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Pharmacogenomic data

Marcelo R Luizon, Daniela A Pereira, Valeria C Sandrim
Hypertension is a leading cause of cardiovascular mortality, but only about half of patients on antihypertensive therapy achieve blood pressure control. Preeclampsia is defined as pregnancy-induced hypertension and proteinuria, and is associated with increased maternal and perinatal mortality and morbidity. Similarly, a large number of patients with preeclampsia are non-responsive to antihypertensive therapy. Pharmacogenomics may help to guide the personalized treatment for non-responsive hypertensive patients...
2018: Frontiers in Pharmacology
Francesca Maria Notarangelo, Giuseppe Maglietta, Paola Bevilacqua, Marco Cereda, Piera Angelica Merlini, Giovanni Quinto Villani, Paolo Moruzzi, Giampiero Patrizi, Guidantonio Malagoli Tagliazucchi, Antonio Crocamo, Angela Guidorossi, Filippo Pigazzani, Elisa Nicosia, Giorgia Paoli, Marco Bianchessi, Mario Angelo Comelli, Caterina Caminiti, Diego Ardissino
BACKGROUND: Clopidogrel is still frequently used in patients with acute coronary syndromes (ACS), but its efficacy is hampered by interpatient response variability, due to genetic polymorphisms associated with clopidogrel metabolism. OBJECTIVE: To evaluate whether selecting antiplatelet therapy (clopidogrel, prasugrel or ticagrelor) on the basis of a patient's genetic and clinical characteristics leads to better clinical outcomes in comparison with the standard of care, which bases the selection on clinical characteristics alone METHODS: Patients hospitalised for ACS were randomly assigned to standard of care or pharmacogenomic arm, which included the genotyping of ABCB1, CYP2C19*2, CYP2C19*17 using an ST Q3 system that provide the data within 70 minutes at each patient's bedside...
February 24, 2018: Journal of the American College of Cardiology
Youqiong Ye, Yu Xiang, Fatma Muge Ozguc, Yoonjin Kim, Chun-Jie Liu, Peter K Park, Qingsong Hu, Lixia Diao, Yanyan Lou, Chunru Lin, An-Yuan Guo, Bingying Zhou, Li Wang, Zheng Chen, Joseph S Takahashi, Gordon B Mills, Seung-Hee Yoo, Leng Han
Cancer chronotherapy, treatment at specific times during circadian rhythms, endeavors to optimize anti-tumor effects and to lower toxicity. However, comprehensive characterization of clock genes and their clinical relevance in cancer is lacking. We systematically characterized the alterations of clock genes across 32 cancer types by analyzing data from The Cancer Genome Atlas, Cancer Therapeutics Response Portal, and The Genomics of Drug Sensitivity in Cancer databases. Expression alterations of clock genes are associated with key oncogenic pathways, patient survival, tumor stage, and subtype in multiple cancer types...
March 1, 2018: Cell Systems
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
Ayman F El-Kattan, Manthena V S Varma
Membrane transporters play an important role in the absorption, distribution, clearance and elimination (ADCE) of the drugs. Supported by the pharmacokinetics data in human, several transporters including organic anion transporting polypeptide (OATP)1B1, OATP1B3, organic anion transporter (OAT)1, OAT3, organic cation transporter (OCT)2, multidrug and toxin extrusion proteins (MATEs), P-glycoprotein and breast cancer resistance protein (BCRP) are suggested to be of clinical relevance. An early understanding of transporters role in the drug disposition and clearance allows reliable prediction/evaluation of the pharmacokinetic changes due to drug-drug interactions (DDIs) or genetic polymorphisms...
March 1, 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
Juan Xie, Anjun Ma, Anne Fennell, Qin Ma, Jing Zhao
Biclustering is a powerful data mining technique that allows clustering of rows and columns, simultaneously, in a matrix-format data set. It was first applied to gene expression data in 2000, aiming to identify co-expressed genes under a subset of all the conditions/samples. During the past 17 years, tens of biclustering algorithms and tools have been developed to enhance the ability to make sense out of large data sets generated in the wake of high-throughput omics technologies. These algorithms and tools have been applied to a wide variety of data types, including but not limited to, genomes, transcriptomes, exomes, epigenomes, phenomes and pharmacogenomes...
February 27, 2018: Briefings in Bioinformatics
Ferdous A Jabir, Wisam H Hoidy
BACKGROUND: Breast cancer is the most common cancer in women characterized by a high variable clinical outcome among individuals treated with targeted therapies. PATIENTS AND METHODS: In this study, we performed a population-based approach intersecting high-throughput genotype data from Iraqi populations with publicly available pharmacogenomics information to estimate the frequency of genotypes correlated with responsiveness to breast cancer treatment thus improving the clinical management of this disease in an efficient and cost effective way...
January 31, 2018: Clinical Breast Cancer
Renaud Tissier, Jeanine Houwing-Duistermaat, Mar Rodríguez-Girondo
Building prediction models based on complex omics datasets such as transcriptomics, proteomics, metabolomics remains a challenge in bioinformatics and biostatistics. Regularized regression techniques are typically used to deal with the high dimensionality of these datasets. However, due to the presence of correlation in the datasets, it is difficult to select the best model and application of these methods yields unstable results. We propose a novel strategy for model selection where the obtained models also perform well in terms of overall predictability...
2018: PloS One
Satoshi Ueshima, Daiki Hira, Yuuma Kimura, Ryo Fujii, Chiho Tomitsuka, Takuya Yamane, Yohei Tabuchi, Tomoya Ozawa, Hideki Itoh, Seiko Ohno, Minoru Horie, Tomohiro Terada, Toshiya Katsura
AIMS: This study aimed to analyse the effects of genetic polymorphisms in drug transporters and metabolising enzymes, and clinical laboratory data on the pharmacokinetic parameters of apixaban. METHODS: Data were collected from 81 Japanese patients with atrial fibrillation. Pharmacogenomic data were stratified by ABCB1, ABCG2, and CYP3A5 polymorphisms. The pharmacokinetic profile of apixaban was described by a one-compartment model with first-order absorption. Population pharmacokinetic analysis was conducted using non-linear mixed effect modelling (NONMEM™) program...
February 19, 2018: British Journal of Clinical Pharmacology
Katherine D Blizinsky, Vence L Bonham
To fully achieve the goals of a genomics-enabled learning health care system, purposeful efforts to understand and reduce health disparities and improve equity of care are essential. This paper highlights three major challenges facing genomics-enabled learning health care systems, as they pertain to ancestrally diverse populations: inequality in the utility of genomic medicine; lack of access to pharmacogenomics in clinical care; and inadequate incorporation of social and environmental data into the electronic health care record (EHR)...
January 2018: Learning Health Systems
Abdelhadi M Habeb, Sarah E Flanagan, Mohamed A Zulali, Mohamed A Abdullah, Renata Pomahačová, Veselin Boyadzhiev, Lesby E Colindres, Guillermo V Godoy, Thiruvengadam Vasanthi, Ramlah Al Saif, Aria Setoodeh, Amirreza Haghighi, Alireza Haghighi, Yomna Shaalan, Andrew T Hattersley, Sian Ellard, Elisa De Franco
AIMS/HYPOTHESIS: Diabetes is one of the cardinal features of thiamine-responsive megaloblastic anaemia (TRMA) syndrome. Current knowledge of this rare monogenic diabetes subtype is limited. We investigated the genotype, phenotype and response to thiamine (vitamin B1 ) in a cohort of individuals with TRMA-related diabetes. METHODS: We studied 32 individuals with biallelic SLC19A2 mutations identified by Sanger or next generation sequencing. Clinical details were collected through a follow-up questionnaire...
February 15, 2018: Diabetologia
Kathrin Blagec, Rudolf Koopmann, Mandy Crommentuijn-van Rhenen, Inge Holsappel, Cathelijne H van der Wouden, Lidija Konta, Hong Xu, Daniela Steinberger, Enrico Just, Jesse J Swen, Henk-Jan Guchelaar, Matthias Samwald
Clinical pharmacogenomics (PGx) has the potential to make pharmacotherapy safer and more effective by utilizing genetic patient data for drug dosing and selection. However, widespread adoption of PGx depends on its successful integration into routine clinical care through clinical decision support tools, which is often hampered by insufficient or fragmented infrastructures. This paper describes the setup and implementation of a unique multimodal, multilingual clinical decision support intervention consisting of digital, paper-, and mobile-based tools that are deployed across implementation sites in seven European countries participating in the Ubiquitous PGx (U-PGx) project...
February 9, 2018: Journal of the American Medical Informatics Association: JAMIA
Yi-An Bi, Jian Lin, Sumathy Mathialagan, Laurie Tylaska, Ernesto Callegari, A David Rodrigues, Manthena V S Varma
Inter-individual variability in warfarin dose requirement demands personalized medicine approaches to balance its therapeutic benefits (anticoagulation) and bleeding risk. Cytochrome P450 2C9 (CYP2C9) genotype-guided warfarin dosing is recommended in the clinic, given the more potent S-warfarin is primarily metabolized by CYP2C9. However, only about 20-30% of inter-patient variability in S-warfarin clearance is associated with CYP2C9 genotype. We evaluated the role of hepatic uptake in the clearance of R- and S-warfarin...
February 12, 2018: Molecular Pharmaceutics
Suhani Almal, Sungwon Jeon, Milee Agarwal, Sweta Patel, Shivangi Patel, Youngjune Bhak, JeHoon Jun, Jong Bhak, Harish Padh
The article presents the analysis of whole genome sequence of a Gujarati Indian individual (IHGP01) that was sequenced at 23.05× coverage with a total of 74.93 Gb of sequence data generated using Illumina HiSeq 2000 platform. Variant analysis revealed over 3.9 million single nucleotide variants (SNVs) and about 393,000 small insertions and deletions (InDels) including novel variants. The known variants were analyzed for their health and disease relevance and pharmacogenomic profile. Mitochondrial and Y-chromosome haplogroup analysis clearly indicated arrival on the continent not more than 20,000-25,000 years ago, following the route out of Africa to central Europe, then into Asian continent and subsequent migration to West part of the Indian subcontinent...
February 9, 2018: Genomics
Miriam S Reuter, Susan Walker, Bhooma Thiruvahindrapuram, Joe Whitney, Iris Cohn, Neal Sondheimer, Ryan K C Yuen, Brett Trost, Tara A Paton, Sergio L Pereira, Jo-Anne Herbrick, Richard F Wintle, Daniele Merico, Jennifer Howe, Jeffrey R MacDonald, Chao Lu, Thomas Nalpathamkalam, Wilson W L Sung, Zhuozhi Wang, Rohan V Patel, Giovanna Pellecchia, John Wei, Lisa J Strug, Sherilyn Bell, Barbara Kellam, Melanie M Mahtani, Anne S Bassett, Yvonne Bombard, Rosanna Weksberg, Cheryl Shuman, Ronald D Cohn, Dimitri J Stavropoulos, Sarah Bowdin, Matthew R Hildebrandt, Wei Wei, Asli Romm, Peter Pasceri, James Ellis, Peter Ray, M Stephen Meyn, Nasim Monfared, S Mohsen Hosseini, Ann M Joseph-George, Fred W Keeley, Ryan A Cook, Marc Fiume, Hin C Lee, Christian R Marshall, Jill Davies, Allison Hazell, Janet A Buchanan, Michael J Szego, Stephen W Scherer
BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant...
February 5, 2018: CMAJ: Canadian Medical Association Journal, Journal de L'Association Medicale Canadienne
Peter H O'Donnell, Kellie Schoolar Reynolds
The theme for the 2018 ASCPT Annual Meeting is "Breaking Down Barriers to Effective Patient Care." This theme refers to the essential contributions of clinical pharmacology to the development of today's discovery into tomorrow's medicine. The various subdisciplines within clinical pharmacology serve to move molecules through the various stages of drug development and also refine or expand use of the drug postapproval. The wide range of topics covered by the 2018 Annual Meeting scientific program demonstrates the breadth of clinical pharmacology's impact...
March 2018: Clinical Pharmacology and Therapeutics
Djillali Annane, Jean-Paul Mira, Lorraine B Ware, Anthony C Gordon, Charles J Hinds, David C Christiani, Jonathan Sevransky, Kathleen Barnes, Timothy G Buchman, Patrick J Heagerty, Robert Balshaw, Nadia Lesnikova, Karen de Nobrega, Hugh F Wellman, Mauricio Neira, Alexandra D J Mancini, Keith R Walley, James A Russell
PURPOSE: To explore potential design for pharmacogenomics trials in sepsis, we investigate the interaction between pharmacogenomic biomarkers and response to drotrecogin alfa (activated) (DrotAA). This trial was designed to validate whether previously identified improved response polymorphisms (IRPs A and B) were associated with an improved response to DrotAA in severe sepsis. METHODS: Patients with severe sepsis at high risk of death, who received DrotAA or not, with DNA available were included and matched to controls adjusting for age, APACHE II or SAPS II, organ dysfunction, ventilation, medical/surgical status, infection site, and propensity score (probability that a patient would have received DrotAA given their baseline characteristics)...
January 31, 2018: Annals of Intensive Care
Gino Antonio Vena, Nicoletta Cassano, Florenzo Iannone
Methotrexate (MTX) is one of the mainstays of treatment for several immune-mediated inflammatory joint and skin diseases, especially rheumatoid arthritis (RA) and moderate-to-severe psoriasis. Oral MTX has been used for the treatment of such diseases for decades for many reasons. There is, however, a relevant interpatient variability of clinical and safety outcomes that can also be related to differences in patients' individual pharmacogenomic profile. Orally administered MTX has been found to have a saturable intestinal absorption and nonlinear pharmacokinetics, with significant consequences on drug bioavailability and clinical efficacy...
2018: Therapeutics and Clinical Risk Management
Alison J Wright, Stephen Sutton, David Armstrong, Paul Aveyard, Ann Louise Kinmonth, Theresa M Marteau
Pharmacogenomics may improve health outcomes in two ways: by more precise and therefore more effective prescribing, tailored to genotype, and by increasing perceived effectiveness of treatments and so motivation for adherence. Little is known about patients' experiences of, and reactions to, receiving pharmacogenomically tailored treatments. The aim of this study was to explore the impact of pharmacogenomic prescribing of nicotine replacement therapy (NRT) on smokers' initial expectations of quit success, adherence, and perceived important differences from previous quit attempts...
January 29, 2018: Translational Behavioral Medicine
Bruno Dias Nani, Marcelo Franchin, Josy Goldoni Lazarini, Irlan Almeida Freires, Marcos Guilherme da Cunha, Bruno Bueno-Silva, Severino Matias de Alencar, Ramiro Mendonça Murata, Pedro Luiz Rosalen
Vestitol and neovestitol are bioactive isoflavonoids isolated from Brazilian red propolis, a unique Apis melifera type of propolis botanically originated from Dalbergia ecastophyllum. Although these molecules have relevant biological effects, including anticancer and immunomodulatory activities, their mechanism(s) of action and the affected pathways remain largely unknown. Here, we carried out a pharmacogenomic analysis to investigate the effects of vestitol and neovestitol on the whole-genome expression in human tumor cells, particularly cancer-related target proteins...
January 29, 2018: Phytotherapy Research: PTR
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