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https://www.readbyqxmd.com/read/28738203/early-detection-monitoring-for-aquatic-non-indigenous-species-optimizing-surveillance-incorporating-advanced-technologies-and%C3%A2-identifying-research-needs
#1
REVIEW
Anett S Trebitz, Joel C Hoffman, John A Darling, Erik M Pilgrim, John R Kelly, Emily A Brown, W Lindsay Chadderton, Scott P Egan, Erin K Grey, Syed A Hashsham, Katy E Klymus, Andrew R Mahon, Jeffrey L Ram, Martin T Schultz, Carol A Stepien, James C Schardt
Following decades of ecologic and economic impacts from a growing list of nonindigenous and invasive species, government and management entities are committing to systematic early- detection monitoring (EDM). This has reinvigorated investment in the science underpinning such monitoring, as well as the need to convey that science in practical terms to those tasked with EDM implementation. Using the context of nonindigenous species in the North American Great Lakes, this article summarizes the current scientific tools and knowledge - including limitations, research needs, and likely future developments - relevant to various aspects of planning and conducting comprehensive EDM...
July 21, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28737972/identifying-health-information-technology-needs-of-oncologists-to-facilitate-the-adoption-of-genomic-medicine-recommendations-from-the-2016-american-society-of-clinical-oncology-omics-and-precision-oncology-workshop
#2
Kevin S Hughes, Edward P Ambinder, Gregory P Hess, Peter Paul Yu, Elmer V Bernstam, Mark J Routbort, Jean Rene Clemenceau, John T Hamm, Phillip G Febbo, Susan M Domchek, James L Chen, Jeremy L Warner
At the ASCO Data Standards and Interoperability Summit held in May 2016, it was unanimously decided that four areas of current oncology clinical practice have serious, unmet health information technology needs. The following areas of need were identified: 1) omics and precision oncology, 2) advancing interoperability, 3) patient engagement, and 4) value-based oncology. To begin to address these issues, ASCO convened two complementary workshops: the Omics and Precision Oncology Workshop in October 2016 and the Advancing Interoperability Workshop in December 2016...
July 24, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28736634/gastrointestinal-stromal-tumors-gists-point-mutations-matter-in-management-a-review
#3
REVIEW
Peter J Oppelt, Angela C Hirbe, Brian A Van Tine
The therapeutic implications of the genomic alterations seen within the drivers of gastrointestinal stromal tumors (GIST) are among the best understood in all of solid tumors. Sequencing of cKIT and PDGFRα should be considered standard practice for the treatment of GIST patients. In this article, we will review the common mutations and how they are utilized in clinical management. In addition, we will review the rare D842V PDGFRα mutation and the diverse molecular group that lacks a mutation in either cKIT or PDGFRα (wild-type GIST) which are best treated on clinical trial...
June 2017: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28736571/evaluation-of-quality-assessment-protocols-for-high-throughput-genome-resequencing-data
#4
REVIEW
Matteo Chiara, Giulio Pavesi
Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human "variome," through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28735962/enhancement-of-antiviral-capacity-of-transgenic-silkworms-against-cytoplasmic-polyhedrosis-virus-via-knockdown-of-multiple-viral-genes
#5
Liang Jiang, Zhengwen Peng, Huizhen Guo, Jingchen Sun, Qiang Sun, Fei Xia, Chunlin Huang, Guowen Xu, Qingyou Xia
Bombyx mori cytoplasmic polyhedrosis virus (BmCPV), a major pathogen of silkworms, causes serious economic losses in sericulture. The BmCPV genome contains 10 discrete dsRNA segments; among these, S1, S2, S3, S4, S6, and S7 encode virus structural proteins, whereas S5, S8, S9, and S10 encode nonstructural proteins. In an attempt to create an anti-BmCPV silkworm strain, we constructed transgenic RNAi vector pb-CNS for knockdown of S5, S8, S9, and S10, and pb-SNS targeting S1, S2, S4, S5, and S8. Transgenic silkworm line CNS and SNS were generated via microinjection of the practical diapause silkworm strain Furong...
July 20, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28735374/changes-in-global-transcriptional-profiling-of-women-following-obesity-surgery-bypass
#6
Marcela Augusta de Souza Pinhel, Natalia Yumi Noronha, Carolina Ferreira Nicoletti, Bruno Affonso Parente de Oliveira, Cristiana Cortes-Oliveira, Vitor Caressato Pinhanelli, Wilson Salgado Junior, Ana Julia Machry, Wilson Araújo da Silva Junior, Dorotéia Rossi Silva Souza, Júlio Sérgio Marchini, Carla Barbosa Nonino
BACKGROUND: Differential gene expression in peripheral blood mononuclear cells (PBMCs) after Roux-en-Y gastric bypass (RYGB) is poorly characterized. Markers of these processes may provide a deeper understanding of the mechanisms that underlie these events. The main goal of this study was to identify changes in PBMC gene expression in women with obesity before and 6 months after RYGB-induced weight loss. METHODS: The ribonucleic acid (RNA) of PBMCs from 13 obese women was analyzed before and 6 months after RYGB; the RNA of PBMCs from nine healthy women served as control...
July 22, 2017: Obesity Surgery
https://www.readbyqxmd.com/read/28735109/design-and-rationale-for-a-real-world-observational-cohort-of-patients-with-nonalcoholic-fatty-liver-disease-the-target-nash-study
#7
A Sidney Barritt, Norman Gitlin, Samuel Klein, Anna S Lok, Rohit Loomba, Laura Malahias, Margaret Powell, Miriam B Vos, L Michael Weiss, Kenneth Cusi, Brent A Neuschwander-Tetri, Arun Sanyal
Nonalcoholic fatty liver disease (NAFLD) is highly prevalent and can lead to cirrhosis, hepatocellular carcinoma, and end-stage liver disease. NAFLD comprises the spectrum from simple steatosis (nonalcoholic fatty liver, NAFL), to steatosis with inflammation (nonalcoholic steatohepatitis, NASH). Current primary therapy recommended for NAFLD is weight loss induced by lifestyle modification. The difficulty in achieving this has led to robust pharmacological therapy development. While new drugs may show efficacy in selected phase II/III clinical trial populations, their real-world effectiveness is unknown...
July 19, 2017: Contemporary Clinical Trials
https://www.readbyqxmd.com/read/28734895/a-sensitive-and-convenient-method-for-clinical-detection-of-non-syndromic-hearing-loss-associated-common-mutations
#8
Er-Feng Yuan, Wei Xia, Jing-Tao Huang, Ling Hu, Xing Liao, Xiang Dai, Song-Mei Liu
BACKGROUND: The majority of non-syndromic hearing loss (NSHL) patients result from causative mutations in GJB2, SLC26A4 and mitochondrial 12S rRNA genes. Accurate detection of these genetic mutations is increasingly recognized for its clinical significance to reduce incidence and guide individual treatment of NSHL. Current methods for clinical practice are labor intensive, expensive or of low sensitivity. METHODS: Genomic DNA from 7 newborns not passing the hearing screening and 94 newborns passing the hearing screening were analyzed for the common mutations using high resolution melting analysis (HRMA) and Sanger sequencing...
July 19, 2017: Gene
https://www.readbyqxmd.com/read/28733559/dynamics-of-egfr-mutations-in-plasma-recapitulates-the-clinical-response-to-egfr-tkis-in-nsclc-patients
#9
Liwen Xiong, Shaohua Cui, Jingyan Ding, Yun Sun, Longfu Zhang, Yizhuo Zhao, Aiqin Gu, Tianqing Chu, Huimin Wang, Hua Zhong, Xin Ye, Yi Gu, Xin Zhang, Min Hu, Liyan Jiang
OBJECTIVES: Genomic profiling using plasma cell-free DNA (cfDNA) represents a non-invasive alternative to tumor re-biopsy, which is challenging in clinical practice. The feasibility of dynamically monitoring epidermal growth factor receptor (EGFR) mutation status using serial plasma samples from non-small cell lung cancer (NSCLC) patients treated by tyrosine kinase inhibitors (TKIs) and its application in tracking clinical response and detection of resistance were investigated. PATIENTS AND METHODS: Forty-five NSCLC patients with EGFR mutation-positive pre-TKI plasma and at least two post-TKI plasma collections were recruited to this study...
July 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732598/high-throughput-imaging-for-the-discovery-of-cellular-mechanisms-of-disease
#10
REVIEW
Gianluca Pegoraro, Tom Misteli
High-throughput imaging (HTI) is a powerful tool in the discovery of cellular disease mechanisms. While traditional approaches to identify disease pathways often rely on knowledge of the causative genetic defect, HTI-based screens offer an unbiased discovery approach based on any morphological or functional defects of disease cells or tissues. In this review, we provide an overview of the use of HTI for the study of human disease mechanisms. We discuss key technical aspects of HTI and highlight representative examples of its practical applications for the discovery of molecular mechanisms of disease, focusing on infectious diseases and host-pathogen interactions, cancer, and rare genetic diseases...
July 18, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28732357/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#11
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
July 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28731043/gastroblastoma-harbors-a-recurrent-somatic-malat1-gli1-fusion-gene
#12
Rondell P Graham, Asha A Nair, Jaime I Davila, Long Jin, Jin Jen, William R Sukov, Tsung-Teh Wu, Henry D Appelman, Jorge Torres-Mora, Kyle D Perry, Lizhi Zhang, Sara M Kloft-Nelson, Ryan A Knudson, Patricia T Greipp, Andrew L Folpe
Gastroblastoma is a rare distinctive biphasic tumor of the stomach. The molecular biology of gastroblastoma has not been studied, and no affirmative diagnostic markers have been developed. We retrieved two gastroblastomas from the consultation practices of the authors and performed transcriptome sequencing on formalin-fixed paraffin-embedded tissue. Recurrent predicted fusion genes were validated at genomic and RNA levels. The presence of the fusion gene was confirmed on two additional paraffin-embedded cases of gastroblastoma...
July 21, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28729406/tumor-evolution-as-a-therapeutic-target
#13
REVIEW
Nabil Amirouchene-Angelozzi, Charles Swanton, Alberto Bardelli
Recent technological advances in the field of molecular diagnostics (including blood-based tumor genotyping) allow the measurement of clonal evolution in patients with cancer, thus adding a new dimension to precision medicine: time. The translation of this new knowledge into clinical benefit implies rethinking therapeutic strategies. In essence, it means considering as a target not only individual oncogenes but also the evolving nature of human tumors. Here, we analyze the limitations of targeted therapies and propose approaches for treatment within an evolutionary framework...
July 20, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28727969/fetal-dysmorphology-still-an-essential-art-analysis-of-the-limitations-of-microarray-in-a-fetal-population-and-a-look-toward-the-genome-sequencing-era
#14
E Fletcher, M Porteous, K J McKenzie, E J Maher, M J Evans
Cytogenomic microarray allows assessment of the genome at higher resolutions than traditional karyotyping. The objective of this study is to evaluate the utility of microarray in a routine fetal autopsy setting before the advent of routine fetal exome/genome sequencing and the issues these technologies may generate. A systematic review of fetal postmortems at 12-24 weeks gestation between January 2011 and December 2014 was undertaken. Cases where there was no consent for audit, research, or genetic testing were excluded as were cases referred to the Procurator Fiscal, stillbirths, and neonatal deaths...
July 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28727725/redgem-systematic-reduction-and-analysis-of-genome-scale-metabolic-reconstructions-for-development-of-consistent-core-metabolic-models
#15
Meric Ataman, Daniel F Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis
Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the complexity of these large metabolic networks often hinders their utility in various practical applications. Although reduced models are commonly used for modeling and in integrating experimental data, they are often inconsistent across different studies and laboratories due to different criteria and detail, which can compromise transferability of the findings and also integration of experimental data from different groups...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28726804/diagnostic-cytogenetic-testing-following-positive-noninvasive-prenatal-screening-results-a-clinical-laboratory-practice-resource-of-the-american-college-of-medical-genetics-and-genomics-acmg
#16
Athena M Cherry, Yassmine M Akkari, Kimberly M Barr, Hutton M Kearney, Nancy C Rose, Sarah T South, James H Tepperberg, Jeanne M Meck
Disclaimer: ACMG Clinical Laboratory Practice Resources are developed primarily as an educational tool for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these practice resources is voluntary and does not necessarily assure a successful medical outcome. This Clinical Laboratory Practice Resource should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results...
July 20, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28725948/genomics-and-epigenomics-in-rheumatic-diseases-what-do-they-provide-in-terms-of-diagnosis-and-disease-management
#17
Patricia Castro-Santos, Roberto Díaz-Peña
Most rheumatic diseases are complex or multifactorial entities with pathogeneses that interact with both multiple genetic factors and a high number of diverse environmental factors. Knowledge of the human genome sequence and its diversity among populations has provided a crucial step forward in our understanding of genetic diseases, identifying many genetic loci or genes associated with diverse phenotypes. In general, susceptibility to autoimmunity is associated with multiple risk factors, but the mechanism of the environmental component influence is poorly understood...
July 20, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/28725230/genetics-and-genomics-of-cotton-leaf-curl-disease-its-viral-causal-agents-and-whitefly-vector-a-way-forward-to-sustain-cotton-fiber-security
#18
REVIEW
Mehboob-Ur- Rahman, Ali Q Khan, Zainab Rahmat, Muhammad A Iqbal, Yusuf Zafar
Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28724393/methicillin-resistant-staphylococcus-aureus-emerged-long-before-the-introduction-of-methicillin-into-clinical-practice
#19
Catriona P Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D Bentley, Angela M Kearns, Matthew T G Holden
BACKGROUND: The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the emergence of resistant strains. Methicillin-resistant Staphylococcus aureus (MRSA) was first observed in 1960, less than one year after the introduction of this second generation beta-lactam antibiotic into clinical practice. Epidemiological evidence has always suggested that resistance arose around this period, when the mecA gene encoding methicillin resistance carried on an SCCmec element, was horizontally transferred to an intrinsically sensitive strain of S...
July 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28724061/multi-locus-mixed-model-analysis-of-stem-rust-resistance-in-winter-wheat
#20
Paul D Mihalyov, Virginia A Nichols, Peter Bulli, Matthew N Rouse, Michael O Pumphrey
Genome-wide association mapping is a powerful tool for dissecting the relationship between phenotypes and genetic variants in diverse populations. With the improved cost efficiency of high-throughput genotyping platforms, association mapping is a desirable method of mining populations for favorable alleles that hold value for crop improvement. Stem rust, caused by the fungus f. sp. is a devastating disease that threatens wheat ( L.) production worldwide. Here, we explored the genetic basis of stem rust resistance in a global collection of 1411 hexaploid winter wheat accessions genotyped with 5390 single nucleotide polymorphism markers...
July 2017: Plant Genome
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