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https://www.readbyqxmd.com/read/27779249/the-global-spectrum-of-protein-coding-pharmacogenomic-diversity
#1
G E B Wright, B Carleton, M R Hayden, C J D Ross
Differences in response to medications have a strong genetic component. By leveraging publically available data, the spectrum of such genomic variation can be investigated extensively. Pharmacogenomic variation was extracted from the 1000 Genomes Project Phase 3 data (2504 individuals, 26 global populations). A total of 12 084 genetic variants were found in 120 pharmacogenes, with the majority (90.0%) classified as rare variants (global minor allele frequency <0.5%), with 52.9% being singletons. Common variation clustered individuals into continental super-populations and 23 pharmacogenes contained highly differentiated variants (FST>0...
October 25, 2016: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/27726640/harnessing-knowledge-on-very-important-pharmacogenes-cyp2c9-and-cyp2c19-variation-for-precision-medicine-in-resource-limited-global-conflict-zones
#2
İbrahim Ömer Barlas, Orhan Sezgin, Collet Dandara, Gözde Türköz, Emre Yengel, Zinhle Cindi, Handan Ankaralı, Semra Şardaş
Pharmacogenomics harnesses the utility of a patient's genome (n = 1) in decisions on which therapeutic drugs and in what amounts should be administered. Often, patients with shared ancestry present with comparable genetic profiles that predict drug response. However, populations are not static, thus, often, population mobility through migration, especially enmasse as is seen for refugees, changes the pharmacogenetic profiles of resultant populations and therefore observed responses to commonly used therapeutic drugs...
October 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27636550/a-european-spectrum-of-pharmacogenomic-biomarkers-implications-for-clinical-pharmacogenomics
#3
Clint Mizzi, Eleni Dalabira, Judit Kumuthini, Nduna Dzimiri, Istvan Balogh, Nazli Başak, Ruwen Böhm, Joseph Borg, Paola Borgiani, Nada Bozina, Henrike Bruckmueller, Beata Burzynska, Angel Carracedo, Ingolf Cascorbi, Constantinos Deltas, Vita Dolzan, Anthony Fenech, Godfrey Grech, Vytautas Kasiulevicius, Ľudevít Kádaši, Vaidutis Kučinskas, Elza Khusnutdinova, Yiannis L Loukas, Milan Macek, Halyna Makukh, Ron Mathijssen, Konstantinos Mitropoulos, Christina Mitropoulou, Giuseppe Novelli, Ioanna Papantoni, Sonja Pavlovic, Giuseppe Saglio, Jadranka Setric, Maja Stojiljkovic, Andrew P Stubbs, Alessio Squassina, Maria Torres, Marek Turnovec, Ron H van Schaik, Konstantinos Voskarides, Salma M Wakil, Anneke Werk, Maria Del Zompo, Branka Zukic, Theodora Katsila, Ming Ta Michael Lee, Alison Motsinger-Rief, Howard L Mc Leod, Peter J van der Spek, George P Patrinos
Pharmacogenomics aims to correlate inter-individual differences of drug efficacy and/or toxicity with the underlying genetic composition, particularly in genes encoding for protein factors and enzymes involved in drug metabolism and transport. In several European populations, particularly in countries with lower income, information related to the prevalence of pharmacogenomic biomarkers is incomplete or lacking. Here, we have implemented the microattribution approach to assess the pharmacogenomic biomarkers allelic spectrum in 18 European populations, mostly from developing European countries, by analyzing 1,931 pharmacogenomics biomarkers in 231 genes...
2016: PloS One
https://www.readbyqxmd.com/read/27414743/genetic-polymorphisms-study-of-pharmacogenomic-vip-variants-in-han-ethnic-of-china-s-shaanxi-province
#4
Tianbo Jin, Ruimin Zhao, Xugang Shi, Na He, Xue He, Yongri Ouyang, Hong Wang, Bo Wang, Longli Kang, Dongya Yuan
BACKGROUND: Multiple factors include genetic and non-genetic interactions induce to different drug response among different individuals. Lots of researches proved that different frequencies of genetic variants exists different ethnic groups. The aim of this study was to screen Han volunteers in Shaanxi for VIP gene polymorphisms. MATERIALS AND METHODS: We genotyped 80 Very Important Pharmacogenes (VIP) (selected from the PharmGKB database) in 192 unrelated, healthy Han ethnic adults from Shaanxi, the northwest of China, and then analyzed genotyping data wtih Structure and F-statistics (Fst) analysis...
September 2016: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/27388693/prediction-of-cyp2d6-phenotype-from-genotype-across-world-populations
#5
Andrea Gaedigk, Katrin Sangkuhl, Michelle Whirl-Carrillo, Teri Klein, J Steven Leeder
PURPOSE: Owing to its highly polymorphic nature and major contribution to the metabolism and bioactivation of numerous clinically used drugs, CYP2D6 is one of the most extensively studied drug-metabolizing enzymes and pharmacogenes. CYP2D6 alleles confer no, decreased, normal, or increased activity and cause a wide range of activity among individuals and between populations. However, there is no standard approach to translate diplotypes into predicted phenotype. METHODS: We exploited CYP2D6 allele-frequency data that have been compiled for Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines (>60,000 subjects, 173 reports) in order to estimate genotype-predicted phenotype status across major world populations based on activity score (AS) assignments...
July 7, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/27304207/cyp2c19-and-cyp2d6-genotypes-in-pacific-peoples
#6
REVIEW
Nuala A Helsby
The study of pharmacogenetic variants in populations which reside in Oceania has been focused mainly on CYP2C19 and CYP2D6. Statements about the high prevalence of CYP2C19 no function genotype in 'Pacific Islanders' can be found in the literature. This review article summarizes the published information about these pharmacogenes in this geographical region and highlights the differences observed between Melanesian and Polynesian populations. It is not appropriate to combine the prevalence data of pharmacogenetic variants, particularly CYP2C19, across this region...
November 2016: British Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/27101133/rare-genetic-variants-in-cellular-transporters-metabolic-enzymes-and-nuclear-receptors-can-be-important-determinants-of-interindividual-differences-in-drug-response
#7
Mikael Kozyra, Magnus Ingelman-Sundberg, Volker M Lauschke
PURPOSE: In this study we characterized the genetic variability of 146 clinically relevant genes influencing drug pharmacokinetics in African and European subpopulations, which are key determinants for interindividual variations in drug efficacy and adverse drug reactions. METHODS: By integrating data from the 1000 Genomes Project (n = 1,092 individuals) and the Exome Sequencing Project (ESP; n = 6,503 individuals), single-nucleotide variants (SNVs) were identified and analyzed regarding frequency, functional consequences, and ethnic diversity...
April 21, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/26858644/cross-comparison-of-exome-analysis-next-generation-sequencing-of-amplicons-and-the-iplex-%C3%A2-adme-pgx-panel-for-pharmacogenomic-profiling
#8
Eng Wee Chua, Simone L Cree, Kim N T Ton, Klaus Lehnert, Phillip Shepherd, Nuala Helsby, Martin A Kennedy
Whole-exome sequencing (WES) has been widely used for analysis of human genetic diseases, but its value for the pharmacogenomic profiling of individuals is not well studied. Initially, we performed an in-depth evaluation of the accuracy of WES variant calling in the pharmacogenes CYP2D6 and CYP2C19 by comparison with MiSeq(®) amplicon sequencing data (n = 36). This analysis revealed that the concordance rate between WES and MiSeq(®) was high, achieving 99.60% for variants that were called without exceeding the truth-sensitivity threshold (99%), defined during variant quality score recalibration (VQSR)...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/26857349/genetic-variation-among-82-pharmacogenes-the-pgrnseq-data-from-the-emerge-network
#9
W S Bush, D R Crosslin, A Owusu-Obeng, J Wallace, B Almoguera, M A Basford, S J Bielinski, D S Carrell, J J Connolly, D Crawford, K F Doheny, C J Gallego, A S Gordon, B Keating, J Kirby, T Kitchner, S Manzi, A R Mejia, V Pan, C L Perry, J F Peterson, C A Prows, J Ralston, S A Scott, A Scrol, M Smith, S C Stallings, T Veldhuizen, W Wolf, S Volpi, K Wiley, R Li, T Manolio, E Bottinger, M H Brilliant, D Carey, R L Chisholm, C G Chute, J L Haines, H Hakonarson, J B Harley, I A Holm, I J Kullo, G P Jarvik, E B Larson, C A McCarty, M S Williams, J C Denny, L J Rasmussen-Torvik, D M Roden, M D Ritchie
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...
August 2016: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/26856248/transcriptomic-variation-of-pharmacogenes-in-multiple-human-tissues-and-lymphoblastoid-cell-lines
#10
A Chhibber, C E French, S W Yee, E R Gamazon, E Theusch, X Qin, A Webb, A C Papp, A Wang, C Q Simmons, A Konkashbaev, A S Chaudhry, K Mitchel, D Stryke, T E Ferrin, S T Weiss, D L Kroetz, W Sadee, D A Nickerson, R M Krauss, A L George, E G Schuetz, M W Medina, N J Cox, S E Scherer, K M Giacomini, S E Brenner
Variation in the expression level and activity of genes involved in drug disposition and action ('pharmacogenes') can affect drug response and toxicity, especially when in tissues of pharmacological importance. Previous studies have relied primarily on microarrays to understand gene expression differences, or have focused on a single tissue or small number of samples. The goal of this study was to use RNA-sequencing (RNA-seq) to determine the expression levels and alternative splicing of 389 Pharmacogenomics Research Network pharmacogenes across four tissues (liver, kidney, heart and adipose) and lymphoblastoid cell lines, which are used widely in pharmacogenomics studies...
February 9, 2016: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/26632549/genetic-polymorphisms-analysis-of-pharmacogenomic-vip-variants-in-miao-ethnic-group-of-southwest-china
#11
Tianbo Jin, Ainiwaer Aikemu, Mingxi Zhang, Tingting Geng, Tian Feng, Longli Kang, Man Lin Luo
BACKGROUND Genetic polymorphisms have a potential clinical role in determining both inter-individual and inter-ethnic differences in drug efficacy, but we have not found any pharmacogenomics information regarding minorities, such as the Miao ethnic group. Our study aimed to screen numbers of the Miao ethnic group for genotype frequencies of VIP variants and to determine differences between the Miao and other human populations worldwide. MATERIAL AND METHODS In this study, we genotyped 66 Very Important Pharmacogene (VIP) variants selected from PharmGKB in 98 unrelated, healthy Miao individuals from the Guizhou province and compared our data with 12 other populations, including 11 populations from the HapMap data set and Xi'an Han Chinese...
December 3, 2015: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/26329523/genetic-polymorphism-of-pharmacogenomic-vip-variants-in-the-deng-people-from-the-himalayas-in-southeast-tibet
#12
Xugang Shi, Li Wang, Shuli Du, Huijuan Wang, Tian Feng, Tianbo Jin, Longli Kang
Little is known about polymorphic distribution of pharmacogenes among ethnicities, including the Deng people. In this study, we recruited 100 unrelated, healthy Deng people and genotyped them with respect to 76 different single-nucleotide polymorphisms by the PharmGKB database. Our results first indicated that the polymorphic distribution of pharmacogenes of the Deng people is most similar to CHD, suggesting that Deng people have a closest genetic relationship with CHD. Our data will enrich the database of pharmacogenomics and provide a theoretical basis for safer drug administration and individualized treatment plans, promoting the development of personalized medicine...
2015: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
https://www.readbyqxmd.com/read/26227544/genetic-polymorphism-of-pharmacogenomic-vip-variants-in-the-deng-people-from-the-himalayas-in-southeast-tibet
#13
Xugang Shi, Li Wang, Shuli Du, Huijuan Wang, Tian Feng, Tianbo Jin, Longli Kang
Little is known about polymorphic distribution of pharmacogenes among ethnicities, including the Deng people. In this study, we recruited 100 unrelated, healthy Deng people and genotyped them with respect to 76 different single-nucleotide polymorphisms by the PharmGKB database. Our results first indicated that the polymorphic distribution of pharmacogenes of the Deng people is most similar to CHD, suggesting that Deng people have a closest genetic relationship with CHD. Our data will enrich the database of pharmacogenomics and provide a theoretical basis for safer drug administration and individualized treatment plans, promoting the development of personalized medicine...
July 31, 2015: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
https://www.readbyqxmd.com/read/25968989/age-related-changes-in-microrna-expression-and-pharmacogenes-in-human-liver
#14
K S Burgess, S Philips, E A Benson, Z Desta, A Gaedigk, R Gaedigk, M W Segar, Y Liu, T C Skaar
Developmental changes in the liver can significantly impact drug disposition. Due to the emergence of microRNAs (miRNAs) as important regulators of drug disposition gene expression, we studied age-dependent changes in miRNA expression. Expression of 533 miRNAs was measured in 90 human liver tissues (fetal, pediatric [1-17 years], and adult [28-80 years]; n = 30 each). In all, 114 miRNAs were upregulated and 72 were downregulated from fetal to pediatric, and 2 and 3, respectively, from pediatric to adult...
August 2015: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/25431893/pharmacogenetics-of-drug-metabolizing-enzymes-in-us-hispanics
#15
REVIEW
Karla Claudio-Campos, Jorge Duconge, Carmen L Cadilla, Gualberto Ruaño
Although the Hispanic population is continuously growing in the United States, they are underrepresented in pharmacogenetic studies. This review addresses the need for compiling available pharmacogenetic data in US Hispanics, discussing the prevalence of clinically relevant polymorphisms in pharmacogenes encoding for drug-metabolizing enzymes. CYP3A5*3 (0.245-0.867) showed the largest frequency in a US Hispanic population. A higher prevalence of CYP2C9*3, CYP2C19*4, and UGT2B7 IVS1+985 A>G was observed in US Hispanic vs...
June 2015: Drug Metabolism and Personalized Therapy
https://www.readbyqxmd.com/read/25379720/copy-number-variability-analysis-of-pharmacogenes-in-patients-with-lymphoma-leukemia-hepatocellular-and-lung-carcinoma-using-the-cancer-genome-atlas-data
#16
In-Wha Kim, Nayoung Han, Myeong Gyu Kim, Therasa Kim, Jung Mi Oh
OBJECTIVE: Individual differences in drug efficacy and toxicity remain an important clinical concern. We investigated copy number variation (CNV) frequencies for pharmacogenes using The Cancer Genome Atlas dataset. MATERIALS AND METHODS: One hundred and fifty-two pharmacogenes were selected from liver hepatocellular carcinoma, lung squamous cell carcinoma (LUSC), acute myeloid leukemia, and lymphoid neoplasm diffuse large B-cell lymphoma (DLBL). The germ line and somatic CNV frequencies were analyzed...
January 2015: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/25266489/genetic-polymorphisms-of-vip-variants-in-the-tajik-ethnic-group-of-northwest-china
#17
Jiayi Zhang, Tianbo Jin, Zulfiya Yunus, Xiaolan Li, Tingting Geng, Hong Wang, Yali Cui, Chao Chen
BACKGROUND: Individual response to medications varies significantly among different populations, and great progress in understanding the molecular basis of drug action has been made in the past 50 years. The field of pharmacogenomics seeks to elucidate inherited differences in drug disposition and effects. While we know that different populations and ethnic groups are genetically heterogeneous, we have not found any pharmacogenomics information regarding minority groups, such as the Tajik ethnic group in northwest China...
2014: BMC Genetics
https://www.readbyqxmd.com/read/25141897/personalized-pharmacogenomics-profiling-using-whole-genome-sequencing
#18
Clint Mizzi, Brock Peters, Christina Mitropoulou, Konstantinos Mitropoulos, Theodora Katsila, Misha R Agarwal, Ron H N van Schaik, Radoje Drmanac, Joseph Borg, George P Patrinos
AIM: Pharmacogenomics holds promise to rationalize drug use by minimizing drug toxicity and at the same time increase drug efficacy. There are currently several assays to screen for known pharmacogenomic biomarkers for the most commonly prescribed drugs. However, these genetic screening assays cannot account for other known or novel pharmacogenomic markers. MATERIALS & METHODS: We analyzed whole-genome sequences of 482 unrelated individuals of various ethnic backgrounds to obtain their personalized pharmacogenomics profiles...
June 2014: Pharmacogenomics
https://www.readbyqxmd.com/read/24960519/design-and-anticipated-outcomes-of-the-emerge-pgx-project-a-multicenter-pilot-for-preemptive-pharmacogenomics-in-electronic-health-record-systems
#19
MULTICENTER STUDY
L J Rasmussen-Torvik, S C Stallings, A S Gordon, B Almoguera, M A Basford, S J Bielinski, A Brautbar, M H Brilliant, D S Carrell, J J Connolly, D R Crosslin, K F Doheny, C J Gallego, O Gottesman, D S Kim, K A Leppig, R Li, S Lin, S Manzi, A R Mejia, J A Pacheco, V Pan, J Pathak, C L Perry, J F Peterson, C A Prows, J Ralston, L V Rasmussen, M D Ritchie, S Sadhasivam, S A Scott, M Smith, A Vega, A A Vinks, S Volpi, W A Wolf, E Bottinger, R L Chisholm, C G Chute, J L Haines, J B Harley, B Keating, I A Holm, I J Kullo, G P Jarvik, E B Larson, T Manolio, C A McCarty, D A Nickerson, S E Scherer, M S Williams, D M Roden, J C Denny
We describe here the design and initial implementation of the eMERGE-PGx project. eMERGE-PGx, a partnership of the Electronic Medical Records and Genomics Network and the Pharmacogenomics Research Network, has three objectives: (i) to deploy PGRNseq, a next-generation sequencing platform assessing sequence variation in 84 proposed pharmacogenes, in nearly 9,000 patients likely to be prescribed drugs of interest in a 1- to 3-year time frame across several clinical sites; (ii) to integrate well-established clinically validated pharmacogenetic genotypes into the electronic health record with associated clinical decision support and to assess process and clinical outcomes of implementation; and (iii) to develop a repository of pharmacogenetic variants of unknown significance linked to a repository of electronic health record-based clinical phenotype data for ongoing pharmacogenomics discovery...
October 2014: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/24831276/using-pharmacogene-polymorphism-panels-to-detect-germline-pharmacodynamic-markers-in-oncology
#20
Daniel L Hertz, Howard L McLeod
The patient (germline) genome can influence the pharmacokinetics and pharmacodynamics of cancer therapy. The field of pharmacogenetics (PGx) has primarily focused on genetic predictors of pharmacokinetics, largely ignoring pharmacodynamics, using a candidate approach to assess single-nucleotide polymorphisms (SNP) with known relevance to drug pharmacokinetics such as enzymes and transporters. A more comprehensive approach, the genome-wide association study, circumvents candidate selection but suffers because of the necessity for substantial statistical correction...
May 15, 2014: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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