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Genomic Association of Single Nucleotide Polymorphisms with Blood Pressure Response to Hydrochlorothiazide Among South African Adults with Hypertension
Journal of Personalized Medicine Article Genomic Association of Single Nucleotide Polymorphisms with Blood Pressure Response to Hydrochlorothiazide among South African Adults with Hypertension Charity Masilela 1,* , Brendon Pearce 1 , Joven Jebio Ongole 2 , Oladele Vincent Adeniyi 3 and Mongi Benjeddou 1 1 Department of Biotechnology, University of the Western Cape, Bellville 7530, South Africa; brendon.biff@gmail.com (B.P.); [email protected] (M.B.) 2 Center for Teaching and Learning, Department of Family Medicine, Piet Retief Hospital, Mkhondo 2380, South Africa; [email protected] 3 Department of Family Medicine, Walter Sisulu University, East London 5200, South Africa; [email protected] * Correspondence: [email protected] Received: 23 October 2020; Accepted: 23 November 2020; Published: 9 December 2020 Abstract: This study described single nucleotide polymorphisms (SNPs) in hydrochlorothiazide- associated genes and further assessed their correlation with blood pressure control among South African adults living with hypertension. A total of 291 participants belonging to the Nguni tribes of South Africa on treatment for hypertension were recruited. Nineteen SNPs in hydrochlorothiazide pharmacogenes were selected and genotyped using MassArray. Uncontrolled hypertension was defined as blood pressure 140/90 mmHg. The association between genotypes, alleles and blood ≥ pressure response to treatment was determined by conducting multivariate logistic regression model analysis. The majority of the study participants were female (73.19%), -
An Update on HLA Alleles Associated with Adverse Drug Reactions
Drug Metabol Pers Ther 2017; 32(2): 73–87 Review Ingrid Fricke-Galindo, Adrián LLerena and Marisol López-López* An update on HLA alleles associated with adverse drug reactions DOI 10.1515/dmpt-2016-0025 Due to the improvement of drug therapy and the economic Received July 27, 2016; accepted February 7, 2017; previously published benefit that HLA screening represents, investigations on online March 18, 2017 HLA alleles associated with ADR should continue. Abstract: Adverse drug reactions (ADRs) are considered as Keywords: abacavir; allopurinol; adverse drug reac- an important cause of morbidity and mortality. The hyper- tions; carbamazepine; human leukocyte antigen (HLA); sensitivity reactions are immune-mediated ADRs, which hypersensitivity syndrome; pharmacogenetics; Stevens- are dose-independent, unpredictable and have been asso- Johnson syndrome. ciated with several HLA alleles. The present review aimed to describe HLA alleles that have been associated with different ADRs in populations worldwide, the recommen- dations of regulatory agencies and pharmacoeconomic Introduction information and databases for the study of HLA alleles in Immunologic-mediated adverse drug reactions (ADRs) are pharmacogenetics. A systematic search was performed in included in type B ADRs which are not related to the dose June 2016 of articles relevant to this issue in indexed jour- and that are uncommon and unpredictable in that they are nals and in scientific databases (PubMed and PharmGKB). not related with the pharmacodynamics of the drug and The information of 95 association studies found was sum- present high mortality [1]. There is evidence that suscep- marized. Several HLA alleles and haplotypes have been tibility to at least some Type B ADR is found under strong associated with ADRs induced mainly by carbamazepine, genetic influence [2], and identifying genetic risk factors allopurinol, abacavir and nevirapine, among other drugs. -
Precision Medicine and Adverse Drug Reactions Related to Cardiovascular Drugs †
diseases Review Precision Medicine and Adverse Drug Reactions Related to Cardiovascular Drugs † James D. Noyes 1 , Ify R. Mordi 1 , Alexander S. Doney 2, Rahman Jamal 3 and Chim C. Lang 1,* 1 Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; [email protected] (J.D.N.); [email protected] (I.R.M.) 2 Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; [email protected] 3 UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur 56000, Malaysia; [email protected] * Correspondence: [email protected]; Tel.: +44-1382-383283 † Precision medicine in cardiology. Abstract: Cardiovascular disease remains the leading global cause of death. Early intervention, with lifestyle advice alongside appropriate medical therapies, is fundamental to reduce patient mortality among high-risk individuals. For those who live with the daily challenges of cardiovascular disease, pharmacological management aims to relieve symptoms and prevent disease progression. Despite best efforts, prescription drugs are not without their adverse effects, which can cause significant patient morbidity and consequential economic burden for healthcare systems. Patients with cardiovascular diseases are often among the most vulnerable to adverse drug reactions due to multiple co-morbidities and advanced age. Examining a patient’s genome to assess for variants that may alter drug efficacy and susceptibility to adverse reactions underpins pharmacogenomics. This strategy is increasingly being implemented in clinical cardiology to tailor patient therapies. The Citation: Noyes, J.D.; Mordi, I.R.; Doney, A.S.; Jamal, R.; Lang, C.C. -
Pharmacogenomics, How to Deal with Different Types of Variants in Next Generation Sequencing Data in the Personalized Medicine Area
Journal of Clinical Medicine Review Pharmacogenomics, How to Deal with Different Types of Variants in Next Generation Sequencing Data in the Personalized Medicine Area Alireza Tafazoli 1,2 , Natalia Wawrusiewicz-Kurylonek 3, Renata Posmyk 3 and Wojciech Miltyk 1,* 1 Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, 15-089 Białystok, Poland; [email protected] 2 Clinical Research Centre, Medical University of Białystok, 15-276 Bialystok, Poland 3 Department of Clinical Genetics, Medical University of Białystok, 15-089 Białystok, Poland; [email protected] (N.W.-K.); [email protected] (R.P.) * Correspondence: [email protected]; Tel.: +48-857485845 Abstract: Pharmacogenomics (PGx) is the knowledge of diverse drug responses and effects in people, based on their genomic profiles. Such information is considered as one of the main directions to reach personalized medicine in future clinical practices. Since the start of applying next generation sequencing (NGS) methods in drug related clinical investigations, many common medicines found their genetic data for the related metabolizing/shipping proteins in the human body. Yet, the employing of technology is accompanied by big obtained data, which most of them have no clear guidelines for consideration in routine treatment decisions for patients. This review article talks about different types of NGS derived PGx variants in clinical studies and try to display the current and newly developed approaches to deal with pharmacogenetic data with/without clear guidelines for considering in clinical settings. Citation: Tafazoli, A.; Keywords: pharmacogenomics; NGS variants; personalized medicine Wawrusiewicz-Kurylonek, N.; Posmyk, R.; Miltyk, W. -
Rational Design and Synthesis of New Nucleoside Analogues Bearing a Cyclohexane Core
Rational Design and Synthesis of New Nucleoside Analogues Bearing a Cyclohexane Core Beatriz Domínguez Pérez Ph.D. Thesis Ph.D. in Chemistry Supervisors: Dr. Ramon Alibés Arqués Dr. Félix Busqué Sánchez Dr. Jean-Didier Márechal Departament de Química Facultat de Ciències 2015 Memòria presentada per aspirar al Grau de Doctor per Beatriz Domínguez Pérez Beatriz Domínguez Pérez Vist i plau, Dr. Ramon Alibés Arqués Dr. Félix Busqué Sánchez Dr. Jean-Didier Maréchal Bellaterra, 13 de maig de 2015 “When you make the finding yourself-even if you’re the last person on Earth to see the light- you’ll never forget it” Carl Sagan A mis padres, a mi hermana A Jonatan Table of contents Abbreviations................................................................................................................................ 1 I. General introduction ............................................................................................. 5 1. Viruses ................................................................................................................................. 7 1.1. Virus replication ............................................................................................................. 8 1.2. Viral diseases in humans ................................................................................................ 9 2. Antiviral drugs ................................................................................................................... 10 2.1. Nucleoside analogues ................................................................................................. -
The Genome-Wide Landscape of Copy Number Variations in the MUSGEN Study Provides Evidence for a Founder Effect in the Isolated Finnish Population
European Journal of Human Genetics (2013) 21, 1411–1416 & 2013 Macmillan Publishers Limited All rights reserved 1018-4813/13 www.nature.com/ejhg ARTICLE The genome-wide landscape of copy number variations in the MUSGEN study provides evidence for a founder effect in the isolated Finnish population Chakravarthi Kanduri1, Liisa Ukkola-Vuoti1, Jaana Oikkonen1, Gemma Buck2, Christine Blancher2, Pirre Raijas3, Kai Karma4, Harri La¨hdesma¨ki5 and Irma Ja¨rvela¨*,1 Here we characterized the genome-wide architecture of copy number variations (CNVs) in 286 healthy, unrelated Finnish individuals belonging to the MUSGEN study, where molecular background underlying musical aptitude and related traits are studied. By using Illumina HumanOmniExpress-12v.1.0 beadchip, we identified 5493 CNVs that were spread across 467 different cytogenetic regions, spanning a total size of 287.83 Mb (B9.6% of the human genome). Merging the overlapping CNVs across samples resulted in 999 discrete copy number variable regions (CNVRs), of which B6.9% were putatively novel. The average number of CNVs per person was 20, whereas the average size of CNV per locus was 52.39 kb. Large CNVs (41 Mb) were present in 4% of the samples. The proportion of homozygous deletions in this data set (B12.4%) seemed to be higher when compared with three other populations. Interestingly, several CNVRs were significantly enriched in this sample set, whereas several others were totally depleted. For example, a CNVR at chr2p22.1 intersecting GALM was more common in this population (P ¼ 3.3706 Â 10 À44) than in African and other European populations. The enriched CNVRs, however, showed no significant association with music-related phenotypes. -
Nucleobase Coupling by Mitsunobu Reaction Towards Nucleoside Analogs
The Free Internet Journal Review for Organic Chemistry Archive for Arkivoc 2021, part iv, 0-0 Organic Chemistry to be inserted by editorial office Nucleobase coupling by Mitsunobu reaction towards nucleoside analogs Eduardo C. de Sousa and Amélia P. Rauter Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa Ed C8, Piso 5, Campo Grande, 1749-016 Lisboa, Portugal Email: [email protected] This paper is dedicated to Prof. Dr. Horst Kunz on the occasion of his 80th anniversary Received 09-21-2020 Accepted Manuscript 11-29-2020 Published on line 12-20-2020 Abstract The coupling of a nucleobase is a key step in the synthesis of most nucleoside analogs, e.g. carbocyclic nucleosides, isonucleosides and acyclic nucleosides. The synthetic strategies for nucleosides based on N- glycosylation are not applied when the nucleobase is not linked to the anomeric center. Thus, other methods have been employed, mainly those based on the alkylation of nucleobases. The Mitsunobu reaction, in which a hydroxy group is replaced by a nucleophile, has also been extensively applied, generating a diversity of molecules, including pharmaceuticals and their precursors. In this review the usefulness of this reaction for the coupling of nucleobases to non-anomeric positions of sugars, carbasugars and other homocyclic and linear structures is highlighted and discussed, covering purines and pyrimidines as pronucleophiles. * Keywords: Mitsunobu reaction, carbocyclic nucleosides, isonucleosides, acyclic nucleosides, synthesis DOI: https://doi.org/10.24820/ark.5550190.p011.377 Page 1 ©AUTHOR(S) Arkivoc 2021, iv, 0-0 de Sousa, E. C. et al. Table of Contents 1. Introduction 1.1. -
Nucleoside Analogs with Fleximer Nucleobase
DOI 10.1007/s10593-020-02713-5 Chemistry of Heterocyclic Compounds 2020, 56(6), 636–643 Nucleoside analogs with fleximer nucleobase Mikhail V. Chudinov1* 1MIREA - Russian Technological University, Lomonosov Institute of Fine Chemical Tehnology, 78 Vernadsky Ave., Moscow 119454, Russia, е-mail: [email protected] Translated from Khimiya Geterotsiklicheskikh Soedinenii, Submitted February 28, 2020 2020, 56(6), 636–643 Accepted after revision April 15, 2020 This review article is devoted to the so-called fleximer nucleoside analogs, containing two or more planar moieties in the heterocyclic base, connected by a bond that permits rotation. Such analogs have been proposed as molecular probes for detecting enzyme–substrate interactions and studying the transcription and translation of nucleic acids, but subsequently have attracted the interest of researchers by their antiviral and antitumor activity. The methods used in the synthesis of such compounds, along with their structural features and also biological activity are considered in this review. Keywords: pyrimidine, riboside, triazole, antitumor activity, antiviral activity, fleximer, nucleoside analogs. The term "fleximers" was introduced in 2001 by the heterocyclic base was the assembly of a fused tricyclic Seley research group,1 referring to synthetic analogs of system with a central thiophene ring. This tricyclic system nucleosides in which the purine base has been "splitted" was subjected to Raney nickel desulfurization, providing into two linked heterocycles – imidazole and pyrimidine. the desired fleximer1 (Scheme 1). Similarly to any other Initially intended as model compounds for studying the synthesis of nucleoside analogs, there was the issue of which binding sites of enzymes and characterizing the interactions synthetic step would be most convenient for the formation between proteins and nucleic acids, compounds of this type of the glycosidic bond. -
The First Intermolecular Interrupted Imino-Nazarov Reaction
Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue The first intermolecular interrupted imino-Nazarov reaction: expeditious access to carbocyclic Cite this: Chem. Sci.,2016,7,1100 nucleoside analogues† Ronny William, Wei Lin Leng, Siming Wang and Xue-Wei Liu* The analogous imino-variant of the Nazarov reaction suffers from unfavorable energetics associated with the ring closure process, thereby limiting the utility of this class of reactions. In this report, the realization of the first intermolecular interrupted imino-Nazarov reaction utilizing silylated pyrimidine derivatives as Received 21st September 2015 nucleophilic trapping partners culminated in an expedient synthetic route to carbocyclic nucleoside Accepted 27th October 2015 analogues. The potential application of silylated nucleobases to intercept the oxyallyl cation in other DOI: 10.1039/c5sc03559g variants of the Nazarov reaction provides vast opportunities to develop new strategies for the formation www.rsc.org/chemicalscience of carbocyclic nucleoside analogues. Creative Commons Attribution 3.0 Unported Licence. Carbocyclic nucleosides represent an emerging class of privi- intercept the cyclopentenyl cation formed following cyclization leged therapeutic compounds which exhibit interesting bio- in inter- or intramolecular fashion, allowing rapid access to logical properties.1,2 Substitution of endocyclic oxygen by more elaborate cyclopentanoid compounds.8 The imino variant a methylene unit in a carbocyclic nucleoside derivative imparts of the Nazarov -
The Role of Nucleotide Excision by Reverse Transcriptase in HIV Drug Resistance
Viruses 2010, 2, 372-394; doi:10.3390/v2020372 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Review The Role of Nucleotide Excision by Reverse Transcriptase in HIV Drug Resistance Antonio J. Acosta-Hoyos and Walter A. Scott * Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, P.O. Box 016129, Miami, FL 33101-6129, USA; E-Mail: [email protected] (A.J.A.-H.) * Author to whom correspondence should be addressed; E-Mail: [email protected] (W.A.S.); Tel.: +1-305-243-6359; Fax: +1-305-243-3955. Received: 10 December 2009; in revised form: 15 January 2010 / Accepted: 25 January 2010 / Published: 28 January 2010 Abstract: Nucleoside reverse transcriptase (RT) inhibitors of HIV block viral replication through the ability of HIV RT to incorporate chain-terminating nucleotide analogs during viral DNA synthesis. Once incorporated, the chain-terminating residue must be removed before DNA synthesis can continue. Removal can be accomplished by the excision activity of HIV RT, which catalyzes the transfer of the 3'-terminal residue on the blocked DNA chain to an acceptor substrate, probably ATP in most infected cells. Mutations of RT that enhance excision activity are the most common cause of resistance to 3'-azido-3'- deoxythymidine (AZT) and exhibit low-level cross-resistance to most other nucleoside RT inhibitors. The resistance to AZT is suppressed by a number of additional mutations in RT, most of which were identified because they conferred resistance to other RT inhibitors. Here we review current understanding of the biochemical mechanisms responsible for increased or decreased excision activity due to these mutations. -
Infinium™ H3africa Consortium Array V2 a Powerful Array for Genetic Studies Focused on African Populations
Design Content | Process BeadChip | Analyze Data Infinium™ H3Africa Consortium Array v2 A powerful array for genetic studies focused on African populations. Overview The Infinium H3Africa Consortium Array v2 (Figure 1, Table 1) is a powerful array for research studies that enables identification of genetic associations with common and rare traits among African populations (Table 2). Specifically designed by the H3Africa consortium, the array harnesses content from Illumina Omni2.5-8 and Omni5-4 BeadChips, in addition to custom content selected by the consortium based on whole-genome sequencing (WGS) data. The custom content was selected by including specific single nucleotide polymorphisms (SNPs) requested by H3Africa consortium projects, SNPs within the MHC region, X-chromosome and mitochondrion SNPs, and SNPs of clinical or pharmacogenomic interest. Remaining custom SNPs were selected to improve coverage, imputation accuracy, and enrichment in novel but common variants in African populations based on sequencing data. Figure 1: Infinium H3Africa Consortium Array v2—The 8-sample Infinium Consortium-selected content H3Africa Consortium Array supports rapid cost-effective studies. The H3Africa consortium selected approximately 10,000 variants relevant to specific diseases of interest including variants known to Table 2: Marker information be associated with kidney disease, diabetes, sickle cell disease, a cardiometabolic diseases and susceptibility to infectious diseases. Marker categories No. of markers b Additional variants from PharmGKB, genome-wide association Exonic markers 88,785 b study (GWAS) catalog, ClinVar and the COSMIC database were also Intronic markers 1,074,881 c identified and selected by the consortium. For PharmGKB and the Nonsense markers 313 c GWAS catalog, 4000 and 24,000 variants, respectively, that occur Missense markers 23,548 c with a minor allele frequency (MAF) ≥ 0.01 in at least one of the African Synonymous markers 21,654 c populations were selected for inclusion. -
Pharmacogenetic Information in Swiss Drug Labels €“ a Systematic Analysis
The Pharmacogenomics Journal (2021) 21:423–434 https://doi.org/10.1038/s41397-020-00195-4 ARTICLE Pharmacogenetic information in Swiss drug labels – a systematic analysis 1 2 1 3 3 3 3,4 2 C. Jeiziner ● K. Suter ● U. Wernli ● J. M. Barbarino ● L. Gong ● M. Whirl-Carrillo ● T. E. Klein ● T. D. Szucs ● 1 5 K. E. Hersberger ● H. E. Meyer zu Schwabedissen Received: 24 March 2020 / Revised: 18 August 2020 / Accepted: 5 October 2020 / Published online: 17 October 2020 © The Author(s) 2020. This article is published with open access Abstract Implementation of pharmacogenetics (PGx) and individualization of drug therapy is supposed to obviate adverse drug reactions or therapy failure. Health care professionals (HCPs) use drug labels (DLs) as reliable information about drugs. We analyzed the Swiss DLs to give an overview on the currently available PGx instructions. We screened 4306 DLs applying natural language processing focusing on drug metabolism (pharmacokinetics) and we assigned PGx levels following the classification system of PharmGKB. From 5979 hits, 2564 were classified as PGx-relevant affecting 167 substances. 55% (n = 93) were classified as “actionable PGx”. Frequently, PGx information appeared in the pharmacokinetics section and in “ ” 1234567890();,: 1234567890();,: DLs of the anatomic group nervous system . Unstandardized wording, appearance of PGx information in different sections and unclear instructions challenge HCPs to identify and interpret PGx information and translate it into practice. HCPs need harmonization and standardization of PGx information in DLs to personalize drug therapies and tailor pharmaceutical care. Introduction However, drug therapies may fail, and/or may induce con- siderable adverse drug reactions (ADRs).