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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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Floris M, Moschella A, Alcalay M, Montella A, Tirelli M, Fontana L, Idda ML, Guarnieri P, Capasso M, Mammì C, Nicoletti P, Miozzo M. Pharmacogenetics in Italy: current landscape and future prospects. Hum Genomics 2024; 18:78. [PMID: 38987819 PMCID: PMC11234611 DOI: 10.1186/s40246-024-00612-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/30/2024] [Indexed: 07/12/2024] Open
Abstract
Pharmacogenetics investigates sequence of genes that affect drug response, enabling personalized medication. This approach reduces drug-induced adverse reactions and improves clinical effectiveness, making it a crucial consideration for personalized medical care. Numerous guidelines, drawn by global consortia and scientific organizations, codify genotype-driven administration for over 120 active substances. As the scientific community acknowledges the benefits of genotype-tailored therapy over traditionally agnostic drug administration, the push for its implementation into Italian healthcare system is gaining momentum. This evolution is influenced by several factors, including the improved access to patient genotypes, the sequencing costs decrease, the growing of large-scale genetic studies, the rising popularity of direct-to-consumer pharmacogenetic tests, and the continuous improvement of pharmacogenetic guidelines. Since EMA (European Medicines Agency) and AIFA (Italian Medicines Agency) provide genotype information on drug leaflet without clear and explicit clinical indications for gene testing, the regulation of pharmacogenetic testing is a pressing matter in Italy. In this manuscript, we have reviewed how to overcome the obstacles in implementing pharmacogenetic testing in the clinical practice of the Italian healthcare system. Our particular emphasis has been on germline testing, given the absence of well-defined national directives in contrast to somatic pharmacogenetics.
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Affiliation(s)
- Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
| | - Antonino Moschella
- Unit of Medical Genetics, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - Myriam Alcalay
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milano, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milano, Italy
| | - Annalaura Montella
- CEINGE Biotecnologie Avanzate, Napoli, Italy
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Matilde Tirelli
- CEINGE Biotecnologie Avanzate, Napoli, Italy
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Laura Fontana
- Medical Genetics Unit, Department of Health Sciences, ASST Santi Paolo e Carlo, Università degli Studi di Milano, Milan, Italy
| | - Maria Laura Idda
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | - Mario Capasso
- CEINGE Biotecnologie Avanzate, Napoli, Italy
- Department of Molecular Medicine and Medical Biotechnology (DMMBM), Università degli Studi di Napoli "Federico II", Napoli, Italy
| | - Corrado Mammì
- Unit of Medical Genetics, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - Paola Nicoletti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monica Miozzo
- Medical Genetics Unit, Department of Health Sciences, ASST Santi Paolo e Carlo, Università degli Studi di Milano, Milan, Italy.
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Haddad A, Radhakrishnan A, McGee S, Smith JD, Karnes JH, Venner E, Wheeler MM, Patterson K, Walker K, Kalra D, Kalla SE, Wang Q, Gibbs RA, Jarvik GP, Sanchez J, Musick A, Ramirez AH, Denny JC, Empey PE. Frequency of pharmacogenomic variation and medication exposures among All of Us Participants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.12.24304664. [PMID: 38946996 PMCID: PMC11213053 DOI: 10.1101/2024.06.12.24304664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Pharmacogenomics promises improved outcomes through individualized prescribing. However, the lack of diversity in studies impedes clinical translation and equitable application of precision medicine. We evaluated the frequencies of PGx variants, predicted phenotypes, and medication exposures using whole genome sequencing and EHR data from nearly 100k diverse All of Us Research Program participants. We report 100% of participants carried at least one pharmacogenomics variant and nearly all (99.13%) had a predicted phenotype with prescribing recommendations. Clinical impact was high with over 20% having both an actionable phenotype and a prior exposure to an impacted medication with pharmacogenomic prescribing guidance. Importantly, we also report hundreds of alleles and predicted phenotypes that deviate from known frequencies and/or were previously unreported, including within admixed American and African ancestry groups.
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Ike JI, Smith IT, Mosley D, Madden C, Grossarth S, Halle BR, Lewis A, Mentch F, Hakonarson H, Bastarache L, Wheless L. Voriconazole metabolism is associated with the number of skin cancers per patient. Arch Dermatol Res 2024; 316:303. [PMID: 38819581 PMCID: PMC11143062 DOI: 10.1007/s00403-024-03135-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
Voriconazole exposure is associated with skin cancer, but it is unknown how the full spectrum of its metabolizer phenotypes impacts this association. We conducted a retrospective cohort study to determine how variation in metabolism of voriconazole as measured by metabolizer status of CYP2C19 is associated with the total number of skin cancers a patient develops and the rate of development of the first skin cancer after treatment. There were 1,739 organ transplant recipients with data on CYP2C19 phenotype. Of these, 134 were exposed to voriconazole. There was a significant difference in the number of skin cancers after transplant based on exposure to voriconazole, metabolizer phenotype, and the interaction of these two (p < 0.01 for all three). This increase was driven primarily by number of squamous cell carcinomas among rapid metabolizes with voriconazole exposure (p < 0.01 for both). Patients exposed to voriconazole developed skin cancers more rapidly than those without exposure (Fine-Grey hazard ratio 1.78, 95% confidence interval 1.19-2.66). This association was similarly driven by development of SCC (Fine-Grey hazard ratio 1.83, 95% confidence interval 1.14-2.94). Differences in voriconazoles metabolism are associated with an increase in the number of skin cancers developed after transplant, particularly SCC.
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Affiliation(s)
| | - Isabelle T Smith
- Vanderbilt University College of Arts and Sciences, Nashville, TN, USA
| | | | - Christopher Madden
- State University of New York Downstate College of Medicine, Brooklyn, NY, USA
| | - Sarah Grossarth
- Quillen College of Medicine, East Tennessee State University, Johnson City, TN, USA
| | - Briana R Halle
- Irvine Department of Dermatology, University of California, Davis, USA
| | - Adam Lewis
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Frank Mentch
- Children's Hospital of Philadelphia Center for Applied Genomics, Philadelphia, USA
| | - Hakon Hakonarson
- Children's Hospital of Philadelphia Center for Applied Genomics, Philadelphia, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lee Wheless
- Tennessee Valley Healthcare System VA Medical Center, Nashville, TN, USA.
- Department of Medicine, Division of Epidemiology, Department of Dermatology, Vanderbilt University Medical Center, 719 Thompson Lane, Suite 26300, Nashville, TN, 37215, USA.
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Ike JI, Smith IT, Mosley D, Madden C, Grossarth S, Halle BR, Lewis A, Mentch F, Hakonarson H, Bastarache L, Wheless L. Voriconazole Metabolism is Associated with the Number of Skin Cancers Per Patient. RESEARCH SQUARE 2024:rs.3.rs-4152279. [PMID: 38699337 PMCID: PMC11065087 DOI: 10.21203/rs.3.rs-4152279/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Voriconazole exposure is associated with skin cancer, but it is unknown how the full spectrum of its metabolizer phenotypes impacts this association. We conducted a retrospective cohort study to determine how variation in metabolism of voriconazole as measured by metabolizer status of CYP2C19 is associated with the total number of skin cancers a patient develops and the rate of development of the first skin cancer after treatment. There were 1,739 organ transplant recipients with data on CYP2C19 phenotype. Of these, 134 were exposed to voriconazole. There was a significant difference in the number of skin cancers after transplant based on exposure to voriconazole, metabolizer phenotype, and the interaction of these two (p < 0.01 for all three). This increase was driven primarily by number of squamous cell carcinomas among rapid metabolizes with voriconazole exposure (p < 0.01 for both). Patients exposed to voriconazole developed skin cancers more rapidly than those without exposure (Fine-Grey hazard ratio 1.78, 95% confidence interval 1.19-2.66). This association was similarly driven by development of SCC (Fine-Grey hazard ratio 1.83, 95% confidence interval 1.14-2.94). Differences in voriconazoles metabolism are associated with an increase in the number of skin cancers developed after transplant, particularly SCC.
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Affiliation(s)
| | | | | | | | - Sarah Grossarth
- Quillen College of Medicine, East Tennessee State University
| | - Briana R Halle
- University of California, Irvine, Department of Dermatology
| | - Adam Lewis
- Vanderbilt University Medical Center, Department of Biomedical Informatics
| | - Frank Mentch
- Children's Hospital of Philadelphia Center for Applied Genomics
| | | | - Lisa Bastarache
- Vanderbilt University Medical Center, Department of Biomedical Informatics
| | - Lee Wheless
- Tennessee Valley Healthcare System VA Medical Center
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Scherf-Clavel M, Weber H, Unterecker S, Müller DJ, Deckert J. Frequencies of CYP2C19 and CYP2D6 gene variants in a German inpatient sample with mood and anxiety disorders. World J Biol Psychiatry 2024; 25:214-221. [PMID: 38493365 DOI: 10.1080/15622975.2024.2321553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/12/2024] [Indexed: 03/18/2024]
Abstract
OBJECTIVES Previous results demonstrated that CYP2D6 and CYP2C19 gene variants affect serum concentrations of antidepressants. We implemented a PGx service determining gene variants in CYP2D6 and CYP2C19 in our clinical routine care and report on our first patient cohort. METHODS We analysed CYP2D6 and CYP2C19 allele, genotype, and phenotype frequencies, and actionable pharmacogenetic variants in this German psychiatric inpatient cohort. Two-tailed z-test was used to investigate for differences in CYP2D6 and CYP2C19 phenotypes and actionable/non-actionable genetic variant frequencies between our cohort and reference cohorts. RESULTS Out of the 154 patients included, 44.8% of patients were classified as CYP2D6 normal metabolizer, 38.3% as intermediate metabolizers, 8.4% as poor metabolizers, and 2.6% as ultrarapid metabolizers. As for CYP2C19, 40.9% of patients were classified as normal metabolizers, 19.5% as intermediate metabolizers, 2.6% as poor metabolizers, 31.2% as rapid metabolizers, and 5.8% as ultrarapid metabolizers. Approximately, 80% of patients had at least one actionable PGx variant. CONCLUSION There is a high prevalence of actionable PGx variants in psychiatric inpatients which may affect treatment response. Physicians should refer to PGx-informed dosing guidelines in carriers of these variants. Pre-emptive PGx testing in general may facilitate precision medicine also for other drugs metabolised by CYP2D6 and/or CYP2C19.
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Affiliation(s)
- Maike Scherf-Clavel
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
| | - Heike Weber
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
| | - Stefan Unterecker
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
| | - Daniel J Müller
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Jürgen Deckert
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital of Würzburg, Würzburg, Germany
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Tippenhauer K, Philips M, Largiadèr C, Sariyar M. Using the PharmCAT tool for Pharmacogenetic clinical decision support. Brief Bioinform 2023; 25:bbad452. [PMID: 38055839 PMCID: PMC10699732 DOI: 10.1093/bib/bbad452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/25/2023] [Accepted: 11/11/2023] [Indexed: 12/08/2023] Open
Abstract
Here, we will provide our insights into the usage of PharmCAT as part of a pharmacogenetic clinical decision support pipeline, which addresses the challenges in mapping clinical dosing guidelines to variants to be extracted from genetic datasets. After a general outline of pharmacogenetics, we describe some features of PharmCAT and how we integrated it into a pharmacogenetic clinical decision support system within a clinical information system. We conclude with promising developments regarding future PharmCAT releases.
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Affiliation(s)
- Kevin Tippenhauer
- Bern University of Applied Sciences, Quellgasse 21, 2500 Biel, Switzerland
| | - Marwin Philips
- Bern University of Applied Sciences, Quellgasse 21, 2500 Biel, Switzerland
| | - Carlo Largiadèr
- Department of Clinical Chemistry at the Bern University Hospital, Bern, Switzerland
| | - Murat Sariyar
- Bern University of Applied Sciences, Quellgasse 21, 2500 Biel, Switzerland
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