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Lantoine J, Brysse A, Dideberg V, Claes K, Symoens S, Coucke W, Benoit V, Rombout S, De Rycke M, Seneca S, Van Laer L, Wuyts W, Corveleyn A, Van Den Bogaert K, Rydlewski C, Wilkin F, Ravoet M, Fastré E, Capron A, Vandevelde NM. Frequency of Participation in External Quality Assessment Programs Focused on Rare Diseases: Belgian Guidelines for Human Genetics Centers. JMIR Med Inform 2021; 9:e27980. [PMID: 34255700 PMCID: PMC8314149 DOI: 10.2196/27980] [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: 03/09/2021] [Accepted: 04/25/2021] [Indexed: 11/23/2022] Open
Abstract
Background Participation in quality controls, also called external quality assessment (EQA) schemes, is required for the ISO15189 accreditation of the Medical Centers of Human Genetics. However, directives on the minimal frequency of participation in genetic quality control schemes are lacking or too heterogeneous, with a possible impact on health care quality. Objective The aim of this project is to develop Belgian guidelines on the frequency of participation in quality controls for genetic testing in the context of rare diseases. Methods A group of experts analyzed 90 EQA schemes offered by accredited providers and focused on analyses used for the diagnosis of rare diseases. On that basis, the experts developed practical recommendations about the minimal frequencies of participation of the Medical Centers of Human Genetics in quality controls and how to deal with poor performances and change management. These guidelines were submitted to the Belgian Accreditation Body and then reviewed and approved by the Belgian College of Human Genetics and Rare Diseases and by the National Institute for Health and Disability Insurance. Results The guidelines offer a decisional algorithm for the minimal frequency of participation in human genetics EQA schemes. This algorithm has been developed taking into account the scopes of the EQA schemes, the levels of experience, and the annual volumes of the Centers of Human Genetics in the performance of the tests considered. They include three key principles: (1) the recommended annual assessment of all genetic techniques and technological platforms, if possible through EQAs covering the technique, genotyping, and clinical interpretation; (2) the triennial assessment of the genotyping and interpretation of specific germline mutations and pharmacogenomics analyses; and (3) the documentation of actions undertaken in the case of poor performances and the participation to quality control the following year. The use of a Bayesian statistical model has been proposed to help the Centers of Human Genetics to determine the theoretical number of tests that should be annually performed to achieve a certain threshold of performance (eg, a maximal error rate of 1%). Besides, the guidelines insist on the role and responsibility of the national public health authorities in the follow-up of the quality of analyses performed by the Medical Centers of Human Genetics and in demonstrating the cost-effectiveness and rationalization of participation frequency in these quality controls. Conclusions These guidelines have been developed based on the analysis of a large panel of EQA schemes and data collected from the Belgian Medical Centers of Human Genetics. They are applicable to other countries and will facilitate and improve the quality management and financing systems of the Medical Centers of Human Genetics.
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Affiliation(s)
- Joséphine Lantoine
- Rare Diseases Unit, Department of Quality of Laboratories, Sciensano, Brussels, Belgium
| | - Anne Brysse
- Center of Human Genetics, CHU of Liège, University of Liège, Liège, Belgium
| | - Vinciane Dideberg
- Center of Human Genetics, CHU of Liège, University of Liège, Liège, Belgium
| | - Kathleen Claes
- Center for Medical Genetics, Ghent University Hospital, Gent, Belgium
| | - Sofie Symoens
- Center for Medical Genetics, Ghent University Hospital, Gent, Belgium
| | - Wim Coucke
- Department of Quality of Laboratories, Sciensano, Brussels, Belgium
| | - Valérie Benoit
- Center of Human Genetics, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Sonia Rombout
- Center of Human Genetics, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Martine De Rycke
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sara Seneca
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lut Van Laer
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Edegem, Belgium
| | - Wim Wuyts
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Edegem, Belgium
| | - Anniek Corveleyn
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Catherine Rydlewski
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Françoise Wilkin
- Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Ravoet
- Center for Human Genetics, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Elodie Fastré
- Center for Human Genetics, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Arnaud Capron
- Department of Quality of Laboratories, Sciensano, Brussels, Belgium
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Soto-Pedre E, Siddiqui MK, Maroteau C, Dawed AY, Doney AS, Palmer CNA, Pearson ER, Leese GP. Polymorphism in INSR Locus Modifies Risk of Atrial Fibrillation in Patients on Thyroid Hormone Replacement Therapy. Front Genet 2021; 12:652878. [PMID: 34249083 PMCID: PMC8260687 DOI: 10.3389/fgene.2021.652878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Aims Atrial fibrillation (AF) is a risk for patients receiving thyroid hormone replacement therapy. No published work has focused on pharmacogenetics relevant to thyroid dysfunction and AF risk. We aimed to assess the effect of L-thyroxine on AF risk stratified by a variation in a candidate gene. Methods and Results A retrospective follow-up study was done among European Caucasian patients from the Genetics of Diabetes Audit and Research in Tayside Scotland cohort (Scotland, United Kingdom). Linked data on biochemistry, prescribing, hospital admissions, demographics, and genetic biobank were used to ascertain patients on L-thyroxine and diagnosis of AF. A GWAS-identified insulin receptor-INSR locus (rs4804416) was the candidate gene. Cox survival models and sensitivity analyses by taking competing risk of death into account were used. Replication was performed in additional sample (The Genetics of Scottish Health Research register, GoSHARE), and meta-analyses across the results of the study and replication cohorts were done. We analyzed 962 exposed to L-thyroxine and 5,840 unexposed patients who were rs4804416 genotyped. The rarer G/G genotype was present in 18% of the study population. The total follow-up was up to 20 years, and there was a significant increased AF risk for patients homozygous carriers of the G allele exposed to L-thyroxine (RHR = 2.35, P = 1.6e-02). The adjusted increased risk was highest within the first 3 years of exposure (RHR = 9.10, P = 8.5e-04). Sensitivity analysis yielded similar results. Effects were replicated in GoSHARE (n = 3,190). Conclusion Homozygous G/G genotype at the INSR locus (rs4804416) is associated with an increased risk of AF in patients on L-thyroxine, independent of serum of free thyroxine and thyroid-stimulating hormone serum concentrations.
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Affiliation(s)
- Enrique Soto-Pedre
- Division of Population Health and Genomics, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Moneeza K Siddiqui
- Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Cyrielle Maroteau
- Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Adem Y Dawed
- Division of Population Health and Genomics, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Alex S Doney
- Medicines Monitoring Unit and Hypertension Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Colin N A Palmer
- Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Ewan R Pearson
- Division of Population Health and Genomics, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Graham P Leese
- Division of Population Health and Genomics, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom.,Department of Endocrinology and Diabetes, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
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Fast screening of covariates in population models empowered by machine learning. J Pharmacokinet Pharmacodyn 2021; 48:597-609. [PMID: 34019213 PMCID: PMC8225540 DOI: 10.1007/s10928-021-09757-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 04/22/2021] [Indexed: 12/15/2022]
Abstract
One of the objectives of Pharmacometry (PMX) population modeling is the identification of significant and clinically relevant relationships between parameters and covariates. Here, we demonstrate how this complex selection task could benefit from supervised learning algorithms using importance scores. We compare various classical methods with three machine learning (ML) methods applied to NONMEM empirical Bayes estimates: random forest, neural networks (NNs), and support vector regression (SVR). The performance of the ML models is assessed using receiver operating characteristic (ROC) curves. The F1 score, which measures test accuracy, is used to compare ML and PMX approaches. Methods are applied to different scenarios of covariate influence based on simulated pharmacokinetics data. ML achieved similar or better F1 scores than stepwise covariate modeling (SCM) and conditional sampling for stepwise approach based on correlation tests (COSSAC). Correlations between covariates and the number of false covariates does not affect the performance of any method, but effect size has an impact. Methods are not equivalent with respect to computational speed; SCM is 30 and 100-times slower than NN and SVR, respectively. The results are validated in an additional scenario involving 100 covariates. Taken together, the results indicate that ML methods can greatly increase the efficiency of population covariate model building in the case of large datasets or complex models that require long run-times. This can provide fast initial covariate screening, which can be followed by more conventional PMX approaches to assess the clinical relevance of selected covariates and build the final model.
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Meyers JL, Salvatore JE. Genetic and Social-Environmental Influences on Substance Use and Disorders. Psychiatr Ann 2021. [DOI: 10.3928/00485713-20210311-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes. PLoS One 2021; 16:e0244876. [PMID: 33411719 PMCID: PMC7790408 DOI: 10.1371/journal.pone.0244876] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
Characterizing the gut microbiota in terms of their capacity to interfere with drug metabolism is necessary to achieve drug efficacy and safety. Although examples of drug-microbiome interactions are well-documented, little has been reported about a computational pipeline for systematically identifying and characterizing bacterial enzymes that process particular classes of drugs. The goal of our study is to develop a computational approach that compiles drugs whose metabolism may be influenced by a particular class of microbial enzymes and that quantifies the variability in the collective level of those enzymes among individuals. The present paper describes this approach, with microbial β-glucuronidases as an example, which break down drug-glucuronide conjugates and reactivate the drugs or their metabolites. We identified 100 medications that may be metabolized by β-glucuronidases from the gut microbiome. These medications included morphine, estrogen, ibuprofen, midazolam, and their structural analogues. The analysis of metagenomic data available through the Sequence Read Archive (SRA) showed that the level of β-glucuronidase in the gut metagenomes was higher in males than in females, which provides a potential explanation for the sex-based differences in efficacy and toxicity for several drugs, reported in previous studies. Our analysis also showed that infant gut metagenomes at birth and 12 months of age have higher levels of β-glucuronidase than the metagenomes of their mothers and the implication of this observed variability was discussed in the context of breastfeeding as well as infant hyperbilirubinemia. Overall, despite important limitations discussed in this paper, our analysis provided useful insights on the role of the human gut metagenome in the variability in drug response among individuals. Importantly, this approach exploits drug and metagenome data available in public databases as well as open-source cheminformatics and bioinformatics tools to predict drug-metagenome interactions.
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Pharmacogenetics Update on Biologic Therapy in Psoriasis. ACTA ACUST UNITED AC 2020; 56:medicina56120719. [PMID: 33419370 PMCID: PMC7766592 DOI: 10.3390/medicina56120719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023]
Abstract
Background and objectives: Psoriasis is a chronic immune-mediated skin disease caused by several complex factors, both environmental and genetic, many of which are still not fully understood. Nowadays, several groups of biological drugs are being used for psoriasis treatment. Although these therapies are very effective, they show significant variability in efficacy among individuals. Therefore, there is a need for biomarkers to predict treatment outcomes in order to guide personalized therapeutic decisions. Pharmacogenetics is the study of variations in DNA sequences related to drug response. Materials and Methods: In this article, we review pharmacogenetics studies on the treatment of moderate-to-severe psoriasis focusing on anti-interleukin (IL) 12/23 (ustekinumab) and anti-IL17 drugs (secukinumab and ixekizumab), as well as recent studies concerning anti-TNF drugs. Results: Several polymorphisms have been studied over the years in reference to anti-TNF drugs; some of the most recent studies included the performance of a genome-wide association study (GWAS) and pharmacogenetics studies focused on the optimization of a treatment regimen. Various polymorphisms in different genes have been related to ustekinumab response; among them, the most commonly studied is the HLA-C*06:02 allele. Conclusions: Although not confirmed in some studies, most studies have shown that patients carrying this allele present a significantly higher response rate to ustekinumab. Some polymorphisms have been studied in patients treated with anti-IL17 drugs, mostly related to secukinumab; however, up to now, no association has been found between any of these polymorphisms and response. Nevertheless, further studies involving larger cohorts are needed in order to confirm these results before the implementation of this biomarker in clinical practice.
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Malsagova KA, Butkova TV, Kopylov AT, Izotov AA, Potoldykova NV, Enikeev DV, Grigoryan V, Tarasov A, Stepanov AA, Kaysheva AL. Pharmacogenetic Testing: A Tool for Personalized Drug Therapy Optimization. Pharmaceutics 2020; 12:E1240. [PMID: 33352764 PMCID: PMC7765968 DOI: 10.3390/pharmaceutics12121240] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022] Open
Abstract
Pharmacogenomics is a study of how the genome background is associated with drug resistance and how therapy strategy can be modified for a certain person to achieve benefit. The pharmacogenomics (PGx) testing becomes of great opportunity for physicians to make the proper decision regarding each non-trivial patient that does not respond to therapy. Although pharmacogenomics has become of growing interest to the healthcare market during the past five to ten years the exact mechanisms linking the genetic polymorphisms and observable responses to drug therapy are not always clear. Therefore, the success of PGx testing depends on the physician's ability to understand the obtained results in a standardized way for each particular patient. The review aims to lead the reader through the general conception of PGx and related issues of PGx testing efficiency, personal data security, and health safety at a current clinical level.
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Affiliation(s)
- Kristina A. Malsagova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (T.V.B.); (A.T.K.); (A.A.I.); (A.A.S.); (A.L.K.)
| | - Tatyana V. Butkova
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (T.V.B.); (A.T.K.); (A.A.I.); (A.A.S.); (A.L.K.)
| | - Arthur T. Kopylov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (T.V.B.); (A.T.K.); (A.A.I.); (A.A.S.); (A.L.K.)
| | - Alexander A. Izotov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (T.V.B.); (A.T.K.); (A.A.I.); (A.A.S.); (A.L.K.)
| | - Natalia V. Potoldykova
- Institute of Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (N.V.P.); (D.V.E.); (V.G.)
| | - Dmitry V. Enikeev
- Institute of Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (N.V.P.); (D.V.E.); (V.G.)
| | - Vagarshak Grigoryan
- Institute of Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (N.V.P.); (D.V.E.); (V.G.)
| | - Alexander Tarasov
- Institute of Linguistics and Intercultural Communication, Sechenov University, 119992 Moscow, Russia;
| | - Alexander A. Stepanov
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (T.V.B.); (A.T.K.); (A.A.I.); (A.A.S.); (A.L.K.)
| | - Anna L. Kaysheva
- Biobanking Group, Branch of Institute of Biomedical Chemistry “Scientific and Education Center”, 109028 Moscow, Russia; (T.V.B.); (A.T.K.); (A.A.I.); (A.A.S.); (A.L.K.)
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Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. Comput Struct Biotechnol J 2020; 18:2535-2546. [PMID: 33033576 PMCID: PMC7522539 DOI: 10.1016/j.csbj.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 12/30/2022] Open
Abstract
Neuropsychiatric disorders (NPDs) such as bipolar disorder (BD), schizophrenia (SZ) and mood disorder (MD) are hard to manage due to overlapping symptoms and lack of biomarkers. Risk alleles of BD/SZ/MD are emerging, with evidence suggesting mitochondrial (mt) dysfunction as a critical factor for disease onset and progression. Mood stabilizing treatments for these disorders are scarce, revealing the need for biomarker discovery and artificial intelligence approaches to design synthetically accessible novel therapeutics. Here, we show mt involvement in NPDs by associating 245 mt proteins to BD/SZ/MD, with 7 common players in these disease categories. Analysis of over 650 publications suggests that 245 NPD-linked mt proteins are associated with 800 other mt proteins, with mt impairment likely to rewire these interactions. High dosage of mood stabilizers is known to alleviate manic episodes, but which compounds target mt pathways is another gap in the field that we address through mood stabilizer-gene interaction analysis of 37 prescriptions and over-the-counter psychotropic treatments, which we have refined to 15 mood-stabilizing agents. We show 26 of the 245 NPD-linked mt proteins are uniquely or commonly targeted by one or more of these mood stabilizers. Further, induced pluripotent stem cell-derived patient neurons and three-dimensional human brain organoids as reliable BD/SZ/MD models are outlined, along with multiomics methods and machine learning-based decision making tools for biomarker discovery, which remains a bottleneck for precision psychiatry medicine.
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The Association of 3-Hydroxy-3-Methylglutaryl-CoA Reductase, Apolipoprotein E, and Solute Carrier Organic Anion Genetic Variants with Atorvastatin Response among Jordanian Patients with Type 2 Diabetes. Life (Basel) 2020; 10:life10100232. [PMID: 33027917 PMCID: PMC7599896 DOI: 10.3390/life10100232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/28/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022] Open
Abstract
Atorvastatin is commonly used among type 2 diabetic (DM2) patients at the University of Jordan Hospital to prevent cardiovascular complication. However, we noticed that there is a wide inter-individual variation in the efficacy and toxicity of atorvastatin. This study aimed to find out the effects of major genetic variants in 3-Hydroxy-3-Methylglutaryl-CoA Reductase (HMGCR), Apolipoprotein E (APOE), and Solute Carrier Organic Anion (SLCO1B1) genes on atorvastatin response among DM2 patients. A sample of 139 DM2 patients on 20 mg of atorvastatin was included in this study. The lipid and glycemic profile and the levels of hepatic enzymes alanine aminotransferase (ALT) and aspartate transaminase were recorded before and after 3 months of atorvastatin treatment. Additionally, the genetic variants HMGCR rs17244841,APOE rs7412 and rs429357, and SLCO1B1 rs2306283 and rs11045818 were genotyped using an Applied Biosystems DNA sequencing method (ABI3730×1). We found that atorvastatin reduced total cholesterol and low-density lipoprotein (LDL) more significantly (p-value < 0.05) in patients with wild genotype than variant alleles APOE rs7412C > T and SLCO1B1 rs2306283A > G. Furthermore, the ALT level was elevated significantly (p-value < 0.05) by 27% in patients with heterozygous SLCO1B1 rs11045818 G/A genotype, while it was not elevated among wild genotype carriers. Additionally, atorvastatin reduced total cholesterol more significantly (p-value < 0.05) in patients with SLCO1B1 rs2306283A and rs11045818G haplotypes and increased ALT levels by 27% (p-value < 0.05) in patients with SLCO1B1 rs2306283G and rs11045818A haplotypes. In conclusion, it was found in this study that APOE rs7412, SLCO1B1 rs2306283, and rs11045818 genotypes can be considered as potential genetic biomarkers of atorvastatin response among DM2 patients of Jordanian Arabic origin. Further clinical studies with larger sample numbers are needed to confirm these findings.
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Crucitta S, Del Re M, Paolieri F, Bloise F, Sbrana A, Sammarco E, Mercinelli C, Cucchiara F, Fontanelli L, Galli L, Danesi R. CYP17A1 polymorphism c.-362T>C predicts clinical outcome in metastatic castration-resistance prostate cancer patients treated with abiraterone. Cancer Chemother Pharmacol 2020; 86:527-533. [PMID: 32945940 DOI: 10.1007/s00280-020-04133-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/22/2020] [Indexed: 01/27/2023]
Abstract
BACKGROUND Abiraterone became a standard hormonal therapy for patients with metastatic castration-resistance prostate cancer (mCRPC). However, patients may experience primary resistance to treatment. To date, few predictive biomarkers of efficacy have been identified. Our aim was to investigate the association between the single nucleotide polymorphism (SNP) c.-362T>C in the CYP17A1 gene, and clinical outcome in mCRPC patients treated with abiraterone. PATIENTS AND METHODS mCRPC patients candidate to receive abiraterone were enrolled in the present retrospective pharmacogenetic study. Based on a literature selection, CYP17A1 rs2486758 (c.-362T > C) was selected and analysed by real-time PCR on genomic DNA extracted from whole blood. Univariate analysis was performed to test the association between the SNP and treatment-related clinical outcomes. RESULTS Sixty mCRPC patients were enrolled in the present study. Patients carrying the mutant CYP17A1 c.-362CT/CC genotypes showed a shorter median progression-free survival (PFS) and prostate-specific antigen-PFS (PSA-PFS) compared to patients carrying the TT genotype (10.7 vs 14.2 months and 8 vs 16 months, respectively; p = 0.04). No association between the selected SNP and the overall survival was found. CONCLUSIONS These findings suggest an association between CYP17A1 c.-362T>C polymorphism and poorer clinical outcome with abiraterone for mCRPC patients. However, further validations on larger cohort of patients are needed to confirm its role as a predictive biomarker for abiraterone resistance.
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Affiliation(s)
- Stefania Crucitta
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, 55, Via Roma, 56126, Pisa, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, 55, Via Roma, 56126, Pisa, Italy.
| | - Federico Paolieri
- Unit of Medical Oncology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Francesco Bloise
- Unit of Medical Oncology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Andrea Sbrana
- Unit of Medical Oncology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Enrico Sammarco
- Unit of Medical Oncology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Chiara Mercinelli
- Unit of Medical Oncology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federico Cucchiara
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, 55, Via Roma, 56126, Pisa, Italy
| | - Lorenzo Fontanelli
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, 55, Via Roma, 56126, Pisa, Italy
| | - Luca Galli
- Unit of Medical Oncology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, 55, Via Roma, 56126, Pisa, Italy
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Almeman AA. Major CYP450 polymorphism Among Saudi Patients. Drug Metab Lett 2020; 14:17-24. [PMID: 32703145 DOI: 10.2174/1872312814666200722122232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Cytochrome P450 (CYP) contributes to a huge collection of medicinal products' Phase I metabolization. We aimed to summarize and investigate the current evidence regarding the frequency of CYP2D6, CYP2C9, CYP2C19, MDR1 in Saudi Arabia. METHODS A computerized search in four databases was done using the relevant keywords. Screening process was done in two steps; title and abstract screening and full-text screening. Data of demographic and characteristics of included studies and patients was extracted and tabulated. RESULTS Ten studies were eligible for our criteria and were included in this systematic review. Age of participants ranged between 17-65 years. Only two subjects showed PM phenotype of CYP2C19 in Saudi population. The most frequent alleles were CYP2C19*1 (62.9%), CYP2C19*2 (11.2%-32%), and CYP2C19*17 (25.7%). The CYP2C19m1 was observed in 97 cases of extensive metabolizing (EM) phenotype CYP2C19. Concerning the CYP2C9, the most frequent alleles were CYP2C9*1 and CYP2C9*2, and the most frequent genotype was CYP2C9*1*1. The CYP2D6*41 allele and C1236T MDR1 were the most frequent allele in this population. CONCLUSION The current evidence suggests that Saudi Arabians resembled European in the frequency of CYP2C19, Caucasians in both the incidence of CYP2C9 and CYP2C19m1 and absence of CYP2C19m2. The CYP2D6*41 allele frequency in Saudi Arabians is relatively high. We recommend a further research to evaluate the basic and clinical relevance of gene polymorphism in such ethnicity.
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Affiliation(s)
- Ahmad Abdulrahman Almeman
- Clinical pharmacology and therapeutics Department, Qassim University, Buraydah, Qassim. Saudi Arabia
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Hamilton WG, Gargiulo JM, Parks NL. Using pharmacogenetics to structure individual pain management protocols in total knee arthroplasty. Bone Joint J 2020; 102-B:73-78. [DOI: 10.1302/0301-620x.102b6.bjj-2019-1539.r1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Aims The purpose of this study was to use pharmacogenetics to determine the frequency of genetic variants in our total knee arthroplasty (TKA) patients that could affect postoperative pain medications. Pharmacogenetic testing evaluates patient DNA to determine if a drug is expected to have a normal clinical effect, heightened effect, or no effect at all on the patient. It also predicts whether patients are likely to experience side effects from medicine. We further sought to determine if changing the multimodal programme based on these results would improve pain control or reduce side effects. Methods In this pilot study, buccal samples were collected from 31 primary TKA patients. Pharmacogenetics testing examined genetic variants in genes OPRM1, CYP1A2, CYP2B6, CYP2C19, CYP3A4, CYP2C9, and CYP2D6. These genes affect the pharmacodynamics and pharmacokinetics of non-steroidal anti-inflammatory drugs and opioids. We examined the frequency of genetic variants to any of the medications we prescribed including celecoxib, hydrocodone, and tramadol. Patients were randomized to one of two groups: the control group received the standard postoperative pain regimen, and the study group received a customized regimen based on the pharmacogenetic results. For the first ten postoperative days, patients recorded pain scores, medication, and side effects. Results Genetic variants involving one or more medications in the multimodal pain protocol occurred in 13 of the 31 patients (42%). In total, eight patients (26%) had variants affecting more than one of the medications. For the 25 patients who recorded pain and medication logs, the mean pain levels and morphine equivalents (MEQs) consumed in the first ten days were higher in the control group than in the custom-guided group (p = 0.019 for pain and p = 0.655 for MEQ). Conclusion Overall, 42% of patients had a variant involving one of the pain medications prescribed in our perioperative pain program for TKA. Ongoing research will help determine if using these data to modify a patient’s medication will improve outcomes. Cite this article: Bone Joint J 2020;102-B(6 Supple A):73–78.
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Affiliation(s)
| | | | - Nancy L. Parks
- Anderson Orthopaedic Research Institute, Alexandria, Virginia, USA
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Zhong Y, De T, Alarcon C, Park CS, Lec B, Perera MA. Discovery of novel hepatocyte eQTLs in African Americans. PLoS Genet 2020; 16:e1008662. [PMID: 32310939 PMCID: PMC7192504 DOI: 10.1371/journal.pgen.1008662] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 04/30/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
African Americans (AAs) are disproportionately affected by metabolic diseases and adverse drug events, with limited publicly available genomic and transcriptomic data to advance the knowledge of the molecular underpinnings or genetic associations to these diseases or drug response phenotypes. To fill this gap, we obtained 60 primary hepatocyte cultures from AA liver donors for genome-wide mapping of expression quantitative trait loci (eQTL) using LAMatrix. We identified 277 eGenes and 19,770 eQTLs, of which 67 eGenes and 7,415 eQTLs are not observed in the Genotype-Tissue Expression Project (GTEx) liver eQTL analysis. Of the eGenes found in GTEx only 25 share the same lead eQTL. These AA-specific eQTLs are less correlated to GTEx eQTLs. in effect sizes and have larger Fst values compared to eQTLs found in both cohorts (overlapping eQTLs). We assessed the overlap between GWAS variants and their tagging variants with AA hepatocyte eQTLs and demonstrated that AA hepatocyte eQTLs can decrease the number of potential causal variants at GWAS loci. Additionally, we identified 75,002 exon QTLs of which 48.8% are not eQTLs in AA hepatocytes. Our analysis provides the first comprehensive characterization of AA hepatocyte eQTLs and highlights the unique discoveries that are made possible due to the increased genetic diversity within the African ancestry genome.
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Affiliation(s)
- Yizhen Zhong
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Tanima De
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Cristina Alarcon
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - C. Sehwan Park
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bianca Lec
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Minoli A. Perera
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- * E-mail:
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Hampel H, Williams C, Etcheto A, Goodsaid F, Parmentier F, Sallantin J, Kaufmann WE, Missling CU, Afshar M. A precision medicine framework using artificial intelligence for the identification and confirmation of genomic biomarkers of response to an Alzheimer's disease therapy: Analysis of the blarcamesine (ANAVEX2-73) Phase 2a clinical study. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2020; 6:e12013. [PMID: 32318621 PMCID: PMC7167374 DOI: 10.1002/trc2.12013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 02/17/2020] [Indexed: 01/02/2023]
Abstract
INTRODUCTION The search for drugs to treat Alzheimer's disease (AD) has failed to yield effective therapies. Here we report the first genome-wide search for biomarkers associated with therapeutic response in AD. Blarcamesine (ANAVEX2-73), a selective sigma-1 receptor (SIGMAR1) agonist, was studied in a 57-week Phase 2a trial (NCT02244541). The study was extended for a further 208 weeks (NCT02756858) after meeting its primary safety endpoint. METHODS Safety, clinical features, pharmacokinetic, and efficacy, measured by changes in the Mini-Mental State Examination (MMSE) and the Alzheimer's Disease Cooperative Study-Activities of Daily Living scale (ADCS-ADL), were recorded. Whole exome and transcriptome sequences were obtained for 21 patients. The relationship between all available patient data and efficacy outcome measures was analyzed with unsupervised formal concept analysis (FCA), integrated in the Knowledge Extraction and Management (KEM) environment. RESULTS Biomarkers with a significant impact on clinical outcomes were identified at week 57: mean plasma concentration of blarcamesine (slope MMSE:P < .041), genomic variants SIGMAR1 p.Gln2Pro (ΔMMSE:P < .039; ΔADCS-ADL:P < .063) and COMT p.Leu146fs (ΔMMSE:P < .039; ΔADCS-ADL:P < .063), and baseline MMSE score (slope MMSE:P < .015). Their combined impact on drug response was confirmed at week 148 with linear mixed effect models. DISCUSSION Confirmatory Phase 2b/3 clinical studies of these patient selection markers are ongoing. This FCA/KEM analysis is a template for the identification of patient selection markers in early therapeutic development for neurologic disorders.
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Affiliation(s)
- Harald Hampel
- Sorbonne UniversityGRC n° 21, Alzheimer Precision Medicine (APM)AP‐HP, Pitié‐Salpêtrière HospitalBoulevard de l'hôpitalParisFrance
| | | | | | | | | | - Jean Sallantin
- Laboratoire d'Intelligence ArtificielleLIRMM, CNRSMontpellierFrance
| | - Walter E. Kaufmann
- Anavex Life Sciences Corp.New YorkNew YorkUSA
- Department of Human GeneticsEmory University School of MedicineAtlantaGeorgiaUSA
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D TK, Jain N, Kumar S U, Jena PP, Ramamoorthy S, Priya Doss C G, Zayed H. Molecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe’s disease. J Biomol Struct Dyn 2020; 39:1795-1810. [DOI: 10.1080/07391102.2020.1742790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Thirumal Kumar D
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Nikita Jain
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Udhaya Kumar S
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Prangya Paramita Jena
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Siva Ramamoorthy
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - George Priya Doss C
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
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Current Concepts in Pharmacometabolomics, Biomarker Discovery, and Precision Medicine. Metabolites 2020; 10:metabo10040129. [PMID: 32230776 PMCID: PMC7241083 DOI: 10.3390/metabo10040129] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 02/07/2023] Open
Abstract
Pharmacometabolomics (PMx) studies use information contained in metabolic profiles (or metabolome) to inform about how a subject will respond to drug treatment. Genome, gut microbiome, sex, nutrition, age, stress, health status, and other factors can impact the metabolic profile of an individual. Some of these factors are known to influence the individual response to pharmaceutical compounds. An individual’s metabolic profile has been referred to as his or her “metabotype.” As such, metabolomic profiles obtained prior to, during, or after drug treatment could provide insights about drug mechanism of action and variation of response to treatment. Furthermore, there are several types of PMx studies that are used to discover and inform patterns associated with varied drug responses (i.e., responders vs. non-responders; slow or fast metabolizers). The PMx efforts could simultaneously provide information related to an individual’s pharmacokinetic response during clinical trials and be used to predict patient response to drugs making pharmacometabolomic clinical research valuable for precision medicine. PMx biomarkers can also be discovered and validated during FDA clinical trials. Using biomarkers during medical development is described in US Law under the 21st Century Cures Act. Information on how to submit biomarkers to the FDA and their context of use is defined herein.
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Novelli G, Biancolella M, Latini A, Spallone A, Borgiani P, Papaluca M. Precision Medicine in Non-Communicable Diseases. High Throughput 2020; 9:ht9010003. [PMID: 32046063 PMCID: PMC7151056 DOI: 10.3390/ht9010003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/31/2019] [Accepted: 02/04/2020] [Indexed: 12/18/2022] Open
Abstract
The increase in life expectancy during the 20th century ranks as one of society's greatest achievements, with massive growth in the numbers and proportion of the elderly, virtually occurring in every country of the world. The burden of chronic diseases is one of the main consequences of this phenomenon, severely hampering the quality of life of elderly people and challenging the efficiency and sustainability of healthcare systems. Non-communicable diseases (NCDs) are considered a global emergency responsible for over 70% of deaths worldwide. NCDs are also the basis for complex and multifactorial diseases such as hypertension, diabetes, and obesity. The epidemics of NCDs are a consequence of a complex interaction between health, economic growth, and development. This interaction includes the individual genome, the microbiome, the metabolome, the immune status, and environmental factors such as nutritional and chemical exposure. To counteract NCDs, it is therefore essential to develop an innovative, personalized, preventative, early care model through the integration of different molecular profiles of individuals to identify both the critical biomarkers of NCD susceptibility and to discover novel therapeutic targets.
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Affiliation(s)
- Giuseppe Novelli
- Department of Biomedicine & Prevention, Genetics Unit, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.L.); (P.B.)
- IRCCS Neuromed, 86077 Pozzilli (IS), Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
- Correspondence: ; Tel.: +39-0620-900-668
| | | | - Andrea Latini
- Department of Biomedicine & Prevention, Genetics Unit, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.L.); (P.B.)
| | - Aldo Spallone
- Department of Neurology and Neurosurgery, Peoples’ Friendship University of Russia (RUDN University), Moscow 117198, Russia;
| | - Paola Borgiani
- Department of Biomedicine & Prevention, Genetics Unit, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.L.); (P.B.)
| | - Marisa Papaluca
- Imperial College, Faculty of Medicine, School of Public Health, SW7 2AZ London, UK;
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Mouse Systems Genetics as a Prelude to Precision Medicine. Trends Genet 2020; 36:259-272. [PMID: 32037011 DOI: 10.1016/j.tig.2020.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/17/2022]
Abstract
Mouse models have been instrumental in understanding human disease biology and proposing possible new treatments. The precise control of the environment and genetic composition of mice allows more rigorous observations, but limits the generalizability and translatability of the results into human applications. In the era of precision medicine, strategies using mouse models have to be revisited to effectively emulate human populations. Systems genetics is one promising paradigm that may promote the transition to novel precision medicine strategies. Here, we review the state-of-the-art resources and discuss how mouse systems genetics helps to understand human diseases and to advance the development of precision medicine, with an emphasis on the existing resources and strategies.
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Basyouni D, Shatnawi A. Pharmacogenomics Instruction Depth, Extent, and Perception in US Medical Curricula. JOURNAL OF MEDICAL EDUCATION AND CURRICULAR DEVELOPMENT 2020; 7:2382120520930772. [PMID: 32782929 PMCID: PMC7385819 DOI: 10.1177/2382120520930772] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/07/2020] [Indexed: 06/09/2023]
Abstract
INTRODUCTION This descriptive study aimed to evaluate the depth, extent, and perception of pharmacogenomics instruction in schools and colleges of medicine in the United States. Changes in medical pharmacogenomics instruction over the past decade were also assessed by comparing our results with those of a previous study. METHODS An electronic survey was emailed to all accredited allopathic and osteopathic medical schools across the US using Qualtrics online survey software. Multiple email reminders were sent to increase the response rate. RESULTS Of 151 targeted eligible medical schools across the United States, 22 responded to the survey. One invalid response was excluded, resulting in a response rate of 13.9%. Of responding schools, 85.7% cover pharmacogenomics in their curriculum, mainly in the second year, however, none teach pharmacogenomics as a stand-alone course. The depth and the extent of pharmacogenomics coverage varied among responding programs. Although 66.7% of respondents believe that neither physicians nor other health care professionals possess appropriate knowledge in pharmacogenomics, only 23.8% plan to increase pharmacogenomics instruction in their curricula in the near future. CONCLUSIONS Most medical schools surveyed include some pharmacogenomics instruction in their curricula, although the depth and the extent of the instruction varies. Most respondents believe that physicians and other health care professionals today do not possess an appropriate level of knowledge in pharmacogenomics; however, few institutions report short-term plans to increase pharmacogenomics instruction. Pharmacogenomics plays a significant role in personalized medicine; greater efforts by medical school decision-makers are needed to improve the level of pharmacogenomics instruction in medical curricula.
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Affiliation(s)
- Dara Basyouni
- Faculty of Dentistry, The University of Jordan, Amman, Jordan
| | - Aymen Shatnawi
- Department of Pharmaceutical and Administrative Sciences, School of Pharmacy, University of Charleston, Charleston, WV, USA
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Peterson RE, Kuchenbaecker K, Walters RK, Chen CY, Popejoy AB, Periyasamy S, Lam M, Iyegbe C, Strawbridge RJ, Brick L, Carey CE, Martin AR, Meyers JL, Su J, Chen J, Edwards AC, Kalungi A, Koen N, Majara L, Schwarz E, Smoller JW, Stahl EA, Sullivan PF, Vassos E, Mowry B, Prieto ML, Cuellar-Barboza A, Bigdeli TB, Edenberg HJ, Huang H, Duncan LE. Genome-wide Association Studies in Ancestrally Diverse Populations: Opportunities, Methods, Pitfalls, and Recommendations. Cell 2019; 179:589-603. [PMID: 31607513 PMCID: PMC6939869 DOI: 10.1016/j.cell.2019.08.051] [Citation(s) in RCA: 385] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/10/2019] [Accepted: 08/26/2019] [Indexed: 12/19/2022]
Abstract
Genome-wide association studies (GWASs) have focused primarily on populations of European descent, but it is essential that diverse populations become better represented. Increasing diversity among study participants will advance our understanding of genetic architecture in all populations and ensure that genetic research is broadly applicable. To facilitate and promote research in multi-ancestry and admixed cohorts, we outline key methodological considerations and highlight opportunities, challenges, solutions, and areas in need of development. Despite the perception that analyzing genetic data from diverse populations is difficult, it is scientifically and ethically imperative, and there is an expanding analytical toolbox to do it well.
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Affiliation(s)
- Roseann E Peterson
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23298, USA.
| | - Karoline Kuchenbaecker
- Division of Psychiatry and UCL Genetics Institute, University College London, London W1T 7NF, UK
| | - Raymond K Walters
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Chia-Yen Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alice B Popejoy
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sathish Periyasamy
- Queensland Brain Institute and Queensland Centre for Mental Health Research, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Max Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Conrad Iyegbe
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Rona J Strawbridge
- Institute of Health and Wellbeing, University of Glasgow, Glasgow G12 8RZ, UK; Department of Medicine Solna, Karolinska Institute, Stockholm, SE 17176, Sweden
| | - Leslie Brick
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI 02906, USA
| | - Caitlin E Carey
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alicia R Martin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jacquelyn L Meyers
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Jinni Su
- Department of Psychology, Arizona State University, Tempe, AZ 85281, USA
| | - Junfang Chen
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Alexis C Edwards
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Allan Kalungi
- Mental Health Section of MRC/UVRI and LSHTM Uganda Research Unit, P.O. Box 49, Entebbe, Uganda; Department of Psychiatry, Faculty of Medicine & Health Sciences, University of Stellenbosch, Cape Town, South Africa; Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Global Initiative for Neuropsychiatric Genetics Education in Research, Harvard T.H. Chan School of Public Health and Broad Institute, Boston, MA 02115, USA
| | - Nastassja Koen
- Department of Psychiatry, Faculty of Medicine & Health Sciences, University of Stellenbosch, Cape Town, South Africa; Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Global Initiative for Neuropsychiatric Genetics Education in Research, Harvard T.H. Chan School of Public Health and Broad Institute, Boston, MA 02115, USA
| | - Lerato Majara
- Global Initiative for Neuropsychiatric Genetics Education in Research, Harvard T.H. Chan School of Public Health and Broad Institute, Boston, MA 02115, USA; MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Emanuel Schwarz
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick F Sullivan
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, SE 17176, Sweden; Genetics and Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Evangelos Vassos
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
| | - Bryan Mowry
- Queensland Brain Institute and Queensland Centre for Mental Health Research, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Miguel L Prieto
- Department of Psychiatry, Faculty of Medicine, Universidad de los Andes, Santiago 7620001, Chile; Mental Health Service, Clínica Universidad de los Andes, Santiago 7620001, Chile; Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Alfredo Cuellar-Barboza
- Department of Psychiatry, University Hospital and School of Medicine, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico; Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Tim B Bigdeli
- Department of Psychiatry, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Laramie E Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
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Jarrar Y, Mosleh R, Hawash M, Jarrar Q. Knowledge And Attitudes Of Pharmacy Students Towards Pharmacogenomics Among Universities In Jordan And West Bank Of Palestine. Pharmgenomics Pers Med 2019; 12:247-255. [PMID: 31632127 PMCID: PMC6789177 DOI: 10.2147/pgpm.s222705] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/09/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Testing by pharmacogenomics (PGx) aims to reduce the side-effects of medicines and to optimize therapy. AIM To ascertain the knowledge and attitudes towards PGx among pharmacy students in Jordan and West Bank of Palestine (WBP). METHODS This cross-sectional study focused on pharmacy students from five universities in Jordan and WBP. Students were asked to answer an online survey comprising 30-closed ended questions measuring the knowledge and attitudes towards PGx. RESULTS The total number of respondents to the questionnaire was 466. Most (96.1%) respondents knew that genetic variations can affect the drug response. Most students stated that the total number of lectures mentioning PGx was fewer than three. Most (>80%) respondents answered that they knew that human genetics can affect the response, inter-individual variation, and ethnic variations in the drug response. However, their knowledge about US Food and Drug Administration recommendations regarding PGx testing of commonly used drugs was weak. Also, 60.3% of respondents stated that the information they received about PGx was insufficient. Most (>92.7%) students wished to know more about PGx and believed that PGx is helpful in choosing the appropriate drug. CONCLUSION Pharmacy students had fair knowledge and good attitudes towards PGx. These factors could aid application of PGx in clinical practice in Jordan and WBP.
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Affiliation(s)
- Yazun Jarrar
- Department of Pharmacy, College of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Rami Mosleh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus00970, Palestine
| | - Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus00970, Palestine
| | - Qais Jarrar
- Department of Pharmaceutical Science, Al-Isra’a University, Amman, Jordan
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Weitzel KW, Duong BQ, Arwood MJ, Owusu-Obeng A, Abul-Husn NS, Bernhardt BA, Decker B, Denny JC, Dietrich E, Gums J, Madden EB, Pollin TI, Wu RR, Haga SB, Horowitz CR. A stepwise approach to implementing pharmacogenetic testing in the primary care setting. Pharmacogenomics 2019; 20:1103-1112. [PMID: 31588877 PMCID: PMC6854439 DOI: 10.2217/pgs-2019-0053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/29/2019] [Indexed: 01/12/2023] Open
Abstract
Pharmacogenetic testing can help identify primary care patients at increased risk for medication toxicity, poor response or treatment failure and inform drug therapy. While testing availability is increasing, providers are unprepared to routinely use pharmacogenetic testing for clinical decision-making. Practice-based resources are needed to overcome implementation barriers for pharmacogenetic testing in primary care.The NHGRI's IGNITE I Network (Implementing GeNomics In pracTicE; www.ignite-genomics.org) explored practice models, challenges and implementation barriers for clinical pharmacogenomics. Based on these experiences, we present a stepwise approach pharmacogenetic testing in primary care: patient identification; pharmacogenetic test ordering; interpretation and application of test results, and patient education. We present clinical factors to consider, test-ordering processes and resources, and provide guidance to apply test results and counsel patients. Practice-based resources such as this stepwise approach to clinical decision-making are important resources to equip primary care providers to use pharmacogenetic testing.
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Affiliation(s)
- Kristin Wiisanen Weitzel
- Department of Pharmacotherapy & Translational Research, University of Florida, Gainesville, FL 32608, USA
| | - Benjamin Q Duong
- Department of Pharmacy, Nemours/Alfred I DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Meghan J Arwood
- Department of Pharmacotherapy & Translational Research, University of Florida, Gainesville, FL 32608, USA
| | - Aniwaa Owusu-Obeng
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noura S Abul-Husn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Barbara A Bernhardt
- Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian Decker
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Joshua C Denny
- Department of Medicine & Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Eric Dietrich
- Department of Pharmacotherapy & Translational Research, University of Florida, Gainesville, FL 32608, USA
| | - John Gums
- Department of Pharmacotherapy & Translational Research, University of Florida, Gainesville, FL 32608, USA
| | - Ebony B Madden
- National Human Genome Research Institute, Division of Genomic Medicine, Bethesda, MD 20892, USA
| | - Toni I Pollin
- Department of Medicine & Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Rebekah Ryanne Wu
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC 27708, USA
| | - Susanne B Haga
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC 27708, USA
| | - Carol R Horowitz
- Department of Health Policy & Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Tuteja S, Ferguson JF. Gut Microbiome and Response to Cardiovascular Drugs. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 12:421-429. [PMID: 31462078 DOI: 10.1161/circgen.119.002314] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The gut microbiome is emerging as an important contributor to both cardiovascular disease risk and metabolism of xenobiotics. Alterations in the intestinal microbiota are associated with atherosclerosis, dyslipidemia, hypertension, and heart failure. The microbiota have the ability to metabolize medications, which can results in altered drug pharmacokinetics and pharmacodynamics or formation of toxic metabolites which can interfere with drug response. Early evidence suggests that the gut microbiome modulates response to statins and antihypertensive medications. In this review, we will highlight mechanisms by which the gut microbiome facilitates the biotransformation of drugs and impacts pharmacological efficacy. A better understanding of the complex interactions of the gut microbiome, host factors, and response to medications will be important for the development of novel precision therapeutics for targeting CVD.
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Affiliation(s)
- Sony Tuteja
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA (S.T.)
| | - Jane F Ferguson
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN (J.F.F.)
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Shi Y, Graves JA, Garbett SP, Zhou Z, Marathi R, Wang X, Harrell FE, Lasko TA, Denny JC, Roden DM, Peterson JF, Schildcrout JS. A Decision-Theoretic Approach to Panel-Based, Preemptive Genotyping. MDM Policy Pract 2019; 4:2381468319864337. [PMID: 31453360 PMCID: PMC6699004 DOI: 10.1177/2381468319864337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 06/01/2019] [Indexed: 12/22/2022] Open
Abstract
We discuss a decision-theoretic approach to building a panel-based, preemptive
genotyping program. The method is based on findings that a large percentage of
patients are prescribed medications that are known to have pharmacogenetic
associations, and over time, a substantial proportion are prescribed additional
such medication. Preemptive genotyping facilitates genotype-guided therapy at
the time medications are prescribed; panel-based testing allows providers to
reuse previously collected genetic data when a new indication arises. Because it
is cost-prohibitive to conduct panel-based genotyping on all patients, we
describe a three-step approach to identify patients with the highest anticipated
benefit. First, we construct prediction models to estimate the risk of being
prescribed one of the target medications using readily available clinical data.
Second, we use literature-based estimates of adverse event rates, variant allele
frequencies, secular death rates, and costs to construct a discrete event
simulation that estimates the expected benefit of having an individual’s genetic
data in the electronic health record after an indication has occurred. Finally,
we combine medication prescription risk with expected benefit of genotyping once
a medication is indicated to calculate the expected benefit of preemptive
genotyping. For each patient-clinic visit, we calculate this expected benefit
across a range of medications and select patients with the highest expected
benefit overall. We build a proof of concept implementation using a cohort of
patients from a single academic medical center observed from July 2010 through
December 2012. We then apply the results of our modeling strategy to show the
extent to which we can improve clinical and economic outcomes in a cohort
observed from January 2013 through December 2015.
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Affiliation(s)
- Yaping Shi
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John A Graves
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shawn P Garbett
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Zilu Zhou
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ramya Marathi
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiaoming Wang
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Frank E Harrell
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Thomas A Lasko
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
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Majoros WH, Kim YS, Barrera A, Li F, Wang X, Cunningham SJ, Johnson GD, Guo C, Lowe WL, Scholtens DM, Hayes MG, Reddy TE, Allen AS. Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. Bioinformatics 2019; 36:331-338. [PMID: 31368479 PMCID: PMC7999138 DOI: 10.1093/bioinformatics/btz545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 06/12/2019] [Accepted: 07/24/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION High-throughput reporter assays dramatically improve our ability to assign function to noncoding genetic variants, by measuring allelic effects on gene expression in the controlled setting of a reporter gene. Unlike genetic association tests, such assays are not confounded by linkage disequilibrium when loci are independently assayed. These methods can thus improve the identification of causal disease mutations. While work continues on improving experimental aspects of these assays, less effort has gone into developing methods for assessing the statistical significance of assay results, particularly in the case of rare variants captured from patient DNA. RESULTS We describe a Bayesian hierarchical model, called Bayesian Inference of Regulatory Differences, which integrates prior information and explicitly accounts for variability between experimental replicates. The model produces substantially more accurate predictions than existing methods when allele frequencies are low, which is of clear advantage in the search for disease-causing variants in DNA captured from patient cohorts. Using the model, we demonstrate a clear tradeoff between variant sequencing coverage and numbers of biological replicates, and we show that the use of additional biological replicates decreases variance in estimates of effect size, due to the properties of the Poisson-binomial distribution. We also provide a power and sample size calculator, which facilitates decision making in experimental design parameters. AVAILABILITY AND IMPLEMENTATION The software is freely available from www.geneprediction.org/bird. The experimental design web tool can be accessed at http://67.159.92.22:8080. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- William H Majoros
- Duke Center for Statistical Genetics and Genomics, Duke University,Division of Integrative Genomics, Department of Biostatistics and Bioinformatics, Duke University Medical School,Center for Genomic and Computational Biology, Duke University Medical School
| | - Young-Sook Kim
- Center for Genomic and Computational Biology, Duke University Medical School,Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710
| | - Alejandro Barrera
- Center for Genomic and Computational Biology, Duke University Medical School
| | - Fan Li
- Department of Biostatistics, Yale University, New Haven, CT 06520
| | - Xingyan Wang
- Present address: PhD Program in Biostatistics, Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA
| | | | - Graham D Johnson
- Center for Genomic and Computational Biology, Duke University Medical School,Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27710
| | - Cong Guo
- Present address: Human Genetics, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - William L Lowe
- Division of Endocrinology Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago
| | - Denise M Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - M Geoffrey Hayes
- Division of Endocrinology Metabolism and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago
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Ramírez B, Niño-Orrego MJ, Cárdenas D, Ariza KE, Quintero K, Contreras Bravo NC, Tamayo-Agudelo C, González MA, Laissue P, Fonseca Mendoza DJ. Copy number variation profiling in pharmacogenetics CYP-450 and GST genes in Colombian population. BMC Med Genomics 2019; 12:110. [PMID: 31324178 PMCID: PMC6642477 DOI: 10.1186/s12920-019-0556-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/05/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Copy Number variation (CNVs) in genes related to drug absorption, distribution, metabolism and excretion (ADME) are relevant in the interindividual variability of drug response. Studies of the CNVs in ADME genes in Latin America population are lacking. The objective of the study was to identify the genetic variability of CNVs in CYP-450 and GST genes in a subgroup of individuals of Colombian origin. METHODS Genomic DNA was isolated from 123 healthy individuals from a Colombian population. Multiplex Ligation-Dependent Probe Amplification (MLPA) was performed for the identification of CNVs in 40 genomic regions of 11 CYP-450 and 3 GST genes. The genetic variability, allelic and genotypic frequencies were analyzed. RESULTS We found that 13 out of 14 genes had CNVs: 5 (35.7%) exhibited deletions and duplications, while 8 (57.1%) presented either deletions or duplications.. 33.3% of individuals carried deletions and duplications while 49.6% had a unique type of CNV (deletion or duplication). The allelic frequencies of the CYP and GST genes were 0 to 47.6% (allele null), 0 to 17.5% (duplicated alleles) and 37 to 100% (normal alleles). CONCLUSIONS Our results describe, for the first time, the genomic profile of CNVs in a subgroup of Colombian population in GST and CYP-450 genes. GST genes indicated greater genetic variability than CYP-450 genes. The data obtained contributes to the knowledge of genetic profiles in Latin American subgroups. Although the clinical relevance of CNVs has not been fully established, it is a valuable source of pharmacogenetic variability data with potential involvement in the response to medications.
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Affiliation(s)
- Brian Ramírez
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - María José Niño-Orrego
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Daniel Cárdenas
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Kevin Enrique Ariza
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Karol Quintero
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Nora Constanza Contreras Bravo
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Caroll Tamayo-Agudelo
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - María Alejandra González
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Paul Laissue
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia
| | - Dora Janeth Fonseca Mendoza
- GENIUROS Research Group, Center For Research in Genetics and Genomics - CIGGUR, School of Medicine and Health Sciences, Universidad Del Rosario, Carrera 24 N° 63C-69, CP 112111, Bogotá DC, Colombia.
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Zhang F, Finkelstein J. Inconsistency in race and ethnic classification in pharmacogenetics studies and its potential clinical implications. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2019; 12:107-123. [PMID: 31308725 PMCID: PMC6612983 DOI: 10.2147/pgpm.s207449] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022]
Abstract
Introduction Racial and ethnic categories are frequently used in pharmacogenetics literature to stratify patients; however, these categories can be inconsistent across different studies. To address the ongoing debate on the applicability of traditional concepts of race and ethnicity in the context of precision medicine, we aimed to review the application of current racial and ethnic categories in pharmacogenetics and its potential impact on clinical care. Methods One hundred and three total pharmacogenetics papers involving the CYP2C9, CYP2C19, and CYP2D6 genes were analyzed for their country of origin, racial, and ethnic categories used, and allele frequency data. Correspondence between the major continental racial categories promulgated by National Institutes of Health (NIH) and those reported by the pharmacogenetics papers was evaluated. Results The racial and ethnic categories used in the papers we analyzed were highly heterogeneous. In total, we found 66 different racial and ethnic categories used which fall under the NIH race category “White”, 47 different racial and ethnic categories for “Asian”, and 62 different categories for “Black”. The number of categories used varied widely based on country of origin: Japan used the highest number of different categories for “White” with 17, Malaysia used the highest number for “Asian” with 24, and the US used the highest number for “Black” with 28. Significant variation in allele frequency between different ethnic subgroups was identified within 3 major continental racial categories. Conclusion Our analysis showed that racial and ethnic classification is highly inconsistent across different papers as well as between different countries. Evidence-based consensus is necessary for optimal use of self-identified race as well as geographical ancestry in pharmacogenetics. Common taxonomy of geographical ancestry which reflects specifics of particular countries and is accepted by the entire scientific community can facilitate reproducible pharmacogenetic research and clinical implementation of its results.
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Affiliation(s)
- Frederick Zhang
- Center for Bioinformatics and Data Analytics, Columbia University Irving Medical Center, New York, NY, USA
| | - Joseph Finkelstein
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Neale SA, Kambara K, Salt TE, Bertrand D. Receptor variants and the development of centrally acting medications. DIALOGUES IN CLINICAL NEUROSCIENCE 2019. [PMID: 31636489 PMCID: PMC6787545 DOI: 10.31887/dcns.2019.21.2/dbertrand] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The progressive changes in research paradigms observed in the largest
pharmaceutical companies and the burgeoning of biotechnology startups over the
last 10 years have generated a need for outsourcing research facilities. In
parallel, progress made in the fields of genomics, protein expression in
recombinant systems, and electrophysiological recording methods have offered new
possibilities for the development of contract research organizations (CROs).
Successful partnering between pharmaceutical companies and CROs largely depends
upon the competences and scientific quality on offer for the discovery of novel
active molecules and targets. Thus, it is critical to review the knowledge in
the field of neuroscience research, how genetic approaches are augmenting our
knowledge, and how they can be applied in the translation from the
identification of potential molecules up to the first clinical trials. Taking
these together, it is apparent that CROs have an important role to play in the
neuroscience of drug discovery.
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Affiliation(s)
- Stuart A Neale
- Neurexpert Limited, The Core, Science Central, Newcastle Upon Tyne, UK
| | | | - Thomas E Salt
- Neurexpert Limited, The Core, Science Central, Newcastle Upon Tyne, UK; Honorary Professor, University of Newcastle, Newcastle, UK
| | - Daniel Bertrand
- HiQScreen Sàrl, Geneva, Switzerland; Emeritus Professor, Medical Faculty, Geneva, Switzerland
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Aroke EN, Hicks TL. Pharmacogenetics of Postoperative Nausea and Vomiting. J Perianesth Nurs 2019; 34:1088-1105. [PMID: 31227296 DOI: 10.1016/j.jopan.2019.03.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 12/17/2022]
Abstract
Postoperative nausea and vomiting (PONV) remains one of the most common adverse effects of anesthesia, affecting up to 80% of high-risk patients within 24 hours after surgery. Patient-related factors, surgical procedure, and perioperative medications such as opioids determine a patient's risk for PONV. To prevent and manage PONV, ondansetron, a 5-hydroxytryptamine type 3 (5-HT3) receptor antagonist, is frequently administered. Ondansetron is metabolized predominantly by hepatic cytochrome P450 (CYP2D6) enzymes, encoded by the CYP2D6 gene, whereas most of the effects of opioids are exerted at the opioid mu-1 receptor, encoded by the OPRM1 gene. Genetic polymorphisms of the CYP2D6 and OPRM1 genes may have a role in interindividual variation in the occurrence of PONV. Specifically, the occurrence of the G-allele produced by the OPRM1 A118G appears to be protective against PONV, whereas CYP2D6 ultrarapid metabolism increases the risk for PONV. The Clinical Pharmacogenetics Implementation Consortium guidelines provide CYP2D6-guided therapeutic recommendations for ondansetron. However, further studies are needed to investigate the role of genetic polymorphism in the occurrence of PONV and response to antiemetics.
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Abstract
Pharmacogenetics is the branch of personalized medicine concerned with the variability in drug response occurring because of heredity. Advances in genetics research, and decreasing costs of gene sequencing, are promoting tremendous growth in pharmacogenetics in all areas of medicine, including sleep medicine. This article reviews the body of research indicating that there are genetic variations that affect the therapeutic actions and adverse effects of agents used for the treatment of sleep disorders to show the potential of pharmacogenetics to improve the clinical practice of sleep medicine.
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Al-Koofee DAF, Ismael JM, Mubarak SMH. Point mutation detection by economic HRM protocol primer design. Biochem Biophys Rep 2019; 18:100628. [PMID: 31008377 DOI: 10.1016/j.bbrep.2019.100628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/13/2019] [Accepted: 03/18/2019] [Indexed: 11/17/2022] Open
Abstract
Globally more than 100 million SNPs in populations. These variations approximately 4-5 million SNPs in a people genome, occur almost every 1000 nucleotides on average and present either unique or in many in individuals. They can act as genetic signs, associated with illness and respond to chemicals and drugs. SNPs occurrence within or near a gene play important role in disease throughout affecting gene task. Frequently many protocols have been used to study single nucleotide polymorphism (SNP) among human variants genome. Restriction fragment length polymorphism (RFLP), Amplification refractory mutation system PCR(ARMS-PCR), sequencing and SNaPshot assays considered familial methods. The potential risk of contamination after PCR is common due to further other steps. In this direction, a high resolution melting (HRM) real-time PCR method is an alternative, reducing the post-PCR transferring steps. uVariants is clarified as appropriate website for designing primers used for SNP recognition by easy and inexpensive protocol called HRM. The researchers can focus on the interest of reference SNP ID number, or "rs" ID to avoid loss time. In this article description how to uses uVariants website for primer design used in HRM technique. Aims To describe uVariants and uDesign software, application and usefulness of HRM technique primer design in the genotyping SNPs among people and public health. Accessibility and requirements uVariants and uDesign are freely accessible at: https://www.dna.utah.edu/variants/;https://www.dna.utah.edu/udesign/app.php respectively.The network server supports the browsers: Chrome, Firefox, Torch, CoolNovo, 360 Browser, Internet Explorer, Opera, and Safari.
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Affiliation(s)
- Dhafer A F Al-Koofee
- Dept. of Clinical Laboratory Science, Faculty of Pharmacy, University of Kufa, Iraq
| | | | - Shaden M H Mubarak
- Dept. of Clinical Laboratory Science, Faculty of Pharmacy, University of Kufa, Iraq
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Landolt HP, Holst SC, Valomon A. Clinical and Experimental Human Sleep-Wake Pharmacogenetics. Handb Exp Pharmacol 2019; 253:207-241. [PMID: 30443785 DOI: 10.1007/164_2018_175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sleep and wakefulness are highly complex processes that are elegantly orchestrated by fine-tuned neurochemical changes among neuronal and non-neuronal ensembles, nuclei, and networks of the brain. Important neurotransmitters and neuromodulators regulating the circadian and homeostatic facets of sleep-wake physiology include melatonin, γ-aminobutyric acid, hypocretin, histamine, norepinephrine, serotonin, dopamine, and adenosine. Dysregulation of these neurochemical systems may cause sleep-wake disorders, which are commonly classified into insomnia disorder, parasomnias, circadian rhythm sleep-wake disorders, central disorders of hypersomnolence, sleep-related movement disorders, and sleep-related breathing disorders. Sleep-wake disorders can have far-reaching consequences on physical, mental, and social well-being and health and, thus, need be treated with effective and rational therapies. Apart from behavioral (e.g., cognitive behavioral therapy for insomnia), physiological (e.g., chronotherapy with bright light), and mechanical (e.g., continuous positive airway pressure treatment of obstructive sleep apnea) interventions, pharmacological treatments often are the first-line clinical option to improve disturbed sleep and wake states. Nevertheless, not all patients respond to pharmacotherapy in uniform and beneficial fashion, partly due to genetic differences. The improved understanding of the neurochemical mechanisms regulating sleep and wakefulness and the mode of action of sleep-wake therapeutics has provided a conceptual framework, to search for functional genetic variants modifying individual drug response phenotypes. This article will summarize the currently known genetic polymorphisms that modulate drug sensitivity and exposure, to partly determine individual responses to sleep-wake pharmacotherapy. In addition, a pharmacogenetic strategy will be outlined how based upon classical and opto-/chemogenetic strategies in animals, as well as human genetic associations, circuit mechanisms regulating sleep-wake functions in humans can be identified. As such, experimental human sleep-wake pharmacogenetics forms a bridge spanning basic research and clinical medicine and constitutes an essential step for the search and development of novel sleep-wake targets and therapeutics.
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Affiliation(s)
- Hans-Peter Landolt
- Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland.
- Zürich Center for Interdisciplinary Sleep Research (ZiS), University of Zürich, Zürich, Switzerland.
| | - Sebastian C Holst
- Neurobiology Research Unit and Neuropharm, Department of Neurology, Rigshospitalet, Copenhagen, Denmark
| | - Amandine Valomon
- Wisconsin Institute for Sleep and Consciousness, University of Wisconsin Madison, Madison, WI, USA
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Jarvis JP, Peter AP, Shaman JA. Consequences of CYP2D6 Copy-Number Variation for Pharmacogenomics in Psychiatry. Front Psychiatry 2019; 10:432. [PMID: 31281270 PMCID: PMC6595891 DOI: 10.3389/fpsyt.2019.00432] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/03/2019] [Indexed: 12/20/2022] Open
Abstract
Pharmacogenomics represents a potentially powerful enhancement to the current standard of care for psychiatric patients. However, a variety of biological and technical challenges must be addressed in order to provide adequate clinical decision support for personalized prescribing and dosing based on genomic data. This is particularly true in the case of CYP2D6, a key drug-metabolizing gene, which not only harbors multiple genetic variants known to affect enzyme function but also shows a broad range of copy-number and hybrid alleles in various patient populations. Here, we describe several challenges in the accurate measurement and interpretation of data from the CYP2D6 locus including the clinical consequences of increased copy number. We discuss best practices for overcoming these challenges and then explore various current and future applications of pharmacogenomic analysis of CYP2D6 in psychiatry.
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A comparative computational approach toward pharmacological chaperones (NN-DNJ and ambroxol) on N370S and L444P mutations causing Gaucher's disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 114:315-339. [DOI: 10.1016/bs.apcsb.2018.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Arbitrio M, Di Martino MT, Scionti F, Barbieri V, Pensabene L, Tagliaferri P. Pharmacogenomic Profiling of ADME Gene Variants: Current Challenges and Validation Perspectives. High Throughput 2018; 7:E40. [PMID: 30567415 PMCID: PMC6306724 DOI: 10.3390/ht7040040] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/29/2018] [Accepted: 12/13/2018] [Indexed: 01/04/2023] Open
Abstract
In the past decades, many efforts have been made to individualize medical treatments, taking into account molecular profiles and the individual genetic background. The development of molecularly targeted drugs and immunotherapy have revolutionized medical treatments but the inter-patient variability in the anti-tumor drug pharmacokinetics (PK) and pharmacodynamics can be explained, at least in part, by genetic variations in genes encoding drug metabolizing enzymes and transporters (ADME) or in genes encoding drug receptors. Here, we focus on high-throughput technologies applied for PK screening for the identification of predictive biomarkers of efficacy or toxicity in cancer treatment, whose application in clinical practice could promote personalized treatments tailored on individual's genetic make-up. Pharmacogenomic tools have been implemented and the clinical utility of pharmacogenetic screening could increase safety in patients for the identification of drug metabolism-related biomarkers for a personalized medicine. Although pharmacogenomic studies were performed in adult cohorts, pharmacogenetic pediatric research has yielded promising results. Additionally, we discuss the current challenges and theoretical bases for the implementation of pharmacogenetic tests for translation in the clinical practice taking into account that pharmacogenomics platforms are discovery oriented and must open the way for the setting of robust tests suitable for daily practice.
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Affiliation(s)
- Mariamena Arbitrio
- Institute of Neurological Sciences, UOS of Pharmacology, 88100 Catanzaro, Italy.
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Vito Barbieri
- Medical Oncology Unit, Mater Domini Hospital, Salvatore Venuta University Campus, 8810 Catanzaro, Italy.
| | - Licia Pensabene
- Department of Medical and Surgical Sciences Pediatric Unit, Magna Graecia University, 88100 Catanzaro, Italy.
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
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Cho YK, Irby DJ, Li J, Sborov DW, Mould DR, Badawi M, Dauki A, Lamprecht M, Rosko AE, Fernandez S, Hade EM, Hofmeister CC, Poi M, Phelps MA. Pharmacokinetic-Pharmacodynamic Model of Neutropenia in Patients With Myeloma Receiving High-Dose Melphalan for Autologous Stem Cell Transplant. CPT Pharmacometrics Syst Pharmacol 2018; 7:748-758. [PMID: 30343510 PMCID: PMC6263666 DOI: 10.1002/psp4.12345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High-dose melphalan (HDM) is part of the conditioning regimen in patients with multiple myeloma (MM) receiving autologous stem cell transplantation (ASCT). However, individual sensitivity to melphalan varies, and many patients experience severe toxicities. Prolonged severe neutropenia is one of the most severe toxicities and contributes to potentially life-threatening infections and failure of ASCT. Granulocyte-colony stimulating factor (G-CSF) is given to stimulate neutrophil proliferation after melphalan administration. The aim of this study was to develop a population pharmacokinetic/pharmacodynamic (PK/PD) model capable of predicting neutrophil kinetics in individual patients with MM undergoing ASCT with high-dose melphalan and G-CSF administration. The extended PK/PD model incorporated several covariates, including G-CSF regimen, stem cell dose, hematocrit, sex, creatinine clearance, p53 fold change, and race. The resulting model explained portions of interindividual variability in melphalan exposure, therapeutic effect, and feedback regulation of G-CSF on neutrophils, thus enabling simulation of various doses and prediction of neutropenia duration.
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Affiliation(s)
- Yu Kyoung Cho
- Division of Pharmaceutics and Pharmaceutical ChemistryCollege of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Donald J. Irby
- Division of Pharmaceutics and Pharmaceutical ChemistryCollege of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Junan Li
- Division of Pharmaceutics and Pharmaceutical ChemistryCollege of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Douglas W. Sborov
- Division of HematologyDepartment of Internal MedicineCollege of MedicineThe Ohio State UniversityColumbusOhioUSA
| | | | - Mohamed Badawi
- Division of Pharmaceutics and Pharmaceutical ChemistryCollege of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Anees Dauki
- Division of Pharmaceutics and Pharmaceutical ChemistryCollege of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Misty Lamprecht
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
| | - Ashley E. Rosko
- Division of HematologyDepartment of Internal MedicineCollege of MedicineThe Ohio State UniversityColumbusOhioUSA
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
| | - Soledad Fernandez
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
- Center for BiostatisticsDepartment of Biomedical InformaticsCollege of MedicineThe Ohio State UniversityColumbusOhioUSA
| | - Erinn M. Hade
- Center for BiostatisticsDepartment of Biomedical InformaticsCollege of MedicineThe Ohio State UniversityColumbusOhioUSA
| | - Craig C. Hofmeister
- Division of HematologyDepartment of Internal MedicineCollege of MedicineThe Ohio State UniversityColumbusOhioUSA
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
| | - Ming Poi
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
- Division of Pharmacy Practice and ScienceCollege of PharmacyThe Ohio State UniversityColumbusOhioUSA
| | - Mitch A. Phelps
- Division of Pharmaceutics and Pharmaceutical ChemistryCollege of PharmacyThe Ohio State UniversityColumbusOhioUSA
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
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88
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Sanghera DK, Bejar C, Sapkota B, Wander GS, Ralhan S. Frequencies of poor metabolizer alleles of 12 pharmacogenomic actionable genes in Punjabi Sikhs of Indian Origin. Sci Rep 2018; 8:15742. [PMID: 30356105 PMCID: PMC6200732 DOI: 10.1038/s41598-018-33981-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 09/28/2018] [Indexed: 12/28/2022] Open
Abstract
Diversity in drug response is attributed to both genetic and non-genetic factors. However, there is paucity of pharmacogenetics information across ethnically and genetically diverse populations of India. Here, we have analyzed 21 SNPs from 12 pharmacogenomics genes in Punjabi Sikhs of Indian origin (N = 1,616), as part of the Sikh Diabetes Study (SDS). We compared the allele frequency of poor metabolism (PM) phenotype among Sikhs across other major global populations from the Exome Aggregation Consortium and 1000 Genomes. The PM phenotype of CYP1A2*1 F for slow metabolism of caffeine and carcinogens was significantly higher in Indians (SDS 42%, GIH [Gujarati] 51%, SAS [Pakistani] 45%) compared to Europeans 29% (pgenotype = 5.3E-05). Similarly, South Asians had a significantly higher frequency of CYP2C9*3 (12% SDS, 13% GIH, 11% SAS) vs. 7% in Europeans (pgenotype = <1.0E-05) and ‘T’ allele of CYP4F2 (36%) SDS, (43%) GIH, 40% (SAS) vs. (29%) in Europeans (pgenotype = <1.0E-05); both associated with a higher risk of bleeding with warfarin. All South Asians –the Sikhs (0.36), GIH (0.34), and SAS (0.36) had a higher frequency of the NAT2*6 allele (linked with slow acetylation of isoniazid) compared to Europeans (0.29). Additionally, the prevalence of the low activity ‘C’ allele of MTHFR (rs1801131) was highest in Sikhs compared to all other ethnic groups [SDS (44%), GIH (39%), SAS (42%) and European (32%) (pgenotype = <1.0E-05)]. SNPs in MTHFR affect metabolism of statins, 5-fluorouracil and methotrexate-based cancer drugs. These findings underscore the need for evaluation of other endogamous ethnic groups of India and beyond for establishing a global benchmark for pre-emptive genotyping in drug metabolizing genes before beginning therapeutic intervention.
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Affiliation(s)
- Dharambir K Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Cynthia Bejar
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Bishwa Sapkota
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | | | - Sarju Ralhan
- Hero DMC Heart Institute, Ludhiana, Punjab, India
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89
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Piñero J, Gonzalez-Perez A, Guney E, Aguirre-Plans J, Sanz F, Oliva B, Furlong LI. Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response. Front Genet 2018; 9:412. [PMID: 30319692 PMCID: PMC6168038 DOI: 10.3389/fgene.2018.00412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/05/2018] [Indexed: 11/13/2022] Open
Abstract
Understanding the mechanisms underlying drug therapeutic action and toxicity is crucial for the prevention and management of drug adverse reactions, and paves the way for a more efficient and rational drug design. The characterization of drug targets, drug metabolism proteins, and proteins associated to side effects according to their expression patterns, their tolerance to genomic variation and their role in cellular networks, is a necessary step in this direction. In this contribution, we hypothesize that different classes of proteins involved in the therapeutic effect of drugs and in their adverse effects have distinctive transcriptomics, genomics and network features. We explored the properties of these proteins within global and organ-specific interactomes, using multi-scale network features, evaluated their gene expression profiles in different organs and tissues, and assessed their tolerance to loss-of-function variants leveraging data from 60K subjects. We found that drug targets that mediate side effects are more central in cellular networks, more intolerant to loss-of-function variation, and show a wider breadth of tissue expression than targets not mediating side effects. In contrast, drug metabolizing enzymes and transporters are less central in the interactome, more tolerant to deleterious variants, and are more constrained in their tissue expression pattern. Our findings highlight distinctive features of proteins related to drug action, which could be applied to prioritize drugs with fewer probabilities of causing side effects.
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Affiliation(s)
- Janet Piñero
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Emre Guney
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Joaquim Aguirre-Plans
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ferran Sanz
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Baldo Oliva
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura I Furlong
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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90
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The gut microbiome and transplantation: An amazon jungle. J Heart Lung Transplant 2018; 37:1043-1044. [DOI: 10.1016/j.healun.2018.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 06/20/2018] [Indexed: 01/16/2023] Open
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91
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Unintended Side Effects of the Digital Transition: European Scientists’ Messages from a Proposition-Based Expert Round Table. SUSTAINABILITY 2018. [DOI: 10.3390/su10062001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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92
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Hemingway H, Asselbergs FW, Danesh J, Dobson R, Maniadakis N, Maggioni A, van Thiel GJM, Cronin M, Brobert G, Vardas P, Anker SD, Grobbee DE, Denaxas S. Big data from electronic health records for early and late translational cardiovascular research: challenges and potential. Eur Heart J 2018; 39:1481-1495. [PMID: 29370377 PMCID: PMC6019015 DOI: 10.1093/eurheartj/ehx487] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/19/2017] [Accepted: 08/08/2017] [Indexed: 12/13/2022] Open
Abstract
Aims Cohorts of millions of people's health records, whole genome sequencing, imaging, sensor, societal and publicly available data present a rapidly expanding digital trace of health. We aimed to critically review, for the first time, the challenges and potential of big data across early and late stages of translational cardiovascular disease research. Methods and results We sought exemplars based on literature reviews and expertise across the BigData@Heart Consortium. We identified formidable challenges including: data quality, knowing what data exist, the legal and ethical framework for their use, data sharing, building and maintaining public trust, developing standards for defining disease, developing tools for scalable, replicable science and equipping the clinical and scientific work force with new inter-disciplinary skills. Opportunities claimed for big health record data include: richer profiles of health and disease from birth to death and from the molecular to the societal scale; accelerated understanding of disease causation and progression, discovery of new mechanisms and treatment-relevant disease sub-phenotypes, understanding health and diseases in whole populations and whole health systems and returning actionable feedback loops to improve (and potentially disrupt) existing models of research and care, with greater efficiency. In early translational research we identified exemplars including: discovery of fundamental biological processes e.g. linking exome sequences to lifelong electronic health records (EHR) (e.g. human knockout experiments); drug development: genomic approaches to drug target validation; precision medicine: e.g. DNA integrated into hospital EHR for pre-emptive pharmacogenomics. In late translational research we identified exemplars including: learning health systems with outcome trials integrated into clinical care; citizen driven health with 24/7 multi-parameter patient monitoring to improve outcomes and population-based linkages of multiple EHR sources for higher resolution clinical epidemiology and public health. Conclusion High volumes of inherently diverse ('big') EHR data are beginning to disrupt the nature of cardiovascular research and care. Such big data have the potential to improve our understanding of disease causation and classification relevant for early translation and to contribute actionable analytics to improve health and healthcare.
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Affiliation(s)
- Harry Hemingway
- Research Department of Clinical Epidemiology, The Farr Institute of Health Informatics Research, University College London, 222 Euston Road, London NW1 2DA, UK
- The National Institute for Health Research, Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, University College London, 222 Euston Road, London NW1 2DA, UK
| | - Folkert W Asselbergs
- Research Department of Clinical Epidemiology, The Farr Institute of Health Informatics Research, University College London, 222 Euston Road, London NW1 2DA, UK
- The National Institute for Health Research, Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, University College London, 222 Euston Road, London NW1 2DA, UK
- Department of Cardiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht 3584 CX, The Netherlands
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Richard Dobson
- Research Department of Clinical Epidemiology, The Farr Institute of Health Informatics Research, University College London, 222 Euston Road, London NW1 2DA, UK
- The National Institute for Health Research, Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, University College London, 222 Euston Road, London NW1 2DA, UK
- NIHR Biomedical Research Centre for Mental Health (IOP), King‘s College London, De Crespigny Park, London SE5 8AF, UK
| | - Nikolaos Maniadakis
- European Society of Cardiology (ESC), 2035 Route des Colles, Les Templiers - CS 80179 Biot, 06903 Sophia Antipolis, France
| | - Aldo Maggioni
- European Society of Cardiology (ESC), 2035 Route des Colles, Les Templiers - CS 80179 Biot, 06903 Sophia Antipolis, France
| | - Ghislaine J M van Thiel
- Department of Cardiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht 3584 CX, The Netherlands
| | - Maureen Cronin
- Vifor Pharma Ltd, lughofstrasse 61, 8152 Glattbrugg, Zurich, Switzerland
| | - Gunnar Brobert
- Department of Epidemiology, Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Panos Vardas
- European Society of Cardiology (ESC), 2035 Route des Colles, Les Templiers - CS 80179 Biot, 06903 Sophia Antipolis, France
| | - Stefan D Anker
- Division of Cardiology and Metabolism—Heart Failure, Cachexia & Sarcopenia; Department of Cardiology (CVK), Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité University Medicine, Charitépl. 1, 10117 Berlin, Germany
- Department of Cardiology and Pneumology, University Medicine Göttingen (UMG), Robert-Koch-Strasse 40, 37099, Göttingen, Germany
| | - Diederick E Grobbee
- Julius Centre for Health Sciences and Primary Care, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Spiros Denaxas
- Research Department of Clinical Epidemiology, The Farr Institute of Health Informatics Research, University College London, 222 Euston Road, London NW1 2DA, UK
- The National Institute for Health Research, Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, University College London, 222 Euston Road, London NW1 2DA, UK
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93
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Saatci Ö, Borgoni S, Akbulut Ö, Durmuş S, Raza U, Eyüpoğlu E, Alkan C, Akyol A, Kütük Ö, Wiemann S, Şahin Ö. Targeting PLK1 overcomes T-DM1 resistance via CDK1-dependent phosphorylation and inactivation of Bcl-2/xL in HER2-positive breast cancer. Oncogene 2018; 37:2251-2269. [PMID: 29391599 DOI: 10.1038/s41388-017-0108-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 10/22/2017] [Accepted: 11/12/2017] [Indexed: 12/18/2022]
Abstract
Trastuzumab-refractory, HER2 (human epidermal growth factor receptor 2)-positive breast cancer is commonly treated with trastuzumab emtansine (T-DM1), an antibody-drug conjugate of trastuzumab and the microtubule-targeting agent, DM1. However, drug response reduces greatly over time due to acquisition of resistance whose molecular mechanisms are mostly unknown. Here, we uncovered a novel mechanism of resistance against T-DM1 by combining whole transcriptome sequencing (RNA-Seq), proteomics and a targeted small interfering RNA (siRNA) sensitization screen for molecular level analysis of acquired and de novo T-DM1-resistant models of HER2-overexpressing breast cancer. We identified Polo-like kinase 1 (PLK1), a mitotic kinase, as a resistance mediator whose genomic as well as pharmacological inhibition restored drug sensitivity. Both acquired and de novo resistant models exhibited synergistic growth inhibition upon combination of T-DM1 with a selective PLK1 inhibitor, volasertib, at a wide concentration range of the two drugs. Mechanistically, T-DM1 sensitization upon PLK1 inhibition with volasertib was initiated by a spindle assembly checkpoint (SAC)-dependent mitotic arrest, leading to caspase activation, followed by DNA damage through CDK1-dependent phosphorylation and inactivation of Bcl-2/xL. Furthermore, we showed that Ser70 phosphorylation of Bcl-2 directly regulates apoptosis by disrupting the binding to and sequestration of the pro-apoptotic protein Bim. Importantly, T-DM1 resistance signature or PLK1 expression correlated with cell cycle progression and DNA repair, and predicted a lower sensitivity to taxane/trastuzumab combination in HER2-positive breast cancer patients. Finally, volasertib in combination with T-DM1 greatly synergized in models of T-DM1 resistance in terms of growth inhibition both in three dimensional (3D) cell culture and in vivo. Altogether, our results provide promising pre-clinical evidence for potential testing of T-DM1/volasertib combination in T-DM1 refractory HER2-positive breast cancer patients for whom there is currently no treatment available.
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Affiliation(s)
- Özge Saatci
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800, Ankara, Turkey
| | - Simone Borgoni
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Özge Akbulut
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800, Ankara, Turkey
| | - Selvi Durmuş
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800, Ankara, Turkey
| | - Umar Raza
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800, Ankara, Turkey
| | - Erol Eyüpoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800, Ankara, Turkey
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, 06800, Ankara, Turkey
| | - Aytekin Akyol
- Department of Pathology, Hacettepe University School of Medicine, 06410, Ankara, Turkey
| | - Özgür Kütük
- Department of Medical Genetics, Başkent University, 01250, Adana, Turkey
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), INF580, Heidelberg, 69120, Germany
| | - Özgür Şahin
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800, Ankara, Turkey.
- National Nanotechnology Research Center (UNAM), Bilkent University, 06800, Ankara, Turkey.
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94
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Ovejero-Benito MC, Muñoz-Aceituno E, Reolid A, Saiz-Rodríguez M, Abad-Santos F, Daudén E. Pharmacogenetics and Pharmacogenomics in Moderate-to-Severe Psoriasis. Am J Clin Dermatol 2018; 19:209-222. [PMID: 28921458 DOI: 10.1007/s40257-017-0322-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pharmacogenetics is the study of variations in DNA sequence related to drug response. Moreover, the evolution of biotechnology and the sequencing of human DNA have allowed the creation of pharmacogenomics, a branch of genetics that analyzes human genes, the RNAs and proteins encoded by them, and the inter-and intra-individual variations in expression and function in relation to drug response. Pharmacogenetics and pharmacogenomics are being used to search for biomarkers that can predict response to systemic treatments, including those for moderate-to-severe psoriasis. Psoriasis is a chronic inflammatory disease with an autoimmune contribution. Although its etiology remains unknown, genetic, epigenetic, and environmental factors play a role in its development. Diverse systemic and biologic therapies are used to treat moderate-to-severe psoriasis. However, these treatments are not curative, and patients exhibit a wide range of responses to them. Moderate-to-severe psoriasis is usually treated with systemic immunomodulators such as acitretin, ciclosporin, and methotrexate. Anti-tumor necrosis factor (TNF) drugs (adalimumab, etanercept, or infliximab) are the first-line treatment for patients resistant to conventional systemic therapies. Although these therapies are very efficient, around 30-50% of patients have inadequate response. Ustekinumab is a monoclonal antibody that targets interleukin (IL)-12 and IL-23 and is used for moderate-to-severe psoriasis. New drugs (apremilast, brodalumab, guselkumab, ixekizumab, and secukinumab) have recently been approved for psoriasis. However, response rates to systemic treatments for moderate-to-severe psoriasis range from 35 to 80%, so it is necessary to identify non-invasive biomarkers that could help predict treatment outcomes of these therapies and individualize care for patients with psoriasis. These biomarkers could improve patient quality of life and reduce health costs and potential side effects. Pharmacogenetic studies have identified potential biomarkers for response to biologic treatments for moderate-to-severe psoriasis. These biomarkers need to be validated in clinical trials involving large cohorts of patients before they can be translated to the clinic. We review pharmacogenetics and pharmacogenomics studies for the treatment of moderate-to-severe plaque psoriasis.
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95
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Robinson JR, Denny JC, Roden DM, Van Driest SL. Genome-wide and Phenome-wide Approaches to Understand Variable Drug Actions in Electronic Health Records. Clin Transl Sci 2018; 11:112-122. [PMID: 29148204 PMCID: PMC5866959 DOI: 10.1111/cts.12522] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/14/2017] [Indexed: 12/24/2022] Open
Affiliation(s)
- Jamie R. Robinson
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of SurgeryVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Joshua C. Denny
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Dan M. Roden
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of PharmacologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Sara L. Van Driest
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of PediatricsVanderbilt University Medical CenterNashvilleTennesseeUSA
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96
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ALARCON-VALDES P, ORTIZ-REYNOSO M, SANTILLAN-BENITEZ J. Perspective on the Genetic Response to Antiparasitics: A Review Article. IRANIAN JOURNAL OF PARASITOLOGY 2017; 12:470-481. [PMID: 29317871 PMCID: PMC5756296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
BACKGROUND Drugs' pharmacokinetics and pharmacodynamics can be affected by diverse genetic variations, within which simple nucleotide polymorphisms (SNPs) are the most common. Genetic variability is one of the factors that could explain questions like why a given drug does not have the desired effect or why do adverse drug reactions arise. METHODS In this retrospective observational study, literature search limits were set within PubMed database as well as the epidemiological bulletins published by the Mexican Ministry of Health, from Jan 1st 2001 to Mar 31st 2017 (16 years). RESULTS Metabolism of antiparasitic drugs and their interindividual responses are mainly modified by variations in cytochrome P450 enzymes. These enzymes show high frequencies of polymorphic variability thus affecting the expression of CYP2C, CYP2A, CYP2A6, CYP2D6, CYP2E6 and CYP2A6 isoforms. Research in this field opens the door to new personalized treatment approaches in medicine. CONCLUSION Clinical and pharmacological utility yield by applying pharmacogenetics to antiparasitic treatments is not intended as a mean to improve the prescription process, but to select or exclude patients that could present adverse drug reactions as well as to evaluate genetic alterations which result in a diversity of responses, ultimately seeking to provide a more effective and safe treatment; therefore choosing a proper dose for the appropriate patient and the optimal treatment duration. Furthermore, pharmacogenetics assists in the development of vaccines. In other words, the aim of this discipline is to find therapeutic targets allowing personalized treatments.
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Schee genannt Halfmann S, Evangelatos N, Schröder-Bäck P, Brand A. European healthcare systems readiness to shift from ‘one-size fits all’ to personalized medicine. Per Med 2017; 14:63-74. [DOI: 10.2217/pme-2016-0061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Personalized medicine (PM) is no longer an abstract healthcare approach. It has become a reality over the last years and is already successfully applied in the various medical fields. Although there are success stories of implementing PM, there are still many more opportunities to further implement and make full use of the potential of PM. We assessed the system readiness of healthcare systems in Europe to shift from the predominant ‘one size fits all’ healthcare approach to PM. We conclude that European healthcare systems are only partially ready for PM. Key challenges such as integration of big data, health literacy, reimbursement and regulatory issues need to be overcome in order to strengthen the implementation and uptake of PM.
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Affiliation(s)
- Sebastian Schee genannt Halfmann
- Maastricht Economic & Social Research Institute on Innovation & Technology (MERIT), Maastricht University, Boschstraat 24, 6211AX Maastricht, The Netherlands
| | - Nikolaos Evangelatos
- Maastricht Economic & Social Research Institute on Innovation & Technology (MERIT), Maastricht University, Boschstraat 24, 6211AX Maastricht, The Netherlands
- University Clinic for Emergency & Intensive Care Medicine, Paracelsus Medical University (PMU), Prof. Ernst-Nathan-Strasse 1, 90419 Nuremberg, Germany
| | - Peter Schröder-Bäck
- Department of International Health, School CAPHRI, Maastricht University, Duboisdomein 30, 6229 GT Maastricht, The Netherlands
- Faculty for Health & Human Sciences, University of Bremen, Grazer Strasse 2, 28359 Bremen, Germany
| | - Angela Brand
- Maastricht Economic & Social Research Institute on Innovation & Technology (MERIT), Maastricht University, Boschstraat 24, 6211AX Maastricht, The Netherlands
- Faculty of Health, Medicine & Life Sciences, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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Bush WS, Crosslin DR, Owusu‐Obeng A, Wallace J, Almoguera B, Basford MA, Bielinski SJ, Carrell DS, Connolly JJ, Crawford D, Doheny KF, Gallego CJ, Gordon AS, Keating B, Kirby J, Kitchner T, Manzi S, Mejia AR, Pan V, Perry CL, Peterson JF, Prows CA, Ralston J, Scott SA, Scrol A, Smith M, Stallings SC, Veldhuizen T, Wolf W, Volpi S, Wiley K, Li R, Manolio T, Bottinger E, Brilliant MH, Carey D, Chisholm RL, Chute CG, Haines JL, Hakonarson H, Harley JB, Holm IA, Kullo IJ, Jarvik GP, Larson EB, McCarty CA, Williams MS, Denny JC, Rasmussen‐Torvik LJ, Roden DM, Ritchie MD. Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network. Clin Pharmacol Ther 2016; 100:160-9. [PMID: 26857349 PMCID: PMC5010878 DOI: 10.1002/cpt.350] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/12/2016] [Accepted: 02/04/2016] [Indexed: 12/20/2022]
Abstract
Genetic variation can affect drug response in multiple ways, although it remains unclear how rare genetic variants affect drug response. The electronic Medical Records and Genomics (eMERGE) Network, collaborating with the Pharmacogenomics Research Network, began eMERGE‐PGx, a targeted sequencing study to assess genetic variation in 82 pharmacogenes critical for implementation of “precision medicine.” The February 2015 eMERGE‐PGx data release includes sequence‐derived data from ∼5,000 clinical subjects. We present the variant frequency spectrum categorized by variant type, ancestry, and predicted function. We found 95.12% of genes have variants with a scaled Combined Annotation‐Dependent Depletion score above 20, and 96.19% of all samples had one or more Clinical Pharmacogenetics Implementation Consortium Level A actionable variants. These data highlight the distribution and scope of genetic variation in relevant pharmacogenes, identifying challenges associated with implementing clinical sequencing for drug treatment at a broader level, underscoring the importance for multifaceted research in the execution of precision medicine.
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Genotyping NUDT15 can predict the dose reduction of 6-MP for children with acute lymphoblastic leukemia especially at a preschool age. J Hum Genet 2016; 61:797-801. [PMID: 27193222 DOI: 10.1038/jhg.2016.55] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 01/25/2023]
Abstract
The pharmacokinetics among children has been altered dynamically. The difference between children and adults is caused by immaturity in things such as metabolic enzymes and transport proteins. The periods when these alterations happen vary from a few days to some years after birth. We hypothesized that the effect of gene polymorphisms associated with the dose of medicine could be influenced by age. In this study, we analyzed 51 patients with childhood acute lymphoblastic leukemia (ALL) retrospectively. We examined the associations between the polymorphism in NUDT15 and clinical data, especially the dose of 6-mercaptopurine (6-MP). Ten of the patients were heterozygous for the variant allele in NUDT15. In patients under 7 years old with NUDT15 variant allele, the average administered dose of 6-MP was lower than that for the patients homozygous for the wild-type allele (P=0.04). Genotyping of NUDT15 could be a beneficial to estimate the tolerated dose of 6-MP for patients with childhood ALL, especially at a preschool age in Japan. Furthermore, the analysis with stratification by age might be useful in pharmacogenomics among children.
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Abstract
Adverse drug reactions (ADRs) are a major public health concern and cause significant patient morbidity and mortality. Pharmacogenomics is the study of how genetic polymorphisms affect an individual's response to pharmacotherapy at the level of a whole genome. This article updates our knowledge on how genetic polymorphisms of important genes alter the risk of ADR occurrence after an extensive literature search. To date, at least 244 pharmacogenes identified have been associated with ADRs of 176 clinically used drugs based on PharmGKB. At least 28 genes associated with the risk of ADRs have been listed by the Food and Drug Administration as pharmacogenomic biomarkers. With the availability of affordable and reliable testing tools, pharmacogenomics looks promising to predict, reduce, and minimize ADRs in selected populations.
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