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https://www.readbyqxmd.com/read/27936512/genome-editing-of-the-disease-susceptibility-gene-cslob1-in-citrus-confers-resistance-to-citrus-canker
#1
Hongge Jia, Yunzen Zhang, Vladimir Orbovic, Jin Xu, Frank White, Jeffrey Jones, Nian Wang
Citrus is a highly valued tree crop worldwide, while, at the same time, citrus production faces many biotic challenges, including bacterial canker and Huanglongbing (HLB). Breeding for disease resistant varieties is the most efficient and sustainable approach to control plant diseases. Traditional breeding of citrus varieties is challenging due to multiple limitations, including polyploidy, polyembryony, extended juvenility, and long crossing cycles. Targeted genome editing technology has the potential to shorten varietal development for some traits, including disease resistance...
December 9, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27936040/a-high-throughput-strategy-for-dissecting-mammalian-genetic-interactions
#2
Victoria B Stockman, Lila Ghamsari, Gorka Lasso, Barry Honig, Sagi D Shapira, Harris H Wang
Comprehensive delineation of complex cellular networks requires high-throughput interrogation of genetic interactions. To address this challenge, we describe the development of a multiplex combinatorial strategy to assess pairwise genetic interactions using CRISPR-Cas9 genome editing and next-generation sequencing. We characterize the performance of combinatorial genome editing and analysis using different promoter and gRNA designs and identified regions of the chimeric RNA that are compatible with next-generation sequencing preparation and quantification...
2016: PloS One
https://www.readbyqxmd.com/read/27935861/microrna-203-predicts-human-survival-after-resection-of-colorectal-liver-metastasis
#3
T Peter Kingham, Hoang C B Nguyen, Jian Zheng, Ioannis T Konstantinidis, Eran Sadot, Jinru Shia, Deborah Kuk, Steven Zhang, Leonard Saltz, Michael I D'Angelica, William R Jarnagin, Hani Goodarzi, Sohail F Tavazoie
BACKGROUND: Resection of colorectal liver metastasis (CRLM) can be curative. Predicting which patients may benefit from resection, however, remains challenging. Some microRNAs (miRNAs) become deregulated in cancers and contribute to cancer progression. We hypothesized that miRNA expression can serve as a prognostic marker of survival after CRLM resection. RESULTS: MiR-203 was significantly overexpressed in tumors of short-term survivors compared to long-term survivors...
December 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27934936/polymer-translocation-through-nano-pores-in-vibrating-thin-membranes
#4
Timothée Menais, Stefano Mossa, Arnaud Buhot
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer can accommodate several bases at the same time, making difficult accurate sequencing applications. More recently, the use of graphene membranes has paved the way to new sequencing capabilities, with the possibility to measure transverse currents, among other advances. The reduced thickness of these new membranes poses new questions on the effect of deformability and vibrations of the membrane on the translocation process, two features which are not taken into account in the well established theoretical frameworks...
December 9, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27934878/activating-cysteinyl-leukotriene-receptor-2-cysltr2-mutations-in-blue-nevi
#5
Inga Möller, Rajmohan Murali, Hansgeorg Müller, Thomas Wiesner, Louise A Jackett, Simone L Scholz, Ioana Cosgarea, Johannes Ap van de Nes, Antje Sucker, Uwe Hillen, Bastian Schilling, Annette Paschen, Heinz Kutzner, Arno Rütten, Martin Böckers, Richard A Scolyer, Dirk Schadendorf, Klaus G Griewank
Blue nevi are common melanocytic tumors arising in the dermal layer of the skin. Similar to uveal melanomas, blue nevi frequently harbor GNAQ and GNA11 mutations. Recently, recurrent CYSLTR2 and PLCB4 mutations were identified in uveal melanomas not harboring GNAQ or GNA11 mutations. All four genes (GNAQ, GNA11, CYSLTR2, and PLCB4) code for proteins involved in the same signaling pathway, which is activated by mutations in these genes. Given the related functional consequences of these mutations and the known genetic similarities between uveal melanoma and blue nevi, we analyzed a cohort of blue nevi to investigate whether CYSLTR2 and PLCB4 mutations occur in tumors lacking GNAQ or GNA11 mutations (as in uveal melanoma)...
December 9, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27933661/mutations-in-the-neb-gene-cause-fetal-akinesia-arthrogryposis-multiplex-congenita
#6
Michal Feingold-Zadok, David Chitayat, Karen Chong, Marie Injeyan, Patrick Shannon, Daphne Chapmann, Ron Maymon, Nir Pillar, Orit Reish
OBJECTIVE: We studied a series of patients with fetal akinesia deformation sequence (FADS)/arthrogryposis multiplex congenita (AMC), with nemaline bodies on muscle specimens, that revealed mutations in the NEB gene. METHOD: We pathologically assessed seven cases from three families, who presented with AMC/FADS. Targeted genetic analysis for Ashkenazi Jewish (AJ) mutation (in relevant patients) was followed by next generation sequencing and Multiplex Ligation-dependent Probe Amplification...
December 9, 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27933528/rna-seq-in-the-collaborative-cross
#7
Richard Green, Courtney Wilkins, Martin T Ferris, Michael Gale
The Collaborative Cross (CC) is a large panel of inbred mouse strains currently being developed for multiple areas of research. Scientists are taking integrated omics-style approaches to collecting data in order to obtain a deeper understanding of the biological mechanisms underlying a number of diverse disease phenotypes. As the cost of the next generation sequencing (NGS) decreases, RNA-sequencing (RNA-seq) has become the favored approach to transcriptomic analyses versus microarrays due to increases in sensitivity and resolution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933214/integrating-next-generation-sequencing-into-clinical-oncology-strategies-promises-and-pitfalls
#8
REVIEW
Peter Horak, Stefan Fröhling, Hanno Glimm
We live in an era of genomic medicine. The past five years brought about many significant achievements in the field of cancer genetics, driven by rapidly evolving technologies and plummeting costs of next-generation sequencing (NGS). The official completion of the Cancer Genome Project in 2014 led many to envision the clinical implementation of cancer genomic data as the next logical step in cancer therapy. Stemming from this vision, the term 'precision oncology' was coined to illustrate the novelty of this individualised approach...
2016: ESMO Open
https://www.readbyqxmd.com/read/27933154/improving-diagnosis-for-congenital-cataract-by-introducing-ngs-genetic-testing
#9
Mohammud Musleh, Jane Ashworth, Graeme Black, Georgina Hall
Childhood cataract (CC) has an incidence of 3.5 per 10,000 by age 15 years. Diagnosis of any underlying cause is important to ensure effective and prompt management of multisystem complications, to facilitate accurate genetic counselling and to streamline multidisciplinary care. Next generation sequencing (NGS) has been shown to be effective in providing an underlying diagnosis in 70% of patients with CC in a research setting. This project aimed to integrate NGS testing in CC within six months of presentation and increase the rate of diagnosis...
2016: BMJ Quality Improvement Reports
https://www.readbyqxmd.com/read/27933111/aberrant-dna-hypermethylation-silenced-sox21-as1-gene-expression-and-its-clinical-importance-in-oral-cancer
#10
Cheng-Mei Yang, Tsung-Han Wang, Hung-Chih Chen, Sung-Chou Li, Ming-Chien Lee, Huei-Han Liou, Pei-Feng Liu, Yu-Kai Tseng, Yow-Ling Shiue, Luo-Ping Ger, Kuo-Wang Tsai
BACKGROUND: Long noncoding RNAs (lncRNAs) are more than 200 nucleotides in length and lack transcriptional ability. The biological function of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. The aim of this study was to identify the dysfunction of lncRNA in OSCC. RESULTS: We analyzed the transcriptome profiles of human OSCC tissues and paired adjacent normal tissues from two patients through a next-generation sequencing approach. A total of 14 lncRNAs were upregulated (fold change ≥3) and 13 were downregulated (fold change ≤-3) in OSCC tissues compared with the adjacent normal tissues...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27932991/cannabidiol-modulates-the-immunophenotype-and-inhibits-the-activation-of-the-inflammasome-in-human-gingival-mesenchymal-stem-cells
#11
Rosaliana Libro, Domenico Scionti, Francesca Diomede, Marco Marchisio, Gianpaolo Grassi, Federica Pollastro, Adriano Piattelli, Placido Bramanti, Emanuela Mazzon, Oriana Trubiani
Human Gingival Mesenchymal Stem Cells (hGMSCs) are multipotential cells that can expand and differentiate in culture under specific and standardized conditions. In the present study, we have investigated whether in vitro pre-treatment of hGMSCs with Cannabidiol (CBD) can influence their expression profile, improving the therapeutic potential of this cell culture. Following CBD treatment (5 μM) for 24 h, gene expression analysis through Next Generation Sequencing (NGS) has revealed several genes differentially expressed between CBD-treated hGMSCs (CBD-hGMSCs) and control cells (CTR-hGMSCs) that were linked to inflammation and apoptosis...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27932415/targeted-next-generation-sequencing-for-diagnostics-and-forensics
#12
Timothy D Minogue, Jeffery W Koehler, David A Norwood
No abstract text is available yet for this article.
December 8, 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27932211/a-novel-class-of-somatic-mutations-in-blood-detected-preferentially-in-cd8-cells
#13
Miko Valori, Lilja Jansson, Anna Kiviharju, Pekka Ellonen, Hanna Rajala, Shady Adnan Awad, Satu Mustjoki, Pentti J Tienari
Somatic mutations have a central role in cancer but their role in other diseases such as autoimmune disorders is poorly understood. Earlier work has provided indirect evidence of rare somatic mutations in autoreactive T-lymphocytes in multiple sclerosis (MS) patients but such mutations have not been identified thus far. We analysed somatic mutations in blood in 16 patients with relapsing MS and 4 with other neurological autoimmune disease. To facilitate the detection of somatic mutations CD4+, CD8+, CD19+ and CD4-/CD8-/CD19- cell subpopulations were separated...
December 5, 2016: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/27931838/routine-use-of-gene-panel-testing-in-hereditary-breast-cancer-should-be-performed-with-caution
#14
REVIEW
Cedric van Marcke, Anne De Leener, Martine Berlière, Miikka Vikkula, Francois P Duhoux
Breast cancer is the most frequent cancer occurring in women. Ten percent of these cancers are considered hereditary. Among them, 30% are attributed to germline mutations in the tumor suppressor genes BRCA1 and BRCA2. Other genes of lower penetrance are also known, explaining together up to 40% of the hereditary risk of breast cancer. New techniques, such as next-generation sequencing, allow the simultaneous analysis of multiple genes in a cost-effective way. As a logical consequence, gene panel testing is entering clinical practice with the promise of personalized care...
December 2016: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/27931678/diagnosing-tuberculosis-in-the-21st-century-dawn-of-a-genomics-revolution
#15
REVIEW
Christopher Jeanes, Justin O'Grady
Tuberculosis (TB) ranks alongside HIV as the leading cause of death worldwide, killing 1.5million people in 2014. Traditional laboratory techniques do not provide sufficiently rapid results to inform clinicians on appropriate treatment, especially in the face of increasingly prevalent drug-resistant TB. Rapid molecular methods such as PCR and LAMP are vital tools in the fight against TB, however, rapid advances in next generation sequencing (NGS) technology are allowing increasingly rapid and accurate sequencing of entire bacterial genomes at ever decreasing cost, providing unprecedented depth of information...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27931010/impact-and-influence-of-omics-technology-on-hyper-tension-studies
#16
REVIEW
Alzenira Costa, Octavio Luiz Franco
BACKGROUND: Hypertension is an important risk factor for cardiovascular diseases. Pathophysiology and molecular mechanisms involved in hypertension regulation are not very well known. Recently, high-throughput Next-Generation Sequencing (NGS) technology has identified hundreds of gene loci associated with multiple cardiovascular pathologies, including blood pressure (BP), generating new expectations in hypertension studies, revealing new pathways and genetic mechanisms underlying BP regulation...
November 23, 2016: International Journal of Cardiology
https://www.readbyqxmd.com/read/27930701/natural-and-undetermined-sudden-death-value-of-post-mortem-genetic-investigation
#17
Olallo Sanchez, Oscar Campuzano, Anna Fernández-Falgueras, Georgia Sarquella-Brugada, Sergi Cesar, Irene Mademont, Jesus Mates, Alexandra Pérez-Serra, Monica Coll, Ferran Pico, Anna Iglesias, Coloma Tirón, Catarina Allegue, Esther Carro, María Ángeles Gallego, Carles Ferrer-Costa, Anna Hospital, Narcís Bardalet, Juan Carlos Borondo, Albert Vingut, Elena Arbelo, Josep Brugada, Josep Castellà, Jordi Medallo, Ramon Brugada
BACKGROUND: Sudden unexplained death may be the first manifestation of an unknown inherited cardiac disease. Current genetic technologies may enable the unraveling of an etiology and the identification of relatives at risk. The aim of our study was to define the etiology of natural deaths, younger than 50 years of age, and to investigate whether genetic defects associated with cardiac diseases could provide a potential etiology for the unexplained cases. METHODS AND FINDINGS: Our cohort included a total of 789 consecutive cases (77...
2016: PloS One
https://www.readbyqxmd.com/read/27930689/determination-of-a-screening-metric-for-high-diversity-dna-libraries
#18
Nicholas J Guido, Steven Handerson, Elaine M Joseph, Devin Leake, Li A Kung
The fields of antibody engineering, enzyme optimization and pathway construction rely increasingly on screening complex variant DNA libraries. These highly diverse libraries allow researchers to sample a maximized sequence space; and therefore, more rapidly identify proteins with significantly improved activity. The current state of the art in synthetic biology allows for libraries with billions of variants, pushing the limits of researchers' ability to qualify libraries for screening by measuring the traditional quality metrics of fidelity and diversity of variants...
2016: PloS One
https://www.readbyqxmd.com/read/27929733/antibody-repertoire-profiling-with-mimotope-arrays
#19
Shina Pashova, Christoph Schneider, Stephan von Gunten, Anastas Pashov
Large-scale profiling and monitoring of antibody repertoires is possible through next generation sequencing (NGS), phage display libraries and microarrays. These methods can be combined in a pipeline, which ultimately maps the antibody reactivities onto defined arrays of structures - peptides or carbohydrates. The arrays can help analyze the individual specificities or can be used as complex patterns. In any case, the targets recognized should formally be considered mimotopes unless they are proven to be epitopes driving the antibody synthesis...
December 8, 2016: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/27929054/in-silico-identification-of-snp-diversity-in-cultivated-and-wild-tomato-species-insight-from-molecular-simulations
#20
Archana Bhardwaj, Yogeshwar Vikram Dhar, Mehar Hasan Asif, Sumit K Bag
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases...
December 8, 2016: Scientific Reports
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