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Pharmacogenomics databases

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https://www.readbyqxmd.com/read/28271979/toward-a-taxonomy-for-multi-omics-science-terminology-development-for-whole-genome-study-approaches-by-omics-technology-and-hierarchy
#1
Nina Pirih, Tanja Kunej
Omics is a form of high-throughput systems science. However, taxonomies for omics studies are limited, inviting us to rethink new ways in which we classify, prioritize, and rank various omics systems science studies. In this overarching context, the genome-wide study approaches have proliferated in number and popularity over the past decade. However, their hierarchy is not well organized and the development of attendant terminology is not controlled. In the present study, we searched the literature in PubMed and the Web of Science databases published from March 1999 to September 2016 using the keywords, including genome-wide, association, whole genome, transcriptome-wide, metabolome, epigenome, and phenome...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28271248/network-reconstruction-reveals-that-valproic-acid-activates-neurogenic-transcriptional-programs-in-adult-brain-following-traumatic-injury
#2
Gerald A Higgins, Patrick Georgoff, Vahagn Nikolian, Ari Allyn-Feuer, Brian Pauls, Richard Higgins, Brian D Athey, Hasan E Alam
OBJECTIVES: To determine the mechanism of action of valproic acid (VPA) in the adult central nervous system (CNS) following traumatic brain injury (TBI) and hemorrhagic shock (HS). METHODS: Data were analyzed from different sources, including experiments in a porcine model, data from postmortem human brain, published studies, public and commercial databases. RESULTS: The transcriptional program in the CNS following TBI, HS, and VPA treatment includes activation of regulatory pathways that enhance neurogenesis and suppress gliogenesis...
March 7, 2017: Pharmaceutical Research
https://www.readbyqxmd.com/read/28270929/changing-paradigms-in-the-management-of-rejection-in-kidney-transplantation-evolving-from-protocol-based-care-to-the-era-of-p4-medicine
#3
Mirela Maier, Tomoko Takano, Ruth Sapir-Pichhadze
PURPOSE OF REVIEW: P4 medicine denotes an evolving field of medicine encompassing predictive, preventive, personalized, and participatory medicine. Using the example of kidney allograft rejection because of donor-recipient incompatibility in human leukocyte antigens, this review outlines P4 medicine's relevance to the various stages of the kidney transplant cycle. SOURCES OF INFORMATION: A search for English articles was conducted in Medline via OvidSP (up to August 18, 2016) using a combination of subject headings (MeSH) and free text in titles, abstracts, and author keywords for the concepts kidney transplantation and P4 medicine...
2017: Canadian Journal of Kidney Health and Disease
https://www.readbyqxmd.com/read/28249909/morphoproteomics-identifies-sirt1-and-ezh2-pathways-as-commonalities-in-b-cell-acute-lymphoblastic-leukemia-pathogenetic-implications-and-opportunities-for-therapeutic-intervention
#4
Robert E Brown, Kristine E Konopka, Priya Weerasinghe, Vanya Jaitly, Amitava Dasgupta, Mary F McGuire, Nghia D Nguyen
B-cell acute lymphoblastic leukemia (ALL) represents a malignant process in which bone marrow-derived lymphoblasts retain their undifferentiated state. Genetic testing has revealed either no identifiable cytogenetic and genomic abnormalities in such patients or a wide range of aberrations that may or may not contribute to the block in differentiation and the associated proliferation of the malignant lymphoblasts in cases of B-cell ALL. In this study, we applied morphoproteomics to a representative spectrum of cases of newly diagnosed B-cell ALL in order to identify pathways that are known to be associated with the maintenance of the undifferentiated state while promoting proliferation...
January 2017: Annals of Clinical and Laboratory Science
https://www.readbyqxmd.com/read/28241745/drug-voyager-a-computational-platform-for-exploring-unintended-drug-action
#5
Min Oh, Jaegyoon Ahn, Taekeon Lee, Giup Jang, Chihyun Park, Youngmi Yoon
BACKGROUND: The dominant paradigm in understanding drug action focuses on the intended therapeutic effects and frequent adverse reactions. However, this approach may limit opportunities to grasp unintended drug actions, which can open up channels to repurpose existing drugs and identify rare adverse drug reactions. Advances in systems biology can be exploited to comprehensively understand pharmacodynamic actions, although proper frameworks to represent drug actions are still lacking. RESULTS: We suggest a novel platform to construct a drug-specific pathway in which a molecular-level mechanism of action is formulated based on pharmacologic, pharmacogenomic, transcriptomic, and phenotypic data related to drug response ( http://databio...
February 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28176638/personalized-medicine-and-adverse-drug-reactions-the-experience-of-an-italian-teaching-hospital
#6
Raffaele La Russa, Vittorio Fineschi, Mariantonia Di Sanzo, Vittorio Gatto, Alessandro Santurro, Gabriella Martini, Matteo Scopetti, Paola Frati
The personalized medicine is a model of medicine based on inherent difference given by the genetic heritage that characterizes us, diversity that can affect also our response to administered therapy. Nowadays, the term "adverse drug reaction" is identified with any harmful effect involuntary resulting from the use of a medicinal product; pharmacogenomics, in this field, has the aim to improve the drug response and to reduce the adverse reaction. We analyzed all reports of adverse reaction collected in the Pharmacovigilance Centre database of an Italian University Hospital, at the Sant'Andrea Hospital Sapienza University of Rome, in a period of two years...
February 7, 2017: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/28139890/pharmacogenomics-of-17-alpha-hydroxyprogesterone-caproate-for-recurrent-preterm-birth-a-case-control-study
#7
T A Manuck, W S Watkins, M S Esplin, J Biggio, R Bukowski, S Parry, H Zhan, H Huang, W Andrews, G Saade, Y Sadovsky, U M Reddy, J Ilekis, M Yandell, M W Varner, L B Jorde
OBJECTIVE: To compare maternal genotypes between women with and without significant prolongation of pregnancy in the setting of 17-alpha hydroxyprogesterone caproate (17-P) administration for the prevention of recurrent preterm birth (PTB). DESIGN: Case-control. SETTING: Three tertiary-care centres across the USA. POPULATION: Women (n = 99) with ≥ 1 prior singleton spontaneous PTB, receiving 17-P. METHODS: Women were classified as having successful prolongation of pregnancy during the 17-P treated pregnancy, in two ways: (1) Definition A: success/non-success based on difference in gestational age at delivery between 17-P-treated and untreated pregnancies (success: delivered ≥ 3 weeks later with 17-P) and (2) Definition B: success/non-success based on reaching term (success: delivered at term with 17-P)...
January 31, 2017: BJOG: An International Journal of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28096076/a-landscape-of-synthetic-viable-interactions-in-cancer
#8
Yunyan Gu, Ruiping Wang, Yue Han, Wenbin Zhou, Zhangxiang Zhao, Tingting Chen, Yuanyuan Zhang, Fuduan Peng, Haihai Liang, Lishuang Qi, Wenyuan Zhao, Da Yang, Zheng Guo
Synthetic viability, which is defined as the combination of gene alterations that can rescue the lethal effects of a single gene alteration, may represent a mechanism by which cancer cells resist targeted drugs. Approaches to detect synthetic viable (SV) interactions in cancer genome to investigate drug resistance are still scarce. Here, we present a computational method to detect synthetic viability-induced drug resistance (SVDR) by integrating the multidimensional data sets, including copy number alteration, whole-exome mutation, expression profile and clinical data...
January 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28069634/a-review-of-connectivity-map-and-computational-approaches-in-pharmacogenomics
#9
Aliyu Musa, Laleh Soltan Ghoraie, Shu-Dong Zhang, Galina Galzko, Olli Yli-Harja, Matthias Dehmer, Benjamin Haibe-Kains, Frank Emmert-Streib
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications...
January 9, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28068459/does-pharmacogenomic-testing-improve-clinical-outcomes-for-major-depressive-disorder-a-systematic-review-of-clinical-trials-and-cost-effectiveness-studies
#10
Joshua D Rosenblat, Yena Lee, Roger S McIntyre
OBJECTIVE: Pharmacogenomic testing has become scalable and available to the general public. Pharmacogenomics has shown promise for predicting antidepressant response and tolerability in the treatment of major depressive disorder (MDD). In theory, pharmacogenomics can improve clinical outcomes by guiding antidepressant selection and dosing. The current systematic review examines the extant literature to determine the impact of pharmacogenomic testing on clinical outcomes in MDD and assesses its cost-effectiveness...
January 3, 2017: Journal of Clinical Psychiatry
https://www.readbyqxmd.com/read/27926382/prediction-of-anti-cancer-drug-response-by-kernelized-multi-task-learning
#11
Mehmet Tan
MOTIVATION: Chemotherapy or targeted therapy are two of the main treatment options for many types of cancer. Due to the heterogeneous nature of cancer, the success of the therapeutic agents differs among patients. In this sense, determination of chemotherapeutic response of the malign cells is essential for establishing a personalized treatment protocol and designing new drugs. With the recent technological advances in producing large amounts of pharmacogenomic data, in silico methods have become important tools to achieve this aim...
October 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27924022/expanded-national-database-collection-and-data-coverage-in-the-findbase-worldwide-database-for-clinically-relevant-genomic-variation-allele-frequencies
#12
Emmanouil Viennas, Angeliki Komianou, Clint Mizzi, Maja Stojiljkovic, Christina Mitropoulou, Juha Muilu, Mauno Vihinen, Panagiota Grypioti, Styliani Papadaki, Cristiana Pavlidis, Branka Zukic, Theodora Katsila, Peter J van der Spek, Sonja Pavlovic, Giannis Tzimas, George P Patrinos
FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27900742/-precision-nursing-individual-based-knowledge-translation
#13
Li-Chi Chiang, Mei-Ling Yeh, Sui-Lung Su
U.S. President Obama announced a new era of precision medicine in the Precision Medicine Initiative (PMI). This initiative aims to accelerate the progress of personalized medicine in light of individual requirements for prevention and treatment in order to improve the state of individual and public health. The recent and dramatic development of large-scale biologic databases (such as the human genome sequence), powerful methods for characterizing patients (such as genomics, microbiome, diverse biomarkers, and even pharmacogenomics), and computational tools for analyzing big data are maximizing the potential benefits of precision medicine...
December 2016: Hu Li za Zhi the Journal of Nursing
https://www.readbyqxmd.com/read/27807747/text-mining-for-precision-medicine-bringing-structure-to-ehrs-and-biomedical-literature-to-understand-genes-and-health
#14
Michael Simmons, Ayush Singhal, Zhiyong Lu
The key question of precision medicine is whether it is possible to find clinically actionable granularity in diagnosing disease and classifying patient risk. The advent of next-generation sequencing and the widespread adoption of electronic health records (EHRs) have provided clinicians and researchers a wealth of data and made possible the precise characterization of individual patient genotypes and phenotypes. Unstructured text-found in biomedical publications and clinical notes-is an important component of genotype and phenotype knowledge...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27746730/using-pharmacogenomic-databases-for-discovering-patient-target-genes-and-small-molecule-candidates-to-cancer-therapy
#15
José E Belizário, Beatriz A Sangiuliano, Marcela Perez-Sosa, Jennifer M Neyra, Dayson F Moreira
With multiple omics strategies being applied to several cancer genomics projects, researchers have the opportunity to develop a rational planning of targeted cancer therapy. The investigation of such numerous and diverse pharmacogenomic datasets is a complex task. It requires biological knowledge and skills on a set of tools to accurately predict signaling network and clinical outcomes. Herein, we describe Web-based in silico approaches user friendly for exploring integrative studies on cancer biology and pharmacogenomics...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/27708512/genetic-factors-affecting-patient-responses-to-pancreatic-cancer-treatment
#16
REVIEW
George Fotopoulos, Konstantinos Syrigos, Muhammad Wasif Saif
Cancer of the exocrine pancreas is a malignancy with a high lethal rate. Surgical resection is the only possible curative mode of treatment. Metastatic pancreatic cancer is incurable with modest results from the current treatment options. New genomic information could prove treatment efficacy. An independent review of PubMed and ScienceDirect databases was performed up to March 2016, using combinations of terms such pancreatic exocrine cancer, chemotherapy, genomic profile, pancreatic cancer pharmacogenomics, genomics, molecular pancreatic pathogenesis, and targeted therapy...
October 2016: Annals of Gastroenterology: Quarterly Publication of the Hellenic Society of Gastroenterology
https://www.readbyqxmd.com/read/27645580/inferences-of-drug-responses-in-cancer-cells-from-cancer-genomic-features-and-compound-chemical-and-therapeutic-properties
#17
Yongcui Wang, Jianwen Fang, Shilong Chen
Accurately predicting the response of a cancer patient to a therapeutic agent is a core goal of precision medicine. Existing approaches were mainly relied primarily on genomic alterations in cancer cells that have been treated with different drugs. Here we focus on predicting drug response based on integration of the heterogeneously pharmacogenomics data from both cell and drug sides. Through a systematical approach, named as PDRCC (Predict Drug Response in Cancer Cells), the cancer genomic alterations and compound chemical and therapeutic properties were incorporated to determine the chemotherapeutic response in cancer patients...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27641153/genetic-polymorphisms-affecting-the-pharmacokinetics-of-antiretroviral-drugs
#18
REVIEW
Andrea Calcagno, Jessica Cusato, Antonio D'Avolio, Stefano Bonora
BACKGROUND: Antiretroviral treatment is highly effective in enhancing HIV-positive patients' survival and quality of life. Despite an increased tolerability in recent years, a substantial amount of patients experience side effects. Antiretrovirals' efficacy and tolerability have been associated with plasma concentrations and single nucleotide polymorphisms in selected genes involved in drug disposition. OBJECTIVE: Our aim was to review the current knowledge in genetic polymorphisms affecting plasma, intracellular or compartmental concentrations of antiretrovirals...
September 19, 2016: Clinical Pharmacokinetics
https://www.readbyqxmd.com/read/27548815/minimum-information-required-for-a-dmet-experiment-reporting
#19
Judit Kumuthini, Mamana Mbiyavanga, Emile R Chimusa, Jyotishman Pathak, Panu Somervuo, Ron Hn Van Schaik, Vita Dolzan, Clint Mizzi, Kusha Kalideen, Raj S Ramesar, Milan Macek, George P Patrinos, Alessio Squassina
AIM: To provide pharmacogenomics reporting guidelines, the information and tools required for reporting to public omic databases. MATERIAL & METHODS: For effective DMET data interpretation, sharing, interoperability, reproducibility and reporting, we propose the Minimum Information required for a DMET Experiment (MIDE) reporting. RESULTS: MIDE provides reporting guidelines and describes the information required for reporting, data storage and data sharing in the form of XML...
September 2016: Pharmacogenomics
https://www.readbyqxmd.com/read/27508329/connection-map-for-compounds-cmc-a-server-for-combinatorial-drug-toxicity-and-efficacy-analysis
#20
Lei Liu, Maria Tsompana, Yong Wang, Dingfeng Wu, Lixin Zhu, Ruixin Zhu
Drug discovery and development is a costly and time-consuming process with a high risk for failure resulting primarily from a drug's associated clinical safety and efficacy potential. Identifying and eliminating inapt candidate drugs as early as possible is an effective way for reducing unnecessary costs, but limited analytical tools are currently available for this purpose. Recent growth in the area of toxicogenomics and pharmacogenomics has provided with a vast amount of drug expression microarray data. Web servers such as CMap and LTMap have used this information to evaluate drug toxicity and mechanisms of action independently; however, their wider applicability has been limited by the lack of a combinatorial drug-safety type of analysis...
September 26, 2016: Journal of Chemical Information and Modeling
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