keyword
https://read.qxmd.com/read/38533129/ursapgx-a-new-r-package-to-annotate-pharmacogenetic-star-alleles-using-phased-whole-genome-sequencing-data
#1
JOURNAL ARTICLE
Gennaro Calendo, Dara Kusic, Jozef Madzo, Neda Gharani, Laura Scheinfeldt
Long-read sequencing technologies offer new opportunities to generate high-confidence phased whole-genome sequencing data for robust pharmacogenetic annotation. Here, we describe a new user-friendly R package, ursaPGx, designed to accept multi-sample phased whole-genome sequencing data VCF input files and output star allele annotations for pharmacogenes annotated in PharmVar.
2024: Front Bioinform
https://read.qxmd.com/read/38476074/pharmacogenetics-of-tamoxifen-in-breast-cancer-patients-of-african-descent-lack-of-data
#2
REVIEW
Bianca Kruger, Delva Shamley, Nyarai Desiree Soko, Collet Dandara
Tamoxifen, a selective estrogen receptor modulator, is used to treat hormone receptor-positive breast cancer. Tamoxifen acts as a prodrug, with its primary therapeutic effect mediated by its principal metabolite, endoxifen. However, tamoxifen has complex pharmacokinetics involving several drug-metabolizing enzymes and transporters influencing its disposition. Genes encoding enzymes involved in tamoxifen disposition exhibit genetic polymorphisms which vary widely across world populations. This review highlights the lack of data on tamoxifen pharmacogenetics among African populations...
March 2024: Clinical and Translational Science
https://read.qxmd.com/read/38462643/genetic-diversity-of-variants-involved-in-drug-response-among-tunisian-and-italian-populations-toward-personalized-medicine
#3
JOURNAL ARTICLE
Haifa Jmel, Stefania Sarno, Cristina Giuliani, Wided Boukhalfa, Sonia Abdelhak, Donata Luiselli, Rym Kefi
Adverse drug reactions (ADR) represent a significant contributor to morbidity and mortality, imposing a substantial financial burden. Genetic ancestry plays a crucial role in drug response. The aim of this study is to characterize the genetic variability of selected pharmacogenes involved with ADR in Tunisians and Italians, with a comparative analysis against global populations. A cohort of 135 healthy Tunisians and 737 Italians were genotyped using a SNP array. Variants located in 25 Very Important Pharmacogenes implicated in ADR were extracted from the genotyping data...
March 10, 2024: Scientific Reports
https://read.qxmd.com/read/38359167/pharmacogenomic-allele-coverage-of-genome-wide-genotyping-arrays-a-comparative-analysis
#4
JOURNAL ARTICLE
Courtney Lenz, Ankita Narang, Chad A Bousman
The use of genome-wide genotyping arrays in pharmacogenomics (PGx) research and clinical implementation applications is increasing but it is unclear which arrays are best suited for these applications. Here, we conduct a comparative coverage analysis of PGx alleles included on genome-wide genotyping arrays, with an emphasis on alleles in genes with PGx-based prescribing guidelines. Genomic manifest files for seven arrays including the Axiom Precision Medicine Diversity Array (PMDA), Axiom PMDA Plus, Axiom PangenomiX, Axiom PangenomiX Plus, Infinium Global Screening Array, Infinium Global Diversity Array (GDA) and Infinium GDA with enhanced PGx (GDA-PGx) Array, were evaluated for coverage of 523 star alleles across 19 pharmacogenes included in prescribing guidelines developed by the Clinical Pharmacogenetic Implementation Consortium and Dutch Pharmacogenomics Working Group...
February 8, 2024: Pharmacogenetics and Genomics
https://read.qxmd.com/read/38346976/haplotype-phasing-of-cyp2d6-an-allelic-ratio-method-using-agena-massarray-data
#5
JOURNAL ARTICLE
Megana Thamilselvan, Cheryl Mather, Yabing Wang, Jerome C Foo, Katherine J Aitchison
Pharmacogenomics aims to use the genetic information of an individual to personalize drug prescribing. There is evidence that pharmacogenomic testing before prescription may prevent adverse drug reactions, increase efficacy, and reduce cost of treatment. CYP2D6 is a key pharmacogene of relevance to multiple therapeutic areas. Indeed, there are prescribing guidelines available for medications based on CYP2D6 enzyme activity as deduced from CYP2D6 genetic data. The Agena MassARRAY system is a cost-effective method of detecting genetic variation that has been clinically applied to other genes...
February 12, 2024: Translational Psychiatry
https://read.qxmd.com/read/38310750/rare-variants-in-pharmacogenes-influence-clozapine-metabolism-in-individuals-with-schizophrenia
#6
JOURNAL ARTICLE
Djenifer B Kappel, Elliott Rees, Eilidh Fenner, Adrian King, John Jansen, Marinka Helthuis, Michael J Owen, Michael C O'Donovan, James T R Walters, Antonio F Pardiñas
Clozapine is the only licensed medication for treatment-resistant schizophrenia (TRS). Few predictors for variation in response to clozapine have been identified, but clozapine metabolism is known to influence therapeutic response and adverse side effects. Here, we expand on genome-wide studies of clozapine metabolism, previously focused on common genetic variation, by analysing whole-exome sequencing data from 2062 individuals with schizophrenia taking clozapine in the UK. We investigated whether rare genomic variation in genes and gene sets involved in the clozapine metabolism pathway influences plasma concentrations of clozapine metabolites, assessed through the longitudinal analysis of 6585 pharmacokinetic assays...
February 3, 2024: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://read.qxmd.com/read/38284696/utilizing-pharmacogenomic-data-for-a-safer-use-of-statins-among-the-emirati-population
#7
JOURNAL ARTICLE
Mais N Alqasrawi, Zeina N Al-Mahayri, Hiba Alblooshi, Habiba Alsafar, Bassam R Ali
BACKGROUND: Statins are the most prescribed lipid-lowering drugs worldwide. The associated adverse events, especially muscle symptoms, have been frequently reported despite their perceived safety. Three pharmacogenes, the solute carrier organic anion transporter family member 1B1 (SLCO1B1), ATP-binding cassette subfamily G member 2 (ABCG2), and cytochrome P450 9C9 (CYP2C9) are suggested as safety biomarkers for statins. The Clinical Pharmacogenomic Implementation Consortium (CPIC) issued clinical guidelines for statin use based on these three genes...
January 26, 2024: Current Vascular Pharmacology
https://read.qxmd.com/read/38276236/the-case-for-pre-emptive-pharmacogenetic-screening-in-south-africa
#8
JOURNAL ARTICLE
Tracey Hurrell, Jerolen Naidoo, Collen Masimirembwa, Janine Scholefield
Lack of equitable representation of global genetic diversity has hampered the implementation of genomic medicine in under-represented populations, including those on the African continent. Data from the multi-national Pre-emptive Pharmacogenomic Testing for Preventing Adverse Drug Reactions (PREPARE) study suggest that genotype guidance for prescriptions reduced the incidence of clinically relevant adverse drug reactions (ADRs) by 30%. In this study, hospital dispensary trends from a tertiary South African (SA) hospital (Steve Biko Academic Hospital; SBAH) were compared with the drugs monitored in the PREPARE study...
January 19, 2024: Journal of Personalized Medicine
https://read.qxmd.com/read/38173046/the-diversity-and-clinical-implications-of-genetic-variants-influencing-clopidogrel-bioactivation-and-response-in-the-emirati-population
#9
JOURNAL ARTICLE
Lubna Q Khasawneh, Habiba Alsafar, Hiba Alblooshi, Mushal Allam, George P Patrinos, Bassam R Ali
BACKGROUND: Clopidogrel is a widely prescribed prodrug that requires activation via specific pharmacogenes to exert its anti-platelet function. Genetic variations in the genes encoding its transporter, metabolizing enzymes, and target receptor lead to variability in its activation and platelet inhibition and, consequently, its efficacy. This variability increases the risk of secondary cardiovascular events, and therefore, some variations have been utilized as genetic biomarkers when prescribing clopidogrel...
January 3, 2024: Human Genomics
https://read.qxmd.com/read/38159139/mining-local-exome-and-hla-data-to-characterize-pharmacogenetic-variants-in-saudi-arabia
#10
JOURNAL ARTICLE
Mohamed Abouelhoda, Noura Almuqati, Ahmed Abogosh, Feras Alfraih, Sateesh Maddirevula, Fowzan S Alkuraya
Pharmacogenomics (PGx) is a promising field of precision medicine where efficacy of drugs is maximized while side effects are minimized for individual patients. Knowledge of the frequency of PGx-relevant variants (pharmacovariants) in the local population is a pre-requisite to informed policy making. Unfortunately, such knowledge is largely lacking from the Middle East. Here, we describe the use of a large clinical exome database (n = 13,473) and HLA haplotypes (n = 64,737) from Saudi Arabia, one of the largest countries in the Middle East, along with previously published data from the local population to ascertain allele frequencies of known pharmacovariants...
December 30, 2023: Human Genetics
https://read.qxmd.com/read/38020121/estimating-the-efficacy-of-pharmacogenomics-over-a-lifetime
#11
JOURNAL ARTICLE
Zhan Ye, John Mayer, Emili J Leary, Terrie Kitchner, Richard A Dart, Murray H Brilliant, Scott J Hebbring
It is well known that common variants in specific genes influence drug metabolism and response, but it is currently unknown what fraction of patients are given prescriptions over a lifetime that could be contraindicated by their pharmacogenomic profiles. To determine the clinical utility of pharmacogenomics over a lifetime in a general patient population, we sequenced the genomes of 300 deceased Marshfield Clinic patients linked to lifelong medical records. Genetic variants in 33 pharmacogenes were evaluated for their lifetime impact on drug prescribing using extensive electronic health records...
2023: Frontiers in Medicine
https://read.qxmd.com/read/37958484/principal-component-analysis-of-alternative-splicing-profiles-revealed-by-long-read-ont-sequencing-in-human-liver-tissue-and-hepatocyte-derived-hepg2-and-huh7-cell-lines
#12
JOURNAL ARTICLE
Elizaveta Sarygina, Anna Kozlova, Kseniia Deinichenko, Sergey Radko, Konstantin Ptitsyn, Svetlana Khmeleva, Leonid K Kurbatov, Pavel Spirin, Vladimir S Prassolov, Ekaterina Ilgisonis, Andrey Lisitsa, Elena Ponomarenko
The long-read RNA sequencing developed by Oxford Nanopore Technology provides a direct quantification of transcript isoforms. That makes the number of transcript isoforms per gene an intrinsically suitable metric for alternative splicing (AS) profiling in the application to this particular type of RNA sequencing. By using this simple metric and recruiting principal component analysis (PCA) as a tool to visualize the high-dimensional transcriptomic data, we were able to group biospecimens of normal human liver tissue and hepatocyte-derived malignant HepG2 and Huh7 cells into clear clusters in a 2D space...
October 24, 2023: International Journal of Molecular Sciences
https://read.qxmd.com/read/37956269/major-genetic-drivers-of-statin-treatment-response-in-african-populations-and-pharmacogenetics-of-dyslipidemia-through-a-one-health-lens
#13
REVIEW
Zizo Lusiki, Dirk Blom, Nyarai D Soko, Smangele Malema, Erika Jones, Brian Rayner, Jonathan Blackburn, Phumla Sinxadi, Michelle T Dandara, Collet Dandara
A One Health lens is increasingly significant to address the intertwined challenges in planetary health concerned with the health of humans, nonhuman animals, plants, and ecosystems. A One Health approach can benefit the public health systems in Africa that are overburdened by noncommunicable, infectious, and environmental diseases. Notably, the COVID-19 pandemic revealed the previously overlooked two-fold importance of pharmacogenetics (PGx), for individually tailored treatment of noncommunicable diseases and environmental pathogens...
November 14, 2023: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/37846556/distribution-of-pharmacogene%C3%A2-allele-and-phenotype-frequencies-in-brazilian-psychiatric-patients
#14
JOURNAL ARTICLE
Guido Boabaid May, Bruna Raquel de Souza, Bárbara Yasmin Gueuvoghlanian-Silva, Esther Camilo Dos Reis, Sofia Rech Mostardeiro, Paula Pedrassani Boabaid May, Elvis Cueva Mateo, Giovanna Grunewald Vietta, Giovana Weber Hoss
Purpose: This work was designed to identify the pharmacogenetic profile of Brazilian psychiatric patients receiving psychoactive drug treatment according to ethnicity. Methods: Based on the GnTech® database, this cross-sectional study analyzed data from self-reported sociodemographic and genetic results from the next-generation sequencing panel composed of 26 pharmacogenes from 359 psychotropic drug users. Results: Variant frequencies of multiple pharmacogenes presented differences between ethnicities ( CYP3A5 , CYP2D6 , CYP1A2 , CYP2B6 , CYP3A4 , UGT1A4 , UGT2B15 , ABCB1 rs1045642 , ADRA2A rs1800544 , COMT rs4680 , GRIK4 rs1954787 , GSK3B rs334558 , GSK3B rs6438552 , HTR1A rs6295 , HTR2A rs7997012 , HTR2C rs1414334 , MTHFR rs1801131 , OPRM1 rs1799971 and 5-HTTLPR ), endorsing the necessity of individual-level analyses in drug treatment...
October 17, 2023: Pharmacogenomics
https://read.qxmd.com/read/37759374/translating-pharmacogenomic-sequencing-data-into-drug-response-predictions-how-to-interpret-variants-of-unknown-significance
#15
REVIEW
Roman Tremmel, Sebastian Pirmann, Yitian Zhou, Volker M Lauschke
The rapid development of sequencing technologies during the past twenty years has provided a variety of methods and tools to interrogate human genomic variations at the population level. Pharmacogenes are well-known to be highly polymorphic and a plethora of pharmacogenomic variants has been identified in population sequencing data. However, so far only a small number of these variants were functionally characterized regarding their impact on drug efficacy and toxicity and the significance of the vast majority remains unknown...
September 27, 2023: British Journal of Clinical Pharmacology
https://read.qxmd.com/read/37757824/frequencies-of-pharmacogenomic-alleles-across-biogeographic-groups-in-a-large-scale-biobank
#16
JOURNAL ARTICLE
Binglan Li, Katrin Sangkuhl, Ryan Whaley, Mark Woon, Karl Keat, Michelle Whirl-Carrillo, Marylyn D Ritchie, Teri E Klein
Pharmacogenomics (PGx) is an integral part of precision medicine and contributes to the maximization of drug efficacy and reduction of adverse drug event risk. Accurate information on PGx allele frequencies improves the implementation of PGx. Nonetheless, curating such information from published allele data is time and resource intensive. The limited number of allelic variants in most studies leads to an underestimation of certain alleles. We applied the Pharmacogenomics Clinical Annotation Tool (PharmCAT) on an integrated 200K UK Biobank genetic dataset (N = 200,044)...
October 5, 2023: American Journal of Human Genetics
https://read.qxmd.com/read/37684227/structural-variation-of-the-coding-and-non-coding-human-pharmacogenome
#17
JOURNAL ARTICLE
Roman Tremmel, Yitian Zhou, Matthias Schwab, Volker M Lauschke
Genetic variants in drug targets and genes encoding factors involved in drug absorption, distribution, metabolism and excretion (ADME) can have pronounced impacts on drug pharmacokinetics, response, and toxicity. While the landscape of genetic variability at the level of single nucleotide variants (SNVs) has been extensively studied in these pharmacogenetic loci, their structural variation is only poorly understood. Thus, we systematically analyzed the genetic structural variability across 908 pharmacogenes (344 ADME genes and 564 drug targets) based on publicly available whole genome sequencing data from 10,847 unrelated individuals...
September 8, 2023: NPJ Genomic Medicine
https://read.qxmd.com/read/37623436/towards-evidence-based-implementation-of-pharmacogenomics-in-southern-africa-comorbidities-and-polypharmacy-profiles-across-diseases
#18
JOURNAL ARTICLE
Nyarai Desiree Soko, Sarudzai Muyambo, Michelle T L Dandara, Elizabeth Kampira, Dirk Blom, Erika S W Jones, Brian Rayner, Delva Shamley, Phumla Sinxadi, Collet Dandara
Pharmacogenomics may improve patient care by guiding drug selection and dosing; however, this requires prior knowledge of the pharmacogenomics of drugs commonly used in a specific setting. The aim of this study was to identify a preliminary set of pharmacogenetic variants important in Southern Africa. We describe comorbidities in 3997 patients from Malawi, South Africa, and Zimbabwe. These patient cohorts were included in pharmacogenomic studies of anticoagulation, dyslipidemia, hypertension, HIV and breast cancer...
July 26, 2023: Journal of Personalized Medicine
https://read.qxmd.com/read/37551613/pharmacogenomic-variation-in-the-malagasy-population-implications-for-the-antimalarial-drug-primaquine-metabolism
#19
JOURNAL ARTICLE
Estee Y Cramer, Jacquelaine Bartlett, Ernest R Chan, Andrea Gaedigk, Arsene C Ratsimbasoa, Rajeev K Mehlotra, Scott M Williams, Peter A Zimmerman
Aim: Antimalarial primaquine (PQ) eliminates liver hypnozoites of Plasmodium vivax.   CYP2D6 gene variation contributes to PQ therapeutic failure. Additional gene variation may contribute to PQ efficacy. Information on pharmacogenomic variation in Madagascar, with vivax malaria and a unique population admixture, is scanty. Methods: The authors performed genome-wide genotyping of 55 Malagasy samples and analyzed data with a focus on a set of 28 pharmacogenes most relevant to PQ. Results: Mainly, the study identified 110 coding or splicing variants, including those that, based on previous studies in other populations, may be implicated in PQ response and copy number variation, specifically in chromosomal regions that contain pharmacogenes...
August 8, 2023: Pharmacogenomics
https://read.qxmd.com/read/37522435/a-real-world-disproportionality-analysis-of-drug-induced-immune-hemolytic-anemia-in-the-fda-adverse-event-reporting-system
#20
JOURNAL ARTICLE
Linlin Tang, Chuanhua Ding, Hongying Li, Xueheng Zhou, Guoqiang Yin
BACKGROUND: Drug-induced immune hemolytic anemia (DIIHA) is a rare but potentially life-threatening pharmacogenic hematological adverse effect. Updating the risk of DIIHA among the currently available drugs based on spontaneously reported adverse event data is of great significance. OBJECTIVE: This study aimed to identify the top 50 drugs associated with immune hemolytic anemia in adults as well as common drugs that could cause immune hemolytic anemia in children based on the United States Food and Drug Administration Adverse Event Reporting System (FAERS) database...
July 31, 2023: Annals of Pharmacotherapy
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