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Genomics Medicine

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https://www.readbyqxmd.com/read/28346484/a-neighborhood-wide-association-study-nwas-example-of-prostate-cancer-aggressiveness
#1
Shannon M Lynch, Nandita Mitra, Michelle Ross, Craig Newcomb, Karl Dailey, Tara Jackson, Charnita M Zeigler-Johnson, Harold Riethman, Charles C Branas, Timothy R Rebbeck
PURPOSE: Cancer results from complex interactions of multiple variables at the biologic, individual, and social levels. Compared to other levels, social effects that occur geospatially in neighborhoods are not as well-studied, and empiric methods to assess these effects are limited. We propose a novel Neighborhood-Wide Association Study(NWAS), analogous to genome-wide association studies(GWAS), that utilizes high-dimensional computing approaches from biology to comprehensively and empirically identify neighborhood factors associated with disease...
2017: PloS One
https://www.readbyqxmd.com/read/28345861/identification-of-gene-transcription-start-sites-and-enhancers-responding-to-pulmonary-carbon-nanotube-exposure-in-vivo
#2
Jette Bornholdt, Anne Thoustrup Saber, Berit Lilje, Mette Boyd, Mette Jørgensen, Yun Chen, Morana Vitezic, Nicklas Raun Jacobsen, Sarah Søs Poulsen, Trine Berthing, Simon Bressendorff, Kristoffer Vitting-Seerup, Robin Andersson, Karin Sørig Hougaard, Carole L Yauk, Sabina Halappanavar, Håkan Wallin, Ulla Vogel, Albin Sandelin
Increased use of nanomaterials in industry, medicine and consumer products has raised concerns over their toxicity. To ensure safe use of nanomaterials, understanding their biological effects at the molecular level is crucial. In particular, the regulatory mechanisms responsible for the cascade of genes activated by nanomaterial exposure are not well characterized. To this end, we profiled the genome-wide usage of gene transcription start sites and linked active enhancer regions in lungs of C57BL/6 mice 24h after intratracheal instillation of a single dose of the multiwalled carbon nanotube Mitsui-7...
March 27, 2017: ACS Nano
https://www.readbyqxmd.com/read/28345409/osteoarthritis-in-football
#3
Gian M Salzmann, Stefan Preiss, Marcy Zenobi-Wong, Laurent P Harder, Dirk Maier, Jirí Dvorák
Football is currently the most popular sporting activity in the world. Multiple reports have shown that a high incidence of osteoarthritis is found in football players. Evidence clearly shows that traumatic injury significantly predisposes players for such pathophysiology. Injuries are frequent in amateur as well as professional football players, with knee and ankle accounting for the most severe injuries. Many professional athletes lose playing time due to injuries and many are forced into early retirement...
April 2017: Cartilage
https://www.readbyqxmd.com/read/28345383/pulmonary-fibrosis-part-i-epidemiology-pathogenesis-and-diagnosis
#4
Keith C Meyer
Many forms of interstitial lung disease (ILD) can progress to extensive fibrosis and respiratory failure. Idiopathic pulmonary fibrosis (IPF), which generally has a poor prognosis, has been thoroughly studied over the past two decades, and many important discoveries have been made that pertain to genetic predisposition, epidemiology, disease pathogenesis, diagnosis, and management. Additionally, non-IPF forms of ILD can have radiologic and histopathologic manifestations that mimic IPF, and making an accurate diagnosis is key to providing personalized medicine to patients with pulmonary fibrosis...
March 26, 2017: Expert Review of Respiratory Medicine
https://www.readbyqxmd.com/read/28345240/prenatal-dna-sequencing-clinical-counseling-and-diagnostic-laboratory-considerations
#5
Ahmad N Abou Tayoun, Nancy B Spinner, Heidi L Rehm, Robert C Green, Diana W Bianchi
Clinical diagnostic laboratories are producing next generation sequencing (NGS)-based test results that are becoming increasingly incorporated into patient care. Whole genome and exome sequencing on fetal material derived from amniocytes, chorionic villi, or products of conception is starting to be offered clinically in specialized centers, but it has not yet become routine practice. The technical, interpretation and ethical challenges are greatest in the area of prenatal medicine because the fetus has a limited health history and the physical examination is only indirectly available via prenatal sonography...
March 27, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28344933/precision-medicine-the-golden-gate-for-detection-treatment-and-prevention-of-alzheimer-s-disease
#6
H Hampel, S E O'Bryant, J I Castrillo, C Ritchie, K Rojkova, K Broich, N Benda, R Nisticò, R A Frank, B Dubois, V Escott-Price, S Lista
During this decade, breakthrough conceptual shifts have commenced to emerge in the field of Alzheimer's disease (AD) recognizing risk factors and the non-linear dynamic continuum of complex pathophysiologies amongst a wide dimensional spectrum of multi-factorial brain proteinopathies/neurodegenerative diseases. As is the case in most fields of medicine, substantial advancements in detecting, treating and preventing AD will likely evolve from the generation and implementation of a systematic precision medicine strategy...
December 2016: Journal of Prevention of Alzheimer's Disease
https://www.readbyqxmd.com/read/28344774/the-dockstore-enabling-modular-community-focused-sharing-of-docker-based-genomics-tools-and-workflows
#7
Brian D O'Connor, Denis Yuen, Vincent Chung, Andrew G Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing...
2017: F1000Research
https://www.readbyqxmd.com/read/28343740/pediatric-oncology-enters-an-era-of-precision-medicine
#8
Nita L Seibel, Katherine Janeway, Carl E Allen, Susan N Chi, Yoon-Jae Cho, Julia L Glade Bender, AeRang Kim, Theodore W Laetsch, Meredith S Irwin, Naoko Takebe, James V Tricoli, Donald Williams Parsons
With the use of high-throughput molecular profiling technologies, precision medicine trials are ongoing for adults with cancer. Similarly, there is an interest in how these techniques can be applied to tumors in children and adolescents to expand our understanding of the biology of pediatric cancers and evaluate the clinical implications of genomic testing for these patients. This article reviews the early studies in pediatric oncology showing the feasibility of this approach, describe the future plans to evaluate the clinical implications in a multicenter clinical trial and identify the challenges of applying genomics in this patient population...
February 1, 2017: Current Problems in Cancer
https://www.readbyqxmd.com/read/28342679/pharmacogenomic-aspects-of-bipolar-disorder-an-update
#9
M Budde, D Degner, J Brockmöller, T G Schulze
The hopes for readily implementable precision medicine are high. For many complex disorders, such as bipolar disorder, these hopes critically hinge on tangible successes in pharmacogenetics of treatment response or susceptibility to adverse events. In this article, we review the current state of pharmacogenomics of bipolar disorder including latest results from candidate genes and genome-wide association studies. The majority of studies focus on response to lithium treatment. Although a host of genes has been studied, hardly any replicated findings have emerged so far...
March 22, 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28341884/mitochondrial-genome-of-the-nematode-endoparasitic-fungus-hirsutella-vermicola-reveals-a-high-level-of-synteny-in-the-family-ophiocordycipitaceae
#10
Yong-Jie Zhang, Hong-Yue Zhang, Xing-Zhong Liu, Shu Zhang
Ophiocordycipitaceae is a diverse fungal family comprising multiple ecologically, economically, medicinally, and culturally important fungal species; however, only four species of the family have available mitochondrial genomes (mitogenomes). In this study, the complete mitogenome of the nematode endoparasitic fungus Hirsutella vermicola in Ophiocordycipitaceae was sequenced, and a comparative mitogenomic analysis of Ophiocordycipitaceae was performed. We found that the 53,793-bp circular mitogenome of H. vermicola, except for standard fungal mitochondrial genes, harbors seven introns acquired possibly through lateral transfer from other fungi and three free-standing open reading frames (ORFs) coding for hypothetical proteins...
March 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28341836/fam46c-is-critical-for-the-anti-proliferation-and-pro-apoptotic-effects-of-norcantharidin-in-hepatocellular-carcinoma-cells
#11
Qiao-Yan Zhang, Xiao-Qiang Yue, Yi-Ping Jiang, Ting Han, Hai-Liang Xin
Norcantharidin (NCTD), a demethylated analog of cantharidin derived from Chinese traditional medicine blister beetle, has been currently used as an anticancer drug for various cancers including hepatocellular carcinoma (HCC). In this study, for a more comprehensive understanding of the targets of NCTD in HCC, next-generation RNA-Seq was utilized. We revealed that the expression of FAM46C, which has been reported as a tumor suppressor for multiple myeloma, was enhanced after NCTD treatment. Re-analysis of TCGA (The Cancer Genome Atlas) LIHC (liver hepatocellular carcinoma) dataset demonstrated that FAM46C expression was significantly lower in HCC tissues than in normal liver tissues...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28339459/functional-classification-of-dna-variants-by-hybrid-minigenes-identification-of-30-spliceogenic-variants-of-brca2-exons-17-and-18
#12
Eugenia Fraile-Bethencourt, Beatriz Díez-Gómez, Valeria Velásquez-Zapata, Alberto Acedo, David J Sanz, Eladio A Velasco
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction of variants of uncertain clinical significance (VUS) whose functional and clinical interpretations pose a challenge for genomic medicine. Likewise, an increasing amount of evidence indicates that genetic variants can have deleterious effects on pre-mRNA splicing. Our goal was to investigate the impact on splicing of a set of reported variants of BRCA2 exons 17 and 18 to assess their role in hereditary breast cancer and to identify critical regulatory elements that may constitute hotspots for spliceogenic variants...
March 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28338645/development-of-44-novel-polymorphic-ssr-markers-for-determination-of-shiitake-mushroom-lentinula-edodes-cultivars
#13
Hwa-Yong Lee, Suyun Moon, Donghwan Shim, Chang Pyo Hong, Yi Lee, Chang-Duck Koo, Jong-Wook Chung, Hojin Ryu
The shiitake mushroom (Lentinulaedodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms...
March 24, 2017: Genes
https://www.readbyqxmd.com/read/28337931/utilizing-nutritional-genomics-to-tailor-diets-for-the-prevention-of-cardiovascular-disease-a-guide-for-upcoming-studies-and-implementations
#14
Dolores Corella, Oscar Coltell, George Mattingley, José V Sorlí, Jose M Ordovas
Personalized diets based on an individual's genome to optimize the success of dietary intervention and reduce genetic cardiovascular disease (CVD) risk, is one of the challenges most frequently discussed in the scientific community. Areas covered: The authors gathered literature-based evidence on nutritional genomics and CVD phenotypes, our own results and research experience to provide a critical overview of the current situation of using nutritional genomics to tailor diets for CVD prevention and to propose guidelines for future studies and implementations...
March 24, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28337071/international-standards-for-genomes-transcriptomes-and-metagenomes
#15
Christopher E Mason, Ebrahim Afshinnekoo, Scott Tighe, Shixiu Wu, Shawn Levy
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous...
March 17, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28334937/dynamically-and-epigenetically-coordinated-gata-ets-sox-transcription-factor-expression-is-indispensable-for-endothelial-cell-differentiation
#16
Yasuharu Kanki, Ryo Nakaki, Teppei Shimamura, Taichi Matsunaga, Kohei Yamamizu, Shiori Katayama, Jun-Ichi Suehiro, Tsuyoshi Osawa, Hiroyuki Aburatani, Tatsuhiko Kodama, Youichiro Wada, Jun K Yamashita, Takashi Minami
Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analysed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334334/p53-and-its-mutants-on-the-slippery-road-from-stemness-to-carcinogenesis
#17
Alina Molchadsky, Varda Rotter
Normal development, tissue homeostasis and regeneration following injury rely on the proper functions of wide repertoire of stem cells (SCs) persisting during embryonic period and throughout the adult life. Therefore, SCs employ robust mechanisms to preserve their genomic integrity and avoid heritage of mutations to their daughter cells. Importantly, propagation of SCs with faulty DNA as well as dedifferentiation of genomically altered somatic cells may result in derivation of cancer SCs, which are considered to be the driving force of the tumorigenic process...
March 15, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28334237/dna-compass-a-secure-client-side-site-for-navigating-personal-genetic-information
#18
Charles Curnin, Assaf Gordon, Yaniv Erlich
Motivation: Millions of individuals have access to raw genomic data using direct-to-consumer companies. The advent of large-scale sequencing projects, such as the Precision Medicine Initiative, will further increase the number of individuals with access to their own genomic information. However, querying genomic data requires a computer terminal and computational skill to analyze the data - an impediment for the general public. Results: DNA Compass is a website designed to empower the public by enabling simple navigation of personal genomic data...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334154/ethical-issues-of-crispr-technology-and-gene-editing-through-the-lens-of-solidarity
#19
John J Mulvihill, Benjamin Capps, Yann Joly, Tamra Lysaght, Hub A E Zwart, Ruth Chadwick
Background: The avalanche of commentaries on CRISPR-Cas9 technology, a bacterial immune system modified to recognize any short DNA sequence, cut it out, and insert a new one, has rekindled hopes for gene therapy and other applications and raised criticisms of engineering genes in future generations. Sources of data: This discussion draws on articles that emphasize ethics, identified partly through PubMed and Google, 2014-2016. Areas of agreement: CRISPR-Cas9 has taken the pace and prospects for genetic discovery and applications to a high level, stoking anticipation for somatic gene engineering to help patients...
February 23, 2017: British Medical Bulletin
https://www.readbyqxmd.com/read/28331464/when-should-genetic-testing-be-performed-in-epilepsy-patients
#20
Annapurna Poduri
This review is a summary of a talk presented at the 2015 American Epilepsy Society Annual Meeting. Its purposes are 1) to review developments in epilepsy genetics, 2) to discuss which groups of patients with epilepsy might benefit from genetic testing, and 3) to present a rational approach to genetic testing in epilepsy in the rapidly evolving era of genomic medicine.
January 2017: Epilepsy Currents
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