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Parvez MM, Thakur A, Mehrotra A, Stancil S, Pearce RE, Basit A, Leeder JS, Prasad B. Age-Dependent Abundance of CYP450 Enzymes Involved in Metronidazole Metabolism: Application to Pediatric PBPK Modeling. Clin Pharmacol Ther 2024; 116:1090-1099. [PMID: 38955794 DOI: 10.1002/cpt.3354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/16/2024] [Indexed: 07/04/2024]
Abstract
The expression of cytochrome P450 (CYP) enzymes is highly variable and associated with factors, such as age, genotype, sex, and disease states. In this study, quantification of metronidazole metabolizing CYP isoforms (CYP2A6, CYP2E1, CYP3A4, CYP3A5, and CYP3A7) in human liver microsomes from 115 children and 35 adults was performed using a quantitative proteomics method. The data confirmed age-dependent increase in CYP2A6, CYP2E1, and CYP3A4 abundance, whereas, as expected, CYP3A7 abundance showed postnatal decrease with age. In particular, the fold difference (neonatal to adulthood levels) in the protein abundance of CYP2A6, CYP2E1, and CYP3A4 was 14, 11, and 20, respectively. In contrast, protein abundance of CYP3A7 was > 125-fold higher in the liver microsomes of neonates than of adults. The abundance of CYP2A6 and CYP3A5 was associated with genotypes, rs4803381 and rs776746, respectively. A proteomics-informed physiologically based pharmacokinetic (PBPK) model was developed to describe the pharmacokinetics of metronidazole and its primary metabolite, 2-hydroxymethylmetronidazole. The model revealed an increase in the metabolite-to-parent ratio with age and showed a strong correlation between CYP2A6 abundance and metabolite formation (r 2 = 0.75). Notably, the estimated contribution of CYP3A7 was ~ 75% in metronidazole clearance in neonates. These data suggest that variability in CYP2A6 and CYP3A7 in younger children poses the risk of variable pharmacokinetics of metronidazole and its active metabolite with a potential impact on drug efficacy and safety. No sex-dependent difference was observed in the protein abundance of the studied CYPs. The successful integration of hepatic CYP ontogeny data derived from a large liver bank into the pediatric PBPK model of metronidazole can be extended to other drugs metabolized by the studied CYPs.
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Affiliation(s)
- Md Masud Parvez
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - Aarzoo Thakur
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - Aanchal Mehrotra
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Stephani Stancil
- 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
| | - Robin E Pearce
- 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
| | - Abdul Basit
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - J Steven Leeder
- 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
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
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Wu A, Raack EJ, Ross CJD, Carleton BC. Implementation and Evaluation Strategies for Pharmacogenetic Testing in Hospital Settings: A Scoping Review. Ther Drug Monit 2024:00007691-990000000-00266. [PMID: 39264345 DOI: 10.1097/ftd.0000000000001243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/01/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND Pharmacogenetic testing in clinical settings has improved the safety and efficacy of drug treatment. There is a growing number of studies evaluating pharmacogenetic implementation and identifying barriers and facilitators. However, no review has focused on bridging the gap between identifying barriers and facilitators of testing and the clinical strategies adopted in response. This review was conducted to understand the implementation and evaluation strategies of pharmacogenetic testing programs. METHODS A PRISMA-compliant scoping review was conducted. The included studies discussed pharmacogenetic testing programs implemented in a hospital setting. Quantitative, qualitative, and mixed design methods were included. RESULTS A total of 232 of the 7043 articles that described clinical pharmacogenetic programs were included. The most common specialties that described pharmacogenetic implementation were psychiatry (26%) and oncology (16%), although many studies described institutional programs implemented across multiple specialties (19%). Different specialties reported different clinical outcomes, but all reported similar program performance indicators, such as test uptake and the number of times the test recommendations were followed. There were benefits and drawbacks to delivering test results through research personnel, pharmacists, and electronic alerts, but active engagement of physicians was necessary for the incorporation of pharmacogenetic results into clinical decision making. CONCLUSIONS Further research is required on the maintenance and sustainability of pharmacogenetic testing initiatives. These findings provide an overview of the implementation and evaluation strategies of different specialties that can be used to improve pharmacogenetic testing.
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Affiliation(s)
- Angela Wu
- Department of Experimental Medicine, University of British Columbia
- BC Children's Hospital Research Institute
| | - Edward J Raack
- BC Children's Hospital Research Institute
- Department of Medical Genetics, University of British Columbia
| | - Colin J D Ross
- BC Children's Hospital Research Institute
- Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia; and
| | - Bruce C Carleton
- BC Children's Hospital Research Institute
- Department of Medical Genetics, University of British Columbia
- Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia; and
- Therapeutic Evaluation Unit, Provincial Health Services Authority, Vancouver, British Columbia, Canada
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3
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Delabays B, Trajanoska K, Walonoski J, Mooser V. Cardiovascular Pharmacogenetics: From Discovery of Genetic Association to Clinical Adoption of Derived Test. Pharmacol Rev 2024; 76:791-827. [PMID: 39122647 DOI: 10.1124/pharmrev.123.000750] [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: 07/29/2023] [Revised: 04/24/2024] [Accepted: 05/28/2024] [Indexed: 08/12/2024] Open
Abstract
Recent breakthroughs in human genetics and in information technologies have markedly expanded our understanding at the molecular level of the response to drugs, i.e., pharmacogenetics (PGx), across therapy areas. This review is restricted to PGx for cardiovascular (CV) drugs. First, we examined the PGx information in the labels approved by regulatory agencies in Europe, Japan, and North America and related recommendations from expert panels. Out of 221 marketed CV drugs, 36 had PGx information in their labels approved by one or more agencies. The level of annotations and recommendations varied markedly between agencies and expert panels. Clopidogrel is the only CV drug with consistent PGx recommendation (i.e., "actionable"). This situation prompted us to dissect the steps from discovery of a PGx association to clinical translation. We found 101 genome-wide association studies that investigated the response to CV drugs or drug classes. These studies reported significant associations for 48 PGx traits mapping to 306 genes. Six of these 306 genes are mentioned in the corresponding PGx labels or recommendations for CV drugs. Genomic analyses also highlighted the wide between-population differences in risk allele frequencies and the individual load of actionable PGx variants. Given the high attrition rate and the long road to clinical translation, additional work is warranted to identify and validate PGx variants for more CV drugs across diverse populations and to demonstrate the utility of PGx testing. To that end, pre-emptive PGx combining genomic profiling with electronic medical records opens unprecedented opportunities to improve healthcare, for CV diseases and beyond. SIGNIFICANCE STATEMENT: Despite spectacular breakthroughs in human molecular genetics and information technologies, consistent evidence supporting PGx testing in the cardiovascular area is limited to a few drugs. Additional work is warranted to discover and validate new PGx markers and demonstrate their utility. Pre-emptive PGx combining genomic profiling with electronic medical records opens unprecedented opportunities to improve healthcare, for CV diseases and beyond.
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Affiliation(s)
- Benoît Delabays
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Joshua Walonoski
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Victor Phillip Dahdaleh Institute of Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada (B.D., K.T., V.M.); and Medeloop Inc., Palo Alto, California, and Montreal, QC, Canada (J.W.)
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4
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Robertson AJ, Mallett AJ, Stark Z, Sullivan C. It Is in Our DNA: Bringing Electronic Health Records and Genomic Data Together for Precision Medicine. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2024; 5:e55632. [PMID: 38935958 PMCID: PMC11211701 DOI: 10.2196/55632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/08/2024] [Accepted: 04/09/2024] [Indexed: 06/29/2024]
Abstract
Health care is at a turning point. We are shifting from protocolized medicine to precision medicine, and digital health systems are facilitating this shift. By providing clinicians with detailed information for each patient and analytic support for decision-making at the point of care, digital health technologies are enabling a new era of precision medicine. Genomic data also provide clinicians with information that can improve the accuracy and timeliness of diagnosis, optimize prescribing, and target risk reduction strategies, all of which are key elements for precision medicine. However, genomic data are predominantly seen as diagnostic information and are not routinely integrated into the clinical workflows of electronic medical records. The use of genomic data holds significant potential for precision medicine; however, as genomic data are fundamentally different from the information collected during routine practice, special considerations are needed to use this information in a digital health setting. This paper outlines the potential of genomic data integration with electronic records, and how these data can enable precision medicine.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, University of Queensland, Hertson, Australia
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- The Genomic Institute, Department of Health, Queensland Government, Brisbane, Australia
| | - Andrew J Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Australian Genomics, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Clair Sullivan
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- Centre for Health Services Research, Faculty of Medicine, University of Queensland, Woolloongabba, Australia
- Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Australia
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5
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Johnson D, Del Fiol G, Kawamoto K, Romagnoli KM, Sanders N, Isaacson G, Jenkins E, Williams MS. Genetically guided precision medicine clinical decision support tools: a systematic review. J Am Med Inform Assoc 2024; 31:1183-1194. [PMID: 38558013 PMCID: PMC11031215 DOI: 10.1093/jamia/ocae033] [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: 08/17/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES Patient care using genetics presents complex challenges. Clinical decision support (CDS) tools are a potential solution because they provide patient-specific risk assessments and/or recommendations at the point of care. This systematic review evaluated the literature on CDS systems which have been implemented to support genetically guided precision medicine (GPM). MATERIALS AND METHODS A comprehensive search was conducted in MEDLINE and Embase, encompassing January 1, 2011-March 14, 2023. The review included primary English peer-reviewed research articles studying humans, focused on the use of computers to guide clinical decision-making and delivering genetically guided, patient-specific assessments, and/or recommendations to healthcare providers and/or patients. RESULTS The search yielded 3832 unique articles. After screening, 41 articles were identified that met the inclusion criteria. Alerts and reminders were the most common form of CDS used. About 27 systems were integrated with the electronic health record; 2 of those used standards-based approaches for genomic data transfer. Three studies used a framework to analyze the implementation strategy. DISCUSSION Findings include limited use of standards-based approaches for genomic data transfer, system evaluations that do not employ formal frameworks, and inconsistencies in the methodologies used to assess genetic CDS systems and their impact on patient outcomes. CONCLUSION We recommend that future research on CDS system implementation for genetically GPM should focus on implementing more CDS systems, utilization of standards-based approaches, user-centered design, exploration of alternative forms of CDS interventions, and use of formal frameworks to systematically evaluate genetic CDS systems and their effects on patient care.
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Affiliation(s)
- Darren Johnson
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Kensaku Kawamoto
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84108, United States
| | - Katrina M Romagnoli
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
| | - Nathan Sanders
- School of Medicine, Geisinger Health Systems, Danville, PA 17822, United States
| | - Grace Isaacson
- Family Medicine, Penn Highlands Healthcare, DuBois, PA 16830, United States
| | - Elden Jenkins
- School of Medicine, Noorda College of Osteopathic Medicine, Provo, UT 84606, United States
| | - Marc S Williams
- Department of Genomic Health, Geisinger Health Systems, Danville, PA 17822, United States
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Bastaki K, Velayutham D, Irfan A, Adnan M, Mohammed S, Mbarek H, Qoronfleh MW, Jithesh PV. Forging the path to precision medicine in Qatar: a public health perspective on pharmacogenomics initiatives. Front Public Health 2024; 12:1364221. [PMID: 38550311 PMCID: PMC10977610 DOI: 10.3389/fpubh.2024.1364221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/20/2024] [Indexed: 04/02/2024] Open
Abstract
Pharmacogenomics (PGx) is an important component of precision medicine that promises tailored treatment approaches based on an individual's genetic information. Exploring the initiatives in research that help to integrate PGx test into clinical setting, identifying the potential barriers and challenges as well as planning the future directions, are all important for fruitful PGx implementation in any population. Qatar serves as an exemplar case study for the Middle East, having a small native population compared to a diverse immigrant population, advanced healthcare system, national genome program, and several educational initiatives on PGx and precision medicine. This paper attempts to outline the current state of PGx research and implementation in Qatar within the global context, emphasizing ongoing initiatives and educational efforts. The inclusion of PGx in university curricula and healthcare provider training, alongside precision medicine conferences, showcase Qatar's commitment to advancing this field. However, challenges persist, including the requirement for population specific implementation strategies, complex genetic data interpretation, lack of standardization, and limited awareness. The review suggests policy development for future directions in continued research investment, conducting clinical trials for the feasibility of PGx implementation, ethical considerations, technological advancements, and global collaborations to overcome these barriers.
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Affiliation(s)
- Kholoud Bastaki
- Clinical and Pharmacy Practice Department, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Dinesh Velayutham
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Areeba Irfan
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Mohd Adnan
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Sawsan Mohammed
- College of Medicine, Pre-Clinical Education Department, QU Health, Qatar University, Doha, Qatar
| | | | - M. Waild Qoronfleh
- Q3 Research Institute (QRI), Research & Policy Division, Ann Arbor, MI, United States
| | - Puthen Veettil Jithesh
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
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7
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Shriver SP, Adams D, McKelvey BA, McCune JS, Miles D, Pratt VM, Ashcraft K, McLeod HL, Williams H, Fleury ME. Overcoming Barriers to Discovery and Implementation of Equitable Pharmacogenomic Testing in Oncology. J Clin Oncol 2024:JCO2301748. [PMID: 38386947 DOI: 10.1200/jco.23.01748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/08/2023] [Accepted: 12/12/2023] [Indexed: 02/24/2024] Open
Abstract
Pharmacogenomics (PGx), the study of inherited genomic variation and drug response or safety, is a vital tool in precision medicine. In oncology, testing to identify PGx variants offers patients the opportunity for customized treatments that can minimize adverse effects and maximize the therapeutic benefits of drugs used for cancer treatment and supportive care. Because individuals of shared ancestry share specific genetic variants, PGx factors may contribute to outcome disparities across racial and ethnic categories when genetic ancestry is not taken into account or mischaracterized in PGx research, discovery, and application. Here, we examine how the current scientific understanding of the role of PGx in differential oncology safety and outcomes may be biased toward a greater understanding and more complete clinical implementation of PGx for individuals of European descent compared with other genetic ancestry groups. We discuss the implications of this bias for PGx discovery, access to care, drug labeling, and patient and provider understanding and use of PGx approaches. Testing for somatic genetic variants is now the standard of care in treatment of many solid tumors, but the integration of PGx into oncology care is still lacking despite demonstrated actionable findings from PGx testing, reduction in avoidable toxicity and death, and return on investment from testing. As the field of oncology is poised to expand and integrate germline genetic variant testing, it is vital that PGx discovery and application are equitable for all populations. Recommendations are introduced to address barriers to facilitate effective and equitable PGx application in cancer care.
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Affiliation(s)
| | | | | | - Jeannine S McCune
- City of Hope/Beckman Research Institute Department of Hematologic Malignancies Translational Sciences, Duarte, CA
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8
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Li LJ, Legeay S, Gagnon AL, Frigon MP, Tessier L, Tremblay K. Moving towards the implementation of pharmacogenetic testing in Quebec. Front Genet 2024; 14:1295963. [PMID: 38234998 PMCID: PMC10791884 DOI: 10.3389/fgene.2023.1295963] [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: 09/17/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Clinical implementation of pharmacogenetics (PGx) into routine care will elevate the current paradigm of treatment decisions. However, while PGx tests are increasingly becoming reliable and affordable, several barriers have limited their widespread usage in Canada. Globally, over ninety successful PGx implementors can serve as models. The purpose of this paper is to outline the PGx implementation barriers documented in Quebec (Canada) to suggest efficient solutions based on existing PGx clinics and propose an adapted clinical implementation model. We conclude that the province of Quebec is ready to implement PGx.
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Affiliation(s)
- Ling Jing Li
- Centre Intégré Universitaire de Santé et de Services Sociaux Du Saguenay-Lac-Saint-Jean (Chicoutimi University Hospital), Research Center, Saguenay, QC, Canada
- Medicine Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Saguenay, QC, Canada
| | - Samuel Legeay
- Centre Intégré Universitaire de Santé et de Services Sociaux Du Saguenay-Lac-Saint-Jean (Chicoutimi University Hospital), Research Center, Saguenay, QC, Canada
- Medicine Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Saguenay, QC, Canada
- University Angers, [CHU Angers], Inserm, CNRS, MINT, Angers, France
| | - Ann-Lorie Gagnon
- Centre Intégré Universitaire de Santé et de Services Sociaux Du Saguenay-Lac-Saint-Jean (Chicoutimi University Hospital), Research Center, Saguenay, QC, Canada
| | - Marie-Pier Frigon
- Centre Intégré Universitaire de Santé et de Services Sociaux Du Saguenay-Lac-Saint-Jean (Chicoutimi University Hospital), Research Center, Saguenay, QC, Canada
- Pediatrics Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Laurence Tessier
- Centre Intégré Universitaire de Santé et de Services Sociaux Du Saguenay-Lac-Saint-Jean (Chicoutimi University Hospital), Research Center, Saguenay, QC, Canada
- Pharmacology-Physiology Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Saguenay, QC, Canada
| | - Karine Tremblay
- Centre Intégré Universitaire de Santé et de Services Sociaux Du Saguenay-Lac-Saint-Jean (Chicoutimi University Hospital), Research Center, Saguenay, QC, Canada
- Pharmacology-Physiology Department, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Saguenay, QC, Canada
- Centre de Recherche Du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC, Canada
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9
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Uber R, Hayduk VA, Pradhan A, Ward T, Flango A, Graham J, Wright EA. Pre-emptive pharmacogenomics implementation among polypharmacy patients 65 years old and older: a clinical pilot. Pharmacogenomics 2023; 24:915-920. [PMID: 37965783 DOI: 10.2217/pgs-2023-0185] [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] [Indexed: 11/16/2023] Open
Abstract
Aim: Pre-emptive testing of pharmacogenomic (PGx) variations has potential to improve medication safety and effectiveness; however, testing is not routine. Given the newfound payor coverage of multigene testing and the potential value of testing within aging patients, it is imperative to test local PGx testing capabilities, report results to patients and providers, and determine the value of testing. Materials & methods: We designed a randomized clinical pilot of a pre-emptive PGx testing process using the electronic health record compared with usual care among an aging primary care population. Results & conclusion: The impact of the program on prescribing patterns, healthcare utilization and costs of care will be evaluated. We hypothesize that implementation of a pre-emptive multigene PGx panel is feasible among elderly, polypharmacy, primary care patients, measured by the number of enrolled patients with PGx results entered in the medical record. Health system wide PGx implementation, including capacity needed to integrate these valuable results, is also described.
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Affiliation(s)
- Ryley Uber
- Center for Pharmacy Innovation & Outcomes, Geisinger, Danville, PA, USA
| | - Vanessa A Hayduk
- Center for Pharmacy Innovation & Outcomes, Geisinger, Danville, PA, USA
| | - Apoorva Pradhan
- Center for Pharmacy Innovation & Outcomes, Geisinger, Danville, PA, USA
| | - Theron Ward
- Enterprise Pharmacy, Geisinger, Danville, PA, USA
| | | | - Jove Graham
- Center for Pharmacy Innovation & Outcomes, Geisinger, Danville, PA, USA
| | - Eric A Wright
- Center for Pharmacy Innovation & Outcomes, Geisinger, Danville, PA, USA
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10
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Peruzzi E, Roncato R, De Mattia E, Bignucolo A, Swen JJ, Guchelaar HJ, Toffoli G, Cecchin E. Implementation of pre-emptive testing of a pharmacogenomic panel in clinical practice: Where do we stand? Br J Clin Pharmacol 2023. [PMID: 37926674 DOI: 10.1111/bcp.15956] [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: 09/13/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
Adverse drug reactions (ADRs) account for a large proportion of hospitalizations among adults and are more common in multimorbid patients, worsening clinical outcomes and burdening healthcare resources. Over the past decade, pharmacogenomics has been developed as a practical tool for optimizing treatment outcomes by mitigating the risk of ADRs. Some single-gene reactive tests are already used in clinical practice, including the DPYD test for fluoropyrimidines, which demonstrates how integrating pharmacogenomic data into routine care can improve patient safety in a cost-effective manner. The evolution from reactive single-gene testing to comprehensive pre-emptive genotyping panels holds great potential for refining drug prescribing practices. Several implementation projects have been conducted to test the feasibility of applying different genetic panels in clinical practice. Recently, the results of a large prospective randomized trial in Europe (the PREPARE study by Ubiquitous Pharmacogenomics consortium) have provided the first evidence that prospective application of a pre-emptive pharmacogenomic test panel in clinical practice, in seven European healthcare systems, is feasible and yielded a 30% reduction in the risk of developing clinically relevant toxicities. Nevertheless, some important questions remain unanswered and will hopefully be addressed by future dedicated studies. These issues include the cost-effectiveness of applying a pre-emptive genotyping panel, the role of multiple co-medications, the transferability of currently tested pharmacogenetic guidelines among patients of non-European origin and the impact of rare pharmacogenetic variants that are not detected by currently used genotyping approaches.
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Affiliation(s)
- Elena Peruzzi
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano, Istituti di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
| | - Rossana Roncato
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano, Istituti di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
- Department of Medicine, University of Udine, Udine, Italy
| | - Elena De Mattia
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano, Istituti di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
| | - Alessia Bignucolo
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano, Istituti di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
| | - Jesse J Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano, Istituti di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
| | - Erika Cecchin
- Experimental and Clinical Pharmacology, Centro di Riferimento Oncologico di Aviano, Istituti di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
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11
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Huebner T, Steffens M, Scholl C. Current status of the analytical validation of next generation sequencing applications for pharmacogenetic profiling. Mol Biol Rep 2023; 50:9587-9599. [PMID: 37787843 PMCID: PMC10635985 DOI: 10.1007/s11033-023-08748-z] [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: 06/05/2023] [Accepted: 08/08/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND Analytical validity is a prerequisite to use a next generation sequencing (NGS)-based application as an in vitro diagnostic test or a companion diagnostic in clinical practice. Currently, in the United States and the European Union, the intended use of such NGS-based tests does not refer to guided drug therapy on the basis of pharmacogenetic profiling of drug metabolizing enzymes, although the value of pharmacogenetic testing has been reported. However, in research, a large variety of NGS-based tests are used and have been confirmed to be at least comparable to array-based testing. METHODS AND RESULTS A systematic evaluation was performed screening and assessing published literature on analytical validation of NGS applications for pharmacogenetic profiling of CYP2C9, CYP2C19, CYP2D6, VKORC1 and/or UGT1A1. Although NGS applications are also increasingly used for implementation assessments in clinical practice, we show in the present systematic literature evaluation that published information on the current status of analytical validation of NGS applications targeting drug metabolizing enzymes is scarce. Furthermore, a comprehensive performance evaluation of whole exome and whole genome sequencing with the intended use for pharmacogenetic profiling has not been published so far. CONCLUSIONS A standard in reporting on analytical validation of NGS-based tests is not in place yet. Therefore, many relevant performance criteria are not addressed in published literature. For an appropriate analytical validation of an NGS-based qualitative test for pharmacogenetic profiling at least accuracy, precision, limit of detection and specificity should be addressed to facilitate the implementation of such tests in clinical use.
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Affiliation(s)
- Tatjana Huebner
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, Bonn, 53175, Germany.
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
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12
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McDermott JH, Newman W. Introduction to pharmacogenetics. Drug Ther Bull 2023; 61:168-172. [PMID: 37788890 DOI: 10.1136/dtb.2023.000009] [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: 10/05/2023]
Abstract
There is considerable interindividual variability in the effectiveness and safety of medicines. Although the reasons for this are multifactorial, it is well recognised that genetic changes impacting the absorption or metabolism of these drugs play a significant contributory role. Understanding how these pharmacogenetic variants impact response to medicines, and leveraging this knowledge to guide prescribing, could have significant benefits for patients and health services. This article provides an introduction to the field of pharmacogenetics, including its nomenclature, the existing evidence base and the current state of implementation globally. We discuss the challenges in translating pharmacogenetic research into clinical practice and highlight the considerable benefits which can emerge in those health services where implementation is successful.
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Affiliation(s)
- John Henry McDermott
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - William Newman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, UK
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13
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Morley TJ, Willimitis D, Ripperger M, Lee H, Han L, Zhou Y, Kang J, Davis LK, Smoller JW, Choi KW, Walsh CG, Ruderfer DM. Evaluating the impact of modeling choices on the performance of integrated genetic and clinical models. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.01.23297927. [PMID: 37961557 PMCID: PMC10635256 DOI: 10.1101/2023.11.01.23297927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The value of genetic information for improving the performance of clinical risk prediction models has yielded variable conclusions. Many methodological decisions have the potential to contribute to differential results across studies. Here, we performed multiple modeling experiments integrating clinical and demographic data from electronic health records (EHR) and genetic data to understand which decision points may affect performance. Clinical data in the form of structured diagnostic codes, medications, procedural codes, and demographics were extracted from two large independent health systems and polygenic risk scores (PRS) were generated across all patients with genetic data in the corresponding biobanks. Crohn's disease was used as the model phenotype based on its substantial genetic component, established EHR-based definition, and sufficient prevalence for model training and testing. We investigated the impact of PRS integration method, as well as choices regarding training sample, model complexity, and performance metrics. Overall, our results show that including PRS resulted in higher performance by some metrics but the gain in performance was only robust when combined with demographic data alone. Improvements were inconsistent or negligible after including additional clinical information. The impact of genetic information on performance also varied by PRS integration method, with a small improvement in some cases from combining PRS with the output of a clinical model (late-fusion) compared to its inclusion an additional feature (early-fusion). The effects of other modeling decisions varied between institutions though performance increased with more compute-intensive models such as random forest. This work highlights the importance of considering methodological decision points in interpreting the impact on prediction performance when including PRS information in clinical models.
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Affiliation(s)
- Theodore J. Morley
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Center for Digital Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville TN
| | - Drew Willimitis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
| | - Michael Ripperger
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
| | - Hyunjoon Lee
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston MA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston MA
| | - Lide Han
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Center for Digital Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville TN
| | - Yu Zhou
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston MA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston MA
| | - Jooeun Kang
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
| | - Lea K. Davis
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Jordan W. Smoller
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston MA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
| | - Karmel W. Choi
- Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston MA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston MA
| | - Colin G. Walsh
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Center for Digital Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Douglas M. Ruderfer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville TN
- Center for Digital Genomic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville TN
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville TN
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN
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14
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Wu P, Liu Z, Tian Z, Wu B, Shao J, Li Q, Geng Z, Pan Y, Lu K, Wang Q, Xu T, Zhou K. CYP2C19 Loss-of-Function Variants Associated With Long-Term Ischemic Stroke Events During Clopidogrel Treatment in the Chinese Population. Clin Pharmacol Ther 2023; 114:1126-1133. [PMID: 37607302 DOI: 10.1002/cpt.3028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/12/2023] [Indexed: 08/24/2023]
Abstract
This study aims to determine whether CYP2C19 loss-of-function (LoF) variants were associated with long-term ischemic stroke risk in Chinese primary care patients treated with clopidogrel. Patients treated with clopidogrel were ascertained from Chinese electronic medical records linked with a biobank for a retrospective cohort study. Their medical information was examined for the period from January 2018 to December 2021. Two CYP2C19 major loss of function variants (*2:rs4244285 and *3: rs4986893) were genotyped. The clinical outcome was ischemic stroke event. Cox regression analysis was used to evaluate the association between the occurrence of ischemic stroke events and CYP2C19 LoF variants. Covariates included age, gender, body mass index, prior ischemic stroke, transient ischemic attack, hypertension, diabetes mellitus, hyperlipoidemia, smoke status, aspirin use, proton-pump inhibitor use, and statin use. Of the 1,141 patients included in the clopidogrel therapy cohort, 61.9% carried at least one CYP2C19 LoF variant. During a median follow-up period of 12 months, 103 patients (9.0%) had an ischemic stroke. After adjusting for other risk factors, carriers of CYP2C19 LoF variants had significantly higher risk of ischemic stroke compared with non-carriers (hazard ratio: 1.64, 95% confidence interval: 1.06-2.53, P = 0.025). This pharmacogenetic study of clopidogrel provides novel insights into the association between the CYP2C19 LoF variant and long-term stroke risk. We established that there is still a need for CYP2C19 genotype-guided personalized antiplatelet therapy in those who have returned to the primary care setting for clopidogrel prescription.
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Affiliation(s)
- Peng Wu
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Ziqing Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zijian Tian
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Benrui Wu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jian Shao
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Qian Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoxu Geng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Pan
- Department of General Practice, Kunshan Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, China
| | - Ke Lu
- Department of General Practice, Kunshan Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, China
| | - Qiang Wang
- Department of General Practice, Kunshan Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu, China
| | - Tao Xu
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kaixin Zhou
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
- College of Public Health, Guangzhou Medical University, Guangzhou, China
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15
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Shue SA, Rowe E, Bell LA, Damush T, DeLong A, Gowan T, Skaar T, Haggstrom D. Pharmacogenomics implementation across multiple clinic settings: a qualitative evaluation. Pharmacogenomics 2023; 24:881-893. [PMID: 37975236 DOI: 10.2217/pgs-2023-0179] [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] [Indexed: 11/19/2023] Open
Abstract
Aim: To advance clinical adoption and implementation of pharmacogenomics (PGx) testing, barriers and facilitators to these efforts must be understood. This study identified and examined barriers and facilitators to active implementation of a PGx program across multiple clinic settings in an academic healthcare system. Materials & methods: 28 contributors to the PGx implementation (e.g., clinical providers, informatics specialists) completed an interview to elicit their perceptions of the implementation. Results: Qualitative analysis identified several barriers and facilitators that spanned different stages of the implementation process. Specifically, unclear test payment mechanisms, decision support tool development, rigid workflows and provider education were noted as barriers to the PGx implementation. A multidisciplinary implementation team and leadership support emerged as key facilitators. Furthermore, participants also suggested strategies to overcome or maintain these factors. Conclusion: Assessing real-world implementation perceptions and suggested strategies from a range of implementation contributors facilitates a more comprehensive framework and best-practice guidelines for PGx implementation.
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Affiliation(s)
- Sarah A Shue
- VA HSR&D Center for Health Information & Communication, Roudebush VA Medical Center, Indianapolis, IN 46202, USA
| | - Elizabeth Rowe
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Lauren A Bell
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Teresa Damush
- VA HSR&D Center for Health Information & Communication, Roudebush VA Medical Center, Indianapolis, IN 46202, USA
- Division of General Internal Medicine & Geriatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Health Services Research, Regenstrief Institute, Indianapolis, IN 46202, USA
| | - Alexis DeLong
- Center for Health Services Research, Regenstrief Institute, Indianapolis, IN 46202, USA
| | - Tayler Gowan
- Center for Health Services Research, Regenstrief Institute, Indianapolis, IN 46202, USA
| | - Todd Skaar
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - David Haggstrom
- VA HSR&D Center for Health Information & Communication, Roudebush VA Medical Center, Indianapolis, IN 46202, USA
- Division of General Internal Medicine & Geriatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Health Services Research, Regenstrief Institute, Indianapolis, IN 46202, USA
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16
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Li B, Sangkuhl K, Whaley R, Woon M, Keat K, Whirl-Carrillo M, Ritchie MD, Klein TE. Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank. Am J Hum Genet 2023; 110:1628-1647. [PMID: 37757824 PMCID: PMC10577080 DOI: 10.1016/j.ajhg.2023.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Pharmacogenomics (PGx) is an integral part of precision medicine and contributes to the maximization of drug efficacy and reduction of adverse drug event risk. Accurate information on PGx allele frequencies improves the implementation of PGx. Nonetheless, curating such information from published allele data is time and resource intensive. The limited number of allelic variants in most studies leads to an underestimation of certain alleles. We applied the Pharmacogenomics Clinical Annotation Tool (PharmCAT) on an integrated 200K UK Biobank genetic dataset (N = 200,044). Based on PharmCAT results, we estimated PGx frequencies (alleles, diplotypes, phenotypes, and activity scores) for 17 pharmacogenes in five biogeographic groups: European, Central/South Asian, East Asian, Afro-Caribbean, and Sub-Saharan African. PGx frequencies were distinct for each biogeographic group. Even biogeographic groups with similar proportions of phenotypes were driven by different sets of dominant PGx alleles. PharmCAT also identified "no-function" alleles that were rare or seldom tested in certain groups by previous studies, e.g., SLCO1B1∗31 in the Afro-Caribbean (3.0%) and Sub-Saharan African (3.9%) groups. Estimated PGx frequencies are disseminated via the PharmGKB (The Pharmacogenomics Knowledgebase: www.pharmgkb.org). We demonstrate that genetic biobanks such as the UK Biobank are a robust resource for estimating PGx frequencies. Improving our understanding of PGx allele and phenotype frequencies provides guidance for future PGx studies and clinical genetic test panel design, and better serves individuals from wider biogeographic backgrounds.
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Affiliation(s)
- Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ryan Whaley
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Mark Woon
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Karl Keat
- Genomics and Computational Biology PhD Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Genetics (by courtesy), Stanford University, Stanford, CA 94305, USA; Department of Medicine (BMIR), Stanford University, Stanford, CA 94305, USA.
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17
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Ramsey LB, Prows CA, Chidambaran V, Sadhasivam S, Quinn CT, Teusink-Cross A, Tang Girdwood S, Dawson DB, Vinks AA, Glauser TA. Implementation of CYP2D6-guided opioid therapy at Cincinnati Children's Hospital Medical Center. Am J Health Syst Pharm 2023; 80:852-859. [PMID: 36715063 PMCID: PMC11004919 DOI: 10.1093/ajhp/zxad025] [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: 01/21/2023] [Indexed: 01/31/2023] Open
Abstract
PURPOSE We describe the implementation of CYP2D6-focused pharmacogenetic testing to guide opioid prescribing in a quaternary care, nonprofit pediatric academic medical center. SUMMARY Children are often prescribed oral opioids after surgeries, for cancer pain, and occasionally for chronic pain. In 2004, Cincinnati Children's Hospital Medical Center implemented pharmacogenetic testing for CYP2D6 metabolism phenotype to inform codeine prescribing. The test and reports were updated to align with changes over time in the testing platform, the interpretation of genotype to phenotype, the electronic health record, and Food and Drug Administration (FDA) guidance. The use of the test increased when a research project required testing and decreased as prescribing of oxycodone increased due to FDA warnings about codeine. Education about the opioid-focused pharmacogenetic test was provided to prescribers (eg, the pain and sickle cell teams) as well as patients and families. Education and electronic health record capability increased provider compliance with genotype-guided postsurgical prescribing of oxycodone, although there was a perceived lack of utility for oxycodone prescribing. CONCLUSION The implementation of pharmacogenetic testing to inform opioid prescribing for children has evolved with accumulating evidence and guidelines, requiring changes in reporting of results and recommendations.
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Affiliation(s)
- Laura B Ramsey
- Department of Pediatrics, Division of Clinical Pharmacology and Division of Research in Patient Services, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Cynthia A Prows
- Division of Human Genetics and Division of Patient Services, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Vidya Chidambaran
- Department of Anesthesiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Senthilkumar Sadhasivam
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Charles T Quinn
- Department of Pediatrics and Division of Hematology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Ashley Teusink-Cross
- Division of Pharmacy, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Sonya Tang Girdwood
- Department of Pediatrics, Division of Clinical Pharmacology; and Division of Hospital Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - D Brian Dawson
- Department of Pediatrics and Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Alexander A Vinks
- Department of Pediatrics, Division of Clinical Pharmacology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Tracy A Glauser
- Department of Pediatrics, Division of Neurology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA
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18
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Smith DM, Wake DT, Dunnenberger HM. Pharmacogenomic Clinical Decision Support: A Scoping Review. Clin Pharmacol Ther 2023; 113:803-815. [PMID: 35838358 DOI: 10.1002/cpt.2711] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/10/2022] [Indexed: 11/06/2022]
Abstract
Clinical decision support (CDS) is often cited as an essential part of pharmacogenomics (PGx) implementations. A multitude of strategies are available; however, it is unclear which strategies are effective and which metrics are used to quantify clinical utility. The objective of this scoping review was to aggregate previous studies into a cohesive depiction of the current state of PGx CDS implementations and identify areas for future research on PGx CDS. Articles were included if they (i) described electronic CDS tools for PGx and (ii) reported metrics related to PGx CDS. Twenty of 3,449 articles were included and provided data on PGx CDS metrics from 15 institutions, with 93% of programs located at academic medical centers. The most common tools in CDS implementations were interruptive post-test alerts. Metrics for clinical response and alert response ranged from 12-73% and 21-98%, respectively. Few data were found on changes in metrics over time and measures that drove the evolution of CDS systems. Relatively few data were available regarding support of optimal approaches for PGx CDS. Post-test alerts were the most widely studied approach, and their effectiveness varied greatly. Further research on the usability, effectiveness, and optimization of CDS tools is needed.
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Affiliation(s)
- D Max Smith
- MedStar Health, Columbia, Maryland, USA.,Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Dyson T Wake
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
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19
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Arnold CG, Sonn B, Meyers FJ, Vest A, Puls R, Zirkler E, Edelmann M, Brooks IM, Monte AA. Accessing and utilizing clinical and genomic data from an electronic health record data warehouse. TRANSLATIONAL MEDICINE COMMUNICATIONS 2023; 8:7. [PMID: 38223535 PMCID: PMC10786622 DOI: 10.1186/s41231-023-00140-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/20/2023] [Indexed: 01/16/2024]
Abstract
Electronic health records (EHRs) and linked biobanks have tremendous potential to advance biomedical research and ultimately improve the health of future generations. Repurposing EHR data for research is not without challenges, however. In this paper, we describe the processes and considerations necessary to successfully access and utilize a data warehouse for research. Although imperfect, data warehouses are a powerful tool for harnessing a large amount of data to phenotype disease. They will have increasing relevance and applications in clinical research with growing sophistication in processes for EHR data abstraction, biobank integration, and cross-institutional linkage.
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Affiliation(s)
- Cosby G. Arnold
- Department of Emergency Medicine, School of Medicine, University of California, Davis, 4150 V Street #2100, Sacramento, CA 95817, USA
| | - Brandon Sonn
- Department of Emergency Medicine, University of Colorado Denver-Anschutz Medical Center, University of Colorado School of Medicine, Mail Stop B-215, 12401 East 17th Avenue, Aurora, CO 80045, USA
| | - Frederick J. Meyers
- Department of Internal Medicine, University of California, Davis, School of Medicine, 4150 V Street #3100, Sacramento, CA 95817, USA
| | - Alexis Vest
- Department of Emergency Medicine, University of Colorado Denver-Anschutz Medical Center, University of Colorado School of Medicine, Mail Stop B-215, 12401 East 17th Avenue, Aurora, CO 80045, USA
| | - Richie Puls
- Department of Emergency Medicine, University of Colorado Denver-Anschutz Medical Center, University of Colorado School of Medicine, Mail Stop B-215, 12401 East 17th Avenue, Aurora, CO 80045, USA
| | - Estelle Zirkler
- Department of Biomedical Informatics, University of Colorado School of Medicine, Anschutz Health Sciences Building, 1890 N. Revere Court, Mailstop F600, Aurora, CO 80045, USA
| | - Michelle Edelmann
- Department of Biomedical Informatics, University of Colorado School of Medicine, Anschutz Health Sciences Building, 1890 N. Revere Court, Mailstop F600, Aurora, CO 80045, USA
| | - Ian M. Brooks
- Department of Biomedical Informatics, University of Colorado School of Medicine, Anschutz Health Sciences Building, 1890 N. Revere Court, Mailstop F600, Aurora, CO 80045, USA
| | - Andrew A. Monte
- Department of Emergency Medicine, School of Medicine, University of California, Davis, 4150 V Street #2100, Sacramento, CA 95817, USA
- Rocky Mountain Poison & Drug Center, Denver Health and Hospital Authority, 1391 Speer Blvd Unit 600, Denver, CO 80204, USA
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20
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Obeng AO, Scott SA, Kaszemacher T, Ellis SB, Mejia A, Gomez A, Nadukuru R, Abul-Husn NS, Vega A, Waite E, Gottesman O, Cho J, Bottinger EP. Prescriber Adoption of SLCO1B1 Genotype-Guided Simvastatin Clinical Decision Support in a Clinical Pharmacogenetics Program. Clin Pharmacol Ther 2023; 113:321-327. [PMID: 36372942 DOI: 10.1002/cpt.2773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/08/2022] [Indexed: 11/15/2022]
Abstract
Pharmacogenetic implementation programs are increasingly feasible due to the availability of clinical guidelines for implementation research. The utilization of these resources has been reported with selected drug-gene pairs; however, little is known about how prescribers respond to pharmacogenetic recommendations for statin therapy. We prospectively assessed prescriber interaction with point-of-care clinical decision support (CDS) to guide simvastatin therapy for a diverse cohort of primary care patients enrolled in a clinical pharmacogenetics program. Of the 1,639 preemptively genotyped patients, 298 (18.2%) had an intermediate function (IF) OATP1B1 phenotype and 25 (1.53%) had a poor function (PF) phenotype, predicted by a common single nucleotide variant in the SLCO1B1 gene (c.521T>C; rs4149056). Clinicians were presented with CDS when simvastatin was prescribed for patients with IF or PF through the electronic health record. Importantly, 64.2% of the CDS deployed at the point-of-care was accepted by the prescribers and resulted in prescription changes. Statin intensity was found to significantly influence prescriber adoption of the pharmacogenetic-guided CDS, whereas patient gender or race, prescriber type, or pharmacogenetic training status did not significantly influence adoption. This study demonstrates that primary care providers readily adopt pharmacogenetic information to guide statin therapy for the majority of patients with preemptive genotype data.
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Affiliation(s)
- Aniwaa Owusu Obeng
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Pharmacy Department, The Mount Sinai Hospital, New York, New York, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stuart A Scott
- Department of Pathology, Stanford University, Stanford, California, USA.,Clinical Genomics Laboratory, Stanford Health Care, Palo Alto, California, USA
| | - Tom Kaszemacher
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen B Ellis
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Mejia
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alanna Gomez
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Rajiv Nadukuru
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,23andMe Inc., Sunnyvale, California, USA
| | - Aida Vega
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Mount Sinai Faculty Practice Associates, Primary Care Program, The Mount Sinai Health system, New York, New York, USA
| | - Eva Waite
- Mount Sinai Faculty Practice Associates, Primary Care Program, The Mount Sinai Health system, New York, New York, USA
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Empirico Inc., San Diego, California, USA
| | - Judy Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erwin P Bottinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
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21
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Abstract
Antiplatelet therapy is used in the treatment of patients with acute coronary syndromes, stroke, and those undergoing percutaneous coronary intervention. Clopidogrel is the most widely used antiplatelet P2Y12 inhibitor in clinical practice. Genetic variation in CYP2C19 may influence its enzymatic activity, resulting in individuals who are carriers of loss-of-function CYP2C19 alleles and thus have reduced active clopidogrel metabolites, high on-treatment platelet reactivity, and increased ischemic risk. Prospective studies have examined the utility of CYP2C19 genetic testing to guide antiplatelet therapy, and more recently published meta-analyses suggest that pharmacogenetics represents a key treatment strategy to individualize antiplatelet therapy. Rapid genetic tests, including bedside genotyping platforms that are validated and have high reproducibility, are available to guide selection of P2Y12 inhibitors in clinical practice. The aim of this review is to provide an overview of the background and rationale for the role of a guided antiplatelet approach to enhance patient care.
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Affiliation(s)
- Matteo Castrichini
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA;
| | - Jasmine A Luzum
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
| | - Naveen Pereira
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA;
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22
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Bai H, Zhang X, Bush WS. Pharmacogenomic and Statistical Analysis. Methods Mol Biol 2023; 2629:305-330. [PMID: 36929083 DOI: 10.1007/978-1-0716-2986-4_14] [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: 03/18/2023]
Abstract
Genetic variants can alter response to drugs and other therapeutic interventions. The study of this phenomenon, called pharmacogenomics, is similar in many ways to other types of genetic studies but has distinct methodological and statistical considerations. Genetic variants involved in the processing of exogenous compounds exhibit great diversity and complexity, and the phenotypes studied in pharmacogenomics are also more complex than typical genetic studies. In this chapter, we review basic concepts in pharmacogenomic study designs, data generation techniques, statistical analysis approaches, and commonly used methods and briefly discuss the ultimate translation of findings to clinical care.
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Affiliation(s)
- Haimeng Bai
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Xueyi Zhang
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
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23
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Public Attitudes toward Pharmacogenomic Testing and Establishing a Statewide Pharmacogenomics Database in the State of Minnesota. J Pers Med 2022; 12:jpm12101615. [PMID: 36294754 PMCID: PMC9604616 DOI: 10.3390/jpm12101615] [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: 08/14/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 11/07/2022] Open
Abstract
The clinical adoption and implementation of pharmacogenomics (PGx) beyond academic medical centers remains slow, restricting the general population from benefitting from this important component of personalized medicine. As an initial step in the statewide initiative of PGx implementation in Minnesota, we engaged community members and assessed attitudes towards PGx testing and acceptability of establishing a secure statewide PGx database for clinical and research use among Minnesota residents. Data was collected from 808 adult attendees at the 2021 Minnesota State Fair through an electronic survey. Eighty-four percent of respondents felt comfortable getting a PGx test for clinical care. Most respondents trusted health professionals (78.2%) and researchers (73.0%) to keep their PGx data private. The majority expressed their support and interest in participating in a statewide PGx database for clinical and research use (64–72%). Higher acceptability of the statewide PGx database was associated with younger age, higher education, higher health literacy, having health insurance, and prior genetic testing. The study sample representing Minnesota residents expressed high acceptability of receiving PGx testing and willingness to participate in PGx data sharing for clinical and research use. Community support and engagement are needed to advance PGx implementation and research on the state scale.
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24
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Harnessing Electronic Medical Records in Cardiovascular Clinical Practice and Research. J Cardiovasc Transl Res 2022:10.1007/s12265-022-10313-1. [DOI: 10.1007/s12265-022-10313-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/29/2022] [Indexed: 10/14/2022]
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25
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Kusic D, Heil J, Zajic S, Brangan A, Dairo O, Smith G, Morales-Scheihing D, Buono RJ, Ferraro TN, Haroz R, Salzman M, Baston K, Bodofsky E, Sabia M, Resch A, Scheinfeldt LB. Patient Perceptions and Potential Utility of Pharmacogenetic Testing in Chronic Pain Management and Opioid Use Disorder in the Camden Opioid Research Initiative. Pharmaceutics 2022; 14:pharmaceutics14091863. [PMID: 36145611 PMCID: PMC9505214 DOI: 10.3390/pharmaceutics14091863] [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: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Pharmacogenetics (PGx) has the potential to improve opioid medication management. Here, we present patient perception data, pharmacogenetic data and medication management trends in patients with chronic pain (arm 1) and opioid use disorder (arm 2) treated at Cooper University Health Care in Camden City, NJ. Our results demonstrate that the majority of patients in both arms of the study (55% and 65%, respectively) are open to pharmacogenetic testing, and most (66% and 69%, respectively) believe that genetic testing has the potential to improve their medical care. Our results further support the potential for CYP2D6 PGx testing to inform chronic pain medication management for poor metabolizers (PMs) and ultrarapid metabolizers (UMs). Future efforts to implement PGx testing in chronic pain management, however, must address patient concerns about genetic test result access and genetic discrimination.
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Affiliation(s)
- Dara Kusic
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | - Jessica Heil
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
- Cooper University Health Care, Camden, NJ 08103, USA
| | - Stefan Zajic
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
- GSK, Collegeville, PA 19426, USA
| | - Andrew Brangan
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
- Geisinger, Danville, PA 17822, USA
| | - Oluseun Dairo
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
- Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Gretchen Smith
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | | | - Russell J. Buono
- Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | | | - Rachel Haroz
- Cooper University Health Care, Camden, NJ 08103, USA
- Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Matthew Salzman
- Cooper University Health Care, Camden, NJ 08103, USA
- Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Kaitlan Baston
- Cooper University Health Care, Camden, NJ 08103, USA
- Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Elliot Bodofsky
- Cooper University Health Care, Camden, NJ 08103, USA
- Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Michael Sabia
- Cooper University Health Care, Camden, NJ 08103, USA
- Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Alissa Resch
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
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26
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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: 17] [Impact Index Per Article: 8.5] [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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27
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McDermott JH, Wright S, Sharma V, Newman WG, Payne K, Wilson P. Characterizing pharmacogenetic programs using the consolidated framework for implementation research: A structured scoping review. Front Med (Lausanne) 2022; 9:945352. [PMID: 36059837 PMCID: PMC9433561 DOI: 10.3389/fmed.2022.945352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/29/2022] [Indexed: 12/11/2022] Open
Abstract
Several healthcare organizations have developed pre-emptive pharmacogenetic testing programs, where testing is undertaken prior to the prescription of a medicine. This review characterizes the barriers and facilitators which influenced the development of these programs. A bidirectional citation searching strategy identified relevant publications before a standardized data extraction approach was applied. Publications were grouped by program and data synthesis was undertaken using the Consolidated Framework for Implementation Research (CFIR). 104 publications were identified from 40 programs and 4 multi-center initiatives. 26 (66%) of the programs were based in the United States and 95% in high-income countries. The programs were heterogeneous in their design and scale. The Characteristics of the Intervention, Inner Setting, and Process domains were referenced by 92.5, 80, and 77.5% of programs, respectively. A positive institutional culture, leadership engagement, engaging stakeholders, and the use of clinical champions were frequently described as facilitators to implementation. Clinician self-efficacy, lack of stakeholder knowledge, and the cost of the intervention were commonly cited barriers. Despite variation between the programs, there were several similarities in approach which could be categorized via the CFIR. These form a resource for organizations planning the development of pharmacogenetic programs, highlighting key facilitators which can be leveraged to promote successful implementation.
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Affiliation(s)
- John H. McDermott
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
- *Correspondence: John H. McDermott,
| | - Stuart Wright
- Division of Population Health, Manchester Centre for Health Economics, Health Services Research and Primary Care, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
| | - Videha Sharma
- Division of Informatics, Centre for Health Informatics, Imaging and Data Science, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution, Infection and Genomics, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - Katherine Payne
- Division of Population Health, Manchester Centre for Health Economics, Health Services Research and Primary Care, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
| | - Paul Wilson
- Division of Population Health, Centre for Primary Care and Health Services Research, Health Services Research and Primary Care, School of Health Sciences, The University of Manchester, Manchester, United Kingdom
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28
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Varughese LA, Bhupathiraju M, Hoffecker G, Terek S, Harr M, Hakonarson H, Cambareri C, Marini J, Landgraf J, Chen J, Kanter G, Lau-Min KS, Massa RC, Damjanov N, Reddy NJ, Oyer RA, Teitelbaum UR, Tuteja S. Implementing Pharmacogenetic Testing in Gastrointestinal Cancers (IMPACT-GI): Study Protocol for a Pragmatic Implementation Trial for Establishing DPYD and UGT1A1 Screening to Guide Chemotherapy Dosing. Front Oncol 2022; 12:859846. [PMID: 35865463 PMCID: PMC9295185 DOI: 10.3389/fonc.2022.859846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background Fluoropyrimidines (fluorouracil [5-FU], capecitabine) and irinotecan are commonly prescribed chemotherapy agents for gastrointestinal (GI) malignancies. Pharmacogenetic (PGx) testing for germline DPYD and UGT1A1 variants associated with reduced enzyme activity holds the potential to identify patients at high risk for severe chemotherapy-induced toxicity. Slow adoption of PGx testing in routine clinical care is due to implementation barriers, including long test turnaround times, lack of integration in the electronic health record (EHR), and ambiguity in test cost coverage. We sought to establish PGx testing in our health system following the Exploration, Preparation, Implementation, Sustainment (EPIS) framework as a guide. Our implementation study aims to address barriers to PGx testing. Methods The Implementing Pharmacogenetic Testing in Gastrointestinal Cancers (IMPACT-GI) study is a non-randomized, pragmatic, open-label implementation study at three sites within a major academic health system. Eligible patients with a GI malignancy indicated for treatment with 5-FU, capecitabine, or irinotecan will undergo PGx testing prior to chemotherapy initiation. Specimens will be sent to an academic clinical laboratory followed by return of results in the EHR with appropriate clinical decision support for the care team. We hypothesize that the availability of a rapid turnaround PGx test with specific dosing recommendations will increase PGx test utilization to guide pharmacotherapy decisions and improve patient safety outcomes. Primary implementation endpoints are feasibility, fidelity, and penetrance. Exploratory analyses for clinical effectiveness of genotyping will include assessing grade ≥3 treatment-related toxicity using available clinical data, patient-reported outcomes, and quality of life measures. Conclusion We describe the formative work conducted to prepare our health system for DPYD and UGT1A1 testing. Our prospective implementation study will evaluate the clinical implementation of this testing program and create the infrastructure necessary to ensure sustainability of PGx testing in our health system. The results of this study may help other institutions interested in implementing PGx testing in oncology care. Clinical Trial Registration https://clinicaltrials.gov/ct2/show/NCT04736472, identifier [NCT04736472].
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Affiliation(s)
- Lisa A. Varughese
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Madhuri Bhupathiraju
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Glenda Hoffecker
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Shannon Terek
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Margaret Harr
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Christine Cambareri
- Department of Pharmacy, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Jessica Marini
- Department of Pharmacy, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Jeffrey Landgraf
- Information Services Applications, Penn Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jinbo Chen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Genevieve Kanter
- Division of Medical Ethics and Health Policy, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kelsey S. Lau-Min
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ryan C. Massa
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nevena Damjanov
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nandi J. Reddy
- Ann B. Barshinger Cancer Institute, Lancaster General Health, Penn Medicine, Lancaster, PA, United States
| | - Randall A. Oyer
- Ann B. Barshinger Cancer Institute, Lancaster General Health, Penn Medicine, Lancaster, PA, United States
| | - Ursina R. Teitelbaum
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sony Tuteja
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Sony Tuteja,
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29
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Auwerx C, Sadler MC, Reymond A, Kutalik Z. From pharmacogenetics to pharmaco-omics: Milestones and future directions. HGG ADVANCES 2022; 3:100100. [PMID: 35373152 PMCID: PMC8971318 DOI: 10.1016/j.xhgg.2022.100100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The origins of pharmacogenetics date back to the 1950s, when it was established that inter-individual differences in drug response are partially determined by genetic factors. Since then, pharmacogenetics has grown into its own field, motivated by the translation of identified gene-drug interactions into therapeutic applications. Despite numerous challenges ahead, our understanding of the human pharmacogenetic landscape has greatly improved thanks to the integration of tools originating from disciplines as diverse as biochemistry, molecular biology, statistics, and computer sciences. In this review, we discuss past, present, and future developments of pharmacogenetics methodology, focusing on three milestones: how early research established the genetic basis of drug responses, how technological progress made it possible to assess the full extent of pharmacological variants, and how multi-dimensional omics datasets can improve the identification, functional validation, and mechanistic understanding of the interplay between genes and drugs. We outline novel strategies to repurpose and integrate molecular and clinical data originating from biobanks to gain insights analogous to those obtained from randomized controlled trials. Emphasizing the importance of increased diversity, we envision future directions for the field that should pave the way to the clinical implementation of pharmacogenetics.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Marie C. Sadler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
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30
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Nadkarni GN, Fei K, Ramos MA, Hauser D, Bagiella E, Ellis SB, Sanderson S, Scott SA, Sabin T, Madden E, Cooper R, Pollak M, Calman N, Bottinger EP, Horowitz CR. Effects of Testing and Disclosing Ancestry-Specific Genetic Risk for Kidney Failure on Patients and Health Care Professionals: A Randomized Clinical Trial. JAMA Netw Open 2022; 5:e221048. [PMID: 35244702 PMCID: PMC8897752 DOI: 10.1001/jamanetworkopen.2022.1048] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
IMPORTANCE Risk variants in the apolipoprotein L1 (APOL1 [OMIM 603743]) gene on chromosome 22 are common in individuals of West African ancestry and confer increased risk of kidney failure for people with African ancestry and hypertension. Whether disclosing APOL1 genetic testing results to patients of African ancestry and their clinicians affects blood pressure, kidney disease screening, or patient behaviors is unknown. OBJECTIVE To determine the effects of testing and disclosing APOL1 genetic results to patients of African ancestry with hypertension and their clinicians. DESIGN, SETTING, AND PARTICIPANTS This pragmatic randomized clinical trial randomly assigned 2050 adults of African ancestry with hypertension and without existing chronic kidney disease in 2 US health care systems from November 1, 2014, through November 28, 2016; the final date of follow-up was January 16, 2018. Patients were randomly assigned to undergo immediate (intervention) or delayed (waiting list control group) APOL1 testing in a 7:1 ratio. Statistical analysis was performed from May 1, 2018, to July 31, 2020. INTERVENTIONS Patients randomly assigned to the intervention group received APOL1 genetic testing results from trained staff; their clinicians received results through clinical decision support in electronic health records. Waiting list control patients received the results after their 12-month follow-up visit. MAIN OUTCOMES AND MEASURES Coprimary outcomes were the change in 3-month systolic blood pressure and 12-month urine kidney disease screening comparing intervention patients with high-risk APOL1 genotypes and those with low-risk APOL1 genotypes. Secondary outcomes compared these outcomes between intervention group patients with high-risk APOL1 genotypes and controls. Exploratory analyses included psychobehavioral factors. RESULTS Among 2050 randomly assigned patients (1360 women [66%]; mean [SD] age, 53 [10] years), the baseline mean (SD) systolic blood pressure was significantly higher in patients with high-risk APOL1 genotypes vs those with low-risk APOL1 genotypes and controls (137 [21] vs 134 [19] vs 133 [19] mm Hg; P = .003 for high-risk vs low-risk APOL1 genotypes; P = .001 for high-risk APOL1 genotypes vs controls). At 3 months, the mean (SD) change in systolic blood pressure was significantly greater in patients with high-risk APOL1 genotypes vs those with low-risk APOL1 genotypes (6 [18] vs 3 [18] mm Hg; P = .004) and controls (6 [18] vs 3 [19] mm Hg; P = .01). At 12 months, there was a 12% increase in urine kidney disease testing among patients with high-risk APOL1 genotypes (from 39 of 234 [17%] to 68 of 234 [29%]) vs a 6% increase among those with low-risk APOL1 genotypes (from 278 of 1561 [18%] to 377 of 1561 [24%]; P = .10) and a 7% increase among controls (from 33 of 255 [13%] to 50 of 255 [20%]; P = .01). In response to testing, patients with high-risk APOL1 genotypes reported more changes in lifestyle (a subjective measure that included better dietary and exercise habits; 129 of 218 [59%] vs 547 of 1468 [37%]; P < .001) and increased blood pressure medication use (21 of 218 [10%] vs 68 of 1468 [5%]; P = .005) vs those with low-risk APOL1 genotypes; 1631 of 1686 (97%) declared they would get tested again. CONCLUSIONS AND RELEVANCE In this randomized clinical trial, disclosing APOL1 genetic testing results to patients of African ancestry with hypertension and their clinicians was associated with a greater reduction in systolic blood pressure, increased kidney disease screening, and positive self-reported behavior changes in those with high-risk genotypes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02234063.
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Affiliation(s)
- Girish N. Nadkarni
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kezhen Fei
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michelle A. Ramos
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Emilia Bagiella
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stephen B. Ellis
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Saskia Sanderson
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stuart A. Scott
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, A Mount Sinai Venture, Stamford, Connecticut
| | - Tatiana Sabin
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ebony Madden
- National Human Genome Research Institute, Bethesda, Maryland
| | - Richard Cooper
- Department of Public Health Sciences, Loyola University Medical School, Maywood, Illinois
| | - Martin Pollak
- Division of Nephrology, Harvard Medical School, Boston, Massachusetts
| | - Neil Calman
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, New York
- Institute for Family Health, New York, New York
| | - Erwin P. Bottinger
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Digital Health Center, Hasso Plattner Institute, Potsdam, Germany
| | - Carol R. Horowitz
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Population Health Sciences and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, New York
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31
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Lee KH, Kang DY, Kim HH, Kim YJ, Kim HJ, Kim JH, Song EY, Yun J, Kang H. Reducing severe cutaneous adverse and type B adverse drug reactions using pre-stored human leukocyte antigen genotypes. Clin Transl Allergy 2022; 12:e12098. [PMID: 35070271 PMCID: PMC8760506 DOI: 10.1002/clt2.12098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/26/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Several type B adverse drug reactions (ADRs), especially severe cutaneous adverse reactions (SCARs), are associated with particular human leukocyte antigen (HLA) genotypes. However, pre-stored HLA information obtained from other clinical workups has not been used to prevent ADRs. We aimed to simulate the preemptive use of pre-stored HLA information in electronic medical records to evaluate whether this information can prevent ADRs. METHODS We analyzed the incidence and the risk of ADRs for selected HLA alleles (HLA-B*57:01, HLA-B*58:01, HLA-A*31:01, HLA-B*15:02, HLA-B*15:11, HLA-B*13:01, HLA-B*59:01, and HLA-A*32:01) and seven drugs (abacavir, allopurinol, carbamazepine, oxcarbazepine, dapsone, methazolamide, and vancomycin) using pre-stored HLA information of transplant patients based on the Pharmacogenomics Knowledge Base guidelines and experts' consensus. RESULTS Among 11,988 HLA-tested transplant patients, 4092 (34.1%) had high-risk HLA alleles, 4583 (38.2%) were prescribed risk drugs, and 580 (4.8%) experienced type B ADRs. Patients with HLA-B*58:01 had a significantly higher incidence of type B ADR and SCARs associated with allopurinol use than that of patients without HLA-B*58:01 (17.2% vs. 11.9%, odds ratio [OR] 1.53 [95% confidence interval {CI} 1.09-2.13], p = 0.001, 2.3% versus 0.3%, OR 7.13 [95% CI 2.19-22.69], p < 0.001). Higher risks of type B ADR and SCARs were observed in patients taking carbamazepine or oxcarbazepine if they had one of HLA-A*31:01, HLA-B*15:02, or HLA-B*15:11 alleles. Vancomycin and dapsone use in HLA-A*32:01 and HLA-B*13:01 carriers, respectively, showed trends toward increased risk of type B ADRs. CONCLUSION Utilization of pre-stored HLA data can prevent type B ADRs including SCARs by screening high-risk patients.
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Affiliation(s)
- Kye Hwa Lee
- Department of Information MedicineAsan Medical CenterSeoulSouth Korea
| | - Dong Yoon Kang
- Drug Safety CenterSeoul National University HospitalSeoulSouth Korea
| | - Hyun Hwa Kim
- Drug Safety CenterSeoul National University HospitalSeoulSouth Korea
| | - Yi Jun Kim
- Institute of Convergence MedicineEwha Womans University Mokdong HospitalSeoulSouth Korea
| | - Hyo Jung Kim
- Department of Digital HealthSamsung Advanced Institute for Health Science and TechnologySungkyunkwan UniversitySeoulSouth Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics and Systems Biomedical Informatics Research CenterDivision of Biomedical InformaticsSeoul National University College of MedicineSeoulSouth Korea
| | - Eun Young Song
- Department of Molecular Medicine and Biopharmaceutical SciencesGraduate School of Convergence Science and Technology and College of MedicineMedical Research CenterSeoul National UniversitySeoulSouth Korea
| | - James Yun
- Department of Immunology and RheumatologyNepean HospitalSydneyNew South WalesAustralia
- Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
| | - Hye‐Ryun Kang
- Drug Safety CenterSeoul National University HospitalSeoulSouth Korea
- Institute of Allergy and Clinical ImmunologySeoul National University Medical Research CenterSeoul National University College of MedicineSeoulSouth Korea
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32
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David SP, Singh L, Pruitt J, Hensing A, Hulick P, Meltzer DO, O’Donnell PH, Dunnenberger HM. The Contribution of Pharmacogenetic Drug Interactions to 90-Day Hospital Readmissions: Preliminary Results from a Real-World Healthcare System. J Pers Med 2021; 11:jpm11121242. [PMID: 34945714 PMCID: PMC8705172 DOI: 10.3390/jpm11121242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 01/09/2023] Open
Abstract
Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines exist for many medications commonly prescribed prior to hospital discharge, yet there are limited data regarding the contribution of gene-x-drug interactions to hospital readmissions. The present study evaluated the relationship between prescription of CPIC medications prescribed within 30 days of hospital admission and 90-day hospital readmission from 2010 to 2020 in a study population (N = 10,104) who underwent sequencing with a 14-gene pharmacogenetic panel. The presence of at least one pharmacogenetic indicator for a medication prescribed within 30 days of hospital admission was considered a gene-x-drug interaction. Multivariable logistic regression analyzed the association between one or more gene-x-drug interactions with 90-day readmission. There were 2211/2354 (93.9%) admitted patients who were prescribed at least one CPIC medication. Univariate analyses indicated that the presence of at least one identified gene-x-drug interaction increased the risk of 90-day readmission by more than 40% (OR = 1.42, 95% confidence interval (CI) 1.09–1.84) (p = 0.01). A multivariable model adjusting for age, race, sex, employment status, body mass index, and medical conditions slightly attenuated the effect (OR = 1.32, 95% CI 1.02–1.73) (p = 0.04). Our results suggest that the presence of one or more CPIC gene-x-drug interactions increases the risk of 90-day hospital readmission, even after adjustment for demographic and clinical risk factors.
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Affiliation(s)
- Sean P. David
- Department of Family Medicine, NorthShore University Health System, Evanston, IL 60201, USA;
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA; (P.H.); (D.O.M.); (P.H.O.)
- Correspondence:
| | - Lavisha Singh
- Department of Statistics, NorthShore University Health System, Evanston, IL 60201, USA;
| | - Jaclyn Pruitt
- Department of Surgery, NorthShore University Health System, Evanston, IL 60201, USA;
- Outcomes Research Network, NorthShore University Health System, Evanston, IL 60201, USA;
| | - Andrew Hensing
- Outcomes Research Network, NorthShore University Health System, Evanston, IL 60201, USA;
| | - Peter Hulick
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA; (P.H.); (D.O.M.); (P.H.O.)
- Center for Personalized Medicine, NorthShore University Health System, Evanston, IL 60201, USA
| | - David O. Meltzer
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA; (P.H.); (D.O.M.); (P.H.O.)
| | - Peter H. O’Donnell
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA; (P.H.); (D.O.M.); (P.H.O.)
| | - Henry M. Dunnenberger
- Department of Family Medicine, NorthShore University Health System, Evanston, IL 60201, USA;
- Outcomes Research Network, NorthShore University Health System, Evanston, IL 60201, USA;
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33
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Clinical implementation of drug metabolizing gene-based therapeutic interventions worldwide. Hum Genet 2021; 141:1137-1157. [PMID: 34599365 DOI: 10.1007/s00439-021-02369-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/09/2021] [Indexed: 02/05/2023]
Abstract
Over the last few years, the field of pharmacogenomics has gained considerable momentum. The advances of new genomics and bioinformatics technologies propelled pharmacogenomics towards its implementation in the clinical setting. Since 2007, and especially the last-5 years, many studies have focused on the clinical implementation of pharmacogenomics while identifying obstacles and proposed strategies and approaches for overcoming them in the real world of primary care as well as outpatients and inpatients clinics. Here, we outline the recent pharmacogenomics clinical implementation projects and provide details of the study designs, including the most predominant and innovative, as well as clinical studies worldwide that focus on outpatients and inpatient clinics, and primary care. According to these studies, pharmacogenomics holds promise for improving patients' health in terms of efficacy and toxicity, as well as in their overall quality of life, while simultaneously can contribute to the minimization of healthcare expenditure.
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Lipschultz E, Danahey K, Truong TM, Schierer E, Volchenboum SL, Ratain MJ, O’Donnell PH. Creation of a pharmacogenomics patient portal complementary to an existing institutional provider-facing clinical decision support system. JAMIA Open 2021; 4:ooab067. [PMID: 34458686 PMCID: PMC8390782 DOI: 10.1093/jamiaopen/ooab067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/29/2021] [Indexed: 11/12/2022] Open
Abstract
Background Applied pharmacogenomics presents opportunities for improving patient care through precision medicine, particularly when paired with appropriate clinical decision support (CDS). However, a lack of patient resources for understanding pharmacogenomic test results may hinder shared decision-making and patient confidence in treatment. We sought to create a patient pharmacogenomics education and results delivery platform complementary to a CDS system to facilitate further research on the relevance of patient education to pharmacogenomics. Methods We conceptualized a model that extended the data access layer of an existing institutional CDS tool to allow for the pairing of decision supports offered to providers with patient-oriented summaries at the same level of phenotypic specificity. We built a two-part system consisting of a secure portal for patient use and an administrative dashboard for patient summary creation. The system was built in an ASP.NET and AngularJS architecture, and all data was housed in a HIPAA-compliant data center, with PHI secure in transit and at rest. Results The YourPGx Patient Portal was deployed on the institutional network in June 2019. Fifty-eight unique patient portal summaries have been written so far, which can provide over 4500 results modules to the pilot population of 544 patients. Patient behavior on the portal is being logged for further research. Conclusions To our knowledge, this is the first automated system designed and deployed to provide detailed, personalized patient pharmacogenomics education complementary to a clinical decision support system. Future work will expand upon this system to allow for telemedicine and patient notification of new or updated results.
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Affiliation(s)
- Elizabeth Lipschultz
- Center for Research Informatics, University of Chicago, Chicago, Illinois, USA
- Center for Personalized Therapeutics, University of Chicago, Chicago, Illinois, USA
| | - Keith Danahey
- Center for Research Informatics, University of Chicago, Chicago, Illinois, USA
- Center for Personalized Therapeutics, University of Chicago, Chicago, Illinois, USA
| | - Tien M Truong
- Center for Personalized Therapeutics, University of Chicago, Chicago, Illinois, USA
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Emily Schierer
- Center for Personalized Therapeutics, University of Chicago, Chicago, Illinois, USA
| | | | - Mark J Ratain
- Center for Personalized Therapeutics, University of Chicago, Chicago, Illinois, USA
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Peter H O’Donnell
- Center for Personalized Therapeutics, University of Chicago, Chicago, Illinois, USA
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Corresponding Author: Peter H. O’Donnell, M.D., University of Chicago, 5841 S. Maryland Avenue, MC 2115, Chicago, IL 60637-1447, USA ()
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Wake DT, Smith DM, Kazi S, Dunnenberger HM. Pharmacogenomic Clinical Decision Support: A Review, How-to Guide, and Future Vision. Clin Pharmacol Ther 2021; 112:44-57. [PMID: 34365648 PMCID: PMC9291515 DOI: 10.1002/cpt.2387] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/28/2021] [Indexed: 02/06/2023]
Abstract
Clinical decision support (CDS) is an essential part of any pharmacogenomics (PGx) implementation. Increasingly, institutions have implemented CDS tools in the clinical setting to bring PGx data into patient care, and several have published their experiences with these implementations. However, barriers remain that limit the ability of some programs to create CDS tools to fit their PGx needs. Therefore, the purpose of this review is to summarize the types, functions, and limitations of PGx CDS currently in practice. Then, we provide an approachable step‐by‐step how‐to guide with a case example to help implementers bring PGx to the front lines of care regardless of their setting. Particular focus is paid to the five “rights” of CDS as a core around designing PGx CDS tools. Finally, we conclude with a discussion of opportunities and areas of growth for PGx CDS.
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Affiliation(s)
- Dyson T Wake
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - D Max Smith
- MedStar Health, Columbia, Maryland, USA.,Georgetown University Medical Center, Washington, DC, USA
| | - Sadaf Kazi
- Georgetown University Medical Center, Washington, DC, USA.,National Center for Human Factors in Healthcare, MedStar Health Research Institute Washington, Washington, DC, USA
| | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
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Taylor CO, Rasmussen LV, Rasmussen-Torvik LJ, Prows CA, Dorr DA, Samal L, Aronson S. Facilitating Genetics Aware Clinical Decision Support: Putting the eMERGE Infrastructure into Practice. ACI OPEN 2021; 5:e54-e58. [PMID: 37920232 PMCID: PMC10621326 DOI: 10.1055/s-0041-1729981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
This editorial provides context for a series of published case reports in ACI Open by summarizing activities and outputs of joint electronic health record integration and pharmacogenomics workgroups in the NIH-funded electronic Medical Records and Genomics (eMERGE) Network. A case report is a useful tool to describe the range of capabilities that an IT infrastructure or a particular technology must support. The activities we describe have informed infrastructure requirements used during eMERGE phase III, provided a venue to share experiences and ask questions among other eMERGE sites, summarized potential hazards that might be encountered for specific clinical decision support (CDS) implementation scenarios, and provided a simple framework that captured progress toward implementing CDS at eMERGE sites in a consistent format.
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Affiliation(s)
- Casey Overby Taylor
- Departments of Medicine and Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
- Geisinger Health System, Genomic Medicine Institute, Danville, Pennsylvania, United States
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois, United States
| | | | - Cynthia A Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - David A Dorr
- Departments of Medical Informatics and Clinical Epidemiology and Medicine, Oregon Health & Science University, Portland, Oregon, United States
| | - Lipika Samal
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Samuel Aronson
- Partners Personalized Medicine, Partners HealthCare, Cambridge, Massachusetts, United States
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37
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Luzum JA, Petry N, Taylor AK, Van Driest SL, Dunnenberger HM, Cavallari LH. Moving Pharmacogenetics Into Practice: It's All About the Evidence! Clin Pharmacol Ther 2021; 110:649-661. [PMID: 34101169 DOI: 10.1002/cpt.2327] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022]
Abstract
The evidence for pharmacogenetics has grown rapidly in recent decades. However, the strength of evidence required for the clinical implementation of pharmacogenetics is highly debated. Therefore, the purpose of this review is to summarize different perspectives on the evidence required for the clinical implementation of pharmacogenetics. First, we present two patient cases that demonstrate how knowledge of pharmacogenetic evidence affected their care. Then we summarize resources that curate pharmacogenetic evidence, types of evidence (with an emphasis on randomized controlled trials [RCT]) and their limitations, and different perspectives from implementers, clinicians, and patients. We compare pharmacogenetics to a historical example (i.e., the evidence required for the clinical implementation of pharmacokinetics/therapeutic drug monitoring), and we provide future perspectives on the evidence for pharmacogenetic panels and the need for more education in addition to evidence. Although there are differences in the interpretation of pharmacogenetic evidence across resources, efforts for standardization are underway. Survey data illustrate the value of pharmacogenetic testing from the patient perspective, with their providers seen as key to ensuring maximum benefit from test results. However, clinicians and practice guidelines from medical societies often rely on RCT data to guide treatment decisions, which are not always feasible or ethical in pharmacogenetics. Thus, recognition of other types of evidence to support pharmacogenetic implementation is needed. Among pharmacogenetic implementers, consistent evidence of pharmacogenetic associations is deemed most critical. Ultimately, moving pharmacogenetics into practice will require consideration of multiple stakeholder perspectives, keeping particularly attuned to the voice of the ultimate stakeholder-the patient.
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Affiliation(s)
- Jasmine A Luzum
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Natasha Petry
- Department of Pharmacy Practice, College of Health Professions, North Dakota State University, Fargo, North Dakota, USA.,Sanford Imagenetics, Sioux Falls, South Dakota, USA
| | - Annette K Taylor
- Colorado Coagulation, Laboratory Corporation of America Holdings, Englewood, Colorado, USA
| | - Sara L Van Driest
- Departments of Pediatrics and Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
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38
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Wendt FR, Koller D, Pathak GA, Jacoby D, Miller EJ, Polimanti R. Biobank Scale Pharmacogenomics Informs the Genetic Underpinnings of Simvastatin Use. Clin Pharmacol Ther 2021; 110:777-785. [PMID: 33837531 DOI: 10.1002/cpt.2260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/01/2021] [Indexed: 12/31/2022]
Abstract
Studying drug-metabolizing enzymes, encoded by pharmacogenes, may inform biological mechanisms underlying the diseases for which a medication is prescribed. Until recently, pharmacogenes could not be studied at biobank scale. In 7,649 unrelated African-ancestry (AFR) and 326,214 unrelated European-ancestry (EUR) participants from the UK Biobank, we associated pharmacogene haplotypes from 50 genes with 265 (EUR) and 17 (AFR) medication use phenotypes using generalized linear models. In EUR, N-acetyltransferase 2 (NAT2) metabolizer phenotype and activity score were associated with simvastatin use. The dose of NAT2*1 was associated with simvastatin use when compared with NAT2*5 (the most common haplotype). This association was robust to effects of low-density lipoprotein cholesterol (LDL-C) concentration (NAT2*1 odds ratio (OR) = 1.07, 95% CI: 1.05-1.09, P = 1.14 × 10-8 ) and polygenic risk for LDL-C concentration (NAT2*1 OR = 1.09, 95% CI: 1.04-1.14, P = 2.26 × 10-4 ). Interactive effects between NAT2*1 and simvastatin use on LDL-C concentration (OR = 0.957, 95% CI: 0.916-0.998, P = 0.045) were replicated in the electronic Medical Records and Genomics Pharmacogenetic Sequencing Pilot (eMERGE-PGx) cohort (OR = 0.987, 95% CI: 0.976-0.998, P = 0.029). We used biobank-scale data to uncover and replicate an association between NAT2 locus variation and better response to statin therapy. Testing NAT2 alleles may be useful for making clinical decisions regarding the potential benefit (e.g., absolute risk reduction) in LDL-C concentration prior to statin treatment.
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Affiliation(s)
- Frank R Wendt
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Dora Koller
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Gita A Pathak
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Daniel Jacoby
- Section of Cardiovascular Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Edward J Miller
- Section of Cardiovascular Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Renato Polimanti
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
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Chan PA, Lewis KL, Biesecker BB, Erby LH, Fasaye GA, Epps S, Biesecker LG, Turbitt E. Preferences for and acceptability of receiving pharmacogenomic results by mail: A focus group study with a primarily African-American cohort. J Genet Couns 2021; 30:1582-1590. [PMID: 33876469 DOI: 10.1002/jgc4.1424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 01/12/2023]
Abstract
Although genetic counseling is traditionally done through in-person, one-on-one visits, workforce shortages call for efficient result return mechanisms. Studies have shown that telephone and in-person return of cancer genetic results are equivalent for patient outcomes. Few studies have been conducted with other modes, result types or racially diverse participants. This study explored participants' perspectives on receiving pharmacogenomic results by mail. Two experienced moderators facilitated six focus groups with 49 individuals who self-identified primarily as African-American and consented to participate in a genome sequencing cohort study. Participants were given a hypothetical pharmacogenomic result report (positive for c.521T>C in SLCO1B1). An accompanying letter explained that the result was associated with statin intolerance along with a recommendation to share it with one's doctor and immediate relatives. Participants reacted to the idea of receiving this type of result by mail, discussing whether the letter's information was sufficient and what they predicted they would do with the result. Two researchers coded the focus group transcripts and identified themes. Many participants thought that it was appropriate to receive the result through the mail, but some suggested a phone call alerting the recipient to the letter. Others emphasized that although a letter was acceptable for disclosing pharmacogenomic results, it would be insufficient for what they perceived as life-threatening results. Most participants found the content sufficient. Some participants suggested resources about statin intolerance and warning signs be added. Most claimed they would share the result with their doctor, yet few participants offered they would share the result with their relatives. This exploratory study advances the evidence that African-American research participants are receptive to return of certain genetic results by approaches that do not involve direct contact with a genetic counselor and intend to share results with providers. ClinSeq: A Large-Scale Medical Sequencing Clinical Research Pilot Study (NCT00410241).
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Affiliation(s)
- Priscilla A Chan
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Katie L Lewis
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Lori H Erby
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Sandra Epps
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Erin Turbitt
- University of Technology Sydney, Sydney, Australia
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40
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Scheinfeldt LB, Brangan A, Kusic DM, Kumar S, Gharani N. Common Treatment, Common Variant: Evolutionary Prediction of Functional Pharmacogenomic Variants. J Pers Med 2021; 11:jpm11020131. [PMID: 33669176 PMCID: PMC7919641 DOI: 10.3390/jpm11020131] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Pharmacogenomics holds the promise of personalized drug efficacy optimization and drug toxicity minimization. Much of the research conducted to date, however, suffers from an ascertainment bias towards European participants. Here, we leverage publicly available, whole genome sequencing data collected from global populations, evolutionary characteristics, and annotated protein features to construct a new in silico machine learning pharmacogenetic identification method called XGB-PGX. When applied to pharmacogenetic data, XGB-PGX outperformed all existing prediction methods and identified over 2000 new pharmacogenetic variants. While there are modest pharmacogenetic allele frequency distribution differences across global population samples, the most striking distinction is between the relatively rare putatively neutral pharmacogene variants and the relatively common established and newly predicted functional pharamacogenetic variants. Our findings therefore support a focus on individual patient pharmacogenetic testing rather than on clinical presumptions about patient race, ethnicity, or ancestral geographic residence. We further encourage more attention be given to the impact of common variation on drug response and propose a new ‘common treatment, common variant’ perspective for pharmacogenetic prediction that is distinct from the types of variation that underlie complex and Mendelian disease. XGB-PGX has identified many new pharmacovariants that are present across all global communities; however, communities that have been underrepresented in genomic research are likely to benefit the most from XGB-PGX’s in silico predictions.
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Affiliation(s)
- Laura B. Scheinfeldt
- Coriell Institute for Medical Research, Camden, NJ 08003, USA; (A.B.); (D.M.K.); (N.G.)
- Correspondence:
| | - Andrew Brangan
- Coriell Institute for Medical Research, Camden, NJ 08003, USA; (A.B.); (D.M.K.); (N.G.)
| | - Dara M. Kusic
- Coriell Institute for Medical Research, Camden, NJ 08003, USA; (A.B.); (D.M.K.); (N.G.)
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA;
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah 21577, Saudi Arabia
| | - Neda Gharani
- Coriell Institute for Medical Research, Camden, NJ 08003, USA; (A.B.); (D.M.K.); (N.G.)
- Gharani Consulting, Surrey KT139PA, UK
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Caspar SM, Schneider T, Stoll P, Meienberg J, Matyas G. Potential of whole-genome sequencing-based pharmacogenetic profiling. Pharmacogenomics 2021; 22:177-190. [PMID: 33517770 DOI: 10.2217/pgs-2020-0155] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pharmacogenetics represents a major driver of precision medicine, promising individualized drug selection and dosing. Traditionally, pharmacogenetic profiling has been performed using targeted genotyping that focuses on common/known variants. Recently, whole-genome sequencing (WGS) is emerging as a more comprehensive short-read next-generation sequencing approach, enabling both gene diagnostics and pharmacogenetic profiling, including rare/novel variants, in a single assay. Using the example of the pharmacogene CYP2D6, we demonstrate the potential of WGS-based pharmacogenetic profiling as well as emphasize the limitations of short-read next-generation sequencing. In the near future, we envision a shift toward long-read sequencing as the predominant method for gene diagnostics and pharmacogenetic profiling, providing unprecedented data quality and improving patient care.
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Affiliation(s)
- Sylvan Manuel Caspar
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich 8952, Switzerland.,Department of Health Sciences & Technology, Laboratory of Translational Nutrition Biology, ETH Zurich, Schwerzenbach 8603, Switzerland
| | - Timo Schneider
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich 8952, Switzerland
| | - Patricia Stoll
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich 8952, Switzerland
| | - Janine Meienberg
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich 8952, Switzerland
| | - Gabor Matyas
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich 8952, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich 8057, Switzerland
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43
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Vassy JL, Gaziano JM, Green RC, Ferguson RE, Advani S, Miller SJ, Chun S, Hage AK, Seo SJ, Majahalme N, MacMullen L, Zimolzak AJ, Brunette CA. Effect of Pharmacogenetic Testing for Statin Myopathy Risk vs Usual Care on Blood Cholesterol: A Randomized Clinical Trial. JAMA Netw Open 2020; 3:e2027092. [PMID: 33270123 PMCID: PMC7716196 DOI: 10.1001/jamanetworkopen.2020.27092] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
IMPORTANCE Nonadherence to statin guidelines is common. The solute carrier organic anion transporter family member 1B1 (SLCO1B1) genotype is associated with simvastatin myopathy risk and is proposed for clinical implementation. The unintended harms of using pharmacogenetic information to guide pharmacotherapy remain a concern for some stakeholders. OBJECTIVE To determine the impact of delivering SLCO1B1 pharmacogenetic results to physicians on the effectiveness of atherosclerotic cardiovascular disease (ASCVD) prevention (measured by low-density lipoprotein cholesterol [LDL-C] levels) and concordance with prescribing guidelines for statin safety and effectiveness. DESIGN, SETTING, AND PARTICIPANTS This randomized clinical trial was performed from December 2015 to July 2019 at 8 primary care practices in the Veterans Affairs Boston Healthcare System. Participants included statin-naive patients with elevated ASCVD risk. Data analysis was performed from October 2019 to September 2020. INTERVENTIONS SLCO1B1 genotyping and results reporting to primary care physicians at baseline (intervention group) vs after 1 year (control group). MAIN OUTCOMES AND MEASURES The primary outcome was the 1-year change in LDL-C level. The secondary outcomes were 1-year concordance with American College of Cardiology-American Heart Association and Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for statin therapy and statin-associated muscle symptoms (SAMS). RESULTS Among 408 patients (mean [SD] age, 64.1 [7.8] years; 25 women [6.1%]), 193 were randomized to the intervention group and 215 were randomized to the control group. Overall, 120 participants (29%) had a SLCO1B1 genotype indicating increased simvastatin myopathy risk. Physicians offered statin therapy to 65 participants (33.7%) in the intervention group and 69 participants (32.1%) in the control group. Compared with patients whose physicians did not know their SLCO1B1 results at baseline, patients whose physicians received the results had noninferior reductions in LDL-C at 12 months (mean [SE] change in LDL-C, -1.1 [1.2] mg/dL in the intervention group and -2.2 [1.3] mg/dL in the control group; difference, -1.1 mg/dL; 90% CI, -4.1 to 1.8 mg/dL; P < .001 for noninferiority margin of 10 mg/dL). The proportion of patients with American College of Cardiology-American Heart Association guideline-concordant statin prescriptions in the intervention group was noninferior to that in the control group (12 patients [6.2%] vs 14 patients [6.5%]; difference, -0.003; 90% CI, -0.038 to 0.032; P < .001 for noninferiority margin of 15%). All patients in both groups were concordant with CPIC guidelines for safe statin prescribing. Physicians documented 2 and 3 cases of SAMS in the intervention and control groups, respectively, none of which was associated with a CPIC guideline-discordant prescription. Among patients with a decreased or poor SLCO1B1 transporter function genotype, simvastatin was prescribed to 1 patient in the control group but none in the intervention group. CONCLUSIONS AND RELEVANCE Clinical testing and reporting of SLCO1B1 results for statin myopathy risk did not result in poorer ASCVD prevention in a routine primary care setting and may have been associated with physicians avoiding simvastatin prescriptions for patients at genetic risk for SAMS. Such an absence of harm should reassure stakeholders contemplating the clinical use of available pharmacogenetic results. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02871934.
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Affiliation(s)
- Jason L. Vassy
- VA Boston Healthcare System, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Ariadne Labs, Boston, Massachusetts
| | - J. Michael Gaziano
- VA Boston Healthcare System, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Robert C. Green
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Ariadne Labs, Boston, Massachusetts
| | - Ryan E. Ferguson
- VA Boston Healthcare System, Boston, Massachusetts
- Department of General Internal Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | | | | | - Sojeong Chun
- Massachusetts College of Pharmacy and Health Sciences, Boston
| | - Anthony K. Hage
- Massachusetts College of Pharmacy and Health Sciences, Boston
| | - Soo-Ji Seo
- Massachusetts College of Pharmacy and Health Sciences, Boston
| | | | | | - Andrew J. Zimolzak
- VA Boston Healthcare System, Boston, Massachusetts
- Baylor College of Medicine, Houston, Texas
- Michael E. DeBakey VA Medical Center, Houston, Texas
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44
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Mauleekoonphairoj J, Chamnanphon M, Khongphatthanayothin A, Sutjaporn B, Wandee P, Poovorawan Y, Nademanee K, Pongpanich M, Chariyavilaskul P. Phenotype prediction and characterization of 25 pharmacogenes in Thais from whole genome sequencing for clinical implementation. Sci Rep 2020; 10:18969. [PMID: 33144648 PMCID: PMC7641128 DOI: 10.1038/s41598-020-76085-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022] Open
Abstract
Publicly available pharmacogenomics (PGx) databases enable translation of genotype data into clinically actionable information. As variation within pharmacogenes is population-specific, this study investigated the spectrum of 25 clinically relevant pharmacogenes in the Thai population (n = 291) from whole genome sequencing. The bioinformatics tool Stargazer was used for phenotype prediction, through assignment of alleles and detection of structural variation. Known and unreported potentially deleterious PGx variants were identified. Over 25% of Thais carried a high-risk diplotype in CYP3A5, CYP2C19, CYP2D6, NAT2, SLCO1B1, and UGT1A1. CYP2D6 structural variants accounted for 83.8% of all high-risk diplotypes. Of 39 known PGx variants identified, six variants associated with adverse drug reactions were common. Allele frequencies of CYP3A5*3 (rs776746), CYP2B6*6 (rs2279343), and NAT2 (rs1041983) were significantly higher in Thais than East-Asian and global populations. 121 unreported variants had potential to exert clinical impact, majority were rare and population-specific, with 60.3% of variants absent from gnomAD database. This study demonstrates the population-specific variation in clinically relevant pharmacogenes, the importance of CYP2D6 structural variation detection in the Thai population, and potential of unreported variants in explaining drug response. These findings are essential in development of dosing guidelines, PGx testing, clinical trials, and drugs.
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Affiliation(s)
- John Mauleekoonphairoj
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand.,Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Monpat Chamnanphon
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apichai Khongphatthanayothin
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand.,Division of Cardiology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Bangkok General Hospital, Bangkok, Thailand
| | - Boosamas Sutjaporn
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Pharawee Wandee
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Koonlawee Nademanee
- Department of Medicine, Faculty of Medicine, Center of Excellence in Arrhythmia Research Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand.,Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Pacific Rim Electrophysiology Research Institute, Bumrungrad Hospital, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Faculty of Science, Omics Sciences and Bioinfomatics Center, Chulalongkorn University, Bangkok, Thailand
| | - Pajaree Chariyavilaskul
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand. .,Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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45
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Roosan D, Hwang A, Law AV, Chok J, Roosan MR. The inclusion of health data standards in the implementation of pharmacogenomics systems: a scoping review. Pharmacogenomics 2020; 21:1191-1202. [PMID: 33124487 DOI: 10.2217/pgs-2020-0066] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background: Despite potential benefits, the practice of incorporating pharmacogenomics (PGx) results in clinical decisions has yet to diffuse widely. In this study, we conducted a review of recent discussions on data standards and interoperability with a focus on sharing PGx test results among health systems. Materials & methods: We conducted a literature search for PGx clinical decision support systems between 1 January 2012 and 31 January 2020. Thirty-two out of 727 articles were included for the final review. Results: Nine of the 32 articles mentioned data standards and only four of the 32 articles provided solutions for the lack of interoperability. Discussions: Although PGx interoperability is essential for widespread implementation, a lack of focus on standardized data creates a formidable challenge for health information exchange. Conclusion: Standardization of PGx data is essential to improve health information exchange and the sharing of PGx results between disparate systems. However, PGx data standards and interoperability are often not addressed in the system-level implementation.
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Affiliation(s)
- Don Roosan
- Assistant Professor, Department of Pharmacy Practice & Administration, College of Pharmacy, Western University of Health Sciences, 309 E 2nd street, Pomona, CA 91766, USA
| | - Angela Hwang
- Research Assistant, Department of Pharmacy Practice & Administration, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Anandi V Law
- Professor, Department of Pharmacy Practice & Administration, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Jay Chok
- Associate Professor, School of Applied Life Sciences, Keck Graduate Institute, Claremont Colleges, Pomona, CA 91711, USA
| | - Moom R Roosan
- Assistant Professor, School of Pharmacy, Department of Pharmacy Practice, Chapman University, Irvine, CA 92618, USA
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46
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Turner RM, Newman WG, Bramon E, McNamee CJ, Wong WL, Misbah S, Hill S, Caulfield M, Pirmohamed M. Pharmacogenomics in the UK National Health Service: opportunities and challenges. Pharmacogenomics 2020; 21:1237-1246. [PMID: 33118435 DOI: 10.2217/pgs-2020-0091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Despite increasing interest in pharmacogenomics, and the potential benefits to improve patient care, implementation into clinical practice has not been widespread. Recently, there has been a drive to implement genomic medicine into the UK National Health Service (NHS), largely spurred on by the success of the 100,000 Genomes Project. The UK Pharmacogenetics and Stratified Medicine Network, NHS England and Genomics England invited experts from academia, the healthcare sector, industry and patient representatives to come together to discuss the opportunities and challenges of implementing pharmacogenomics into the NHS. This report highlights the discussions of the workshop to provide an overview of the issues that need to be considered to enable pharmacogenomic medicine to become mainstream within the NHS.
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Affiliation(s)
- Richard M Turner
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, L69 3GL, UK
| | - William G Newman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Elvira Bramon
- Division of Psychiatry, University College London, Charles Bell House, 67-73 Riding House Street, London, W1W 7EJ, UK
| | - Christine J McNamee
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, L69 3GL, UK
| | - Wai Lup Wong
- East & North Hertfordshire NHS Trust, Coreys Mill Lane, Stevenage, SG1 4AB, UK
| | - Siraj Misbah
- John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - Sue Hill
- NHS England, Skipton House, 80 London Road, London, SE1 6LH, UK
| | - Mark Caulfield
- William Harvey Research Institute, Charterhouse Square, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Munir Pirmohamed
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, L69 3GL, UK
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47
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Monserrat Villatoro J, García García I, Bueno D, de la Cámara R, Estébanez M, López de la Guía A, Abad-Santos F, Antón C, Mejía G, Otero MJ, Ramírez García E, Frías Iniesta J, Carcas A, Borobia AM. Randomised multicentre clinical trial to evaluate voriconazole pre-emptive genotyping strategy in patients with risk of aspergillosis: vorigenipharm study protocol. BMJ Open 2020; 10:e037443. [PMID: 33004392 PMCID: PMC7534724 DOI: 10.1136/bmjopen-2020-037443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION Invasive aspergillosis is the most important cause of morbidity and mortality in patients with haematological diseases. At present, voriconazole is the first-line treatment for invasive fungal disease. The pharmacokinetic interindividual variability of voriconazole depends on genetic factors. CYP450 is involved in 70%-75% of total metabolism of voriconazole, mainly CYP3A4 and CYP2C19, with the remaining 25%-30% of metabolism conducted by monooxygenase flavins. CYP2C19 single nucleotide polymorphisms could explain 50%-55% of variability in voriconazole metabolism. MATERIALS AND METHODS The main objective is to compare efficiency of pre-emptive voriconazole genotyping with routine practice. The primary outcome is serum voriconazole on the fifth day within the therapeutic range. The secondary outcome is the combined variables of therapeutic failure and adverse events within 90 days of first administration, associated with voriconazole. A total of 146 patients at risk of invasive aspergillosis who will potentially receive voriconazole will be recruited, and CYP2C19 will be genotyped. If the patient ultimately receives voriconazole, they will be randomised (1:1 experimental/control). In the experimental arm, patients will receive a dose according to a pharmacogenetic algorithm, including CYP2C19 genotype and clinical and demographic information. In the control arm, patients will receive a dose according to clinical practice guidelines. In addition, a Spanish National Healthcare System (NHS) point-of-view cost-effectiveness evaluation will be performed. Direct cost calculations for each arm will be performed. CONCLUSION This trial will provide information about the viability and cost-effectiveness of the implementation of a pre-emptive voriconazole genotyping strategy in the Spanish NHS. ETHICS AND DISSEMINATION A Spanish version of this protocol has been evaluated and approved by the La Paz University Hospital Ethics Committee and the Spanish Agency of Medicines and Medical Devices. Trial results will be submitted for publication in an open peer-reviewed medical speciality-specific publication. TRIAL REGISTRATION NUMBER Eudra-CT: 2019-000376-41 and NCT04238884; Pre-results.
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Affiliation(s)
| | - Irene García García
- Clinical Pharmacology Department, Hospital Universitario La Paz IdiPAZ, Madrid, Spain
| | - David Bueno
- Pediatric Oncology and Haematology Department, Hospital Universitario La Paz, Madrid, Spain
| | - Rafael de la Cámara
- Haematology Department, Hospital Universitario de la Princesa, Madrid, Spain
| | - Miriam Estébanez
- Internal Medicine Department, Hospital Central de la Defensa Gómez Ulla, Madrid, Spain
| | | | - Francisco Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Madrid, Spain
- Pharmacology Department, Universidad Autonoma de Madrid, Madrid, Spain
| | - Cristina Antón
- Health Technology Assessment Department, Universidad Francisco de Vitoria, Pozuelo de Alarcon, Madrid, Spain
| | - Gina Mejía
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Madrid, Spain
| | - María José Otero
- Haematology Department, Hospital Central de la Defensa Gómez Ulla, Madrid, Spain
| | - Elena Ramírez García
- Clinical Pharmacology Department, Hospital Universitario La Paz IdiPAZ, Madrid, Spain
- Pharmacology Department, Universidad Autonoma de Madrid, Madrid, Spain
| | - Jesús Frías Iniesta
- Clinical Pharmacology Department, Hospital Universitario La Paz IdiPAZ, Madrid, Spain
- Pharmacology Department, Universidad Autonoma de Madrid, Madrid, Spain
| | - Antonio Carcas
- Clinical Pharmacology Department, Hospital Universitario La Paz IdiPAZ, Madrid, Spain
- Pharmacology Department, Universidad Autonoma de Madrid, Madrid, Spain
| | - Alberto M Borobia
- Clinical Pharmacology Department, Hospital Universitario La Paz IdiPAZ, Madrid, Spain
- Pharmacology Department, Universidad Autonoma de Madrid, Madrid, Spain
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48
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Walters CE, Nitin R, Margulis K, Boorom O, Gustavson DE, Bush CT, Davis LK, Below JE, Cox NJ, Camarata SM, Gordon RL. Automated Phenotyping Tool for Identifying Developmental Language Disorder Cases in Health Systems Data (APT-DLD): A New Research Algorithm for Deployment in Large-Scale Electronic Health Record Systems. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2020; 63:3019-3035. [PMID: 32791019 PMCID: PMC7890229 DOI: 10.1044/2020_jslhr-19-00397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/23/2020] [Accepted: 05/19/2020] [Indexed: 05/13/2023]
Abstract
Purpose Data mining algorithms using electronic health records (EHRs) are useful in large-scale population-wide studies to classify etiology and comorbidities (Casey et al., 2016). Here, we apply this approach to developmental language disorder (DLD), a prevalent communication disorder whose risk factors and epidemiology remain largely undiscovered. Method We first created a reliable system for manually identifying DLD in EHRs based on speech-language pathologist (SLP) diagnostic expertise. We then developed and validated an automated algorithmic procedure, called, Automated Phenotyping Tool for identifying DLD cases in health systems data (APT-DLD), that classifies a DLD status for patients within EHRs on the basis of ICD (International Statistical Classification of Diseases and Related Health Problems) codes. APT-DLD was validated in a discovery sample (N = 973) using expert SLP manual phenotype coding as a gold-standard comparison and then applied and further validated in a replication sample of N = 13,652 EHRs. Results In the discovery sample, the APT-DLD algorithm correctly classified 98% (concordance) of DLD cases in concordance with manually coded records in the training set, indicating that APT-DLD successfully mimics a comprehensive chart review. The output of APT-DLD was also validated in relation to independently conducted SLP clinician coding in a subset of records, with a positive predictive value of 95% of cases correctly classified as DLD. We also applied APT-DLD to the replication sample, where it achieved a positive predictive value of 90% in relation to SLP clinician classification of DLD. Conclusions APT-DLD is a reliable, valid, and scalable tool for identifying DLD cohorts in EHRs. This new method has promising public health implications for future large-scale epidemiological investigations of DLD and may inform EHR data mining algorithms for other communication disorders. Supplemental Material https://doi.org/10.23641/asha.12753578.
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Affiliation(s)
- Courtney E. Walters
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
- Neuroscience Program, College of Arts and Science, Vanderbilt University, Nashville, TN
| | - Rachana Nitin
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN
| | - Katherine Margulis
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN
- Kennedy Krieger Institute, Baltimore, MD
| | - Olivia Boorom
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Daniel E. Gustavson
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Catherine T. Bush
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Lea K. Davis
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Jennifer E. Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Nancy J. Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Stephen M. Camarata
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Reyna L. Gordon
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
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49
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Scott SA, Scott ER, Seki Y, Chen AJ, Wallsten R, Owusu Obeng A, Botton MR, Cody N, Shi H, Zhao G, Brake P, Nicoletti P, Yang Y, Delio M, Shi L, Kornreich R, Schadt EE, Edelmann L. Development and Analytical Validation of a 29 Gene Clinical Pharmacogenetic Genotyping Panel: Multi-Ethnic Allele and Copy Number Variant Detection. Clin Transl Sci 2020; 14:204-213. [PMID: 32931151 PMCID: PMC7877843 DOI: 10.1111/cts.12844] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/16/2020] [Indexed: 12/12/2022] Open
Abstract
To develop a novel pharmacogenetic genotyping panel, a multidisciplinary team evaluated available evidence and selected 29 genes implicated in interindividual drug response variability, including 130 sequence variants and additional copy number variants (CNVs). Of the 29 genes, 11 had guidelines published by the Clinical Pharmacogenetics Implementation Consortium. Targeted genotyping and CNV interrogation were accomplished by multiplex single‐base extension using the MassARRAY platform (Agena Biosciences) and multiplex ligation‐dependent probe amplification (MRC Holland), respectively. Analytical validation of the panel was accomplished by a strategic combination of > 500 independent tests performed on 170 unique reference material DNA samples, which included sequence variant and CNV accuracy, reproducibility, and specimen (blood, saliva, and buccal swab) controls. Among the accuracy controls were 32 samples from the 1000 Genomes Project that were selected based on their enrichment of sequence variants included in the pharmacogenetic panel (VarCover.org). Coupled with publicly available samples from the Genetic Testing Reference Materials Coordination Program (GeT‐RM), accuracy validation material was available for the majority (77%) of interrogated sequence variants (100% with average allele frequencies > 0.1%), as well as additional structural alleles with unique copy number signatures (e.g., CYP2D6*5, *13, *36, *68; CYP2B6*29; and CYP2C19*36). Accuracy and reproducibility for both genotyping and copy number were > 99.9%, indicating that the optimized panel platforms were precise and robust. Importantly, multi‐ethnic allele frequencies of the interrogated variants indicate that the vast majority of the general population carries at least one of these clinically relevant pharmacogenetic variants, supporting the implementation of this panel for pharmacogenetic research and/or clinical implementation programs.
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Affiliation(s)
- Stuart A Scott
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erick R Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Aniwaa Owusu Obeng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariana R Botton
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Neal Cody
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Paola Nicoletti
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Lisong Shi
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruth Kornreich
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Edelmann
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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50
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Hoffman JM, Flynn AJ, Juskewitch JE, Freimuth RR. Biomedical Data Science and Informatics Challenges to Implementing Pharmacogenomics with Electronic Health Records. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-020320-093614] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pharmacogenomic information must be incorporated into electronic health records (EHRs) with clinical decision support in order to fully realize its potential to improve drug therapy. Supported by various clinical knowledge resources, pharmacogenomic workflows have been implemented in several healthcare systems. Little standardization exists across these efforts, however, which limits scalability both within and across clinical sites. Limitations in information standards, knowledge management, and the capabilities of modern EHRs remain challenges for the widespread use of pharmacogenomics in the clinic, but ongoing efforts are addressing these challenges. Although much work remains to use pharmacogenomic information more effectively within clinical systems, the experiences of pioneering sites and lessons learned from those programs may be instructive for other clinical areas beyond genomics. We present a vision of what can be achieved as informatics and data science converge to enable further adoption of pharmacogenomics in the clinic.
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Affiliation(s)
- James M. Hoffman
- Department of Pharmaceutical Sciences and the Office of Quality and Patient Care, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Allen J. Flynn
- Department of Learning Health Sciences, Medical School, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Justin E. Juskewitch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Robert R. Freimuth
- Division of Digital Health Sciences, Department of Health Sciences Research, Center for Individualized Medicine, and Information and Knowledge Management, Mayo Clinic, Rochester, Minnesota 55905, USA
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