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Pharmacogenomic data

Siva Sai Krishna Dasa, Galina Diakova, Ryo Suzuki, Anne M Mills, Michael F Gutknecht, Alexander L Klibanov, Jill K Slack-Davis, Kimberly A Kelly
Advances in genomics and proteomics drive precision medicine by providing actionable genetic alterations and molecularly targeted therapies, respectively. While genomic analysis and medicinal chemistry have advanced patient stratification with treatments tailored to the genetic profile of a patient's tumor, proteomic targeting has the potential to enhance the therapeutic index of drugs like poly(ADP-ribose) polymerase (PARP) inhibitors. PARP inhibitors in breast and ovarian cancer patients with BRCA1/2 mutations have shown promise...
2018: Theranostics
Joseph D Tucci, Paul P Pumuye, Nuala A Helsby, Daniel T Barratt, Percy P Pokeya, Francis Hombhanje, Andrew A Somogyi
Papua New Guinea (PNG) can be roughly divided into highland, coastal and island peoples with significant mitochondrial DNA differentiation reflecting early and recent distinct migrations from Africa and East Asia, respectively. Infectious diseases such as tuberculosis, malaria and HIV severely impact on the health of its peoples for which drug therapy is the major treatment and pharmacogenetics has clinical relevance for many of these drugs. Although there is generally little information about known single nucleotide polymorphisms in the population, in some instances, their frequencies have been shown to be higher than anywhere worldwide...
June 2018: Pharmacogenetics and Genomics
Nina Pirih, Tanja Kunej
The volume of publications and the type of research approaches used in omics system sciences are vast and continue to expand rapidly. This increased complexity and heterogeneity of omics data are challenging data extraction, sensemaking, analyses, knowledge translation, and interpretation. An extended and dynamic taxonomy for the classification and summary of omics studies are essential. We present an updated taxonomy for classification of omics research studies based on four criteria: (1) type and number of genomic loci in a research study, (2) number of species and biological samples, (3) the type of omics technology (e...
May 2018: Omics: a Journal of Integrative Biology
Shannon Manzi
Safe prescribing of medications has become increasingly challenging with dozens of new drugs and drug classes added each year. Maximizing the ability to find a medication that will work as intended while minimizing side effects can be difficult, particularly when a patient does not respond as expected. Some of the variability in response may be attributed to the patient's genetics. Pharmacogenomics is the science of examining a patient's genotype in the context of medication selection and dosing. Used correctly, the clinical application of pharmacogenomic data can be useful in decreasing the trial and error approach to medication therapy...
May 1, 2018: Pediatric Annals
Blagoj Ristevski, Ming Chen
This paper surveys big data with highlighting the big data analytics in medicine and healthcare. Big data characteristics: value, volume, velocity, variety, veracity and variability are described. Big data analytics in medicine and healthcare covers integration and analysis of large amount of complex heterogeneous data such as various - omics data (genomics, epigenomics, transcriptomics, proteomics, metabolomics, interactomics, pharmacogenomics, diseasomics), biomedical data and electronic health records data...
May 10, 2018: Journal of Integrative Bioinformatics
Scott J Warchal, John C Dawson, Neil O Carragher
Principal component analysis enables dimensional reduction of multivariate datasets that are typical in high-content screening. A common analysis utilizing principal components is a distance measurement between a perturbagen-such as small-molecule treatment or shRNA knockdown-and a negative control. This method works well to identify active perturbagens, though it cannot discern between distinct phenotypic responses. Here, we describe an extension of the principal component analysis approach to multivariate high-content screening data to enable quantification of differences in direction in principal component space...
2018: Methods in Molecular Biology
Rabea Asleh, Alexandros Briasoulis, Elliot M Berinstein, Joshua B Wiener, Mohan Palla, Sudhir S Kushwaha, Andrew P Levy
Objectives: The objectives of the study were to compile and summarize the data from all of the clinical trials designed to examine the association between haptoglobin (Hp) genotype and incidence of cardiovascular (CV) events in patients with diabetes mellitus (DM) and to assess the impact of vitamin E treatment on CV outcomes according to the Hp genotype. Background: The Hp genotype could serve as a predictive biomarker to DM patients who may benefit from vitamin E therapy...
2018: Pharmacogenomics and Personalized Medicine
Sarah Yoon, Eun-Ju Lee, Ji-Hye Choi, Taek Chung, Do Young Kim, Jong-Yeop Im, Myung-Ho Bae, Jung-Hee Kwon, Hyuk-Hoon Kim, Hyung Chul Kim, Young Nyun Park, Hee-Jung Wang, Hyun Goo Woo
Gene mutations play critical roles during cancer development and progression, and therefore represent targets for precision medicine. Here we recapitulated the pharmacogenomic data to delineate novel candidates for actionable mutations and therapeutic target drugs. As a proof-of-concept, we demonstrated that the loss-of-function of SULF2 by mutation (N491K) or inhibition enhanced sorafenib sensitivity in liver cancer cells and in vivo mouse models. This effect was mediated by deregulation of EGFR signaling and downstream expression of LCN2...
May 3, 2018: Oncogene
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
A Costanzo, L Bianchi, M L Flori, G Malara, L Stingeni, M Bartezaghi, L Carraro, G Castellino
BACKGROUND: Understanding genetic variations is important in predicting the treatment response and forms the basis for identifying new pharmacogenetic and pharmacogenomic targets for the treatment of psoriasis. Limited data are available for the efficacy of secukinumab in relation to genetic markers. OBJECTIVE: To evaluate the efficacy and safety of secukinumab 300 mg in HLA-Cw6-positive (Cw6-POS) and HLA-Cw6-negative (Cw6-NEG) patients with moderate-to-severe chronic plaque-type psoriasis...
April 28, 2018: British Journal of Dermatology
Jing Li, Chenghao Guo, Mengdan Yan, Fanglin Niu, Peng Chen, Bin Li, Tianbo Jin
Pharmacogenomics, the study of the role of genetics in drug response, has recently become a focal point of research. Previous studies showed that genes associated with drug detoxification vary among different populations. However, pharmacogenomic information of the Zhuang ethnic group is scarce. The aim of the present study was to screen members of the Zhuang ethnicity in southwestern China for genotype frequencies of very important pharmacogenomic (VIP) variants and to determine the differences between the Zhuang ethnicity and other human populations...
April 2018: Medicine (Baltimore)
Nicola Mulder, Alash'le Abimiku, Sally N Adebamowo, Jantina de Vries, Alice Matimba, Paul Olowoyo, Michele Ramsay, Michelle Skelton, Dan J Stein
Precision medicine is being enabled in high-income countries by the growing availability of health data, increasing knowledge of the genetic determinants of disease and variation in response to treatment (pharmacogenomics), and the decreasing costs of data generation, which promote routine application of genomic technologies in the health sector. However, there is uncertainty about the feasibility of applying precision medicine approaches in low- and middle-income countries, due to the lack of population-specific knowledge, skills, and resources...
2018: Pharmacogenomics and Personalized Medicine
Jiazhen Liu, Joseph Finkelstein
The main objective of this project was to introduce approaches for comprehensive medication risk assessment in people with polypharmacy that simultaneously account for multiple drug and gene effects. To achieve this goal, we developed an integrated knowledge repository of actionable pharmacogenes and a scoring algorithm that was pilot-tested using a data set containing pharmacogenomic information of people with polypharmacy. Metabolic phenotyping using resulting database demonstrated recall of 83.6% and precision of 87...
2018: Studies in Health Technology and Informatics
Marc Hinderer, Melanie Boerries, Martin Boeker, Michael Neumaier, Frank-Peter Loubal, Till Acker, Manfred Brunner, Hans-Ulrich Prokosch, Jan Christoph
BACKGROUND: Pharmacogenomic Clinical Decision Support Systems (CDSS) are considered to be the most feasible tool for adopting pharmacogenomic testing into clinical routine. OBJECTIVE: To discuss important factors for implementing pharmacogenomic CDSS into German hospitals. METHODS: We analyzed two relevant studies. Furthermore, we interviewed data privacy officers of three German university hospitals and examined relevant legal regulations in literature...
2018: Studies in Health Technology and Informatics
Haifa Jmel, Lilia Romdhane, Yosra Ben Halima, Meriem Hechmi, Chokri Naouali, Hamza Dallali, Yosr Hamdi, Jingxuan Shan, Abdelmajid Abid, Henda Jamoussi, Sameh Trabelsi, Lotfi Chouchane, Donata Luiselli, Sonia Abdelhak, Rym Kefi
Genetic variation is an important determinant affecting either drug response or susceptibility to adverse drug reactions. Several studies have highlighted the importance of ethnicity in influencing drug response variability that should be considered during drug development. Our objective is to characterize the genetic variability of some pharmacogenes involved in the response to drugs used for the treatment of Metabolic Syndrome (MetS) in Tunisia and to compare our results to the worldwide populations. A set of 135 Tunisians was genotyped using the Affymetrix Chip 6...
2018: PloS One
Caitrin W McDonough, Oyunbileg Magvanjav, Ana C C Sá, Nihal M El Rouby, Chintan Dave, Amelia N Deitchman, Marina Kawaguchi-Suzuki, Wenbin Mei, Yong Shen, Ravi Shankar Prasad Singh, Mohamed Solayman, Kent R Bailey, Eric Boerwinkle, Arlene B Chapman, John G Gums, Amy Webb, Steven E Scherer, Wolfgang Sadee, Stephen T Turner, Rhonda M Cooper-DeHoff, Yan Gong, Julie A Johnson
BACKGROUND: Plasma renin is an important regulator of blood pressure (BP). Plasma renin activity (PRA) has been shown to correlate with variability in BP response to antihypertensive agents. We conducted a genome-wide association study to identify single-nucleotide polymorphisms (SNPs) associated with baseline PRA using data from the PEAR study (Pharmacogenomic Evaluation of Antihypertensive Responses). METHODS: Multiple linear regression analysis was performed in 461 whites and 297 blacks using an additive model, adjusting for age, sex, and ancestry-specific principal components...
April 2018: Circulation. Genomic and precision medicine
Faizal Z Asumda, Konstantinos E Hatzistergos, Derek M Dykxhoorn, Silvia Jakubski, Jasmine Edwards, Emmanuel Thomas, Eugene R Schiff
A variety of approaches have been developed for the derivation of hepatocyte-like cells from pluripotent stem cells. Currently, most of these strategies employ step-wise differentiation approaches with recombinant growth-factors or small-molecule analogs to recapitulate developmental signaling pathways. Here, we tested the efficacy of a small-molecule based differentiation protocol for the generation of hepatocyte-like cells from human pluripotent stem cells. Quantitative gene-expression, immunohistochemical, and western blot analyses for SOX17, FOXA2, CXCR4, HNF4A, AFP, indicated the stage-specific differentiation into definitive endoderm, hepatoblast and hepatocyte-like derivatives...
March 27, 2018: Differentiation; Research in Biological Diversity
Jai N Patel, Lauren A Wiebe, Henry M Dunnenberger, Howard L McLeod
Genomic medicine provides opportunities to personalize cancer therapy for an individual patient. Although novel targeted therapies prolong survival, most patients with cancer continue to suffer from burdensome symptoms including pain, depression, neuropathy, nausea and vomiting, and infections, which significantly impair quality of life. Suboptimal management of these symptoms can negatively affect response to cancer treatment and overall prognosis. The effect of genetic variation on drug response-otherwise known as pharmacogenomics-is well documented and directly influences an individual patient's response to antiemetics, opioids, neuromodulators, antidepressants, antifungals, and more...
April 5, 2018: Oncologist
Kevin T Bain, Emily J Schwartz, Orsula V Knowlton, Calvin H Knowlton, Jacques Turgeon
OBJECTIVES: To determine the feasibility of implementing a pharmacist-led pharmacogenomics (PGx) service for the Program of All-Inclusive Care for the Elderly (PACE). SETTING: A national centralized pharmacy providing PGx services to community-based PACE centers. PRACTICE DESCRIPTION: Individuals 55 years of age and older enrolled in PACE who underwent PGx testing as part of their medical care (n = 296). PRACTICE INNOVATION: Pharmacist-led PGx testing, interpreting, and consulting...
March 27, 2018: Journal of the American Pharmacists Association: JAPhA
Stephen Hyter, Jeff Hirst, Harsh Pathak, Ziyan Y Pessetto, Devin C Koestler, Rama Raghavan, Dong Pei, Andrew K Godwin
There is a lack of personalized treatment options for women with recurrent platinum-resistant ovarian cancer. Outside of bevacizumab and a group of poly ADP-ribose polymerase inhibitors, few options are available to women that relapse. We propose that efficacious drug combinations can be determined via molecular characterization of ovarian tumors along with pre-established pharmacogenomic profiles of repurposed compounds. To that end, we selectively performed multiple two-drug combination treatments in ovarian cancer cell lines that included reactive oxygen species inducers and HSP90 inhibitors...
March 13, 2018: Oncotarget
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