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Hernandez S, Hindorff LA, Morales J, Ramos EM, Manolio TA. Patterns of pharmacogenetic variation in nine biogeographic groups. Clin Transl Sci 2024; 17:e70017. [PMID: 39206687 PMCID: PMC11358764 DOI: 10.1111/cts.70017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 08/02/2024] [Accepted: 08/10/2024] [Indexed: 09/04/2024] Open
Abstract
Frequencies of pharmacogenetic (PGx) variants are known to differ substantially across populations but much of the available PGx literature focuses on one or a few population groups, often defined in nonstandardized ways, or on a specific gene or variant. Guidelines produced by the Clinical Pharmacogenetic Implementation Consortium (CPIC) provide consistent methods of literature extraction, curation, and reporting, including comprehensive curation of allele frequency data across nine defined "biogeographic groups" from the PGx literature. We extracted data from 23 CPIC guidelines encompassing 19 genes to compare the sizes of the populations from each group and allele frequencies of altered function alleles across groups. The European group was the largest in the curated literature for 16 of the 19 genes, while the American and Oceanian groups were the smallest. Nearly 200 alleles were detected in nonreference groups that were not reported in the largest (reference) group. The genes CYP2B6 and CYP2C9 were more likely to have higher frequencies of altered function alleles in nonreference groups compared to the reference group, while the genes CYP4F2, DPYD, SLCO1B1, and UGT1A1 were less likely to have higher frequencies in nonreference groups. PGx allele frequencies and function differ substantially across nine biogeographic groups, all but two of which are underrepresented in available PGx data. Awareness of these differences and increased efforts to characterize the breadth of global PGx variation are needed to ensure that implementation of PGx-guided drug selection does not further widen existing health disparities among populations currently underrepresented in PGx data.
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Affiliation(s)
- Sophia Hernandez
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Lucia A. Hindorff
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Joannella Morales
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Erin M. Ramos
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Teri A. Manolio
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
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2
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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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3
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Ji Y, Zhao J, Gong J, Sedlazeck FJ, Fan S. Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations. Mol Genet Genomics 2024; 299:65. [PMID: 38972030 DOI: 10.1007/s00438-024-02158-x] [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: 12/06/2023] [Accepted: 06/16/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND A large number of challenging medically relevant genes (CMRGs) are situated in complex or highly repetitive regions of the human genome, hindering comprehensive characterization of genetic variants using next-generation sequencing technologies. In this study, we employed long-read sequencing technology, extensively utilized in studying complex genomic regions, to characterize genetic alterations, including short variants (single nucleotide variants and short insertions and deletions) and copy number variations, in 370 CMRGs across 41 individuals from 19 global populations. RESULTS Our analysis revealed high levels of genetic variants in CMRGs, with 68.73% exhibiting copy number variations and 65.20% containing short variants that may disrupt protein function across individuals. Such variants can influence pharmacogenomics, genetic disease susceptibility, and other clinical outcomes. We observed significant differences in CMRG variation across populations, with individuals of African ancestry harboring the highest number of copy number variants and short variants compared to samples from other continents. Notably, 15.79% to 33.96% of short variants were exclusively detectable through long-read sequencing. While the T2T-CHM13 reference genome significantly improved the assembly of CMRG regions, thereby facilitating variant detection in these regions, some regions still lacked resolution. CONCLUSION Our results provide an important reference for future clinical and pharmacogenetic studies, highlighting the need for a comprehensive representation of global genetic diversity in the reference genome and improved variant calling techniques to fully resolve medically relevant genes.
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Affiliation(s)
- Yanfeng Ji
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Junfan Zhao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Jiao Gong
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China.
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Skokou M, Karamperis K, Koufaki MI, Tsermpini EE, Pandi MT, Siamoglou S, Ferentinos P, Bartsakoulia M, Katsila T, Mitropoulou C, Patrinos GP. Clinical implementation of preemptive pharmacogenomics in psychiatry. EBioMedicine 2024; 101:105009. [PMID: 38364700 PMCID: PMC10879811 DOI: 10.1016/j.ebiom.2024.105009] [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: 08/03/2023] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Pharmacogenomics (PGx) holds promise to revolutionize modern healthcare. Although there are several prospective clinical studies in oncology and cardiology, demonstrating a beneficial effect of PGx-guided treatment in reducing adverse drug reactions, there are very few such studies in psychiatry, none of which spans across all main psychiatric indications, namely schizophrenia, major depressive disorder and bipolar disorder. In this study we aim to investigate the clinical effectiveness of PGx-guided treatment (occurrence of adverse drug reactions, hospitalisations and re-admissions, polypharmacy) and perform a cost analysis of the intervention. METHODS We report our findings from a multicenter, large-scale, prospective study of pre-emptive genome-guided treatment named as PREemptive Pharmacogenomic testing for preventing Adverse drug REactions (PREPARE) in a large cohort of psychiatric patients (n = 1076) suffering from schizophrenia, major depressive disorder and bipolar disorder. FINDINGS We show that patients with an actionable phenotype belonging to the PGx-guided arm (n = 25) present with 34.1% less adverse drug reactions compared to patients belonging to the control arm (n = 36), 41.2% less hospitalisations (n = 110 in the PGx-guided arm versus n = 187 in the control arm) and 40.5% less re-admissions (n = 19 in the PGx-guided arm versus n = 32 in the control arm), less duration of initial hospitalisations (n = 3305 total days of hospitalisation in the PGx-guided arm from 110 patients, versus n = 6517 in the control arm from 187 patients) and duration of hospitalisation upon readmission (n = 579 total days of hospitalisation upon readmission in the PGx-guided arm, derived from 19 patients, versus n = 928 in the control arm, from 32 patients respectively). It was also shown that in the vast majority of the cases, there was less drug dose administrated per drug in the PGx-guided arm compared to the control arm and less polypharmacy (n = 124 patients prescribed with at least 4 psychiatric drugs in the PGx-guided arm versus n = 143 in the control arm) and smaller average number of co-administered psychiatric drugs (2.19 in the PGx-guided arm versus 2.48 in the control arm. Furthermore, less deaths were reported in the PGx-guided arm (n = 1) compared with the control arm (n = 9). Most importantly, we observed a 48.5% reduction of treatment costs in the PGx-guided arm with a reciprocal slight increase of the quality of life of patients suffering from major depressive disorder (0.935 versus 0.925 QALYs in the PGx-guided and control arm, respectively). INTERPRETATION While only a small proportion (∼25%) of the entire study sample had an actionable genotype, PGx-guided treatment can have a beneficial effect in psychiatric patients with a reciprocal reduction of treatment costs. Although some of these findings did not remain significant when all patients were considered, our data indicate that genome-guided psychiatric treatment may be successfully integrated in mainstream healthcare. FUNDING European Union Horizon 2020.
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Affiliation(s)
- Maria Skokou
- Department of Psychiatry, University of Patras General Hospital, Patras, Greece
| | - Kariofyllis Karamperis
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece; The Golden Helix Foundation, London, UK
| | - Margarita-Ioanna Koufaki
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece; The Golden Helix Foundation, London, UK
| | - Evangelia-Eirini Tsermpini
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece
| | - Maria-Theodora Pandi
- Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Pathology, Clinical Bioinformatics Unit, Rotterdam, the Netherlands
| | - Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece
| | - Panagiotis Ferentinos
- 2nd Department of Psychiatry, National and Kapodistrian University of Athens, ATIKON University General Hospital, Athens, Greece
| | - Marina Bartsakoulia
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece
| | - Theodora Katsila
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece
| | | | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece; Erasmus University Medical Center, Faculty of Medicine and Health Sciences, Department of Pathology, Clinical Bioinformatics Unit, Rotterdam, the Netherlands; Department of Genetics and Genomics, United Arab Emirates University, College of Medicine and Health Sciences, Al-Ain, Abu Dhabi, United Arab Emirates; United Arab Emirates University, Zayed Center for Health Sciences, Al-Ain, Abu Dhabi, United Arab Emirates.
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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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Abouelhoda M, Almuqati N, Abogosh A, Alfraih F, Maddirevula S, Alkuraya FS. Mining local exome and HLA data to characterize pharmacogenetic variants in Saudi Arabia. Hum Genet 2024; 143:125-136. [PMID: 38159139 DOI: 10.1007/s00439-023-02628-z] [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: 02/16/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
Pharmacogenomics (PGx) is a promising field of precision medicine where efficacy of drugs is maximized while side effects are minimized for individual patients. Knowledge of the frequency of PGx-relevant variants (pharmacovariants) in the local population is a pre-requisite to informed policy making. Unfortunately, such knowledge is largely lacking from the Middle East. Here, we describe the use of a large clinical exome database (n = 13,473) and HLA haplotypes (n = 64,737) from Saudi Arabia, one of the largest countries in the Middle East, along with previously published data from the local population to ascertain allele frequencies of known pharmacovariants. In addition, we queried another exome database (n = 816) of well-phenotyped research subjects from Saudi Arabia to discover novel candidate variants in known PGx genes (pharmacogenes). Although our results show that only 26% (63/242) of class 1A/1B PharmGKB variants were identified, we estimate that 99.57% of the local population have at least one such variant. This translates to a minimum estimated impact of 9% of medications dispensed by our medical center annually. We also highlight the contribution of rare variants where 71% of the pharmacogenes devoid of common pharmacovariants had at least one potentially deleterious rare variant. Thus, we show that approaches that go beyond the use of commercial PGx kits that have been optimized for other populations should be implemented to ensure universal and equitable access of all members of the local population to personalized prescription practices.
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Affiliation(s)
- Mohamed Abouelhoda
- Department of Computational Sciences, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Noura Almuqati
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ahmed Abogosh
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Feras Alfraih
- Oncology Centre, Faisal Specialist Hospital and Research Centre, Riyadh, King, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia.
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Alqasrawi MN, Al-Mahayri ZN, Alblooshi H, Alsafar H, Ali BR. Utilizing Pharmacogenomic Data for a Safer Use of Statins among the Emirati Population. Curr Vasc Pharmacol 2024; 22:218-229. [PMID: 38284696 DOI: 10.2174/0115701611283841231227064343] [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: 09/23/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Statins are the most prescribed lipid-lowering drugs worldwide. The associated adverse events, especially muscle symptoms, have been frequently reported despite their perceived safety. Three pharmacogenes, the solute carrier organic anion transporter family member 1B1 (SLCO1B1), ATP-binding cassette subfamily G member 2 (ABCG2), and cytochrome P450 2C9 (CYP2C9) are suggested as safety biomarkers for statins. The Clinical Pharmacogenomic Implementation Consortium (CPIC) issued clinical guidelines for statin use based on these three genes. OBJECTIVES The present study aimed to examine variants in these pharmacogenes to predict the safety of statin use among the Emirati population. METHODS Analyzing 242 whole exome sequencing data at the three genes enabled the determination of the frequencies of the single nucleotide polymorphisms (SNPs), annotating the haplotypes and the predicted functions of their proteins. RESULTS In our cohort, 29.8% and 5.4% had SLCO1B1 decreased and poor function, respectively. The high frequency warns of the possibility of significant side effects of some statins and the importance of pharmacogenomic testing. We found a low frequency (6%) of the ABCG2:rs2231142 variant, which indicates the low probability of Emirati patients being recommended against higher rosuvastatin doses compared with other populations with higher frequencies of this variant. In contrast, we found high frequencies of the functionally impaired CYP2C9 alleles, which makes fluvastatin a less favorable choice. CONCLUSION Among the sparse studies available, the present one demonstrates all SLCO1B1 and CYP2C9 function-impairing alleles among Emiratis. We highlighted how population-specific pharmacogenomic data can predict safer choices of statins, especially in understudied populations.
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Affiliation(s)
- Mais N Alqasrawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Zeina N Al-Mahayri
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hiba Alblooshi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Habiba Alsafar
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
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Turner AJ, Haidar CE, Yang W, Boone EC, Offer SM, Empey PE, Haddad A, Tahir S, Scharer G, Broeckel U, Gaedigk A. Updated DPYD HapB3 haplotype structure and implications for pharmacogenomic testing. Clin Transl Sci 2024; 17:e13699. [PMID: 38129972 PMCID: PMC10777430 DOI: 10.1111/cts.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/22/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
The DPYD gene encodes dihydropyrimidine dehydrogenase, the rate-limiting enzyme for the metabolism of fluoropyrimidines 5-fluorouracil and capecitabine. Genetic variants in DPYD have been associated with altered enzyme activity, therefore accurate detection and interpretation is critical to predict metabolizer status for individualized fluoropyrimidine therapy. The most commonly observed deleterious variation is the causal variant linked to the previously described HapB3 haplotype, c.1129-5923C>G (rs75017182) in intron 10, which introduces a cryptic splice site. A benign synonymous variant in exon 11, c.1236G>A (rs56038477) is also linked to HapB3 and is commonly used for testing. Previously, these single-nucleotide polymorphisms (SNPs) have been reported to be in perfect linkage disequilibrium (LD); therefore, c.1236G>A is often utilized as a proxy for the function-altering intronic variant. Clinical genotyping of DPYD identified a patient who had c.1236G>A, but not c.1129-5923C>G, suggesting that these two SNPs may not be in perfect LD, as previously assumed. Additional individuals with c.1236G>A, but not c.1129-5923C>G, were identified in the Children's Mercy Data Warehouse and the All of Us Research Program version 7 cohort substantiating incomplete SNP linkage. Consequently, testing only c.1236G>A can generate false-positive results in some cases and lead to suboptimal dosing that may negatively impact patient therapy and prospect of survival. Our data show that DPYD genotyping should include the functional variant c.1129-5923C>G, and not the c.1236G>A proxy, to accurately predict DPD activity.
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Affiliation(s)
| | - Cyrine E. Haidar
- Department of Pharmacy and Pharmaceutical SciencesSt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical SciencesSt. Jude Children's Research HospitalMemphisTennesseeUSA
| | - Erin C. Boone
- Division of Clinical Pharmacology, Toxicology & Therapeutic InnovationChildren's Mercy Research Institute (CMRI)Kansas CityMissouriUSA
| | - Steven M. Offer
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Philip E. Empey
- Department of Pharmacy and TherapeuticsUniversity of Pittsburgh School of PharmacyPittsburghPennsylvaniaUSA
| | - Andrew Haddad
- Department of Pharmaceutical SciencesUniversity of Pittsburgh School of PharmacyPittsburghPennsylvaniaUSA
| | - Saba Tahir
- Medical College of Wisconsin, School of PharmacyMilwaukeeWisconsinUSA
| | | | | | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic InnovationChildren's Mercy Research Institute (CMRI)Kansas CityMissouriUSA
- School of MedicineUniversity of Missouri‐Kansas CityKansas CityMissouriUSA
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Stöllberger C, Finsterer J. Cannabidiol's impact on drug-metabolization. Eur J Intern Med 2023; 118:6-13. [PMID: 37541924 DOI: 10.1016/j.ejim.2023.07.029] [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: 04/17/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 08/06/2023]
Abstract
IMPORTANCE Products containing cannabidiol(CBD) are easily accessible. CBD is reported to inhibit the drug-metabolizing proteins(DMP) Cytochrome P450(CYP)3A4/5, CYP2C9, CYP2B6, CYP2D6, CYP2E1, CYP1A2, CYP2C19, carboxylesterase 1(CES1), uridine 5'diphospho-glucoronosyltransferase(UGT)1A9, UGT2B7, P-glycoprotein(P-gp) and Breast Cancer Resistance Protein(BCRP). The relevance of CBD-drug interactions is largely unknown. Aim of the study was to identify drugs, potentially interacting with orally ingested CBD, to assess whether CBD-drug interactions have been reported, and if substrates of DMP are frequently prescribed drugs. OBSERVATIONS Identified were 403 drugs as substrates of DMP. CBD-drug interactions were reported for 53/403 substrates in humans (n = 25), in vivo (n = 13) or in vitro (n = 15). In 31/53 substrates, CBD induced an increase, in 1/53 a decrease, in 4/53 no change in the substrate level. For 5/53 substrates, the results were controversial, and in 12/53 no substrate levels were reported. Among the 30 most frequently prescribed drugs in Germany were 67% substrates of DMP and among the 50 most frequently prescribed drugs in the USA 68%. RELEVANCE AND CONCLUSIONS There is an urgent need for pharmacologic studies on CBD-drug interactions. Patients should be educated on the potential risk and awareness should be increased among physicians. Regulatory authorities should become aware of the problem and start an initiative on an international level to increase the safety of CBD.
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Gallardo-Cóndor J, Naranjo P, Atarihuana S, Coello D, Guevara-Ramírez P, Flores-Espinoza R, Burgos G, López-Cortés A, Cabrera-Andrade A. Population-Specific Distribution of TPMT Deficiency Variants and Ancestry Proportions in Ecuadorian Ethnic Groups: Towards Personalized Medicine. Ther Clin Risk Manag 2023; 19:1005-1018. [PMID: 38050617 PMCID: PMC10693761 DOI: 10.2147/tcrm.s432856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
Purpose Thiopurine S-methyltransferase (TPMT) is an enzyme that metabolizes purine analogs, agents used in the treatment of acute lymphoblastic leukemia. Improper drug metabolism leads to toxicity in chemotherapy patients and reduces treatment effectiveness. TPMT variants associated with reduced enzymatic activity vary across populations. Therefore, studying these variants in heterogeneous populations, such as Ecuadorians, can help identify molecular causes of deficiency for this enzyme. Methods We sequenced the entire TPMT coding region in 550 Ecuadorian individuals from Afro-Ecuadorian, Indigenous, Mestizo, and Montubio ethnicities. Moreover, we conducted an ancestry analysis using 46 informative ancestry markers. Results We identified 8 single nucleotide variants in the coding region of TPMT. The most prevalent alleles were TPMT*3A, TPMT*3B, and TPMT*3C, with frequencies of 0.055, 0.012, and 0.015, respectively. Additionally, we found rare alleles TPMT*4 and TPMT*8 with frequencies of 0.005 and 0.003. Correlating the ancestry proportions with TPMT-deficient genotypes, we observed that the Native American ancestry proportion influenced the distribution of the TPMT*1/TPMT*3A genotype (OR = 5.977, p = 0.002), while the contribution of African ancestral populations was associated with the TPMT*1/TPMT*3C genotype (OR = 9.769, p = 0.003). The rates of TPMT-deficient genotypes observed in Mestizo (f = 0.121) and Indigenous (f = 0.273) groups provide evidence for the influence of Native American ancestry and the prevalence of the TPMT*3A allele. In contrast, although Afro-Ecuadorian groups demonstrate similar deficiency rates (f = 0.160), the genetic factors involved are associated with contributions from African ancestral populations, specifically the prevalent TPMT*3C allele. Conclusion The distribution of TPMT-deficient variants offers valuable insights into the populations under study, underscoring the necessity for genetic screening strategies to prevent thiopurine toxicity events among Latin American minority groups.
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Affiliation(s)
| | - Pablo Naranjo
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Sebastián Atarihuana
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Dayana Coello
- Laboratorios de Investigación, Universidad de Las Américas, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Rodrigo Flores-Espinoza
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Germán Burgos
- One Health Research Group, Facultad de Medicina, Universidad de Las Américas, Quito, Ecuador
- Grupo de Medicina Xenomica, Instituto de Ciencias Forenses, Universidad de Santiago de Compostela, Satiago de Compostela, Spain
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Alejandro Cabrera-Andrade
- Escuela de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
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Kreutz RP. Clopidogrel Pharmacogenomics: Validation in a Population of South-Asian Ancestry. JACC. ADVANCES 2023; 2:100572. [PMID: 38939475 PMCID: PMC11198343 DOI: 10.1016/j.jacadv.2023.100572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Affiliation(s)
- Rolf P. Kreutz
- Division of Cardiovascular Medicine, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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12
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Degaga A, Sirgu S, Huri HZ, Sim MS, Kebede T, Tegene B, Loganadan NK, Engidawork E, Shibeshi W. Association of Met420del Variant of Metformin Transporter Gene SLC22A1 with Metformin Treatment Response in Ethiopian Patients with Type 2 Diabetes. Diabetes Metab Syndr Obes 2023; 16:2523-2535. [PMID: 37641646 PMCID: PMC10460611 DOI: 10.2147/dmso.s426632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023] Open
Abstract
Objective This study aimed to evaluate whether the M420del variants of SLC22A1 (rs72552763) is associated with metformin treatment response in Ethiopian patients with type 2 diabetes mellitus (T2DM). Patients and Methods A prospective observational cohort study was conducted on 86 patients with T2DM who had been receiving metformin monotherapy for <1 year. Patients showing ≥0.5% reduction in HbA1c levels from baseline within 3 months and remained low for at least another 3 months were defined as responders while those patients with <0.5% reduction in HbA1c levels and/or those whom started a new class of glucose-lowering drug(s) because of unsatisfactory reduction were defined as non-responders. In addition, good glycemic control was observed when HbA1c ≤7.0%, and the above values were regarded as poor. Genotyping of rs72552763 SNP was performed using TaqMan® Drug Metabolism Enzyme Genotyping Assay and its association with metformin response and glycemic control were assessed by measuring the change in HbA1c and fasting blood glucose levels using Chi-square, logistic regression and Mann-Whitney U-test. Statistical significance was set at p <0.05. Results The minor allele frequency of the rs72552763 SNP of SLC22A1 was 9.3%. Metformin response was significantly higher in deletion_GAT (del_G) genotypes as compared to the wild-type GAT_GAT (G_G) genotypes. Furthermore, a significantly lower median treatment HbA1 level was found in del_G genotypes as compared to G_G genotypes. However, the association of rs72552763 with metformin response was not replicated at the allele level. In contrast, the minor del_allele was significantly associated with good glycemic control compared to the G_allele, though not replicated at del_G genotypes level. Conclusion This study demonstrated that metformin response was significantly higher in study participants with a heterozygous carrier of M420del variants of SLC22A1 as compared to the wild-type G_G genotypes after 3 months of treatment.
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Affiliation(s)
- Abraham Degaga
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Clinical Pharmacy & Pharmacy Practice, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Sisay Sirgu
- Department of Internal Medicine, Diabetes and Endocrinology Unit, Saint Paul Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Hasniza Zaman Huri
- Department of Clinical Pharmacy & Pharmacy Practice, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Maw Shin Sim
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Tedla Kebede
- Department of Internal Medicine, Diabetes and Endocrinology Unit, Addis Ababa University, Addis Ababa, Ethiopia
| | - Birhanemeskel Tegene
- Department of Microbiology, Saint Paul Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | | | - Ephrem Engidawork
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Workineh Shibeshi
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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Padmanabhan S, du Toit C, Dominiczak AF. Cardiovascular precision medicine - A pharmacogenomic perspective. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e28. [PMID: 38550953 PMCID: PMC10953758 DOI: 10.1017/pcm.2023.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 05/16/2024]
Abstract
Precision medicine envisages the integration of an individual's clinical and biological features obtained from laboratory tests, imaging, high-throughput omics and health records, to drive a personalised approach to diagnosis and treatment with a higher chance of success. As only up to half of patients respond to medication prescribed following the current one-size-fits-all treatment strategy, the need for a more personalised approach is evident. One of the routes to transforming healthcare through precision medicine is pharmacogenomics (PGx). Around 95% of the population is estimated to carry one or more actionable pharmacogenetic variants and over 75% of adults over 50 years old are on a prescription with a known PGx association. Whilst there are compelling examples of pharmacogenomic implementation in clinical practice, the case for cardiovascular PGx is still evolving. In this review, we shall summarise the current status of PGx in cardiovascular diseases and look at the key enablers and barriers to PGx implementation in clinical practice.
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Affiliation(s)
- Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Clea du Toit
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Anna F. Dominiczak
- BHF Glasgow Cardiovascular Research Centre, School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
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Samarasinghe SR, Hoy W, Jadhao S, McMorran BJ, Guchelaar HJ, Nagaraj SH. The pharmacogenomic landscape of an Indigenous Australian population. Front Pharmacol 2023; 14:1180640. [PMID: 37284308 PMCID: PMC10241071 DOI: 10.3389/fphar.2023.1180640] [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: 03/06/2023] [Accepted: 04/07/2023] [Indexed: 06/08/2023] Open
Abstract
Background: Population genomic studies of individuals of Indigenous ancestry have been extremely limited comprising <0.5% of participants in international genetic databases and genome-wide association studies, contributing to a "genomic gap" that limits their access to personalised medicine. While Indigenous Australians face a high burden of chronic disease and associated medication exposure, corresponding genomic and drug safety datasets are sorely lacking. Methods: To address this, we conducted a pharmacogenomic study of almost 500 individuals from a founder Indigenous Tiwi population. Whole genome sequencing was performed using short-read Illumina Novaseq6000 technology. We characterised the pharmacogenomics (PGx) landscape of this population by analysing sequencing results and associated pharmacological treatment data. Results: We observed that every individual in the cohort carry at least one actionable genotype and 77% of them carry at least three clinically actionable genotypes across 19 pharmacogenes. Overall, 41% of the Tiwi cohort were predicted to exhibit impaired CYP2D6 metabolism, with this frequency being much higher than that for other global populations. Over half of the population predicted an impaired CYP2C9, CYP2C19, and CYP2B6 metabolism with implications for the processing of commonly used analgesics, statins, anticoagulants, antiretrovirals, antidepressants, and antipsychotics. Moreover, we identified 31 potentially actionable novel variants within Very Important Pharmacogenes (VIPs), five of which were common among the Tiwi. We further detected important clinical implications for the drugs involved with cancer pharmacogenomics such as thiopurines and tamoxifen, immunosuppressants like tacrolimus and certain antivirals used in the hepatitis C treatment due to potential differences in their metabolic processing. Conclusion: The pharmacogenomic profiles generated in our study demonstrate the utility of pre-emptive PGx testing and have the potential to help guide the development and application of precision therapeutic strategies tailored to Tiwi Indigenous patients. Our research provides valuable insights on pre-emptive PGx testing and the feasibility of its use in ancestrally diverse populations, emphasizing the need for increased diversity and inclusivity in PGx investigations.
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Affiliation(s)
| | - Wendy Hoy
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Sudhir Jadhao
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Brendan J McMorran
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, ACT, Australia
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, Netherlands
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
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15
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Giorgetti A, Amurri S, Fazio G, Bini C, Anniballi L, Pirani F, Pelletti G, Pelotti S. The Evaluation of CYP2D6, CYP2C9, CYP2C19, and CYP2B6 Phenoconversion in Post-Mortem Casework: The Challenge of Forensic Toxicogenetics. Metabolites 2023; 13:metabo13050661. [PMID: 37233702 DOI: 10.3390/metabo13050661] [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: 04/05/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/27/2023] Open
Abstract
In toxicogenetics, an integrative approach including the prediction of phenotype based on post-mortem genotyping of drug-metabolising enzymes might help explain the cause of death (CoD) and manner of death (MoD). The use of concomitant drugs, however, might lead to phenoconversion, a mismatch between the phenotype based on the genotype and the metabolic profile actually observed after phenoconversion. The aim of our study was to evaluate the phenoconversion of CYP2D6, CYP2C9, CYP2C19, and CYP2B6 drug-metabolising enzymes in a series of autopsy cases tested positive for drugs that are substrates, inducers, or inhibitors of these enzymes. Our results showed a high rate of phenoconversion for all enzymes and a statistically significant higher frequency of poor and intermediate metabolisers for CYP2D6, CYP2C9, and CYP2C19 after phenoconversion. No association was found between phenotypes and CoD or MoD, suggesting that, although phenoconversion might be useful for a forensic toxicogenetics approach, more research is needed to overcome the challenges arising from the post-mortem setting.
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Affiliation(s)
- Arianna Giorgetti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Sara Amurri
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Giulia Fazio
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Carla Bini
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Laura Anniballi
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Filippo Pirani
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Guido Pelletti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
| | - Susi Pelotti
- Unit of Legal Medicine, Department of Medical and Surgical Sciences, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy
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16
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Developing supervised machine learning algorithms to evaluate the therapeutic effect and laboratory-related adverse events of cyclosporine and tacrolimus in renal transplants. Int J Clin Pharm 2023:10.1007/s11096-023-01545-5. [PMID: 36848022 DOI: 10.1007/s11096-023-01545-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/18/2023] [Indexed: 03/01/2023]
Abstract
BACKGROUND Single nucleotide polymorphisms influence the effects of tacrolimus and cyclosporine in renal transplants. AIM We set out to use machine learning algorithms (MLAs) to identify variables that predict the therapeutic effects and adverse events following tacrolimus and cyclosporine administration in renal transplant patients. METHOD We sampled 120 adult renal transplant patients (on cyclosporine or tacrolimus). Generalized linear model (GLM), support vector machine (SVM), artificial neural network (ANN), Chi-square automatic interaction detection, classification and regression tree, and K-nearest neighbors were the chosen MLAs. The mean absolute error (MAE), relative mean square error (RMSE), and regression coefficient (β) with a 95% confidence interval (CI) were used as the model parameters. RESULTS For a stable dose of tacrolimus, the MAEs (RMSEs) of GLM, SVM, and ANN were 1.3 (1.5), 1.3 (1.8), and 1.7 (2.3) mg/day, respectively. GLM revealed that the POR*28 genotype and age significantly predicted the stable dose of tacrolimus as follows: POR*28 (β -1.8; 95% CI -3, -0.5; p = 0.006), and age (β -0.04; 95% CI -0.1, -0.006; p = 0.02). For a stable dose of cyclosporine, MAEs (RMSEs) of 93.2 (103.4), 79.1 (115.2), and 73.7 (91.7) mg/day were observed with GLM, SVM, and ANN, respectively. GLM revealed the following predictors of a stable dose of cyclosporine: CYP3A5*3 (β -80.8; 95% CI -130.3, -31.2; p = 0.001), and age (β -3.4; 95% CI -5.9, -0.9; p = 0.007). CONCLUSION We observed that various MLAs could identify significant predictors that were useful to optimize tacrolimus and cyclosporine dosing regimens; yet, the findings must be externally validated.
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17
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Zhou Y, Lauschke VM. The genetic landscape of major drug metabolizing cytochrome P450 genes-an updated analysis of population-scale sequencing data. THE PHARMACOGENOMICS JOURNAL 2022; 22:284-293. [PMID: 36068297 PMCID: PMC9674520 DOI: 10.1038/s41397-022-00288-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Genes encoding cytochrome P450 enzymes (CYPs) are extremely polymorphic and multiple CYP variants constitute clinically relevant biomarkers for the guidance of drug selection and dosing. We previously reported the distribution of the most relevant CYP alleles using population-scale sequencing data. Here, we update these findings by making use of the increasing wealth of data, incorporating whole exome and whole genome sequencing data from 141,614 unrelated individuals across 12 human populations. We furthermore extend our previous studies by systematically considering also uncharacterized rare alleles and reveal that they contribute between 1.5% and 17.5% to the overall genetically encoded functional variability. By using established guidelines, we aggregate and translate the available sequencing data into population-specific patterns of metabolizer phenotypes. Combined, the presented data refine the worldwide landscape of ethnogeographic variability in CYP genes and aspire to provide a relevant resource for the optimization of population-specific genotyping strategies and precision public health.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden.
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University of Tuebingen, Tuebingen, Germany.
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Farinango C, Gallardo-Cóndor J, Freire-Paspuel B, Flores-Espinoza R, Jaramillo-Koupermann G, López-Cortés A, Burgos G, Tejera E, Cabrera-Andrade A. Genetic Variations of the DPYD Gene and Its Relationship with Ancestry Proportions in Different Ecuadorian Trihybrid Populations. J Pers Med 2022; 12:jpm12060950. [PMID: 35743735 PMCID: PMC9225136 DOI: 10.3390/jpm12060950] [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: 05/04/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022] Open
Abstract
Dihydropyrimidine dehydrogenase is one of the main pharmacological metabolizers of fluoropyrimidines, a group of drugs widely used in clinical oncology. Around 20 to 30% of patients treated with fluoropyrimidines experience severe toxicity caused by a partial or total decrease in enzymatic activity. This decrease is due to molecular variants in the DPYD gene. Their prevalence and allelic frequencies vary considerably worldwide, so their description in heterogeneous groups such as the Ecuadorian population will allow for the description of pharmacogenetic variants and proper characterization of this population. Thus, we genotyped all the molecular variants with a predictive value for DPYD in a total of 410 Ecuadorian individuals belonging to Mestizo, Afro-Ecuadorian, and Indigenous ethnic groups. Moreover, we developed a genetic ancestry analysis using 46 autosomal ancestry informative markers. We determined 20 genetic variations in 5 amplified regions, including 3 novel single nucleotide variants. The allele frequencies for DPYD variants c.1627G>A (*5, rs1801159), c.1129-15T>C (rs56293913), c.1218G>A (rs61622928), rs1337752, rs141050810, rs2786783, rs2811178, and g.97450142G>A (chr1, GRCh38.p13) are significantly related to Native American and African ancestry proportions. In addition, the FST calculated from these variants demonstrates the closeness between Indigenous and Mestizo populations, and evidences genetic divergence between Afro-Ecuadorian groups when compared with Mestizo and Indigenous ethnic groups. In conclusion, the genetic variability in the DPYD gene is related to the genetic component of ancestral populations in different Ecuadorian ethnic groups. The absence and low frequency of variants with predictive value for fluoropyrimidine toxicity such as DPYD *2A, HapB3, and c.2846A>T (prevalent in populations with European ancestry) is consistent with the genetic background found.
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Affiliation(s)
- Camila Farinango
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito 170125, Ecuador; (C.F.); (J.G.-C.); (E.T.)
| | - Jennifer Gallardo-Cóndor
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito 170125, Ecuador; (C.F.); (J.G.-C.); (E.T.)
| | - Byron Freire-Paspuel
- Laboratorios de Investigación, Universidad de Las Américas, Quito 170125, Ecuador; (B.F.-P.); (R.F.-E.)
- Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Rodrigo Flores-Espinoza
- Laboratorios de Investigación, Universidad de Las Américas, Quito 170125, Ecuador; (B.F.-P.); (R.F.-E.)
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20550-013, Brazil
| | - Gabriela Jaramillo-Koupermann
- Laboratorio de Biología Molecular, Subproceso de Anatomía Patológica, Hospital de Especialidades Eugenio Espejo, Quito 170403, Ecuador;
| | - Andrés López-Cortés
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito 170125, Ecuador; (A.L.-C.); (G.B.)
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito 170302, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28001 Madrid, Spain
| | - Germán Burgos
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito 170125, Ecuador; (A.L.-C.); (G.B.)
| | - Eduardo Tejera
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito 170125, Ecuador; (C.F.); (J.G.-C.); (E.T.)
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito 170125, Ecuador
| | - Alejandro Cabrera-Andrade
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito 170125, Ecuador
- Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito 170125, Ecuador
- Correspondence:
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Patrinos GP, Shuldiner AR. Pharmacogenomics: the low-hanging fruit in the personalized medicine tree. Hum Genet 2022; 141:1109-1111. [PMID: 35482087 DOI: 10.1007/s00439-022-02456-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- George P Patrinos
- Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, University of Patras School of Health Sciences, University Campus, Rion, 265 04, Patras, Greece. .,College of Medicine and Health Sciences, Department of Genetics and Genomics, United Arab Emirates University, Al-Ain, United Arab Emirates. .,Zayed Center for Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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