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Genomics Medicine

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https://www.readbyqxmd.com/read/30019526/radaa-a-command-line-tool-for-identification-of-radical-amino-acid-changes-in-multiple-sequence-alignments
#1
Inge Seim, Andrew M Baker, Lisa K Chopin
High-throughput sequencing has revolutionised biology and medicine. Numerous genomes and transcriptome assemblies are now available, and these genomic data sets lend themselves to comparisons between species, strains, and other strata. Researchers often need to rapidly identify changes, in particular amino acid substitutions that could confer biological function in their system of interest. However, we are not aware of an easy-to-use tool that can be used to detect such changes, and researchers currently rely on idiosyncratic computer code...
July 17, 2018: Molecular Informatics
https://www.readbyqxmd.com/read/30018749/pharmacogenetic-studies-with-oral-anticoagulants-genome-wide-association-studies-in-vitamin-k-antagonist-and-direct-oral-anticoagulants
#2
REVIEW
Natalia Cullell, Caty Carrera, Elena Muiño, Nuria Torres, Jerzy Krupinski, Israel Fernandez-Cadenas
Oral anticoagulants (OAs) are the recommended drugs to prevent cardiovascular events and recurrence in patients with atrial fibrillation (AF) and cardioembolic stroke. We conducted a literature search to review the current state of OAs pharmacogenomics, focusing on Genome Wide Association Studies (GWAs) in patients treated with vitamin K antagonists (VKAs) and direct oral anticoagulants (DOACs). VKAs: Warfarin, acenocoumarol, fluindione and phenprocoumon have long been used, but their interindividual variability and narrow therapeutic/safety ratio makes their dosage difficult...
June 26, 2018: Oncotarget
https://www.readbyqxmd.com/read/30018380/integrated-genetic-and-epigenetic-analysis-of-myxofibrosarcoma
#3
Koichi Ogura, Fumie Hosoda, Yasuhito Arai, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Momoko Nagai, Mamoru Kato, Erika Arakawa, Wakako Mukai, Hirofumi Rokutan, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Myxofibrosarcoma (MFS) is a common adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high local recurrence rate. Here we report the genetic and epigenetic landscape of MFS based on the results of whole-exome sequencing (N = 41), RNA sequencing (N = 29), and methylation analysis (N = 41), using 41 MFSs as a discovery set, and subsequent targeted sequencing of 140 genes in the entire cohort of 99 MFSs and 17 MFSs' data from TCGA. Fourteen driver genes are identified, including potentially actionable therapeutic targets seen in 37% of cases...
July 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/30018232/authentication-of-herbal-medicines-dipsacus-asper-and-phlomoides-umbrosa-using-dna-barcodes-chloroplast-genome-and-sequence-characterized-amplified-region-scar-marker
#4
Inkyu Park, Sungyu Yang, Wook Jin Kim, Pureum Noh, Hyun Oh Lee, Byeong Cheol Moon
Dried roots of Dipsacus asper (Caprifoliaceae) are used as important traditional herbal medicines in Korea. However, the roots are often used as a mixture or contaminated with Dipsacus japonicus in Korean herbal markets. Furthermore, the dried roots of Phlomoides umbrosa (Lamiaceae) are used indiscriminately with those of D. asper , with the confusing Korean names of Sok-Dan and Han-Sok-Dan for D. asper and P. umbrosa , respectively. Although D. asper and P. umbrosa are important herbal medicines, the molecular marker and genomic information available for these species are limited...
July 17, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/30018130/machine-learning-for-better-prognostic-stratification-and-driver-gene-identification-using-somatic-copy-number-variations-in-anaplastic-oligodendroglioma
#5
Shai Rosenberg, Francois Ducray, Agusti Alentorn, Caroline Dehais, Nabila Elarouci, Aurelie Kamoun, Yannick Marie, Marie-Laure Tanguy, Aurélien De Reynies, Karima Mokhtari, Dominique Figarella-Branger, Jean-Yves Delattre, Ahmed Idbaih
BACKGROUND: 1p/19q-codeleted anaplastic gliomas have variable clinical behavior. We have recently shown that the common 9p21.3 allelic loss is an independent prognostic factor in this tumor type. The aim of this study is to identify less frequent genomic copy number variations (CNVs) with clinical importance that may shed light on molecular oncogenesis of this tumor type. MATERIALS AND METHODS: A cohort of 197 patients with anaplastic oligodendroglioma was collected as part of the French POLA network...
July 17, 2018: Oncologist
https://www.readbyqxmd.com/read/30017092/the-human-genome-editing-race-loosening-regulatory-standards-for-commercial-advantage
#6
Toni Cathomen, Silke Schüle, Martina Schüßler-Lenz, Mohamed Abou-El-Enein
Medicinal products based on genome editing must undergo rigorous preclinical testing and are subject to regulatory oversight for proper risk assessment prior to first evaluation in humans. We give a European perspective on the regulatory expectations to translate genome editing to the clinic to ensure their timely progress to market.
July 12, 2018: Trends in Biotechnology
https://www.readbyqxmd.com/read/30016991/thrombopoietin-knock-in-augments-platelet-generation-from-human-embryonic-stem-cells
#7
Leisheng Zhang, Cuicui Liu, Hongtao Wang, Dan Wu, Pei Su, Mengge Wang, Jiaojiao Guo, Shixuan Zhao, Shuxu Dong, Wen Zhou, Cameron Arakaki, Xiaobing Zhang, Jiaxi Zhou
BACKGROUND: Refinement of therapeutic-scale platelet production in vitro will provide a new source for transfusion in patients undergoing chemotherapy or radiotherapy. However, procedures for cost-effective and scalable platelet generation remain to be established. METHODS: In this study, we established human embryonic stem cell (hESC) lines containing knock-in of thrombopoietin (TPO) via CRISPR/Cas9-mediated genome editing. The expression and secretion of TPO was detected by western blotting and enzyme-linked immunosorbent assay...
July 17, 2018: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/30016813/highmed-an-open-platform-approach-to-enhance-care-and-research-across-institutional-boundaries
#8
Birger Haarbrandt, Björn Schreiweis, Sabine Rey, Ulrich Sax, Simone Scheithauer, Otto Rienhoff, Petra Knaup-Gregori, Udo Bavendiek, Christoph Dieterich, Benedikt Brors, Inga Kraus, Caroline Marieken Thoms, Dirk Jäger, Volker Ellenrieder, Björn Bergh, Ramin Yahyapour, Roland Eils, HiGHmed Consortium, Michael Marschollek
INTRODUCTION: This article is part of the Focus Theme of Methods of Information in Medicine on the German Medical Informatics Initiative. HiGHmed brings together 24 partners from academia and industry, aiming at improvements in care provision, biomedical research and epidemiology. By establishing a shared information governance framework, data integration centers and an open platform architecture in cooperation with independent healthcare providers, the meaningful reuse of data will be facilitated...
July 2018: Methods of Information in Medicine
https://www.readbyqxmd.com/read/30016722/an-unsupervised-machine-learning-method-for-discovering-patient-clusters-based-on-genetic-signatures
#9
Christian Lopez, Scott Tucker, Tarik Salameh, Conrad Tucker
INTRODUCTION: Many chronic disorders have genomic etiology, disease progression, clinical presentation, and response to treatment that vary on a patient-to-patient basis. Such variability creates a need to identify characteristics within patient populations that have clinically relevant predictive value in order to advance personalized medicine. Unsupervised machine learning methods are suitable to address this type of problem, in which no a priori class label information is available to guide this search...
July 14, 2018: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/30016002/pediatric-cancer-families-participation-in-whole-genome-sequencing-research-in-denmark-parent-perspectives
#10
Anna Byrjalsen, Ulrik Stoltze, Karin Wadt, Lisa Lyngsie Hjalgrim, Anne-Marie Gerdes, Kjeld Schmiegelow, Ayo Wahlberg
With an impending introduction of genome sequencing into paediatric oncology to facilitate personalised medicine, this study examines parent perspectives on participating in whole genome sequencing (WGS) research in the difficult weeks following diagnosis. As an embedded part of Sequencing Tumor and Germline DNA-Implications and National Guidelines (STAGING), a project aiming to implement WGS of all newly diagnosed paediatric cancer patients in Denmark, a parent perspective study was conducted by a clinical geneticist and anthropologist to document pragmatic, social and ethical dilemmas...
July 17, 2018: European Journal of Cancer Care
https://www.readbyqxmd.com/read/30014471/crispr-cas9-a-cornerstone-for-the-evolution-of-precision-medicine
#11
REVIEW
Sleiman Razzouk
Modern genetic therapy incorporates genomic testing and genome editing. It is the finest approach for precision medicine. Genome editing is a state-of-the-art technology to manipulate gene expression thus generating a particular genotype. It encompasses multiple programmable nuclease-based approaches leading to genetic changes. Not surprisingly, this method triggered internationally a wide array of controversies in the scientific community and in the public since it transforms the human genome. Given its importance, the pace of this technology is exceptionally fast...
July 16, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/30014448/ovarian-environment-aging-follicular-fluid-lipidomic-and-related-metabolic-pathways
#12
Fernanda Bertuccez Cordeiro, Daniela Antunes Montani, Eduardo Jorge Pilau, Fábio Cesar Gozzo, Renato Fraietta, Edson Guimaraes Lo Turco
PURPOSE: The decline in female fecundity with age may be caused by decreased oocyte quality, a factor that may be associated with the altered composition of follicular fluid (FF). METHODS: In an effort to better understand follicular aging and the role of lipids in a given biological system, we present a prospective study that compares lipid profiles of FF from women older than 35 years (aging group, n = 12) to women equal or younger than 35 years old (control group, n = 17)...
July 16, 2018: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/30013180/deep-learning-sequence-based-ab-initio-prediction-of-variant-effects-on-expression-and-disease-risk
#13
Jian Zhou, Chandra L Theesfeld, Kevin Yao, Kathleen M Chen, Aaron K Wong, Olga G Troyanskaya
Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understanding the transcriptional effects of genome variation. However, this is extremely difficult because of the enormous scale of the noncoding mutation space. We developed a deep learning-based framework, ExPecto, that can accurately predict, ab initio from a DNA sequence, the tissue-specific transcriptional effects of mutations, including those that are rare or that have not been observed...
July 16, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30011882/computational-methodologies-in-the-exploration-of-marine-natural-product-leads
#14
REVIEW
Florbela Pereira, Joao Aires-de-Sousa
Computational methodologies are assisting the exploration of marine natural products (MNPs) to make the discovery of new leads more efficient, to repurpose known MNPs, to target new metabolites on the basis of genome analysis, to reveal mechanisms of action, and to optimize leads. In silico efforts in drug discovery of NPs have mainly focused on two tasks: dereplication and prediction of bioactivities. The exploration of new chemical spaces and the application of predicted spectral data must be included in new approaches to select species, extracts, and growth conditions with maximum probabilities of medicinal chemistry novelty...
July 13, 2018: Marine Drugs
https://www.readbyqxmd.com/read/30011878/harmonizing-outcomes-for-genomic-medicine-comparison-of-emerge-outcomes-to-clingen-outcome-intervention-pairs
#15
Janet L Williams, Wendy K Chung, Alex Fedotov, Krzysztof Kiryluk, Chunhua Weng, John J Connolly, Margaret Harr, Hakon Hakonarson, Kathleen A Leppig, Eric B Larson, Gail P Jarvik, David L Veenstra, Christin Hoell, Maureen E Smith, Ingrid A Holm, Josh F Peterson, Marc S Williams
Genomic medicine is moving from research to the clinic. There is a lack of evidence about the impact of genomic medicine interventions on health outcomes. This is due in part to a lack of standardized outcome measures that can be used across different programs to evaluate the impact of interventions targeted to specific genetic conditions. The eMERGE Outcomes working group (OWG) developed measures to collect information on outcomes following the return of genomic results to participants for several genetic disorders...
July 13, 2018: Healthcare (Basel, Switzerland)
https://www.readbyqxmd.com/read/30011215/gender-differences-in-the-hepatotoxicity-and-toxicokinetics-of-emodin-the-potential-mechanisms-mediated-by-ugt2b7-and-mrp2
#16
Lili Wu, Weichao Han, Yulian Chen, Tao Zhang, Junjin Liu, Shilong Zhong, Han Liu, Congcong Han, Zhongyi Zhang, Shu-Wen Liu, Lan Tang
Emodin is a main anthraquinone compound which exists in Chinese traditional medicines including Polygonum multiflorum and Rhubarb. It is documented to have obvious liver and kidney toxicity. This study aims to (a) estimate gender differences of hepatotoxicity and toxicokinetics in rats after oral administration of emodin (60 and 150 mg/kg/d) for consecutive 28 days; (b) clarify relative mechanisms caused by glucuronidation and disposition. Hepatotoxicity was significantly higher in female rats than that in male rats as evidenced by histopathological and biochemical tests...
July 16, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/30009200/whole-exome-sequencing-in-20-197-persons-for-rare-variants-in-alzheimer-s-disease
#17
Neha S Raghavan, Adam M Brickman, Howard Andrews, Jennifer J Manly, Nicole Schupf, Rafael Lantigua, Charles J Wolock, Sitharthan Kamalakaran, Slave Petrovski, Giuseppe Tosto, Badri N Vardarajan, David B Goldstein, Richard Mayeux
Objective: The genetic bases of Alzheimer's disease remain uncertain. An international effort to fully articulate genetic risks and protective factors is underway with the hope of identifying potential therapeutic targets and preventive strategies. The goal here was to identify and characterize the frequency and impact of rare and ultra-rare variants in Alzheimer's disease, using whole-exome sequencing in 20,197 individuals. Methods: We used a gene-based collapsing analysis of loss-of-function ultra-rare variants in a case-control study design with data from the Washington Heights-Inwood Columbia Aging Project, the Alzheimer's Disease Sequencing Project and unrelated individuals from the Institute of Genomic Medicine at Columbia University...
July 2018: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/30008703/organic-peroxide-sensing-repressor-ohrr-regulates-organic-hydroperoxide-stress-resistance-and-avermectin-production-in-streptomyces-avermitilis
#18
Meng Sun, Mengya Lyu, Ying Wen, Yuan Song, Jilun Li, Zhi Chen
The bacterium Streptomyces avermitilis is an industrial-scale producer of avermectins, which are important anthelmintic agents widely used in agriculture, veterinary medicine, and human medicine. During the avermectin fermentation process, S. avermitilis is exposed to organic peroxides generated by aerobic respiration. We investigated the role of MarR-family transcriptional regulator OhrR in oxidative stress response and avermectin production in S. avermitilis . The S. avermitilis genome encodes two organic hydroperoxide resistance proteins: OhrB1 and OhrB2...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30006420/genomic-medicine-takes-the-stage-again
#19
Margaret Tempero
No abstract text is available yet for this article.
July 2018: Journal of the National Comprehensive Cancer Network: JNCCN
https://www.readbyqxmd.com/read/30005861/support-of-precision-medicine-through-risk-stratification-in-autoimmune-liver-diseases-histology-scoring-systems-and-non-invasive-markers
#20
REVIEW
Lars Bossen, Alessio Gerussi, Vasiliki Lygoura, George F Mells, Marco Carbone, Pietro Invernizzi
Autoimmune liver diseases (AILDs) are complex conditions, which arise from the interaction between a genetic susceptibility and unknown environmental triggers. They represent a relevant cause of liver failure and liver transplantation worldwide. As a testimony of our progress in understanding the biology of AILDs and the disease progression is the overall median survival which has increased over the last decade. However, there are still major challenges such as the lack of therapies and surveillance strategies in primary sclerosing cholangitis (PSC), the management and treatment of non-responders to first-line therapies in primary biliary cholangitis (PBC) and the need for tailoring immunosuppressive drugs in autoimmune hepatitis (AIH)...
July 10, 2018: Autoimmunity Reviews
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