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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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2
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Gallego-Fabrega C, Muiño E, Cárcel-Márquez J, Llucià-Carol L, Lledós M, Martín-Campos JM, Cullell N, Fernández-Cadenas I. Genome-Wide Studies in Ischaemic Stroke: Are Genetics Only Useful for Finding Genes? Int J Mol Sci 2022; 23:6840. [PMID: 35743317 PMCID: PMC9224543 DOI: 10.3390/ijms23126840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023] Open
Abstract
Ischaemic stroke is a complex disease with some degree of heritability. This means that heritability factors, such as genetics, could be risk factors for ischaemic stroke. The era of genome-wide studies has revealed some of these heritable risk factors, although the data generated by these studies may also be useful in other disciplines. Analysis of these data can be used to understand the biological mechanisms associated with stroke risk and stroke outcome, to determine the causality between stroke and other diseases without the need for expensive clinical trials, or to find potential drug targets with higher success rates than other strategies. In this review we will discuss several of the most relevant studies regarding the genetics of ischaemic stroke and the potential use of the data generated.
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Affiliation(s)
- Cristina Gallego-Fabrega
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Elena Muiño
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Jara Cárcel-Márquez
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Laia Llucià-Carol
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
- Institute for Biomedical Research of Barcelona (IIBB), National Spanish Research Council (CSIC), 08036 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Miquel Lledós
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Jesús M. Martín-Campos
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Natalia Cullell
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
| | - Israel Fernández-Cadenas
- Stroke Pharmacogenomics and Genetics Group, Institut de Recerca de l’Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; (C.G.-F.); (E.M.); (J.C.-M.); (L.L.-C.); (M.L.); (J.M.M.-C.); (N.C.)
- Stroke Pharmacogenomics and Genetics Group, Fundació MútuaTerrassa per la Docència i la Recerca, 08221 Terrassa, Spain
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3
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Huang Q, Cao L, Luo N, Qian H, Wei M, Xue L, Zhou Q, Zou B, Tan L, Chu Y, Ma X, Wang C, Wu H, Zhang L, Sun L, Li D, Fan X, Miao L, Zhou G. Predicting Range of Initial Warfarin Dose Based on Pharmacometabolomic and Genetic Inputs. Clin Pharmacol Ther 2021; 110:1585-1594. [PMID: 34460938 DOI: 10.1002/cpt.2407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/22/2021] [Indexed: 12/29/2022]
Abstract
Anticoagulation response to warfarin during the initial stage of therapy varies among individuals. In this study, we aimed to combine pharmacometabolomic and pharmacogenetic data to predict interindividual variation in warfarin response, and, on this basis, suggest an initial daily dose range. The baseline metabolic profiles, genotypes, and clinical information of 160 patients with heart valve disease served as the variables of the function of the last international normalized ratio measured before a patient's discharge (INRday7 ) to screen for potential biomarkers. The partial least-squares model showed that two baseline metabolites (uridine and guanosine), one single-nucleotide variation (VKORC1), and four clinical parameters (weight, creatinine level, amiodarone usage, and initial daily dose) had good predictive power for INRday7 (R2 = 0.753 for the training set, 0.643 for the test set). With these biomarkers, a machine learning algorithm (two-dimensional linear discriminant analysis-multinomial logit model) was used to predict the subgroups with extremely warfarin-sensitive or less warfarin-sensitive patients with a prediction accuracy of 91% for the training set and 90% for the test set, indicating that individual responses to warfarin could be effectively predicted. Based on this model, we have successfully designed an algorithm,"IniWarD," for predicting an effective dose range in the initial 7-day warfarin therapy. The results indicate that the daily dose range suggested by the IniWarD system is more appropriate than that of the conventional genotype-based method, and the risk of bleeding or thrombus due to warfarin could thus be avoided.
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Affiliation(s)
- Qing Huang
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Ling Cao
- National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Nan Luo
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hanyu Qian
- National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Meng Wei
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Ling Xue
- Department of Clinical Pharmacology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiang Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Li Tan
- National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Changtian Wang
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Haiwei Wu
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Lei Zhang
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Lei Sun
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Demin Li
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Xialei Fan
- National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Liyan Miao
- Department of Clinical Pharmacology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
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4
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McInnes G, Yee SW, Pershad Y, Altman RB. Genomewide Association Studies in Pharmacogenomics. Clin Pharmacol Ther 2021; 110:637-648. [PMID: 34185318 PMCID: PMC8376796 DOI: 10.1002/cpt.2349] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022]
Abstract
The increasing availability of genotype data linked with information about drug-response phenotypes has enabled genomewide association studies (GWAS) that uncover genetic determinants of drug response. GWAS have discovered associations between genetic variants and both drug efficacy and adverse drug reactions. Despite these successes, the design of GWAS in pharmacogenomics (PGx) faces unique challenges. In this review, we analyze the last decade of GWAS in PGx. We review trends in publications over time, including the drugs and drug classes studied and the clinical phenotypes used. Several data sharing consortia have contributed substantially to the PGx GWAS literature. We anticipate increased focus on biobanks and highlight phenotypes that would best enable future PGx discoveries.
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Affiliation(s)
- Gregory McInnes
- Biomedical Informatics Training Program, Stanford University, Stanford, California, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, California, USA
| | - Yash Pershad
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Departments of Genetics, Medicine, Biomedical Data Science, Stanford, California, USA
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5
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Davis BH, Williams K, Absher D, Korf B, Limdi NA. Evaluation of population-level pharmacogenetic actionability in Alabama. Clin Transl Sci 2021; 14:2327-2338. [PMID: 34121327 PMCID: PMC8604228 DOI: 10.1111/cts.13097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/14/2021] [Accepted: 05/16/2021] [Indexed: 12/20/2022] Open
Abstract
The evolution of evidence and availability of Clinical Pharmacogenetic Implementation Consortium (CPIC) guidelines have enabled assessment of pharmacogenetic (PGx) actionability and clinical implementation. However, population‐level actionability is not well‐characterized. We leveraged the Alabama Genomic Health Initiative (AGHI) to evaluate population‐level PGx actionability. Participants (>18 years), representing all 67 Alabama counties, were genotyped using the Illumina Global Screening array. Using CPIC guidelines, actionability was evaluated using (1) genotype data and genetic ancestry, (2) prescribing data, and (3) combined genotype and medication data. Of 6,331 participants, 4230 had genotype data and 3386 had genotype and prescription data (76% women; 76% White/18% Black [self‐reported]). Genetic ancestry was concordant with self‐reported race. For CPIC level A genes, 98.6% had an actionable genotype (99.4% Blacks/African; 98.5% White/European). With the exception of DPYD and CYP2C19, the prevalence of actionable genotypes by gene differed significantly by race. Based on prescribing, actionability was highest for CYP2D6 (70.9%), G6PD (54.1%), CYP2C19 (53.5%), and CYP2C9 (47.5%). Among participants prescribed atenolol, carvedilol, or metoprolol, ~ 50% had an actionable ADRB1 genotype, associated with decreased therapeutic response, with higher actionability among Blacks compared to Whites (62.5% vs. 47.4%; p < 0.0001). Based on both genotype and prescribing frequencies, no significant differences in actionability were observed between men and women. This statewide effort highlights PGx population‐level impact to help optimize pharmacotherapy. Almost all Alabamians harbor an actionable genotype, and a significant proportion are prescribed affected medications. Statewide efforts, such as AGHI, lay the foundation for translational research and evaluate “real‐world” outcomes of PGx.
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Affiliation(s)
- Brittney H Davis
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kelly Williams
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Devin Absher
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bruce Korf
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Nita A Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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6
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Al Ammari M, AlBalwi M, Sultana K, Alabdulkareem IB, Almuzzaini B, Almakhlafi NS, Aldrees M, Alghamdi J. The effect of the VKORC1 promoter variant on warfarin responsiveness in the Saudi WArfarin Pharmacogenetic (SWAP) cohort. Sci Rep 2020; 10:11613. [PMID: 32669629 PMCID: PMC7363835 DOI: 10.1038/s41598-020-68519-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/25/2020] [Indexed: 11/09/2022] Open
Abstract
Warfarin is a frequently prescribed oral anticoagulant with a narrow therapeutic index, requiring careful dosing and monitoring. However, patients respond with significant inter-individual variability in terms of the dose and responsiveness of warfarin, attributed to genetic polymorphisms within the genes responsible for the pharmacokinetics and pharmacodynamics of warfarin. Extensive warfarin pharmacogenetic studies have been conducted, including studies resulting in genotype-guided dosing guidelines, but few large scale studies have been conducted with the Saudi population. In this study, we report the study design and baseline characteristics of the Saudi WArfarin Pharmacogenomics (SWAP) cohort, as well as the association of the VKORC1 promoter variants with the warfarin dose and the time to a stable INR. In the 936 Saudi patients recruited in the SWAP study, the minor allele C of rs9923231 was significantly associated with a 8.45 mg higher weekly warfarin dose (p value = 4.0 × 10-46), as well as with a significant delay in achieving a stable INR level. The addition of the rs9923231 status to the model, containing all the significant clinical variables, doubled the warfarin dose explained variance to 31%. The SWAP cohort represents a valuable resource for future research with the objective of identifying rare and prevalent genetic variants, which can be incorporated in personalized anticoagulation therapy for the Saudi population.
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Affiliation(s)
- Maha Al Ammari
- Pharmaceutical Care Services, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mohammed AlBalwi
- Department of Pathology and Laboratory, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Khizra Sultana
- Research Office, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Ibrahim B Alabdulkareem
- Health Sciences Research Center, King Abdullah Bin Abdulaziz University Hospital, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Bader Almuzzaini
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Nada S Almakhlafi
- Pharmaceutical Care Services, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mohammed Aldrees
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Jahad Alghamdi
- King Abdullah International Medical Research Center, The Saudi Biobank, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.
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7
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Asiimwe IG, Zhang EJ, Osanlou R, Krause A, Dillon C, Suarez-Kurtz G, Zhang H, Perini JA, Renta JY, Duconge J, Cavallari LH, Marcatto LR, Beasly MT, Perera MA, Limdi NA, Santos PCJL, Kimmel SE, Lubitz SA, Scott SA, Kawai VK, Jorgensen AL, Pirmohamed M. Genetic Factors Influencing Warfarin Dose in Black-African Patients: A Systematic Review and Meta-Analysis. Clin Pharmacol Ther 2020; 107:1420-1433. [PMID: 31869433 PMCID: PMC7217737 DOI: 10.1002/cpt.1755] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022]
Abstract
Warfarin is the most commonly used oral anticoagulant in sub-Saharan Africa. Dosing is challenging due to a narrow therapeutic index and high interindividual variability in dose requirements. To evaluate the genetic factors affecting warfarin dosing in black-Africans, we performed a meta-analysis of 48 studies (2,336 patients). Significant predictors for CYP2C9 and stable dose included rs1799853 (CYP2C9*2), rs1057910 (CYP2C9*3), rs28371686 (CYP2C9*5), rs9332131 (CYP2C9*6), and rs28371685 (CYP2C9*11) reducing dose by 6.8, 12.5, 13.4, 8.1, and 5.3 mg/week, respectively. VKORC1 variants rs9923231 (-1639G>A), rs9934438 (1173C>T), rs2359612 (2255C>T), rs8050894 (1542G>C), and rs2884737 (497T>G) decreased dose by 18.1, 21.6, 17.3, 11.7, and 19.6 mg/week, respectively, whereas rs7294 (3730G>A) increased dose by 6.9 mg/week. Finally, rs12777823 (CYP2C gene cluster) was associated with a dose reduction of 12.7 mg/week. Few studies were conducted in Africa, and patient numbers were small, highlighting the need for further work in black-Africans to evaluate genetic factors determining warfarin response.
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Affiliation(s)
- Innocent G. Asiimwe
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Eunice J. Zhang
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Rostam Osanlou
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, Johannesburg, South Africa
| | - Chrisly Dillon
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | | | - Honghong Zhang
- Department of Pharmacology, Center for Pharmacogenomics, Northwestern University, Chicago IL
| | - Jamila A Perini
- Research Laboratory of Pharmaceutical Sciences, West Zone State University-UEZO, Rio de Janeiro, Brazil
| | - Jessicca Y. Renta
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067
| | - Jorge Duconge
- University of Puerto Rico School of Pharmacy, Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067
| | - Larisa H Cavallari
- Center for Pharmacogenomics, Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL, USA
| | - Leiliane R. Marcatto
- Laboratory of Genetics and Molecular Cardiology, Faculdade de Medicina FMUSP, Heart Institute (InCor), Universidade de São Paulo, São Paulo, Brazil
| | - Mark T. Beasly
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | - Minoli A Perera
- Department of Pharmacology, Center for Pharmacogenomics, Northwestern University, Chicago IL
| | - Nita A. Limdi
- Department of Neurology & Epidemiology, Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham
| | - Paulo C. J. L. Santos
- Department of Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, EPM-Unifesp, São Paulo, Brazil
| | - Stephen E. Kimmel
- Perelman School of Medicine at the University of Pennsylvania, Department of Biostatistics, Epidemiology, and Informatics
| | - Steven A. Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Vivian K. Kawai
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrea L. Jorgensen
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool
- These authors contributed equally: Andrea Jorgensen and Munir Pirmohamed
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool
- These authors contributed equally: Andrea Jorgensen and Munir Pirmohamed
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8
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Gulilat M, Lamb T, Teft WA, Wang J, Dron JS, Robinson JF, Tirona RG, Hegele RA, Kim RB, Schwarz UI. Targeted next generation sequencing as a tool for precision medicine. BMC Med Genomics 2019; 12:81. [PMID: 31159795 PMCID: PMC6547602 DOI: 10.1186/s12920-019-0527-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/13/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) enables rapid identification of common and rare genetic variation. The detection of variants contributing to therapeutic drug response or adverse effects is essential for implementation of individualized pharmacotherapy. Successful application of short-read based NGS to pharmacogenes with high sequence homology, nearby pseudogenes and complex structure has been previously shown despite anticipated technical challenges. However, little is known regarding the utility of such panels to detect copy number variation (CNV) in the highly polymorphic cytochrome P450 (CYP) 2D6 gene, or to identify the promoter (TA)7 TAA repeat polymorphism UDP glucuronosyltransferase (UGT) 1A1*28. Here we developed and validated PGxSeq, a targeted exome panel for pharmacogenes pertinent to drug disposition and/or response. METHODS A panel of capture probes was generated to assess 422 kb of total coding region in 100 pharmacogenes. NGS was carried out in 235 subjects, and sequencing performance and accuracy of variant discovery validated in clinically relevant pharmacogenes. CYP2D6 CNV was determined using the bioinformatics tool CNV caller (VarSeq). Identified SNVs were assessed in terms of population allele frequency and predicted functional effects through in silico algorithms. RESULTS Adequate performance of the PGxSeq panel was demonstrated with a depth-of-coverage (DOC) ≥ 20× for at least 94% of the target sequence. We showed accurate detection of 39 clinically relevant gene variants compared to standard genotyping techniques (99.9% concordance), including CYP2D6 CNV and UGT1A1*28. Allele frequency of rare or novel variants and predicted function in 235 subjects mirrored findings from large genomic datasets. A large proportion of patients (78%, 183 out of 235) were identified as homozygous carriers of at least one variant necessitating altered pharmacotherapy. CONCLUSIONS PGxSeq can serve as a comprehensive, rapid, and reliable approach for the detection of common and novel SNVs in pharmacogenes benefiting the emerging field of precision medicine.
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Affiliation(s)
- Markus Gulilat
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Tyler Lamb
- Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Wendy A Teft
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada
| | - Jian Wang
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Jacqueline S Dron
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - John F Robinson
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Rommel G Tirona
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Robert A Hegele
- Robarts Research Institute, Western University, 1151 Richmond St. N, London, ON, N6A 5B7, Canada
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.,Department of Physiology and Pharmacology, Western University, Medical Sciences Building, Room 216, London, ON, N6A 5C1, Canada
| | - Ute I Schwarz
- Division of Clinical Pharmacology, Department of Medicine, Western University, London Health Sciences Centre - University Hospital, 339 Windermere Road, London, ON, N6A 5A5, Canada.
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9
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Li X, Li D, Wu JC, Liu ZQ, Zhou HH, Yin JY. Precision dosing of warfarin: open questions and strategies. THE PHARMACOGENOMICS JOURNAL 2019; 19:219-229. [PMID: 30745565 DOI: 10.1038/s41397-019-0083-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/17/2018] [Accepted: 12/21/2018] [Indexed: 12/30/2022]
Abstract
Warfarin has a very narrow therapeutic window and obvious interindividual variability in its effects, with many factors contributing to the body's response. Algorithms incorporating multiple genetic, environment and clinical factors have been established to select a precision dose for each patient. A number of randomized controlled trials (RCTs) were conducted to explore whether patients could benefit from these algorithms; however, the results were inconsistent. Some questions remain to be resolved. Recently, new genetic and non-genetic factors have been discovered to contribute to variability in optimal warfarin doses. The results of further RCTs have been unveiled, and guidelines for pharmacogenetically guided warfarin dosing have been updated. Based on these most recent advancements, we summarize some open questions in this field and try to propose possible strategies to resolve them.
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Affiliation(s)
- Xi Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China
| | - Dan Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China
| | - Ji-Chu Wu
- Department of Cardiovascular, Central Hospital of Shaoyang, Shaoyang, 422000, P. R. China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China.,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, P. R. China. .,Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China. .,Hunan Provincial Gynecological Cancer Diagnosis and Treatment Engineering Research Center, Changsha, 410078, P. R. China.
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Abstract
Precision medicine is an approach in which the characteristics of patients as well as their diseases are used to identify optimal therapy; it links researchers, patients, health care providers, and clinical laboratories. In precision medicine, specific molecular characteristics of an untreatable cancer can be targeted by specific molecular-based therapy. Access to high-quality human tissues is necessary to determine many characteristics of patients and their diseases (such as targetable molecules). There are ethical issues in using human tissues in precision medicine, including informed consent and confidentiality, optimal utilization, quality of tissues, and minimization of bias. When human tissues are obtained for patient therapy, the bioresource should be a component certified by Clinical Laboratory Improvement Amendments. For precision medicine to benefit medically underserved populations requires extensive focused research, planning, and resources, some of which are currently unavailable at rural and other sites where care is provided to underserved populations.
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11
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Guo C, Lin X, Yin J, Xie X, Li J, Meng X, Wu J, Huang L, Huang Z, Yang G, Zhou H, Chen X. Pharmacogenomics signature: A novel strategy on the individual differences in drug response. Cancer Lett 2018; 420:190-194. [DOI: 10.1016/j.canlet.2018.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 01/04/2023]
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12
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Affiliation(s)
- Sarah Jones
- Future Science Group, Unitec House, 2 Albert Place, London N31QB, UK
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