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Pharmacogenomics Journal

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https://www.readbyqxmd.com/read/29720721/pharmacogenomic-survey-of-qatari-populations-using-whole-genome-and-exome-sequences
#1
Ambily Sivadas, Vinod Scaria
The Arabs represent one of the most genetically heterogeneous populations characterized by a high prevalence of Mendelian disorders due to consanguinity. Population-scale genomic datasets provide a unique opportunity to understand the epidemiology of variants associated with differential therapeutic response. We analyzed publicly available genomic data for 1005 Qatari individuals encompassing five subpopulations. The frequencies of known and novel pharmacogenetic variants were compared with global populations...
May 3, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29720720/gamma-aminobutyric-acid-gaba-receptors-genes-polymorphisms-and-risk-for-restless-legs-syndrome
#2
Félix Javier Jiménez-Jiménez, Gara Esguevillas, Hortensia Alonso-Navarro, Martín Zurdo, Laura Turpín-Fenoll, Jorge Millán-Pascual, Teresa Adeva-Bartolomé, Esther Cubo, Francisco Navacerrada, Gemma Amo, Ana Rojo-Sebastián, Lluisa Rubio, Mónica Díez-Fairén, Pau Pastor, Marisol Calleja, José Francisco Plaza-Nieto, Belén Pilo-de-la-Fuente, Margarita Arroyo-Solera, Esteban García-Albea, José A G Agúndez, Elena García-Martín
The possible role of gammaaminobutyric acid (GABA) in the pathophysiology of restless legs syndrome (RLS) is suggested by the symptomatic improvement achieved with GABAergic drugs. Thalamic GABA levels have shown positive correlation with periodic limb movements indices and with RLS severity. We tried to investigate the possible association between the most common single nucleotide polymorphisms (SNPs) in the GABA receptors (GABR) genes rho1, 2, and 3 (GABRR1, GABRR2, GABRR3), alpha4 (GABRA4), epsilon (GABRE), and theta (GABRQ) with the risk of developing RLS...
May 3, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29713005/genetic-structure-of-pharmacogenetic-biomarkers-in-brazil-inferred-from-a-systematic-review-and-population-based-cohorts-a-ribef-epigen-brazil-initiative
#3
Fernanda Rodrigues-Soares, Fernanda S G Kehdy, Julia Sampaio-Coelho, Poliana X C Andrade, Carolina Céspedes-Garro, Camila Zolini, Marla M Aquino, Mauricio L Barreto, Bernardo L Horta, Maria Fernanda Lima-Costa, Alexandre C Pereira, Adrián LLerena, Eduardo Tarazona-Santos
We present allele frequencies involving 39 pharmacogenetic biomarkers studied in Brazil, and their distribution on self-reported race/color categories that: (1) involve a mix of perceptions about ancestry, morphological traits, and cultural/identity issues, being social constructs pervasively used in Brazilian society and medical studies; (2) are associated with disparities in access to health services, as well as in their representation in genetic studies, and (3), as we report here, explain a larger portion of the variance of pharmaco-allele frequencies than geography...
May 1, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29662106/pharmacogenetics-of-platinum-based-chemotherapy-impact-of-dna-repair-and-folate-metabolism-gene-polymorphisms-on-prognosis-of-non-small-cell-lung-cancer-patients
#4
Cristina Pérez-Ramírez, Marisa Cañadas-Garre, Ahmed Alnatsha, Eduardo Villar, Javier Valdivia-Bautista, María José Faus-Dáder, Miguel Ángel Calleja-Hernández
Chemotherapy based on platinum compounds is the standard treatment for NSCLC patients with EGFR wild type, and is also used as second line in mutated EGFR patients. Nevertheless, this therapy presents poor clinical outcomes. ERCC1, ERCC2, XRCC1, MDM2, MTHFR, MTR, and SLC19A1 gene polymorphisms may contribute to individual variation in response and survival to platinum-based chemotherapy. The aim of this study was to investigate the influence of these polymorphisms on response and survival of NSCLC patients treated with platinum-based chemotherapy...
April 17, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29618765/associations-between-genetic-polymorphisms-of-membrane-transporter-genes-and-prognosis-after-chemotherapy-meta-analysis-and-finding-from-seoul-breast-cancer-study-sebcs
#5
Ji-Eun Kim, Jaesung Choi, JooYong Park, Chulbum Park, Se Mi Lee, Seong Eun Park, Nan Song, Seokang Chung, Hyuna Sung, Wonshik Han, Jong Won Lee, Sue K Park, Mi Kyung Kim, Dong-Young Noh, Keun-Young Yoo, Daehee Kang, Ji-Yeob Choi
Membrane transporters can be major determinants of the pharmacokinetic profiles of anticancer drugs. The associations between genetic variations of ATP-binding cassette (ABC) and solute carrier (SLC) genes and cancer survival were investigated through a meta-analysis and an association study in the Seoul Breast Cancer Study (SEBCS). Including the SEBCS, the meta-analysis was conducted among 38 studies of genetic variations of transporters on various cancer survivors. The population of SEBCS consisted of 1338 breast cancer patients who had been treated with adjuvant chemotherapy...
April 4, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29520081/evaluation-of-a-clinical-pharmacogenetics-model-to-predict-methotrexate-response-in-patients-with-rheumatoid-arthritis
#6
Rosario López-Rodríguez, Aida Ferreiro-Iglesias, Aurea Lima, Miguel Bernardes, Andrzej Pawlik, Agnieszka Paradowska-Gorycka, Jerzy Świerkot, Ryszard Slezak, Isidoro Gonzalez-Alvaro, Javier Narvaez, Eva Pérez-Pampín, Antonio Mera-Varela, Laura Vidal-Bralo, José Gorgonio Acuña-Ochoa, Carmen Conde, Antonio Gonzalez
Variability of response to treatment hinders successful management of rheumatoid arthritis (RA). Consequently, a clinical pharmacogenetics model for predicting response to methotrexate (CP-MTX) has been previously proposed that includes four clinical variables (disease activity, sex, the presence of rheumatoid factor and smoking status) and four SNPs (rs2236225, rs17602729, rs1127354, and rs2372536) in genes of the folate pathway. It showed good performance, but failed to attract attention, likely, in relation with lack of clear clinical benefit...
March 8, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29520080/impact-of-cyp2c19-polymorphism-in-prognosis-of-minor-stroke-or-tia-patients-with-declined-egfr-on-dual-antiplatelet-therapy-chance-substudy
#7
Yu Wu, Yilun Zhou, Yuesong Pan, Xingquan Zhao, Liping Liu, David Wang, Chunxue Wang, Hao Li, S Claiborne Johnston, Xia Meng, Yilong Wang, Yongjun Wang
Clopidogrel resistance is prevalent in chronic kidney disease (CKD) patients. Genetic polymorphism is considered to be the most important factor that influences clopidogrel resistance. Limited data exist as to the role of pharmacogenetics in prognosis of stroke patients with impaired renal function on clopidogrel. We sought to explore whether decreased kidney function alters the association between CYP2C19 genetic variants and clinical outcome in patients with minor stroke or transient ischemic attack (TIA) receiving clopidogrel therapy...
March 8, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29520079/a-6-week-laboratory-research-rotation-in-pharmacogenomics-a-model-for-preparing-pharmacy-students-to-practice-precision-medicine
#8
Prema S Rao, Ryan Endicott, Randy Mullins, U Subrahmanyeswara Rao
Comparison of human genome sequences from different individuals has unraveled that genes involved in the drug efficacy and metabolism are polymorphic, harboring mutations, splicing variations and other alterations. These data provide a reasonable explanation for the inter-individual variations observed in drug therapy. Thus, a detailed molecular analysis and an in-depth knowledge of these genes is a prerequisite to practice pharmacogenomics-based medicine. We have introduced a 6-week laboratory research rotation to train students in the expression analysis of different pharmacogenes combined with bioinformatics tools...
March 8, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29472587/association-of-brca1-ercc1-rap80-pkm2-rrm1-rrm2-ts-tsp1-and-txr1-mrna-expression-levels-between-primary-tumors-and-infiltrated-regional-lymph-nodes-in-patients-with-resectable-non-small-cell-lung-cancer
#9
K Tryfonidis, C Papadaki, S Assele, E Lagoudaki, J Menis, A Koutsopoulos, M Trypaki, E Tsakalaki, M Sfakianaki, B Hasan, E Stathopoulos, V Georgoulias, J Souglakos
Differences in gene expression levels between the primary tumors (PTs) and matched regional lymph nodal metastases (LNs) in patients with totally excised non-small cell lung cancer (NSCLC) were explored. Microdissected formalin-fixed paraffin-embedded (FFPE) samples from (PT) and their matched infiltrated LNs, from 239 patients [183 (with matched PT and LNs samples)-case and 56 PT only samples-control cohorts] were analyzed for BRCA1, ERCC1, RAP80, PKM2, RRM1, RRM2, TS, TSP1, and TXR1 mRNA expression by quantitative real-time polymerase-chain reaction (PCR)...
February 22, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29352165/construction-of-full-length-japanese-reference-panel-of-class-i-hla-genes-with-single-molecule-real-time-sequencing
#10
Takahiro Mimori, Jun Yasuda, Yoko Kuroki, Tomoko F Shibata, Fumiki Katsuoka, Sakae Saito, Naoki Nariai, Akira Ono, Naomi Nakai-Inagaki, Kazuharu Misawa, Keiko Tateno, Yosuke Kawai, Nobuo Fuse, Atsushi Hozawa, Shinichi Kuriyama, Junichi Sugawara, Naoko Minegishi, Kichiya Suzuki, Kengo Kinoshita, Masao Nagasaki, Masayuki Yamamoto
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used...
January 19, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29305589/astrocyte-specific-transcriptome-responses-to-chronic-ethanol-consumption
#11
Emma K Erickson, Sean P Farris, Yuri A Blednov, R Dayne Mayfield, R Adron Harris
Astrocytes play critical roles in central nervous system (CNS) homeostasis and are implicated in the pathogenesis of neurological and psychiatric conditions, including drug dependence. Little is known about the effects of chronic ethanol consumption on astrocyte gene expression. To address this gap in knowledge, we performed transcriptome-wide RNA sequencing of astrocytes isolated from the prefrontal cortex (PFC) of mice following chronic ethanol consumption. Differential expression analysis revealed ethanol-induced changes unique to astrocytes that were not identified in total homogenate preparations...
January 5, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29302041/analysis-of-cytokine-immune-response-profile-in-response-to-inflammatory-stimuli-in-mice-with-genetic-defects-in-fetal-and-adult-hemoglobin-chain-expression
#12
Ismat Khatri, Christian Alexander, Klaus Brandenburg, Zhiqi Chen, Adrian Heini, Didier Heumann, Jean-Pierre Mach, Vienna Mazzoli, Ernst Rietschel, Alexey Tersikh, Artur Ulmer, Kai Yu, Ulrich Zähringer, Reginald Gorczynski
Injections of a crude fetal sheep liver extract (FSLE) containing fetal hemoglobin, MPLA, and glutathione (GSSH) reversed cytokine changes in aged mice. To investigate the role of fetal hemoglobin we derived mice with homzygous deletions for either of the two major βchains, Hgbβma KO or Hgbβmi KO. Hgbβmi is the most prominent fetal Hgbβ chain, with Hgbβma more prominent in adult mice. Mice lacking another fetal Hgb chain, HgbεKO, died in utero. CHO cells transfected with cloned Hgb chains were used to produce proteins for preparation of rabbit heteroantibodes...
January 4, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29298996/the-phosphatidylinositide-3-kinase-pi3k-signaling-pathway-is-a-determinant-of-zileuton-response-in-adults-with-asthma
#13
Amber Dahlin, Weiliang Qiu, Augusto A Litonjua, John J Lima, Mayumi Tamari, Michiaki Kubo, Charles G Irvin, Stephen P Peters, Ann C Wu, Scott T Weiss, Kelan G Tantisira
Variable responsiveness to zileuton, a leukotriene antagonist used to treat asthma, may be due in part to genetic variation. While individual SNPs were previously associated with zileuton-related lung function changes, specific quantitative trait loci (QTLs) and biological pathways that may contribute have not been identified. In this study, we investigated the hypothesis that genetic variation within biological pathways is associated with zileuton response. We performed an integrative QTL mapping and pathway enrichment study to investigate data from a GWAS of zileuton response, in addition to mRNA expression profiles and leukotriene production data from lymphoblastoid cell lines (LCLs) (derived from asthmatics) that were treated with zileuton or ethanol (control)...
January 3, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29298995/nuclear-receptor-gene-polymorphisms-and-warfarin-dose-requirements-in-the-quebec-warfarin-cohort
#14
Payman Shahabi, Félix Lamothe, Stéphanie Dumas, Étienne Rouleau-Mailloux, Yassamin Feroz Zada, Sylvie Provost, Geraldine Asselin, Ian Mongrain, Diane Valois, Marie-Josée Gaulin Marion, Louis-Philippe Lemieux Perreault, Sylvie Perreault, Marie-Pierre Dubé
Warfarin is primarily metabolized by cytochrome 2C9, encoded by gene CYP2C9. Here, we investigated whether variants in nuclear receptor genes which regulate the expression of CYP2C9 are associated with warfarin response. We used data from 906 warfarin users from the Quebec Warfarin Cohort (QWC) and tested the association of warfarin dose requirement at 3 months following the initiation of therapy in nine nuclear receptor genes: NR1I3, NR1I2, NR3C1, ESR1, GATA4, RXRA, VDR, CEBPA, and HNF4A. Three correlated SNPs in the VDR gene (rs4760658, rs11168292, and rs11168293) were associated with dose requirements of warfarin (P = 2...
January 3, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29298994/cost-effectiveness-of-hla-dqb1-hla-b-pharmacogenetic-guided-treatment-and-blood-monitoring-in-us-patients-taking-clozapine
#15
François R Girardin, Antoine Poncet, Arnaud Perrier, Nathalie Vernaz, Mark Pletscher, Caroline F Samer, Jeffrey A Lieberman, Jean Villard
Less than 1% of adult patients with schizophrenia taking clozapine develop agranulocytosis, and most of these cases occur within the first weeks of treatment. The human leukocyte antigen (HLA) region has been associated with genetic susceptibility to clozapine-induced agranulocytosis (single amino acid changes in HLA-DQB1 (126Q) and HLA-B (158T)). The current study aimed to evaluate the cost-effectiveness, from a healthcare provider's perspective, of an HLA genotype-guided approach in patients with treatment-resistant schizophrenia who were taking clozapine and to compare the results with the current absolute neutrophil count monitoring (ANCM) schemes used in the USA...
January 3, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28631723/pharmacogenetic-biomarkers-of-response-in-crohn-s-disease
#16
REVIEW
T M Linares-Pineda, M Cañadas-Garre, A Sánchez-Pozo, M Á Calleja-Hernández
Crohn's disease (CD) is a chronic condition, which affects the immune system. It can also affect any part of the digestive tract and be associated with external manifestations. The causes of the disease remain unknown, although it seems to be the result of a combination of factors, such as genetic predisposition, environment, lifestyle and the composition of the microbiota, among others. The treatment protocol begins with a change in eating and smoking habits, and is continued with different lines of treatment, including corticosteroids, immunomodulators and biologic therapy (infliximab and adalimumab), which have shown differences in response among patients, especially with biologic treatment...
January 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28607505/predictive-genetic-markers-in-neoadjuvant-chemoradiotherapy-for-locally-advanced-esophageal-cancer-a-long-way-to-go-review-of-the-literature
#17
REVIEW
M Gusella, E Pezzolo, Y Modena, C Barile, D Menon, G Crepaldi, F La Russa, A P Fraccon, F Pasini
The role of genetic molecular markers in neoadjuvant treatment for locally advanced esophageal cancer has been reviewed, focusing strictly on concurrent chemoradiation protocols followed by surgery. Eleven studies evaluated the role of mRNA expression profile; the end point was overall survival (OS) in two studies and different definitions of histological response in nine. Genes reported as significant were involved in cell cycle control (30), apoptosis (7), structural molecules (9), cell metabolism (6) and DNA repair (1)...
January 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28290528/nicotine-dependence-is-associated-with-functional-variation-in-fmo3-an-enzyme-that-metabolizes-nicotine-in-the-brain
#18
A M Teitelbaum, S E Murphy, G Akk, T B Baker, A Germann, L B von Weymarn, L J Bierut, A Goate, E D Kharasch, A J Bloom
A common haplotype of the flavin-containing monooxygenase gene FMO3 is associated with aberrant mRNA splicing, a twofold reduction in in vivo nicotine N-oxidation and reduced nicotine dependence. Tobacco remains the largest cause of preventable mortality worldwide. CYP2A6, the primary hepatic nicotine metabolism gene, is robustly associated with cigarette consumption but other enzymes contribute to nicotine metabolism. We determined the effects of common variants in FMO3 on plasma levels of nicotine-N-oxide in 170 European Americans administered deuterated nicotine...
January 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28139755/genetically-determined-high-activity-of-il-12-and-il-18-in-ulcerative-colitis-and-tlr5-in-crohns-disease-were-associated-with-non-response-to-anti-tnf-therapy
#19
S Bank, P S Andersen, J Burisch, N Pedersen, S Roug, J Galsgaard, S Y Turino, J B Brodersen, S Rashid, B K Rasmussen, S Avlund, T B Olesen, H J Hoffmann, B A Nexø, J Sode, U Vogel, V Andersen
Anti-tumour necrosis factor-α (TNF-α) is used for treatment of severe cases of inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC). However, one-third of the patients do not respond to the treatment. A recent study indicated that genetically determined high activity of pro-inflammatory cytokines, including interleukin-1β (IL-1β), IL-6 and interferon gamma (IFN-γ), are associated with non-response to anti-TNF therapy. Using a candidate gene approach, 21 functional single-nucleotide polymorphisms (SNPs) in 14 genes in the Toll-like receptors, the inflammasome and the IFNG pathways were assessed in 482 and 256 prior anti-TNF naïve Danish patients with CD and UC, respectively...
January 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28117434/genetic-polymorphisms-as-predictive-biomarker-of-survival-in-patients-with-gastrointestinal-stromal-tumors-treated-with-sunitinib
#20
J S L Kloth, M C Verboom, J J Swen, T van der Straaten, S Sleijfer, A K L Reyners, N Steeghs, H Gelderblom, H J Guchelaar, R H J Mathijssen
This study aimed to identify single-nucleotide polymorphisms (SNPs) that are associated with outcome to treatment with sunitinib in patients with advanced gastrointestinal stromal tumors (GIST). Forty-nine SNPS involved in the pharmacokinetic and pharmacodynamic pathway of sunitinib were associated with progression-free survival (PFS) and overall survival (OS) in 127 patients with advanced GIST who have been treated with sunitinib. PFS was significantly longer in carriers of the TT genotype in POR rs1056878 (hazards ratio (HR) 4...
January 2018: Pharmacogenomics Journal
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