden, NJ, United States
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, NJ, United States
- Cooper Medical School of Rowan University, Camden, NJ, United States
| | - Neda Gharani
- Coriell Institute for Medical Research, Camden, NJ, United States
- Gharani Consulting Limited, London, United Kingdom
| | - Laura Scheinfeldt
- Coriell Institute for Medical Research, Camden, NJ, United States
- Cooper Medical School of Rowan University, Camden, NJ, United States
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6
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Jolly B, Scaria V. Ethnic differences in pharmacogenomic variants: a south Asian perspective. Pharmacogenomics 2024; 25:171-174. [PMID: 38511426 DOI: 10.2217/pgs-2024-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/14/2024] [Indexed: 03/22/2024] Open
Affiliation(s)
- Bani Jolly
- Karkinos Healthcare Private Limited (KHPL), Aurbis Business Parks, Bellandur, Bengaluru, Karnataka, 560103, India
| | - Vinod Scaria
- Vishwanath Cancer Care Foundation (VCCF), Neelkanth Business Park Kirol Village, West Mumbai, Maharashtra, 400086, India
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7
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Malik S, Verma P, Ruaño G, Al Siaghy A, Dilawar A, Bishop JR, Strawn JR, Namerow LB. Pharmacogenetics in Child and Adolescent Psychiatry: Background and Evidence-Based Clinical Applications. J Child Adolesc Psychopharmacol 2024; 34:4-20. [PMID: 38377525 DOI: 10.1089/cap.2023.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The efficacy and tolerability of psychotropic medications can vary significantly among children and adolescents, and some of this variability relates to pharmacogenetic factors. Pharmacogenetics (PGx) in child and adolescent psychiatry can potentially improve treatment outcomes and minimize adverse drug reactions. This article reviews key pharmacokinetic and pharmacodynamic genes and principles of pharmacogenetic testing and discusses the evidence base for clinical decision-making concerning PGx testing. This article reviews current guidelines from the United States Food and Drug Administration (FDA), the Clinical Pharmacogenetics Implementation Consortium (CPIC), and the Dutch Pharmacogenetics Working Group (DPWG) and explores potential future directions. This review discusses key clinical considerations for clinicians prescribing psychotropic medications in children and adolescents, focusing on antidepressants, antipsychotics, stimulants, norepinephrine reuptake inhibitors, and alpha-2 agonists. Finally, this review synthesizes the practical use of pharmacogenetic testing and clinical decision support systems.
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Affiliation(s)
- Salma Malik
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut, USA
- Division of Child and Adolescent Psychiatry, Institute of Living/Hartford Hospital, Hartford, Connecticut, USA
| | - Pragya Verma
- Division of Child and Adolescent Psychiatry, Institute of Living/Hartford Hospital, Hartford, Connecticut, USA
| | - Gualberto Ruaño
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Areej Al Siaghy
- Division of Child and Adolescent Psychiatry, Institute of Living/Hartford Hospital, Hartford, Connecticut, USA
| | | | - Jeffrey R Bishop
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, Minnesota, USA
- Department of Psychiatry, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Jeffrey R Strawn
- Department of Psychiatry & Behavioral Neuroscience, University of Cincinnati, College of Medicine, Cincinnati, Ohio, USA
| | - Lisa B Namerow
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut, USA
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8
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Abad-Santos F, Aliño SF, Borobia AM, García-Martín E, Gassó P, Maroñas O, Agúndez JAG. Developments in pharmacogenetics, pharmacogenomics, and personalized medicine. Pharmacol Res 2024; 200:107061. [PMID: 38199278 DOI: 10.1016/j.phrs.2024.107061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
The development of Pharmacogenetics and Pharmacogenomics in Western Europe is highly relevant in the worldwide scenario. Despite the usually low institutional support, many research groups, composed of basic and clinical researchers, have been actively working for decades in this field. Their contributions made an international impact and paved the way for further studies and pharmacogenomics implementation in clinical practice. In this manuscript, that makes part of the Special Issue entitled Spanish Pharmacology, we present an analysis of the state of the art of Pharmacogenetics and Pharmacogenomics research in Europe, we compare it with the developments in Spain, and we summarize the most salient contributions since 1988 to the present, as well as recent developments in the clinical application of pharmacogenomics knowledge. Finally, we present some considerations on how we could improve translation to clinical practice in this specific scenario.
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Affiliation(s)
- Francisco Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de La Princesa, Universidad Autónoma de Madrid (UAM), CIBEREHD, Instituto de Investigación Sanitaria La Princesa (IP), Madrid, Spain.
| | - Salvador F Aliño
- Gene Therapy and Pharmacogenomics Group, Department of Pharmacology, Faculty of Medicine, Universitat de València, Av. Blasco Ibáñez 15, 46010 Valencia, Spain
| | - Alberto M Borobia
- Clinical Pharmacology Department, La Paz University Hospital, School of Medicine, Universidad Autónoma de Madrid (UAM), IdiPAZ, Madrid, Spain
| | - Elena García-Martín
- Department of Pharmacology, Universidad de Extremadura, Avda de la Universidad s/n, 10071 Cáceres, Spain
| | - Patricia Gassó
- Basic Clinical Practice Department, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona Clínic Schizophrenia Unit (BCSU), IDIBAPS, CIBERSAM, Barcelona, Spain
| | - Olalla Maroñas
- Public Foundation of Genomic Medicine, Santiago University Hospital, Genomic Medicine group, Pharmacogenetics and Drug Discovery (GenDeM), CIBERER, Santiago Health Research Institute (IDIS), Galicia, Spain
| | - José A G Agúndez
- Universidad de Extremadura. University Institute of Molecular Pathology Biomarkers, Avda de las Ciencias s/n, 10071 Cáceres, Spain.
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Friedman JM, Bombard Y, Carleton B, Issa AM, Knoppers B, Plon SE, Rahimzadeh V, Relling MV, Williams MS, van Karnebeek C, Vears D, Cornel MC. Should secondary pharmacogenomic variants be actively screened and reported when diagnostic genome-wide sequencing is performed in a child? Genet Med 2024; 26:101033. [PMID: 38007624 DOI: 10.1016/j.gim.2023.101033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023] Open
Abstract
This white paper was prepared by the Global Alliance for Genomics and Health Regulatory and Ethics Work Stream's Pediatric Task Team to review and provide perspective with respect to ethical, legal, and social issues regarding the return of secondary pharmacogenomic variants in children who have a serious disease or developmental disorder and are undergoing exome or genome sequencing to identify a genetic cause of their condition. We discuss actively searching for and reporting pharmacogenetic/genomic variants in pediatric patients, different methods of returning secondary pharmacogenomic findings to the patient/parents and/or treating clinicians, maintaining these data in the patient's health record over time, decision supports to assist using pharmacogenetic results in future treatment decisions, and sharing information in public databases to improve the clinical interpretation of pharmacogenetic variants identified in other children. We conclude by presenting a series of points to consider for clinicians and policymakers regarding whether, and under what circumstances, routine screening and return of pharmacogenomic variants unrelated to the indications for testing is appropriate in children who are undergoing genome-wide sequencing to assist in the diagnosis of a suspected genetic disease.
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Affiliation(s)
- Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Bruce Carleton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pharmaceutical Outcomes Programme, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Amalia M Issa
- Personalized Precision Medicine & Targeted Therapeutics, Springfield, MA; Health Policy, University of the Sciences, Philadelphia, PA; Pharmaceutical Sciences, University of the Sciences, Philadelphia, PA; Family Medicine, McGill University, Montreal, Quebec, Canada
| | - Bartha Knoppers
- Centre of Genomics and Policy, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Sharon E Plon
- Department of Pediatrics, Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Vasiliki Rahimzadeh
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Mary V Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Clara van Karnebeek
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Departments of Pediatrics and Human Genetics, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands; Radboud Center for Mitochondrial and Metabolic Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Danya Vears
- University of Melbourne, Carlton, Melbourne, Australia; Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Martina C Cornel
- Department of Human Genetics and Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands
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Kraus MB, Bingham JS, Kekic A, Erickson C, Grilli CB, Seamans DP, Upjohn DP, Hentz JG, Clarke HD, Spangehl MJ. Does Preoperative Pharmacogenomic Testing of Patients Undergoing TKA Improve Postoperative Pain? A Randomized Trial. Clin Orthop Relat Res 2024; 482:291-300. [PMID: 37594401 PMCID: PMC10776165 DOI: 10.1097/corr.0000000000002767] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/09/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Pharmacogenomics is an emerging and affordable tool that may improve postoperative pain control. One challenge to successful pain control is the large interindividual variability among analgesics in their efficacy and adverse drug events. Whether preoperative pharmacogenomic testing is worthwhile for patients undergoing TKA is unclear. QUESTIONS/PURPOSES (1) Are the results of preoperative pharmacogenetic testing associated with lower postoperative pain scores as measured by the Overall Benefit of Analgesic Score (OBAS)? (2) Do the results of preoperative pharmacogenomic testing lead to less total opioids given? (3) Do the results of preoperative pharmacogenomic testing lead to changes in opioid prescribing patterns? METHODS Participants of this randomized trial were enrolled from September 2018 through December 2021 if they were aged 18 to 80 years and were undergoing primary TKA under general anesthesia. Patients were excluded if they had chronic kidney disease, a history of chronic pain or narcotic use before surgery, or if they were undergoing robotic surgery. Preoperatively, patients completed pharmacogenomic testing (RightMed, OneOME) and a questionnaire and were randomly assigned to the experimental group or control group. Of 99 patients screened, 23 were excluded, one before randomization; 11 allocated patients in each group did not receive their allocated interventions for reasons such as surgery canceled, patients ultimately undergoing spinal anesthesia, and change in surgery plan. Another four patients in each group were excluded from the analysis because they were missing an OBAS report. This left 30 patients for analysis in the control group and 38 patients in the experimental group. The control and experimental groups were similar in age, gender, and race. Pharmacogenomic test results for patients in the experimental group were reviewed before surgery by a pharmacist, who recommended perioperative medications to the clinical team. A pharmacist also assessed for clinically relevant drug-gene interactions and recommended drug and dose selection according to guidelines from the Clinical Pharmacogenomics Implementation Consortium for each patient enrolled in the study. Patients were unaware of their pharmacogenomic results. Pharmacogenomic test results for patients in the control group were not reviewed before surgery; instead, standard perioperative medications were administered in adherence to our institutional care pathways. The OBAS (maximum 28 points) was the primary outcome measure, recorded 24 hours postoperatively. A two-sample t-test was used to compare the mean OBAS between groups. Secondary measures were the mean 24-hour pain score, total morphine milligram equivalent, and frequency of opioid use. Postoperatively, patients were assessed for pain with a VAS (range 0 to 10). Opioid use was recorded preoperatively, intraoperatively, in the postanesthesia care unit, and 24 hours after discharge from the postanesthesia care unit. Changes in perioperative opioid use based on pharmacogenomic testing were recorded, as were changes in prescription patterns for postoperative pain control. Preoperative characteristics were also compared between patients with and without various phenotypes ascertained from pharmacogenomic test results. RESULTS The mean OBAS did not differ between groups (mean ± SD 4.7 ± 3.7 in the control group versus 4.2 ± 2.8 in the experimental group, mean difference 0.5 [95% CI -1.1 to 2.1]; p = 0.55). Total opioids given did not differ between groups or at any single perioperative timepoint (preoperative, intraoperative, or postoperative). We found no difference in opioid prescribing pattern. After adjusting for multiple comparisons, no difference was observed between the treatment and control groups in tramadol use (41% versus 71%, proportion difference 0.29 [95% CI 0.05 to 0.53]; nominal p = 0.02; adjusted p > 0.99). CONCLUSION Routine use of pharmacogenomic testing for patients undergoing TKA did not lead to better pain control or decreased opioid consumption. Future studies might focus on at-risk populations, such as patients with chronic pain or those undergoing complex, painful surgical procedures, to test whether pharmacogenomic results might be beneficial in certain circumstances. LEVEL OF EVIDENCE Level I, therapeutic study.
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Affiliation(s)
- Molly B. Kraus
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Phoenix, AZ, USA
| | | | | | - Colby Erickson
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | | | - David P. Seamans
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Phoenix, AZ, USA
| | - David P. Upjohn
- Center for Regenerative Biotherapeutics, Mayo Clinic, Phoenix, AZ, USA
| | - Joseph G. Hentz
- Department of Quantitative Health Sciences, Mayo Clinic, Scottsdale, AZ, USA
| | - Henry D. Clarke
- Department of Orthopedic Surgery, Mayo Clinic, Phoenix, AZ, USA
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11
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Principi N, Petropulacos K, Esposito S. Impact of Pharmacogenomics in Clinical Practice. Pharmaceuticals (Basel) 2023; 16:1596. [PMID: 38004461 PMCID: PMC10675377 DOI: 10.3390/ph16111596] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Polymorphisms of genes encoding drug metabolizing enzymes and transporters can significantly modify pharmacokinetics, and this can be associated with significant differences in drug efficacy, safety, and tolerability. Moreover, genetic variants of some components of the immune system can explain clinically relevant drug-related adverse events. However, the implementation of drug dose individualization based on pharmacogenomics remains scarce. In this narrative review, the impact of genetic variations on the disposition, safety, and tolerability of the most commonly prescribed drugs is reported. Moreover, reasons for poor implementation of pharmacogenomics in everyday clinical settings are discussed. The literature analysis showed that knowledge of how genetic variations can modify the effectiveness, safety, and tolerability of a drug can lead to the adjustment of usually recommended drug dosages, improve effectiveness, and reduce drug-related adverse events. Despite some efforts to introduce pharmacogenomics in clinical practice, presently very few centers routinely use genetic tests as a guide for drug prescription. The education of health care professionals seems critical to keep pace with the rapidly evolving field of pharmacogenomics. Moreover, multimodal algorithms that incorporate both clinical and genetic factors in drug prescribing could significantly help in this regard. Obviously, further studies which definitively establish which genetic variations play a role in conditioning drug effectiveness and safety are needed. Many problems must be solved, but the advantages for human health fully justify all the efforts.
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Affiliation(s)
| | | | - Susanna Esposito
- Pediatric Clinic, Department of Medicine and Surgery, University Hospital of Parma, 43126 Parma, Italy
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Bianchini ML, Aquilante CL, Kao DP, Martin JL, Anderson HD. Patient-Level Exposure to Actionable Pharmacogenomic Medications in a Nationally Representative Insurance Claims Database. J Pers Med 2023; 13:1574. [PMID: 38003889 PMCID: PMC10672722 DOI: 10.3390/jpm13111574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND The prevalence of exposure to pharmacogenomic medications is well established but little is known about how long patients are exposed to these medications. AIM Our objective was to describe the amount of exposure to actionable pharmacogenomic medications using patient-level measures among a large nationally representative population using an insurance claims database. METHODS Our retrospective cohort study included adults (18+ years) from the IQVIA PharMetrics® Plus for Academics claims database with incident fills of 72 Clinical Pharmacogenetics Implementation Consortium level A, A/B, or B medications from January 2012 through September 2018. Patient-level outcomes included the proportion of days covered (PDC), number of fills, and average days supplied per fill over a 12-month period. RESULTS Over 1 million fills of pharmacogenetic medications were identified for 605,355 unique patients. The mean PDC for all medications was 0.21 (SD 0.3), suggesting patients were exposed 21% (77 days) of the year. Medications with the highest PDC (0.55-0.89) included ivacaftor, tamoxifen, clopidogrel, HIV medications, transplant medications, and statins; with the exception of statins, these medications were initiated by fewer patients. Pharmacogenomic medications were filled an average of 2.8 times (SD 3.0, range 1-81) during the year following the medication's initiation, and the average days supplied for each fill was 22.3 days (SD 22.4, range 1-180 days). CONCLUSION Patient characteristics associated with more medication exposure were male sex, older age, and comorbid chronic conditions. Prescription fill data provide patient-level exposure metrics that can further our understanding of pharmacogenomic medication utilization and help inform opportunities for pharmacogenomic testing.
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Affiliation(s)
- Monica L. Bianchini
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (M.L.B.); (C.L.A.); (J.L.M.)
| | - Christina L. Aquilante
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (M.L.B.); (C.L.A.); (J.L.M.)
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - David P. Kao
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - James L. Martin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (M.L.B.); (C.L.A.); (J.L.M.)
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Heather D. Anderson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (M.L.B.); (C.L.A.); (J.L.M.)
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
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Nogueiras-Álvarez R. Pharmacogenomics in clinical trials: an overview. Front Pharmacol 2023; 14:1247088. [PMID: 37927590 PMCID: PMC10625420 DOI: 10.3389/fphar.2023.1247088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
With the trend towards promoting personalised medicine (PM), the application of pharmacogenetics and pharmacogenomics (PGx) is of growing importance. For the purposes of clinical trials, the inclusion of PGx is an additional tool that should be considered for improving our knowledge about the effectiveness and safety of new drugs. A search of available clinical trials containing pharmacogenetic and PGx information was conducted on ClinicalTrials.gov. The results show there has been an increase in the number of trials containing PGx information since the 2000 s, with particular relevance in the areas of Oncology (28.43%) and Mental Health (10.66%). Most of the clinical trials focus on treatment as their primary purpose. In those clinical trials entries where the specific genes considered for study are detailed, the most frequently explored genes are CYP2D6 (especially in Mental Health and Pain), CYP2C9 (in Hematology), CYP2C19 (in Cardiology and Mental Health) and ABCB1 and CYP3A5 (particularly prominent in Transplantation and Cardiology), among others. Researchers and clinicans should be trained in pharmacogenetics and PGx in order to be able to make a proper interpretation of this data, contributing to better prescribing decisions and an improvement in patients' care, which would lead to the performance of PM.
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Biswas M, Sukasem C. Pharmacogenomics of chloroquine and hydroxychloroquine: current evidence and future implications. Pharmacogenomics 2023; 24:831-840. [PMID: 37846548 DOI: 10.2217/pgs-2023-0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
As substrates of CYP2C8, CYP3A4/5 and CYP2D6, chloroquine's (CQ) and hydroxychloroquine's (HCQ) efficacy and safety may be affected by variants in the genes encoding these enzymes. This paper aims to assimilate the current evidence on the pharmacogenomics of CQ/HCQ and to identify risk phenotypes affecting the safety or efficacy of these drugs. It has been found that some CYP3A5, CYP2D6 and CYP2C8 genetic variants may affect the safety or effectiveness of CQ/HCQ. The phenotypes predictively representing ultra-rapid and poor metabolizers have been considered high-risk phenotypes. After considering these high-risk phenotypes in different ethnic groups, it is predicted that a considerable proportion of patients taking CQ/HCQ may be at risk of either therapeutic failure or severe toxicities.
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Affiliation(s)
- Mohitosh Biswas
- Department of Pharmacy, University of Rajshahi, Rajshahi, 6205, Bangladesh
- Division of Pharmacogenomics & Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok, 10400, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics & Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok, 10400, Thailand
- Pharmacogenomics & Precision Medicine Clinic, Bumrungrad Genomic Medicine Institute (BGMI), Bumrungrad International Hospital, 10110, Bangkok, Thailand
- Faculty of Pharmaceutical Sciences, Burapha University, Saensuk, Mueang, Chonburi, 20131, Thailand
- MRC Centre for Drug Safety Science, Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, L69 3GL, UK
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Godoy Torso ND, Jl Santos PC, Moriel P. Challenges for the application of pharmacogenomics associated with the nomenclature of allelic variants. Pharmacogenomics 2023; 24:793-796. [PMID: 37846553 DOI: 10.2217/pgs-2023-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Affiliation(s)
- Nadine de Godoy Torso
- School of Medical Sciences, Universidade Estadual de Campinas, Campinas, 13083-894, Brazil
| | - Paulo Caleb Jl Santos
- Department of Pharmacology, Universidade Federal de São Paulo (EPM-Unifesp), São Paulo, 04044-020, Brazil
| | - Patricia Moriel
- Faculty of Pharmaceutical Sciences, Universidade Estadual de Campinas, Campinas, 13083-970, Brazil
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Chen LS, Baker TB, Ramsey A, Amos CI, Bierut LJ. Genomic medicine to reduce tobacco and related disorders: Translation to precision prevention and treatment. ADDICTION NEUROSCIENCE 2023; 7:100083. [PMID: 37602286 PMCID: PMC10434839 DOI: 10.1016/j.addicn.2023.100083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Genomic medicine can enhance prevention and treatment. First, we propose that advances in genomics have the potential to enhance assessment of disease risk, improve prognostic predictions, and guide treatment development and application. Clinical implementation of polygenic risk scores (PRSs) has emerged as an area of active research. The pathway from genomic discovery to implementation is an iterative process. Second, we provide examples on how genomic medicine has the potential to solve problems in prevention and treatment using two examples: Lung cancer screening and evidence-based tobacco treatment are both under-utilized and great opportunities for genomic interventions. Third, we discuss the translational process for developing genomic interventions from evidence to implementation by presenting a model to evaluate genomic evidence for clinical implementation, mechanisms of genomic interventions, and patient desire for genomic interventions. Fourth, we present potential challenges in genomic interventions including a great need for evidence in all diverse populations, little evidence on treatment algorithms, challenges in accommodating a dynamic evidence base, and implementation challenges in real world clinical settings. Finally, we conclude that research to identify genomic markers that are associated with smoking cessation success and the efficacy of smoking cessation treatments is needed to empower people of all diverse ancestry. Importantly, genomic data can be used to help identify patients with elevated risk for nicotine addiction, difficulty quitting smoking, favorable response to specific pharmacotherapy, and tobacco-related health problems.
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Affiliation(s)
- Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, United States
| | - Timothy B. Baker
- Center for Tobacco Research and Intervention, School of Medicine and Public Health, University of Wisconsin, Madison, WI, United States
| | - Alex Ramsey
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, United States
| | - Christopher I. Amos
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, United States
- Department of Medicine, Baylor College of Medicine, Institute for Clinical and Translational Research, Houston, TX, United States
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, MO, United States
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Brady A, Misra S, Abdelmalek M, Kekic A, Kunze K, Lim E, Jakob N, Mour G, Keddis MT. The Value of Pharmacogenomics for White and Indigenous Americans after Kidney Transplantation. PHARMACY 2023; 11:125. [PMID: 37624080 PMCID: PMC10457738 DOI: 10.3390/pharmacy11040125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND There is a paucity of evidence to inform the value of pharmacogenomic (PGx) results in patients after kidney transplant and how these results differ between Indigenous Americans and Whites. This study aims to identify the frequency of recommended medication changes based on PGx results and compare the pharmacogenomic (PGx) results and patients' perceptions of the findings between a cohort of Indigenous American and White kidney transplant recipients. METHODS Thirty-one Indigenous Americans and fifty White kidney transplant recipients were studied prospectively. Genetic variants were identified using the OneOme RightMed PGx test of 27 genes. PGx pharmacist generated a report of the genetic variation and recommended changes. Pre- and post-qualitative patient surveys were obtained. RESULTS White and Indigenous American subjects had a similar mean number of medications at the time of PGx testing (mean 13 (SD 4.5)). In the entire cohort, 53% received beta blockers, 30% received antidepressants, 16% anticoagulation, 47% pain medication, and 25% statin therapy. Drug-gene interactions that warranted a clinical action were present in 21.5% of patients. In 12.7%, monitoring was recommended. Compared to the Whites, the Indigenous American patients had more normal CYP2C19 (p = 0.012) and CYP2D6 (p = 0.012) activities. The Indigenous American patients had more normal CYP4F2 (p = 0.004) and lower VKORC (p = 0.041) activities, phenotypes for warfarin drug dosing, and efficacy compared to the Whites. SLC6A4, which affects antidepressant metabolism, showed statistical differences between the two cohorts (p = 0.017); specifically, SLC6A4 had reduced expression in 45% of the Indigenous American patients compared to 20% of the White patients. There was no significant difference in patient perception before and after PGx. CONCLUSIONS Kidney transplant recipients had several drug-gene interactions that were clinically actionable; over one-third of patients were likely to benefit from changes in medications or drug doses based on the PGx results. The Indigenous American patients differed in the expression of drug-metabolizing enzymes and drug transporters from the White patients.
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Affiliation(s)
- Alexandra Brady
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Suman Misra
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Mina Abdelmalek
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Adrijana Kekic
- Department of Pharmacy Clinical Practice, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Katie Kunze
- Department of Statistics, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Elisabeth Lim
- Department of Statistics, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Nicholas Jakob
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Girish Mour
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Mira T. Keddis
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
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Cecchin E, Posocco B, Mezzalira S, Appetecchia M, Toffoli G. The Role of Gender Pharmacogenetics in the Personalization of Drug Treatment. J Pharmacol Exp Ther 2023; 386:190-197. [PMID: 37001987 DOI: 10.1124/jpet.122.001416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 03/21/2023] [Indexed: 07/20/2023] Open
Abstract
The use of pharmacogenetic guidelines in personalizing treatments has shown the potential to reduce interindividual variability in drug response by enabling genotype-matched dosing and drug selection. However, other important factors, such as patient gender, may interact strongly with pharmacogenetics in determining the individual profile of toxicity and efficacy but are still rarely considered when planning pharmacological treatment. The literature indicates that males and females respond differently to drugs, with women being at higher risk for toxicity and having different plasma exposure to drugs at standard doses. Recent studies have shown that pharmacogenetic variants may have different predictive value in different sexes, as in the case of treatment with opioids, angiotensin-converting enzyme inhibitors, or proton pump inhibitors. Of particular interest is the case of treatment with fluoropyrimidines for cancer. A significant increase in toxicity has been described in female patients, with a more pronounced effect of specific DPYD and TYMS polymorphisms also noted. This manuscript reviews the major findings in the field of sex-specific pharmacogenomics. SIGNIFICANCE STATEMENT: Interindividual variability in drug response is an emerging issue in pharmacology. The genetic profile of patients, as well as their gender, may play a role in the identification of patients more exposed to the risk of adverse drug reactions or poor efficacy. This article reviews the current state of research on the interaction between gender and pharmacogenetics in addressing interindividual variability.
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Affiliation(s)
- Erika Cecchin
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano PN, Italy (E.C., B.P., S.M., G.T.); and Oncological Endocrinology Unit, IRCCS Regina Elena National Cancer Institute-IFO, Rome, Italy (M.A.)
| | - Bianca Posocco
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano PN, Italy (E.C., B.P., S.M., G.T.); and Oncological Endocrinology Unit, IRCCS Regina Elena National Cancer Institute-IFO, Rome, Italy (M.A.)
| | - Silvia Mezzalira
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano PN, Italy (E.C., B.P., S.M., G.T.); and Oncological Endocrinology Unit, IRCCS Regina Elena National Cancer Institute-IFO, Rome, Italy (M.A.)
| | - Marialuisa Appetecchia
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano PN, Italy (E.C., B.P., S.M., G.T.); and Oncological Endocrinology Unit, IRCCS Regina Elena National Cancer Institute-IFO, Rome, Italy (M.A.)
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano PN, Italy (E.C., B.P., S.M., G.T.); and Oncological Endocrinology Unit, IRCCS Regina Elena National Cancer Institute-IFO, Rome, Italy (M.A.)
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Katsukunya JN, Soko ND, Naidoo J, Rayner B, Blom D, Sinxadi P, Chimusa ER, Dandara M, Dzobo K, Jones E, Dandara C. Pharmacogenomics of Hypertension in Africa: Paving the Way for a Pharmacogenetic-Based Approach for the Treatment of Hypertension in Africans. Int J Hypertens 2023; 2023:9919677. [PMID: 38633331 PMCID: PMC11022520 DOI: 10.1155/2023/9919677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/21/2023] [Accepted: 05/22/2023] [Indexed: 04/19/2024] Open
Abstract
In Africa, the burden of hypertension has been rising at an alarming rate for the last two decades and is a major cause for cardiovascular disease (CVD) mortality and morbidity. Hypertension is characterised by elevated blood pressure (BP) ≥ 140/90 mmHg. Current hypertension guidelines recommend the use of antihypertensives belonging to the following classes: calcium channel blockers (CCB), angiotensin converting inhibitors (ACEI), angiotensin receptor blockers (ARB), diuretics, β-blockers, and mineralocorticoid receptor antagonists (MRAs), to manage hypertension. Still, a considerable number of hypertensives in Africa have their BP uncontrolled due to poor drug response and remain at the risk of CVD events. Genetic factors are a major contributing factor, accounting for 20% to 80% of individual variability in therapy and poor response. Poor response to antihypertensive drug therapy is characterised by elevated BPs and occurrence of adverse drug reactions (ADRs). As a result, there have been numerous studies which have examined the role of genetic variation and its influence on antihypertensive drug response. These studies are predominantly carried out in non-African populations, including Europeans and Asians, with few or no Africans participating. It is important to note that the greatest genetic diversity is observed in African populations as well as the highest prevalence of hypertension. As a result, this warrants a need to focus on how genetic variation affects response to therapeutic interventions used to manage hypertension in African populations. In this paper, we discuss the implications of genetic diversity in CYP11B2, GRK4, NEDD4L, NPPA, SCNN1B, UMOD, CYP411, WNK, CYP3A4/5, ACE, ADBR1/2, GNB3, NOS3, B2, BEST3, SLC25A31, LRRC15 genes, and chromosome 12q loci on hypertension susceptibility and response to antihypertensive therapy. We show that African populations are poorly explored genetically, and for the few characterised genes, they exhibit qualitative and quantitative differences in the profile of pharmacogene variants when compared to other ethnic groups. We conclude by proposing prioritization of pharmacogenetics research in Africa and possible adoption of pharmacogenetic-guided therapies for hypertension in African patients. Finally, we outline the implications, challenges, and opportunities these studies present for populations of non-European descent.
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Affiliation(s)
- Jonathan N. Katsukunya
- Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation Unit, University of Cape Town, Cape Town, South Africa
| | - Nyarai D. Soko
- Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation Unit, University of Cape Town, Cape Town, South Africa
| | - Jashira Naidoo
- Department of Medicine, Division of Nephrology and Hypertension, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Brian Rayner
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation Unit, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Division of Nephrology and Hypertension, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Dirk Blom
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation Unit, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Division of Lipidology and Cape Heart Institute, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Phumla Sinxadi
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation Unit, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Division of Clinical Pharmacology, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R. Chimusa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear NE1 8ST, UK
| | - Michelle Dandara
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation Unit, University of Cape Town, Cape Town, South Africa
| | - Kevin Dzobo
- Medical Research Council-SA Wound Healing Unit, Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Groote Schuur Hospital, Faculty of Health Sciences University of Cape Town, Anzio Road Observatory, Cape Town 7925, South Africa
| | - Erika Jones
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation Unit, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Division of Nephrology and Hypertension, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology and Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- UCT/South African Medical Research Council (SAMRC) Platform for Pharmacogenomics Research and Translation Unit, University of Cape Town, Cape Town, South Africa
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Bignucolo A, De Mattia E, Roncato R, Peruzzi E, Scarabel L, D’Andrea M, Sartor F, Toffoli G, Cecchin E. Ten-year experience with pharmacogenetic testing for DPYD in a national cancer center in Italy: Lessons learned on the path to implementation. Front Pharmacol 2023; 14:1199462. [PMID: 37256229 PMCID: PMC10225682 DOI: 10.3389/fphar.2023.1199462] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023] Open
Abstract
Background: Awareness about the importance of implementing DPYD pharmacogenetics in clinical practice to prevent severe side effects related to the use of fluoropyrimidines has been raised over the years. Since 2012 at the National Cancer Institute, CRO-Aviano (Italy), a diagnostic DPYD genotyping service was set up. Purpose: This study aims to describe the evolution of DPYD diagnostic activity at our center over the last 10 years as a case example of a successful introduction of pharmacogenetic testing in clinical practice. Methods: Data related to the diagnostic activity of in-and out-patients referred to our service between January 2012 and December 2022 were retrieved from the hospital database. Results: DPYD diagnostic activity at our center has greatly evolved over the years, shifting gradually from a post-toxicity to a pre-treatment approach. Development of pharmacogenetic guidelines by national and international consortia, genotyping, and IT technology evolution have impacted DPYD testing uptake in the clinics. Our participation in a large prospective implementation study (Ubiquitous Pharmacogenomics) increased health practitioners' and patients' awareness of pharmacogenetic matters and provided additional standardized infrastructures for genotyping and reporting. Nationwide test reimbursement together with recommendations by regulatory agencies in Europe and Italy in 2020 definitely changed the clinical practice guidelines of fluoropyrimidines prescription. A dramatic increase in the number of pre-treatment DPYD genotyping and in the coverage of new fluoropyrimidine prescriptions was noticed by the last year of observation (2022). Conclusion: The long path to a successful DPYD testing implementation in the clinical practice of a National Cancer Center in Italy demonstrated that the development of pharmacogenetic guidelines and genotyping infrastructure standardization as well as capillary training and education activity for all the potential stakeholders are fundamental. However, only national health politics of test reimbursement and clear recommendations by drug regulatory agencies will definitely move the field forward.
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Li B, Sangkuhl K, Keat K, Whaley RM, Woon M, Verma S, Dudek S, Tuteja S, Verma A, Whirl-Carrillo M, Ritchie MD, Klein TE. How to Run the Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clin Pharmacol Ther 2023; 113:1036-1047. [PMID: 36350094 PMCID: PMC10121724 DOI: 10.1002/cpt.2790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022]
Abstract
Pharmacogenomics (PGx) investigates the genetic influence on drug response and is an integral part of precision medicine. While PGx testing is becoming more common in clinical practice and may be reimbursed by Medicare/Medicaid and commercial insurance, interpreting PGx testing results for clinical decision support is still a challenge. The Pharmacogenomics Clinical Annotation Tool (PharmCAT) has been designed to tackle the need for transparent, automatic interpretations of patient genetic data. PharmCAT incorporates a patient's genotypes, annotates PGx information (allele, genotype, and phenotype), and generates a report with PGx guideline recommendations from the Clinical Pharmacogenetics Implementation Consortium (CPIC) and/or the Dutch Pharmacogenetics Working Group (DPWG). PharmCAT has introduced new features in the last 2 years, including a variant call format (VCF) Preprocessor, the inclusion of DPWG guidelines, and functionalities for PGx research. For example, researchers can use the VCF Preprocessor to prepare biobank-scale data for PharmCAT. In addition, PharmCAT enables the assessment of novel partial and combination alleles that are composed of known PGx variants and can call CYP2D6 genotypes based on single and deletions in the input VCF file. This tutorial provides materials and detailed step-by-step instructions for how to use PharmCAT in a versatile way that can be tailored to users' individual needs.
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Affiliation(s)
- Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Karl Keat
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan M. Whaley
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Shefali Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, PA, USA
| | - Scott Dudek
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sony Tuteja
- Department of Medicine, University of Pennsylvania, PA, USA
| | - Anurag Verma
- Department of Medicine, University of Pennsylvania, PA, USA
| | | | - Marylyn D. Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Medicine (BMIR), Stanford University, Stanford, CA, USA
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22
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Ramsey LB, Gong L, Lee SB, Wagner JB, Zhou X, Sangkuhl K, Adams SM, Straka RJ, Empey PE, Boone EC, Klein TE, Niemi M, Gaedigk A. PharmVar GeneFocus: SLCO1B1. Clin Pharmacol Ther 2023; 113:782-793. [PMID: 35797228 PMCID: PMC10900141 DOI: 10.1002/cpt.2705] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/24/2022] [Indexed: 11/06/2022]
Abstract
The Pharmacogene Variation Consortium (PharmVar) is now providing star (*) allele nomenclature for the highly polymorphic human SLCO1B1 gene encoding the organic anion transporting polypeptide 1B1 (OATP1B1) drug transporter. Genetic variation within the SLCO1B1 gene locus impacts drug transport, which can lead to altered pharmacokinetic profiles of several commonly prescribed drugs. Variable OATP1B1 function is of particular importance regarding hepatic uptake of statins and the risk of statin-associated musculoskeletal symptoms. To introduce this important drug transporter gene into the PharmVar database and serve as a unified reference of haplotype variation moving forward, an international group of gene experts has performed an extensive review of all published SLCO1B1 star alleles. Previously published star alleles were self-assigned by authors and only loosely followed the star nomenclature system that was first developed for cytochrome P450 genes. This nomenclature system has been standardized by PharmVar and is now applied to other important pharmacogenes such as SLCO1B1. In addition, data from the 1000 Genomes Project and investigator-submitted data were utilized to confirm existing haplotypes, fill knowledge gaps, and/or define novel star alleles. The PharmVar-developed SLCO1B1 nomenclature has been incorporated by the Clinical Pharmacogenetics Implementation Consortium (CPIC) 2022 guideline on statin-associated musculoskeletal symptoms.
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Affiliation(s)
- Laura B Ramsey
- Divisions of Clinical Pharmacology and Research in Patient Services, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Li Gong
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Seung-Been Lee
- Precision Medicine Institute, Macrogen Inc., Seoul, Korea
| | - Jonathan B Wagner
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Xujia Zhou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Solomon M Adams
- School of Pharmacy, Shenandoah University, Fairfax, Virginia, USA
| | - Robert J Straka
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Philip E Empey
- School of Pharmacy and Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Department of Medicine (BMIR), Stanford University, Stanford, California, USA
| | - Mikko Niemi
- Department of Clinical Pharmacology, University of Helsinki, Helsinki, Finland
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Clinical Pharmacology, HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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Anderson JD, Davis BH, Giang G, Jones A, Lee CR, Parker K, Searcy H, Benner K, Limdi N, Guimbellot JS. Pharmacogenetic actionability and medication prescribing in people with cystic fibrosis. Clin Transl Sci 2023; 16:662-672. [PMID: 36760155 PMCID: PMC10087076 DOI: 10.1111/cts.13479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 02/11/2023] Open
Abstract
Although major advancements have been made in the therapeutics for people with cystic fibrosis (PwCF), many still require the use of multiple medications to manage acute exacerbations of disease and maintain health. Iterative trial and error processes of pharmacotherapeutic management can be optimized by assessing and incorporating pharmacogenetics. For 82 PwCF, we reviewed 2 years of medication use and response history and interrogated metabolizer status for common pharmacogenes, revealing 3336 medication exposure events (MEEs) to 286 unique medications. As expected, the more frequent MEEs were those commonly used to treat cystic fibrosis (CF), such as antibiotics and respiratory medications. Antibiotics also comprised 56.7% of the undesirable drug responses. The impact of gene variants on drug responses was assessed using Pharmacogenomics Knowledgebase (PharmGKB) and Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. Thirty-three (11.5%) medications have strong evidence of genetic influence on response as evidenced by gene-based dosing guidelines. 110 (38.5%) unique medications had at least one association with a very important pharmacogene, whereas 143 (50%) were associated with at least one clinical or variant annotation. Over 97% of participants had at least one actionable genotype. Eleven (13.4%) patients with an actionable genotype, taking the impacted medication, had an undesirable drug response described in the CPIC guidelines that could potentially have been mitigated with a priori knowledge of the genotype. PwCF take many medications for disease management, with frequent dose changes to elicit a desired clinical effect. As CF care evolves, implementing pharmacogenetics testing can improve efficiency and safety of prescribing practices using precision selection and dosing at medication initiation.
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Affiliation(s)
- Justin D. Anderson
- Gregory Fleming James Cystic Fibrosis Research CenterUniversity of Alabama at Birmingham (UAB)BirminghamAlabamaUSA
- Division of Pulmonary and Sleep Medicine, Department of PediatricsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Brittney H. Davis
- Department of Neurology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Gracie Giang
- McWhorter School of PharmacySamford UniversityBirminghamAlabamaUSA
| | - April Jones
- McWhorter School of PharmacySamford UniversityBirminghamAlabamaUSA
| | - Cameron R. Lee
- McWhorter School of PharmacySamford UniversityBirminghamAlabamaUSA
| | - Kennedy Parker
- Gregory Fleming James Cystic Fibrosis Research CenterUniversity of Alabama at Birmingham (UAB)BirminghamAlabamaUSA
- Division of Pulmonary and Sleep Medicine, Department of PediatricsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Heather Searcy
- Division of Pulmonary and Sleep Medicine, Department of PediatricsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Kim Benner
- McWhorter School of PharmacySamford UniversityBirminghamAlabamaUSA
| | - Nita A. Limdi
- Department of Neurology, School of MedicineUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Jennifer S. Guimbellot
- Gregory Fleming James Cystic Fibrosis Research CenterUniversity of Alabama at Birmingham (UAB)BirminghamAlabamaUSA
- Division of Pulmonary and Sleep Medicine, Department of PediatricsUniversity of Alabama at BirminghamBirminghamAlabamaUSA
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Scorcella C, Domizi R, Amoroso S, Carsetti A, Casarotta E, Castaldo P, D’angelo C, Damiani E, Gasparri F, Donati A, Adrario E. Pharmacogenetics in critical care: association between CYP3A5 rs776746 A/G genotype and acetaminophen response in sepsis and septic shock. BMC Anesthesiol 2023; 23:55. [PMID: 36797680 PMCID: PMC9933278 DOI: 10.1186/s12871-023-02018-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Pharmacogenetics could represent a further resource to understand the interindividual heterogeneity of response of the host to sepsis and to provide a personalized approach to the critical care patient. METHODS Secondary analysis of data from the prospective observational study NCT02750163, in 50 adult septic and septic shock patients treated with Acetaminophen (ACT) for pyrexia. We investigated the presence of two polymorphisms, located respectively in the genes UGT1A1 and CYP3A5, that encode for proteins related to the hepatic metabolism of ACT. The main dependent variables explored were plasmatic concentration of ACT, body temperature and hepatic parameters. RESULTS 8% of the patients carried CYP3A5 rs776746 A/G genotypes and showed significantly higher plasma levels of ACT than GG wild type patients, and than patients with UGT1A1 rs8330 C/G genotypes. CONCLUSIONS Identifying specific genotypes of response to ACT may be helpful to guide a more personalized titration of therapy in sepsis and septic shock. CYP3A5 might be a good biomarker for ACT metabolism; however further studies are needed to confirm this result. TRIAL REGISTRATION NCT02750163.
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Affiliation(s)
- C. Scorcella
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy
| | - R. Domizi
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy
| | - S. Amoroso
- grid.7010.60000 0001 1017 3210Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, via Tronto 10/a, Torrette di Ancona, 60020 Italy
| | - A. Carsetti
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy ,grid.7010.60000 0001 1017 3210Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, via Tronto 10/a, Torrette di Ancona, 60020 Italy
| | - E. Casarotta
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy ,grid.7010.60000 0001 1017 3210Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, via Tronto 10/a, Torrette di Ancona, 60020 Italy
| | - P. Castaldo
- grid.7010.60000 0001 1017 3210Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, via Tronto 10/a, Torrette di Ancona, 60020 Italy
| | - C. D’angelo
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy ,grid.7010.60000 0001 1017 3210Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, via Tronto 10/a, Torrette di Ancona, 60020 Italy
| | - E. Damiani
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy ,grid.7010.60000 0001 1017 3210Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, via Tronto 10/a, Torrette di Ancona, 60020 Italy
| | - F. Gasparri
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy
| | - A. Donati
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy ,grid.7010.60000 0001 1017 3210Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, via Tronto 10/a, Torrette di Ancona, 60020 Italy
| | - E. Adrario
- Anesthesia and Intensive Care Unit, Azienda Ospedaliero Universitaria delle Marche, via Conca 71, Torrette di Ancona, 60126 Italy ,grid.7010.60000 0001 1017 3210Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, via Tronto 10/a, Torrette di Ancona, 60020 Italy
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Devanathan R, Alladi CG, Ravichandran M, Ramasamy K, Uppugunduri CRS. Impact of pharmacogenomics in achieving personalized/precision medicine in the clinical setting: a symposium report. Pharmacogenomics 2023; 24:123-129. [PMID: 36786192 DOI: 10.2217/pgs-2022-0194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The Indo-Swiss symposium on pharmacogenomic strategies for the implementation of personalized medicine was conducted as part of the Jawaharlal Institute of Postgraduate Medical Education and Research Integrated Pharmacogenomics Program in Puducherry, India, on 19 November 2022. The symposium was conducted in hybrid mode. The theme of symposium was the impact of pharmacogenomics on the achievement of personalized medicine/precision medicine in the clinical setting. The symposium sought to promote interaction among the participants to initiate future collaborative research projects. The symposium also served as a platform for young researchers to present their research findings as posters to the audience.
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Affiliation(s)
- Reka Devanathan
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India
| | - Charanraj Goud Alladi
- Department of Biochemistry, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India
| | - Mirunalini Ravichandran
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India
| | - Kesavan Ramasamy
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, 605006, India
| | - Chakradhara Rao S Uppugunduri
- CANSEARCH Research Platform in Pediatric Oncology & Hematology, Department of Pediatrics, Gynecology & Obstetrics, Faculty of Medicine, University of Geneva, Geneva 4, Switzerland
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26
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Liu Y, Lin Z, Chen Q, Chen Q, Sang L, Wang Y, Shi L, Guo L, Yu Y. PAnno: A pharmacogenomics annotation tool for clinical genomic testing. Front Pharmacol 2023; 14:1008330. [PMID: 36778023 PMCID: PMC9909284 DOI: 10.3389/fphar.2023.1008330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction: Next-generation sequencing (NGS) technologies have been widely used in clinical genomic testing for drug response phenotypes. However, the inherent limitations of short reads make accurate inference of diplotypes still challenging, which may reduce the effectiveness of genotype-guided drug therapy. Methods: An automated Pharmacogenomics Annotation tool (PAnno) was implemented, which reports prescribing recommendations and phenotypes by parsing the germline variant call format (VCF) file from NGS and the population to which the individual belongs. Results: A ranking model dedicated to inferring diplotypes, developed based on the allele (haplotype) definition and population allele frequency, was introduced in PAnno. The predictive performance was validated in comparison with four similar tools using the consensus diplotype data of the Genetic Testing Reference Materials Coordination Program (GeT-RM) as ground truth. An annotation method was proposed to summarize prescribing recommendations and classify drugs into avoid use, use with caution, and routine use, following the recommendations of the Clinical Pharmacogenetics Implementation Consortium (CPIC), etc. It further predicts phenotypes of specific drugs in terms of toxicity, dosage, efficacy, and metabolism by integrating the high-confidence clinical annotations in the Pharmacogenomics Knowledgebase (PharmGKB). PAnno is available at https://github.com/PreMedKB/PAnno. Discussion: PAnno provides an end-to-end clinical pharmacogenomics decision support solution by resolving, annotating, and reporting germline variants.
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Affiliation(s)
- Yaqing Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zipeng Lin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qingwang Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Qiaochu Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Leqing Sang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yunjin Wang
- Department of Breast Surgery, Precision Cancer Medicine Center, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Li Guo
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Li Guo, ; Ying Yu,
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China,*Correspondence: Li Guo, ; Ying Yu,
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27
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Dodson C, Layman L. Refinement of a pharmacogenomics app for dosing guidelines for oncology: findings from the usability evaluation. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1261. [PMID: 36618784 PMCID: PMC9816840 DOI: 10.21037/atm-2022-68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/19/2022] [Indexed: 11/21/2022]
Abstract
Background This study extended a precision medicine clinical decision support mobile application (app) for use with oncology medications. Two gene variants (CYP2D6 and DPYD) associated with pharmacogenomic dosing algorithms in oncology was added to a prototype app. Usability of the app was evaluated. The use of smartphones and mobile apps for prescribing medications has exponentially increased since the introduction of physician order entry. Decision support apps have improved provider performance and studies have shown broader adoption is crucial for the success of these tools. Therefore, successful use of mobile apps will depend on perceptions of users. Rogers' Diffusion of Innovation theory will be the guiding framework for this study. Methods The main research variable is usability as measured by effectiveness, efficiency, and satisfaction. A mixed method design was used. The setting was inpatient and outpatient oncology practices within North Carolina. The sample included registered nurses and nurse practitioners within the oncology field. A functioning mobile app was extended based on the Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines to address the most common gene variants seen in oncology patients. Usability testing is divided into two main categories, inspection and testing methods. Prior to the field study, a heuristic evaluation was conducted. This evaluation inspected the user interface, comparing the elements and aspects of it to a set of principles, heuristics, as a guideline to evaluate the usability of the mobile app. Results The testing evaluation was conducted with a sample of 51 health care providers to evaluate usability, measured by the System Usability Scale and open-ended questions. Descriptive statistics was used to summarize usefulness and end-user perceived ease of use. In addition, a thematic analysis of the open-ended questions was conducted. Conclusions The development of this mobile app is relevant to nurses who have prescriptive privileges, as well as an educational tool for nurses to understand the rationale behind prescribing certain medications and alternate dosages by providing specific recommendations. Translation of precision medicine into practice will benefit patients by improving care, reducing adverse reactions, and lowering costs.
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Affiliation(s)
- Crystal Dodson
- School of Nursing, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Lucas Layman
- Department of Computer Science, University of North Carolina Wilmington, Wilmington, NC, USA
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Morris SA, Alsaidi AT, Verbyla A, Cruz A, Macfarlane C, Bauer J, Patel JN. Cost Effectiveness of Pharmacogenetic Testing for Drugs with Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines: A Systematic Review. Clin Pharmacol Ther 2022; 112:1318-1328. [PMID: 36149409 PMCID: PMC9828439 DOI: 10.1002/cpt.2754] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/17/2022] [Indexed: 01/31/2023]
Abstract
The objective of this study was to evaluate the evidence on cost-effectiveness of pharmacogenetic (PGx)-guided treatment for drugs with Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. A systematic review was conducted using multiple biomedical literature databases from inception to June 2021. Full articles comparing PGx-guided with nonguided treatment were included for data extraction. Quality of Health Economic Studies (QHES) was used to assess robustness of each study (0-100). Data are reported using descriptive statistics. Of 108 studies evaluating 39 drugs, 77 (71%) showed PGx testing was cost-effective (CE) (N = 48) or cost-saving (CS) (N = 29); 21 (20%) were not CE; 10 (9%) were uncertain. Clopidogrel had the most articles (N = 23), of which 22 demonstrated CE or CS, followed by warfarin (N = 16), of which 7 demonstrated CE or CS. Of 26 studies evaluating human leukocyte antigen (HLA) testing for abacavir (N = 8), allopurinol (N = 10), or carbamazepine/phenytoin (N = 8), 15 demonstrated CE or CS. Nine of 11 antidepressant articles demonstrated CE or CS. The median QHES score reflected high-quality studies (91; range 48-100). Most studies evaluating cost-effectiveness favored PGx testing. Limited data exist on cost-effectiveness of preemptive and multigene testing across disease states.
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Affiliation(s)
- Sarah A. Morris
- Department of Cancer Pharmacology and PharmacogenomicsLevine Cancer Institute, Atrium HealthCharlotteNorth CarolinaUSA
| | | | - Allison Verbyla
- Health Economics and Outcomes Research, Department of BiostatisticsLevine Cancer Institute, Atrium HealthCharlotteNorth CarolinaUSA
| | - Adilen Cruz
- Health Economics and Outcomes Research, Department of BiostatisticsLevine Cancer Institute, Atrium HealthCharlotteNorth CarolinaUSA
| | | | - Joseph Bauer
- Health Economics and Outcomes Research, Department of BiostatisticsLevine Cancer Institute, Atrium HealthCharlotteNorth CarolinaUSA
| | - Jai N. Patel
- Department of Cancer Pharmacology and PharmacogenomicsLevine Cancer Institute, Atrium HealthCharlotteNorth CarolinaUSA
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Kidwai-Khan F, Rentsch CT, Pulk R, Alcorn C, Brandt CA, Justice AC. Pharmacogenomics driven decision support prototype with machine learning: A framework for improving patient care. Front Big Data 2022; 5:1059088. [DOI: 10.3389/fdata.2022.1059088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
IntroductionA growing number of healthcare providers make complex treatment decisions guided by electronic health record (EHR) software interfaces. Many interfaces integrate multiple sources of data (e.g., labs, pharmacy, diagnoses) successfully, though relatively few have incorporated genetic data.MethodThis study utilizes informatics methods with predictive modeling to create and validate algorithms to enable informed pharmacogenomic decision-making at the point of care in near real-time. The proposed framework integrates EHR and genetic data relevant to the patient's current medications including decision support mechanisms based on predictive modeling. We created a prototype with EHR and linked genetic data from the Department of Veterans Affairs (VA), the largest integrated healthcare system in the US. The EHR data included diagnoses, medication fills, and outpatient clinic visits for 2,600 people with HIV and matched uninfected controls linked to prototypic genetic data (variations in single or multiple positions in the DNA sequence). We then mapped the medications that patients were prescribed to medications defined in the drug-gene interaction mapping of the Clinical Pharmacogenomics Implementation Consortium's (CPIC) level A (i.e., sufficient evidence for at least one prescribing action) guidelines that predict adverse events. CPIC is a National Institute of Health funded group of experts who develop evidence based pharmacogenomic guidelines. Preventable adverse events (PAE) can be defined as a harmful outcome from an intervention that could have been prevented. For this study, we focused on potential PAEs resulting from a medication-gene interaction.ResultsThe final model showed AUC scores of 0.972 with an F1 score of 0.97 with genetic data as compared to 0.766 and 0.73 respectively, without genetic data integration.DiscussionOver 98% of people in the cohort were on at least one medication with CPIC level a guideline in their lifetime. We compared predictive power of machine learning models to detect a PAE between five modeling methods: Random Forest, Support Vector Machine (SVM), Extreme Gradient Boosting (XGBoost), K Nearest neighbors (KNN), and Decision Tree. We found that XGBoost performed best for the prototype when genetic data was added to the framework and improved prediction of PAE. We compared area under the curve (AUC) between the models in the testing dataset.
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Fricke-Galindo I, Falfán-Valencia R. Current pharmacogenomic recommendations in chronic respiratory diseases: Is there a biomarker ready for clinical implementation? Expert Rev Respir Med 2022; 16:1145-1152. [PMID: 36416606 DOI: 10.1080/17476348.2022.2149496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION The study of genetic variants in response to different drugs has predominated in fields of medicine such as oncology and infectious diseases. In chronic respiratory diseases, the available pharmacogenomic information is scarce but not less relevant. AREAS COVERED We searched the pharmacogenomic recommendations for respiratory diseases in the Table of Pharmacogenomic Biomarkers in Drug Labeling (U.S. Food and Drug Administration), the Clinical Pharmacogenomics Implementation Consortium (CPIC), and PharmGKB. The main pharmacogenomics recommendation in this field is to assess CFTR variants for using ivacaftor and its combination. The drugs' labels for arformoterol, indacaterol, and umeclidinium indicate a lack of influence of genetic variants in the pharmacokinetics of these drugs. Further studies should evaluate the contribution of CYP2D6 and CYP2C19 variants for formoterol. In addition, there are reports of potential pharmacogenetic variants in the treatment with acetylcysteine (TOLLIP rs3750920) and captopril (ACE rs1799752). The genetic variations for warfarin also are presented in PharmGKB and CPIC for patients with pulmonary hypertension. EXPERT OPINION The pharmacogenomics recommendations for lung diseases are limited. The clinical implementation of pharmacogenomics in treating respiratory diseases will contribute to the quality of life of patients with chronic respiratory diseases.
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Affiliation(s)
- Ingrid Fricke-Galindo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, 14080, Mexico City, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, 14080, Mexico City, Mexico
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Cicali EJ, Lemke L, Al Alshaykh H, Nguyen K, Cavallari LH, Wiisanen K. How to Implement a Pharmacogenetics Service at your Institution. JOURNAL OF THE AMERICAN COLLEGE OF CLINICAL PHARMACY 2022; 5:1161-1175. [PMID: 36589694 PMCID: PMC9799247 DOI: 10.1002/jac5.1699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023]
Abstract
The vast majority of patients possess one or more pharmacogenetic variants that can influence optimal medication use. When pharmacogenetic data are used to guide drug choice and dosing, evidence points to improved disease outcomes, fewer adverse effects, and lower healthcare spending. Although its science is well established, clinical use of pharmacogenetic data to guide drug therapy is still in its infancy. Pharmacogenetics essentially involves the intersection of an individual's genetic data with their medications, which makes pharmacists uniquely qualified to provide clinical support and education in this field. In fact, most pharmacogenetics implementations, to date, have been led by pharmacists as leaders or members of a multidisciplinary team or as individual practitioners. A successful large-scale pharmacogenetics implementation requires coordination and synergy among administrators, clinicians, informatics teams, laboratories, and patients. Because clinical implementation of pharmacogenetics is in its early stages, there is an urgent need for guidance and dissemination of shared experiences to provide a framework for clinicians. Many early adopters of pharmacogenetics have explored various strategies among diverse practice settings. This article relies on the experiences of early adopters to provide guidance for critical steps along the pathway to implementation, including strategies to engage stakeholders; evaluate pharmacogenetic evidence; coordinate laboratory testing, results interpretation and their integration into the electronic health record; identify reimbursement avenues; educate providers and patients; and maintain a successful program. Learning from early adopters' published experiences and strategies can allow clinicians leading a new pharmacogenetics implementation to avoid pitfalls and adapt and apply lessons learned by others to their own practice.
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Affiliation(s)
- Emily J Cicali
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
| | - Lauren Lemke
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
| | - Hana Al Alshaykh
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
| | - Khoa Nguyen
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
| | - Kristin Wiisanen
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, Gainesville, FL, USA
- Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Fl, USA
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Skryabin V, Rozochkin I, Zastrozhin M, Lauschke V, Franck J, Bryun E, Sychev D. Meta-analysis of pharmacogenetic clinical decision support systems for the treatment of major depressive disorder. THE PHARMACOGENOMICS JOURNAL 2022; 23:45-49. [PMID: 36273107 DOI: 10.1038/s41397-022-00295-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022]
Abstract
The study aimed to conduct a meta-analysis of studies comparing pharmacogenetically guided dosing of antidepressants with empiric standard of care. Publications referring to genotype-guided antidepressant therapy were identified via PubMed, Google Scholar, Scopus, Web of Science, Embase, and Cochrane databases from the inception of the databases to 2021. In addition, bibliographies of all articles were manually searched for additional references not identified in primary searches. Studies comparing clinical outcomes between two groups of patients who received antidepressant treatment were included in meta-analysis. Analysis of the data revealed statistically significant differences between the experimental group receiving pharmacogenetically guided dosing and the empirically treated controls. Specifically, genotype-guided treatment significantly improved response and remission of patients after both eight and twelve weeks of therapy, whereas no effect on the development of adverse drug reactions was observed. This meta-analysis indicates that the use of preemptive genotyping to guide dosing of antidepressants might increase treatment efficacy.
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Haidar CE, Crews KR, Hoffman JM, Relling MV, Caudle KE. Advancing Pharmacogenomics from Single-Gene to Preemptive Testing. Annu Rev Genomics Hum Genet 2022; 23:449-473. [PMID: 35537468 PMCID: PMC9483991 DOI: 10.1146/annurev-genom-111621-102737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pharmacogenomic testing can be an effective tool to enhance medication safety and efficacy. Pharmacogenomically actionable medications are widely used, and approximately 90-95% of individuals have an actionable genotype for at least one pharmacogene. For pharmacogenomic testing to have the greatest impact on medication safety and clinical care, genetic information should be made available at the time of prescribing (preemptive testing). However, the use of preemptive pharmacogenomic testing is associated with some logistical concerns, such as consistent reimbursement, processes for reporting preemptive results over an individual's lifetime, and result portability. Lessons can be learned from institutions that have implemented preemptive pharmacogenomic testing. In this review, we discuss the rationale and best practices for implementing pharmacogenomics preemptively.
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Affiliation(s)
- Cyrine E Haidar
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , ,
| | - Kristine R Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , ,
| | - James M Hoffman
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , ,
- Office of Quality and Safety, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Mary V Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , ,
| | - Kelly E Caudle
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , ,
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Mbavha BT, Kanji CR, Stadler N, Stingl J, Stanglmair A, Scholl C, Wekwete W, Masimirembwa C. Population genetic polymorphisms of pharmacogenes in Zimbabwe, a potential guide for the safe and efficacious use of medicines in people of African ancestry. Pharmacogenet Genomics 2022; 32:173-182. [PMID: 35190514 DOI: 10.1097/fpc.0000000000000467] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Pharmacogenomics (PGx) is a clinically significant factor in the safe and efficacious use of medicines. While PGx knowledge is abundant for other populations, there are scarce PGx data on African populations and is little knowledge on drug-gene interactions for medicines used to treat diseases common in Africa. The aim of this study was to use a custom-designed open array to genotype clinically actionable variants in a Zimbabwean population. This study also identified some of the commonly used drugs in Zimbabwe and the associated genes involved in their metabolism. METHODS A custom-designed open array that covers 120 genetic variants was used to genotype 522 black Zimbabwean healthy volunteers using TaqMan-based single nucleotide polymorphism genotyping. Data were also accessed from Essential Drugs' List in Zimbabwe (EDLIZ), and the medicines were grouped into the associated biomarker groups based on their metabolism. We also estimated the national drug procurement levels for medicines that could benefit from PGx-guided use based on the data obtained from the national authorities in Zimbabwe. RESULTS The results demonstrate the applicability of an open-array chip in simultaneously determining multiple genetic variants in an individual, thus significantly reducing cost and time to generate PGx data. There were significantly high frequencies of African-specific variants, such as the CYP2D6*17 and *29 variants and the CYP2B6*18 variant. The data obtained showed that the Zimbabwean population exhibits PGx variations in genes important for the safe and efficacious use of drugs approved by the EDLIZ and are procured at significantly large amounts annually. The study has established a cohort of genotyped healthy volunteers that can be accessed and used in the conduct of clinical pharmacogenetic studies for drugs entering a market of people of predominantly African ancestry. CONCLUSION Our study demonstrated the potential benefit of integrating PGx in Zimbabwe for the safe and efficacious use of drugs that are commonly used.
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Affiliation(s)
- Bianza T Mbavha
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Harare, Zimbabwe
| | - Comfort R Kanji
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Harare, Zimbabwe
| | - Nadina Stadler
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn
| | - Julia Stingl
- Institute of Clinical Pharmacology, University Hospital RWTH Aachen, Aachen, Germany
| | - Andrea Stanglmair
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn
| | - William Wekwete
- Evaluations and Registration Division, Medicines Control Authority of Zimbabwe (MCAZ), Harare, Zimbabwe
| | - Collen Masimirembwa
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Harare, Zimbabwe
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Richtlinie der Gendiagnostik-Kommission (GEKO) für die Beurteilung genetischer Eigenschaften hinsichtlich ihrer Bedeutung für die Wirkung eines Arzneimittels bei einer Behandlung gemäß § 23 Abs. 2 Nr. 1b GenDG. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2022; 65:958-962. [PMID: 35776150 DOI: 10.1007/s00103-022-03559-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Blazy C, Ellingrod V, Ward K. Variability Between Clinical Pharmacogenetics Implementation Consortium (CPIC®) Guidelines and a Commercial Pharmacogenetics Laboratory in Genotype to Phenotype Interpretations For Patients Utilizing Psychotropics. Front Pharmacol 2022; 13:939313. [PMID: 35814245 PMCID: PMC9263441 DOI: 10.3389/fphar.2022.939313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/06/2022] [Indexed: 11/19/2022] Open
Abstract
Clinical practice environments without in-house pharmacogenetic testing often rely on commercial laboratories, especially in the setting of pharmacogenetic testing intended to guide psychotropic use. There are occasionally differences in phenotype assignment and medication recommendations between commercial laboratories and the Clinical Pharmacogenetics Implementation Consortium (CPIC). This may be problematic as many institutions that implement pharmacogenetics consider CPIC to be an important source of guidelines for recommended prescribing actions based on genetics, as well as a tool towards standardizing pharmacogenetics implementation. Here, we completed a retrospective chart review of our academic health system’s (Michigan Medicine) electronic health record with the goal of comparing phenotypic assignment of CYP2D6 and CYP2C19 genotypes between the commercial pharmacogenetic lab used most at our institution, and CPIC. Ultimately, we identified 205 patients with available pharmacogenetic results from this lab. The prevalence of conflicting phenotype assignment was 28.8% for CYP2D6 and 32.2% for CYP2C19 genotypes when comparing the commercial lab to CPIC guidelines. In several cases, the phenotypic assignment differences for antidepressants led to significant differences in medication recommendations when comparing the commercial lab report and CPIC guidelines. These results may also have implications for medications outside of psychiatry with recommendations for dose adjustments based on CYP2D6 or CYP2C19 metabolizing phenotype.
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Affiliation(s)
- Christopher Blazy
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
| | - Vicki Ellingrod
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
| | - Kristen Ward
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, United States
- Clinical Pharmacy Department, Michigan Medicine, Ann Arbor, MI, United States
- *Correspondence: Kristen Ward,
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Blagec K, Swen JJ, Koopmann R, Cheung KC, Crommentuijn-van Rhenen M, Holsappel I, Konta L, Ott S, Steinberger D, Xu H, Cecchin E, Dolžan V, Dávila-Fajardo CL, Patrinos GP, Sunder-Plassmann G, Turner RM, Pirmohamed M, Guchelaar HJ, Samwald M. Pharmacogenomics decision support in the U-PGx project: Results and advice from clinical implementation across seven European countries. PLoS One 2022; 17:e0268534. [PMID: 35675343 PMCID: PMC9176797 DOI: 10.1371/journal.pone.0268534] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 04/26/2022] [Indexed: 12/18/2022] Open
Abstract
Background The clinical implementation of pharmacogenomics (PGx) could be one of the first milestones towards realizing personalized medicine in routine care. However, its widespread adoption requires the availability of suitable clinical decision support (CDS) systems, which is often impeded by the fragmentation or absence of adequate health IT infrastructures. We report results of CDS implementation in the large-scale European research project Ubiquitous Pharmacogenomics (U-PGx), in which PGx CDS was rolled out and evaluated across more than 15 clinical sites in the Netherlands, Spain, Slovenia, Italy, Greece, United Kingdom and Austria, covering a wide variety of healthcare settings. Methods We evaluated the CDS implementation process through qualitative and quantitative process indicators. Quantitative indicators included statistics on generated PGx reports, median time from sampled upload until report delivery and statistics on report retrievals via the mobile-based CDS tool. Adoption of different CDS tools, uptake and usability were further investigated through a user survey among healthcare providers. Results of a risk assessment conducted prior to the implementation process were retrospectively analyzed and compared to actual encountered difficulties and their impact. Results As of March 2021, personalized PGx reports were produced from 6884 genotyped samples with a median delivery time of twenty minutes. Out of 131 invited healthcare providers, 65 completed the questionnaire (response rate: 49.6%). Overall satisfaction rates with the different CDS tools varied between 63.6% and 85.2% per tool. Delays in implementation were caused by challenges including institutional factors and complexities in the development of required tools and reference data resources, such as genotype-phenotype mappings. Conclusions We demonstrated the feasibility of implementing a standardized PGx decision support solution in a multinational, multi-language and multi-center setting. Remaining challenges for future wide-scale roll-out include the harmonization of existing PGx information in guidelines and drug labels, the need for strategies to lower the barrier of PGx CDS adoption for healthcare institutions and providers, and easier compliance with regulatory and legal frameworks.
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Affiliation(s)
- Kathrin Blagec
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Jesse J Swen
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rudolf Koopmann
- Diagnosticum Center for Human Genetics, Frankfurt am Main, Germany.,Institute for Human Genetics, Justus Liebig University, Giessen, Germany
| | - Ka-Chun Cheung
- Medicines Information Centre, Royal Dutch Pharmacists Association (KNMP), The Hague, The Netherlands
| | | | - Inge Holsappel
- Medicines Information Centre, Royal Dutch Pharmacists Association (KNMP), The Hague, The Netherlands
| | - Lidija Konta
- Diagnosticum Center for Human Genetics, Frankfurt am Main, Germany
| | - Simon Ott
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Daniela Steinberger
- Diagnosticum Center for Human Genetics, Frankfurt am Main, Germany.,Institute for Human Genetics, Justus Liebig University, Giessen, Germany
| | - Hong Xu
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano, Italy
| | - Vita Dolžan
- Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, Pharmacogenetics Laboratory, University of Ljubljana, Ljubljana, Slovenia
| | - Cristina Lucía Dávila-Fajardo
- Clinical Pharmacy Department, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria Granada (Ibs.Granada), Granada, Spain
| | - George P Patrinos
- Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras School of Health Sciences, Patras, Greece
| | - Gere Sunder-Plassmann
- Division of Nephrology and Dialysis, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Richard M Turner
- The Wolfson Centre for Personalised Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, Royal Liverpool University Hospital and University of Liverpool, Liverpool, United Kingdom
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias Samwald
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
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Sakon CM, Tillman EM. Pharmacogenomics: a tool to improve medication safety and efficacy in patients with cystic fibrosis. Pharmacogenomics 2022; 23:559-556. [PMID: 35670256 DOI: 10.2217/pgs-2022-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cystic fibrosis is a genetic, multiorgan system disease that involves the use of many medications to control symptoms associated with the underlying condition. Many of these medications have Clinical Pharmacogenetics Implementation Consortium evidence-based guidelines for pharmacogenomics that are available to guide dosing. The aim of this article is to review relevant literature and evaluate the utility of preemptive pharmacogenomics testing for persons with cystic fibrosis and propose a pharmacogenomics panel that could be considered standard of care for persons with cystic fibrosis.
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Affiliation(s)
- Colleen M Sakon
- Pharmacy Department, Indiana University Health, Indianapolis, IN, USA
| | - Emma M Tillman
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, USA
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Hamilton WG, Gargiulo JM, Reynolds TR, Parks NL. Prospective Randomized Study Using Pharmacogenetics to Customize Postoperative Pain Medication Following Hip and Knee Arthroplasty. J Arthroplasty 2022; 37:S76-S81. [PMID: 35279338 DOI: 10.1016/j.arth.2022.02.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The purpose of this study is to determine whether pharmacogenetic testing could be used to effectively customize postoperative pain medicine following total joint replacement. METHODS Buccal swabs were collected preoperatively from 107 patients. Pharmacogenetic testing was performed for genetic variants on a panel of 16 genes, including CYP2D6, CYP2C9, OPRM1, and CYP1A2, which affect the pharmacodynamics and pharmacokinetics of non-steroidal anti-inflammatory drugs and many opioids. Patients were randomized to a control group or custom group and blinded to their group. The control group was prescribed oxycodone, tramadol, and celecoxib for postoperative pain management. If any of those were not normally metabolized, they were not prescribed to the patients in the custom group, who were given an alternative drug (hydromorphone for narcotics, meloxicam for non-steroidal anti-inflammatory drugs). Patients recorded their pain level (0-10 numeric scale) and all medications taken daily for the first 10 days following surgery. Medication was converted to milligram morphine equivalents (MMEs). RESULTS Genetic variations to medications in our standard postoperative pain management protocol occurred in 24 of the 107 patients (22.4%). The 10-day MME consumed by patients in the control group with genetic variants was 162.6 mg. Patients with variants who had custom postoperative medication consumed only 86.7 MME in the same timeframe (P = .126). The control group demonstrated a higher 10-day average pain level of 4.2 vs the custom group pain level of only 3.1 (P < .05). CONCLUSION With custom postoperative pain prescriptions based on pharmacogenetic testing, patients were able to achieve lower pain levels while reducing the consumption of pain medication.
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Affiliation(s)
| | | | | | - Nancy L Parks
- Anderson Orthopaedic Research Institute, Alexandria, Virginia
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40
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Roosan D. The promise of digital health in healthcare equity and medication adherence in the disadvantaged dementia population. Pharmacogenomics 2022; 23:505-508. [PMID: 35698906 DOI: 10.2217/pgs-2022-0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tweetable abstract Pharmacogenomics cascade testing in a digital health solution can improve medication adherence in dementia care for disadvantaged populations.
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Affiliation(s)
- Don Roosan
- College of Pharmacy, Western University of Health Sciences, 309 E. 2nd Street, Pomona, CA 91766, USA
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Lopez-Medina AI, Chahal CAA, Luzum JA. The genetics of drug-induced QT prolongation: evaluating the evidence for pharmacodynamic variants. Pharmacogenomics 2022; 23:543-557. [PMID: 35698903 DOI: 10.2217/pgs-2022-0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Drug-induced long QT syndrome (diLQTS) is an adverse effect of many commonly prescribed drugs, and it can increase the risk for lethal ventricular arrhythmias. Genetic variants in pharmacodynamic genes have been associated with diLQTS, but the strength of the evidence for each of those variants has not yet been evaluated. Therefore, the purpose of this review was to evaluate the strength of the evidence for pharmacodynamic genetic variants associated with diLQTS using a novel, semiquantitative scoring system modified from the approach used for congenital LQTS. KCNE1-D85N and KCNE2-T8A had definitive and strong evidence for diLQTS, respectively. The high level of evidence for these variants supports current consideration as risk factors for patients that will be prescribed a QT-prolonging drug.
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Affiliation(s)
- Ana I Lopez-Medina
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Choudhary Anwar A Chahal
- Division of Cardiovascular Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA.,Barts Heart Centre, St. Bartholomew's Hospital, West Smithfield, London, EC1A 7BE, UK.,WellSpan Health, Lancaster, PA 17607, USA
| | - Jasmine A Luzum
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
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Cerezo-Arias MDLO, Gómez-Tabales J, Martí M, García-Martín E, Agúndez JAG. Common UGT1A6 Variant Alleles Determine Acetaminophen Pharmacokinetics in Man. J Pers Med 2022; 12:jpm12050720. [PMID: 35629143 PMCID: PMC9143054 DOI: 10.3390/jpm12050720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 11/18/2022] Open
Abstract
Acetaminophen (paracetamol) is a widely used drug that causes adverse drug events that are often dose-dependent and related to plasma drug concentrations. Acetaminophen metabolism strongly depends on UGT1A enzymes. We aimed to investigate putative factors influencing acetaminophen pharmacokinetics. We analyzed acetaminophen pharmacokinetics after intravenous administration in 186 individuals, and we determined the effect of sex; body mass index (BMI); previous and concomitant therapy with UGT1A substrates, inhibitors, and inducers; as well as common variations in the genes coding for UGT1A1, UGT1A6, and UGT1A9. We identified sex and UGT1A6 genetic variants as major factors influencing acetaminophen pharmacokinetics, with women showing lower clearance (p < 0.001) and higher area under the plasma drug concentration-time curve (AUC) values than men (p < 0.001). UGT1A6 genetic variants were related to decreased acetaminophen biodisposition. Individuals who were homozygous or double-heterozygous for variant UGT1A6 alleles showed a 22.5% increase in t1/2 values and a 22.8 increase in drug exposure (p < 0.001, and 0.006, respectively) after correction by sex. The effect is related to the UGT1A6*2 and UGT1A6*4 variant alleles, whereas no effect of UGT1A6*3 and UGT1A9*3 alleles, BMI, or drug−drug interaction was identified in this study. We conclude that sex and UGT1A6 variants determine acetaminophen pharmacokinetics, thus providing evidence to eventually developing pharmacogenomics procedures and recommendations for acetaminophen use.
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Affiliation(s)
- María de las Olas Cerezo-Arias
- Intensive Care Medicine Department, University Hospital, Badajoz, University of Extremadura (UEX), 06006 Badajoz, Spain;
| | - Javier Gómez-Tabales
- Universidad de Extremadura, University Institute of Molecular Pathology Biomarkers, ARADyAL Instituto de Salud Carlos III, 10071 Caceres, Spain; (J.G.-T.); (M.M.)
| | - Manuel Martí
- Universidad de Extremadura, University Institute of Molecular Pathology Biomarkers, ARADyAL Instituto de Salud Carlos III, 10071 Caceres, Spain; (J.G.-T.); (M.M.)
| | - Elena García-Martín
- Universidad de Extremadura, University Institute of Molecular Pathology Biomarkers, ARADyAL Instituto de Salud Carlos III, 10071 Caceres, Spain; (J.G.-T.); (M.M.)
- Correspondence: (E.G.-M.); (J.A.G.A.); Tel.: +34-927251514 (E.G.-M.); +34-927251323 (J.A.G.A)
| | - José A. G. Agúndez
- Universidad de Extremadura, University Institute of Molecular Pathology Biomarkers, ARADyAL Instituto de Salud Carlos III, 10071 Caceres, Spain; (J.G.-T.); (M.M.)
- Correspondence: (E.G.-M.); (J.A.G.A.); Tel.: +34-927251514 (E.G.-M.); +34-927251323 (J.A.G.A)
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Integration of Omics and Phenotypic Data for Precision Medicine. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2486:19-35. [PMID: 35437716 DOI: 10.1007/978-1-0716-2265-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Over the past two decades, biomedical research is moving toward a big-data-driven approach. The underlying causes of this transition include the ability to gather genetic or molecular profiles of humans faster, the increasing adoption of electronic health record (EHR) system, and the growing interest in linking omics and phenotypic data for analysis. The integration of individual's biology data (e.g., genomics, proteomics, metabolomics), and health-care data has created unprecedented opportunities for precision medicine, that is, a medical model that uses a patient's unique information, mainly genetic, to prevent, diagnose, or treat disease. This chapter reviewed the research opportunities and applications of integrating omics and phenotypic data for precision medicine, such as understanding the relationship between genotype and phenotype, disease subtyping, and diagnosis or prediction of adverse outcomes. We reviewed the recent advanced methods, particularly the machine learning and deep learning-based approaches used for harnessing and harmonizing the multiomics and phenotypic data to address these applications. We finally discussed the challenges and future directions.
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Goddard KAB, Lee K, Buchanan AH, Powell BC, Hunter JE. Establishing the Medical Actionability of Genomic Variants. Annu Rev Genomics Hum Genet 2022; 23:173-192. [PMID: 35363504 PMCID: PMC10184682 DOI: 10.1146/annurev-genom-111021-032401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Actionability is an important concept in medicine that does not have a well-accepted standard definition, nor is there a general consensus on how to establish it. Medical actionability is often conflated with clinical utility, a related but distinct concept. This lack of clarity contributes to practice variation and inconsistent coverage decisions in genomic medicine, leading to the potential for systematic bias in the use of evidence-based interventions. We clarify how medical actionability and clinical utility are distinct and then discuss the spectrum of actionability, including benefits for the person, the family, and society. We also describe applications across the life course, including prediction, diagnosis, and treatment. Current challenges in assessing the medical actionability of identified genomic variants include gaps in the evidence, limited contexts with practice guidelines, and subjective aspects of medical actionability. A standardized and authoritative assessment of medical actionability is critical to implementing genomic medicine in a fashion that improves population health outcomes and reduces health disparities. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Kristy Lee
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Adam H Buchanan
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Bradford C Powell
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
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45
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Klanderman BJ, Koch C, Machini K, Parpattedar SS, Bandyadka S, Lin CF, Hynes E, Lebo MS, Amr SS. Automated Pharmacogenomic Reports for Clinical Genome Sequencing. J Mol Diagn 2022; 24:205-218. [PMID: 35041930 DOI: 10.1016/j.jmoldx.2021.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/09/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022] Open
Abstract
Clinical laboratories offering genome sequencing have the opportunity to return pharmacogenomic findings to patients, providing the added benefit of preemptive testing that could help inform medication selection or dosing throughout the lifespan. Implementation of pharmacogenomic reporting must address several challenges, including inherent limitations in short-read genome sequencing methods, gene and variant selection, standardization of genotype and phenotype nomenclature, and choice of guidelines and drugs to report. An automated pipeline, lmPGX, was developed as an end-to-end solution that produces two versions of a pharmacogenomic report, presenting either Clinical Pharmacogenetics Implementation Consortium or US Food and Drug Administration guidelines for 12 genes. The pipeline was validated for performance using reference samples and pharmacogenetic data from the Genetic Testing Reference Materials Coordination Program. To determine performance and limitations, lmPGX was compared with three additional publicly available pharmacogenomic pipelines. The lmPGX pipeline offers clinical laboratories an opportunity for seamless integration of pharmacogenomic results with genome reporting.
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Affiliation(s)
- Barbara J Klanderman
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Kalotina Machini
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Shruti S Parpattedar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Shruthi Bandyadka
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Chiao-Feng Lin
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts; Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
| | - Sami S Amr
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Deparment of Pathology, Harvard Medical School, Boston, Massachusetts.
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46
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Fekete F, Mangó K, Minus A, Tóth K, Monostory K. CYP1A2 mRNA Expression Rather than Genetic Variants Indicate Hepatic CYP1A2 Activity. Pharmaceutics 2022; 14:pharmaceutics14030532. [PMID: 35335907 PMCID: PMC8954692 DOI: 10.3390/pharmaceutics14030532] [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: 01/14/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
CYP1A2, one of the most abundant hepatic cytochrome P450 enzymes, is involved in metabolism of several drugs and carcinogenic compounds. Data on the significance of CYP1A2 genetic polymorphisms in enzyme activity are highly inconsistent; therefore, the impact of CYP1A2 genetic variants (−3860G>A, −2467delT, −739T>G, −163C>A, 2159G>A) on mRNA expression and phenacetin O-dealkylation selective for CYP1A2 was investigated in human liver tissues and in psychiatric patients belonging to Caucasian populations. CYP1A2*1F, considered to be associated with high CYP1A2 inducibility, is generally identified by the presence of −163C>A polymorphism; however, we demonstrated that −163C>A existed in several haplotypes (CYP1A2*1F, CYP1A2*1L, CYP1A2*1M, CYP1A2*1V, CYP1A2*1W), and consequently, CYP1A2*1F was a much rarer allelic variant (0.4%) than reported in Caucasian populations. Of note, −163C>A polymorphism was found to result in an increase of neither mRNA nor the activity of CYP1A2. Moreover, hepatic CYP1A2 activity was associated with hepatic or leukocyte mRNA expression rather than genetic polymorphisms of CYP1A2. Consideration of non-genetic phenoconverting factors (co-medication with CYP1A2-specific inhibitors/inducers, tobacco smoking and non-specific factors, including amoxicillin+clavulanic acid therapy or chronic alcohol consumption) did not much improve genotype−phenotype estimation. In conclusion, CYP1A2-genotyping is inappropriate for the prediction of CYP1A2 function; however, CYP1A2 mRNA expression in leukocytes can inform about patients’ CYP1A2-metabolizing capacity.
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Affiliation(s)
- Ferenc Fekete
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (F.F.); (K.M.); (A.M.); (K.T.)
- Doctoral School of Biology and Institute of Biology, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Katalin Mangó
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (F.F.); (K.M.); (A.M.); (K.T.)
| | - Annamária Minus
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (F.F.); (K.M.); (A.M.); (K.T.)
| | - Katalin Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (F.F.); (K.M.); (A.M.); (K.T.)
| | - Katalin Monostory
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, H-1117 Budapest, Hungary; (F.F.); (K.M.); (A.M.); (K.T.)
- Correspondence:
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Keathley J, Garneau V, Marcil V, Mutch DM, Robitaille J, Rudkowska I, Sofian G, Desroches S, Vohl MC. Clinical Practice Guidelines Using GRADE and AGREE II for the Impact of Genetic Variants on Plasma Lipid/Lipoprotein/Apolipoprotein Responsiveness to Omega-3 Fatty Acids. Front Nutr 2022; 8:768474. [PMID: 35237638 PMCID: PMC8883048 DOI: 10.3389/fnut.2021.768474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Background A recent systematic review, which used the GRADE methodology, concluded that there is strong evidence for two gene-diet associations related to omega-3 and plasma triglyceride (TG) responses. Systematic reviews can be used to inform the development of clinical practice guidelines (CPGs). Objective To provide guidance for clinical practice related to genetic testing for evaluating responsiveness to dietary/supplemental omega-3s and their impact on plasma lipids/lipoproteins/apolipoproteins. Design Using the results of the abovementioned systematic review, the first CPGs in nutrigenetics were developed using the established GRADE methodology and AGREE II approach. Results Three clinical practice recommendations were developed. Most gene-diet associations identified in the literature lack adequate scientific and clinical validity to warrant consideration for implementing in a practice setting. However, two gene-diet associations with strong evidence (GRADE quality: moderate and high) can be considered for implementation into clinical practice in certain cases: male APOE-E4 carriers (rs429358, rs7412) and TG changes in response to the omega-3 fatty acids eicosapentaenoic acid (EPA) and/or docosahexaenoic acid (DHA) as well as a 31-SNP nutrigenetic risk score and TG changes in response to EPA+DHA among adults with overweight/obesity. Ethical and regulatory implications must be considered when providing APOE nutrigenetic tests given the well-established link between APOE genetic variation and Alzheimer's Disease. Conclusion Most of the evidence in this area is not ready for implementation into clinical practice primarily due to low scientific validity (low quality of evidence). However, the first CPGs in nutrigenetics have been developed for two nutrigenetic associations with strong scientific validity, related to dietary/supplemental omega-3 and TG responses.
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Affiliation(s)
- Justine Keathley
- Centre Nutrition, Santé et Société (NUTRISS), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec City, QC, Canada
- School of Nutrition, Université Laval, Québec City, QC, Canada
| | - Véronique Garneau
- Centre Nutrition, Santé et Société (NUTRISS), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec City, QC, Canada
- School of Nutrition, Université Laval, Québec City, QC, Canada
| | - Valérie Marcil
- Research Centre, Sainte-Justine University Health Centre, Montréal, QC, Canada
- Department of Nutrition, Université de Montréal, Montréal, QC, Canada
| | - David M. Mutch
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada
| | - Julie Robitaille
- Centre Nutrition, Santé et Société (NUTRISS), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec City, QC, Canada
- School of Nutrition, Université Laval, Québec City, QC, Canada
| | - Iwona Rudkowska
- Endocrinology and Nephrology Unit, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Québec City, QC, Canada
- Department of Kinesiology, Université Laval, Québec City, QC, Canada
| | | | - Sophie Desroches
- Centre Nutrition, Santé et Société (NUTRISS), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec City, QC, Canada
- School of Nutrition, Université Laval, Québec City, QC, Canada
| | - Marie-Claude Vohl
- Centre Nutrition, Santé et Société (NUTRISS), Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec City, QC, Canada
- School of Nutrition, Université Laval, Québec City, QC, Canada
- *Correspondence: Marie-Claude Vohl
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48
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Bousman CA, Mukerjee G, Men X, Dorfman R, Müller DJ, Thomas RE. Encountering Pharmacogenetic Test Results in the Psychiatric Clinic. CANADIAN JOURNAL OF PSYCHIATRY. REVUE CANADIENNE DE PSYCHIATRIE 2022; 67:95-100. [PMID: 34783587 PMCID: PMC8892046 DOI: 10.1177/07067437211058847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chad A Bousman
- Departments of Medical Genetics, Psychiatry, Physiology & Pharmacology, and Community Health Sciences, University of Calgary, Calgary, Alberta, Canada.,Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada.,Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Xiaoyu Men
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada
| | - Ruslan Dorfman
- GeneYouIn Inc, Toronto, Ontario, Canada.,Department of Anesthesia, McMaster University, Hamilton, Ontario, Canada
| | - Daniel J Müller
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Roger E Thomas
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
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49
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Tortajada-Genaro LA. DNA Genotyping Based on Isothermal Amplification and Colorimetric Detection by Consumer Electronics Devices. Methods Mol Biol 2022; 2393:163-178. [PMID: 34837179 DOI: 10.1007/978-1-0716-1803-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The point-of-care testing of DNA biomarkers requires compact biosensing systems and consumer electronic technologies provide fascinating opportunities. Their portability, mass-produced components, and high-performance readout capabilities are the main advantages for the development of novel bioanalytical methods.This chapter describes the detection of single nucleotide polymorphisms (SNP) through methods based on user-friendly optical devices (e.g., USB digital microscope, flatbed scanner, smartphone, and DVD drive). Loop mediated isothermal amplification (LAMP) enables the required discrimination of each specific variant prior to the optical reading. In the first method, products are directly hybridized to the allele-specific probes attached to plastic chips in an array format. The second method, allele-specific primers are used, enabling the direct end-point detection based a colorimetric dyer and a microfluidic chamber chip. In both approaches, devices are employed for chip scanning.A representative application to the genotyping of a clinically relevant SNP from human samples is provided, showing the excellent features achieved. Consumer electronic devices are able to register sensitive precise measurements in terms of signal-to-noise ratios, image resolution, and scan-to-scan reproducibility. The integrated DNA-based method lead a low detection limit (100 genomic DNA copies), reproducible (variation <15%), high specificity (genotypes validated by reference method), and cheap assays (<10 €/test). The underlying challenge is the reliable implementation into minimal-specialized clinical laboratories, incorporating additional advantages, such as user-friendly interface, low cost, and connectivity for telemedicine needs.
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Affiliation(s)
- Luis Antonio Tortajada-Genaro
- Chemistry Department, Universitat Politècnica de València, Valencia, Spain.
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Valencia, Spain.
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50
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Gene-drug pairings for antidepressants and antipsychotics: level of evidence and clinical application. Mol Psychiatry 2022; 27:593-605. [PMID: 34754108 DOI: 10.1038/s41380-021-01340-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/23/2021] [Accepted: 10/01/2021] [Indexed: 11/09/2022]
Abstract
Substantial inter-individual discrepancies exist in both therapeutic effectiveness and adverse effects of antidepressant and antipsychotic medications, which can, in part, be explained by genetic variation. Here, we searched the Pharmacogenomics Knowledge Base for gene-antidepressant and gene-antipsychotic pairs with the highest level of evidence. We then extracted and compared the associated prescribing recommendations for these pairs developed by the Clinical Pharmacogenomics Implementation Consortium, the Dutch Pharmacogenetics Working Group or approved product labels in the US, Canada, Europe, and Asia. Finally, we highlight key economical, educational, regulatory, and ethical issues that, if not appropriately considered, can hinder the implementation of these recommendations in clinical practice. Our review indicates that evidence-based guidelines are available to assist with the implementation of pharmacogenetic-guided antidepressant and antipsychotic prescribing, although the maximum impact of these guidelines on patient care will not be realized until key barriers are minimized or eliminated.
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