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https://www.readbyqxmd.com/read/29029145/blood-meal-source-characterization-using-illumina-sequencing-in-the-chagas-disease-vector-rhodnius-pallescens-hemiptera-reduviidae-in-panam%C3%A3
#1
Troy J Kieran, Nicole L Gottdenker, Christina P Varian, Azael Saldaña, Nicolas Means, Darlisha Owens, Jose E Calzada, Travis C Glenn
Accurate blood meal identification is critical to understand hematophagous vector-host relationships. This study describes a customizable Next-Generation Sequencing (NGS) approach to identify blood meals from Rhodnius pallescens (Hemiptera: Reduviidae) triatomines using multiple barcoded primers and existing software to pick operational taxonomic units and match sequences for blood meal identification. We precisely identified all positive control samples using this method and further examined 74 wild-caught R...
October 4, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/29029115/whole-genome-next-generation-sequencing-to-study-within-host-evolution-of-chronic-norovirus-infection-among-immunocompromised-patients
#2
J van Beek, M de Graaf, S L Smits, C M E Schapendonk, G M G M Verjans, H Vennema, A A van der Eijk, M V T Phan, M L Cotten, M P G Koopmans
Background: The genus Norovirus comprises large genetic diversity and new GII.4 variants emerge every 2-3 years. It is unknown in which host these new variants originate. Here we study whether prolonged shedders within the immunocompromised population could be a reservoir for newly emerging strains. Methods: Faecal samples (n=65) from immunocompromised patients (n=16) were retrospectively selected. Isolated viral RNA was enriched by hybridization with a custom norovirus whole-genome RNA bait set and deep sequenced on the Illumina MiSeq platform...
September 27, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29028941/dysregulation-of-cortical-neuron-dna-methylation-profile-in-autism-spectrum-disorder
#3
Stefano Nardone, Dev Sharan Sams, Antonino Zito, Eli Reuveni, Evan Elliott
Autism Spectrum Disorder (ASD) is a complex neuropsychiatric syndrome whose etiology includes genetic and environmental components. Since epigenetic marks are sensitive to environmental insult, they may be involved in the development of ASD. Initial brain studies have suggested a dysregulation of epigenetic marks in ASD. However, due to cellular heterogeneity in the brain, these studies have not determined if there is a true change in the neuronal epigenetic signature. Here, we report a genome-wide methylation study on fluorescence-activated cell sorting-sorted neuronal nuclei from the frontal cortex of 16 male ASD and 15 male control subjects...
September 28, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/29028885/hotresdb-host-transcriptional-response-database-for-viral-hemorrhagic-fevers
#4
Jonathan Lo, Deric Zhang, Emily Speranza, Jose A Negron, John H Connor
Summary: High-throughput screening of the host transcriptional response to various viral infections provides a wealth of data but utilization of microarray and next generation sequencing (NGS) data for analysis can be difficult. The Host Transcriptional Response DataBase (HoTResDB), allows visitors to access already processed microarray and NGS data from non-human primate models of viral hemorrhagic fever to better understand the host transcriptional response. Availability: HoTResDB is freely available at http://hotresdb...
September 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028854/clinical-insights-and-emerging-strategies-in-managing-cutaneous-t-cell-lymphoma
#5
Christina C Patrone, Larisa J Geskin
<p>Mycosis Fungoides and Sézary Syndrome, the two most common types of Cutaneous T-Cell Lymphoma (CTCL), present many management challenges for dermatologists. Here, we provide a comprehensive review of up-to-date literature, guidelines, and expert clinical insights. We highlight the updates in the World Health Organization Classification of Cutaneous Lymphomas; we summarize the epidemiology, including a recently observed stabilization of increasing incidence of CTCL in the past decade and increased incidence in males, blacks, and veterans; we also provide the most recent updates on prognostic factors for CTCL...
May 1, 2017: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/29028646/advances-in-understanding-the-molecular-underpinnings-of-adrenocortical-tumors
#6
Norman G Nicolson, Jianling Man, Tobias Carling
PURPOSE OF REVIEW: Adrenocortical tumors are divided into benign adenomas and malignant carcinomas. The former is relatively common and carries a favorable prognosis, whereas the latter is rare and frequently presents at an advanced stage, with poor outcomes. Advances in next-generation sequencing, genome analysis, and bioinformatics have allowed for high-throughput molecular characterization of adrenal tumorigenesis. RECENT FINDINGS: Although recent genomic, epigenomic, and transcriptomic studies in large tumor cohorts have confirmed the central roles of aberrant Wnt/ß-catenin signaling, constitutive protein kinase A pathway activation, cell cycle dysregulation, and ion channelopathies in adrenal tumorigenesis, these studies also revealed novel signature events underlying malignant differentiation of adrenocortical carcinomas...
October 11, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29028645/an-update-on-the-status-of-molecular-testing-for-the-indeterminate-thyroid-nodule-and-risk-stratification-of-differentiated-thyroid-cancer
#7
Kristina J Nicholson, Linwah Yip
PURPOSE OF REVIEW: Correct identification of malignancy in cytologically indeterminate thyroid nodules is a diagnostic challenge, leading to potentially unnecessary surgery in patients for whom final histology is benign. Similarly, many patients with differentiated thyroid cancer (DTC) undergo aggressive surgical management of tumors, which may ultimately have low-risk histologic features. Use of molecular testing strategies can aid in both the diagnosis of indeterminate thyroid nodules and preoperative risk stratification of DTC...
October 11, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29028431/interferon-tau-regulates-cytokine-production-and-cellular-function-in-human-trophoblast-cell-line
#8
Nao Tanikawa, Kotomi Seno, Ryouka Kawahara-Miki, Koji Kimura, Shuichi Matsuyama, Hisataka Iwata, Takehito Kuwayama, Koumei Shirasuna
Type I interferons (IFN), including IFN-beta (IFNB), activate multiple STAT signaling to drive various biological responses. Another type I IFN, IFN-tau (IFNT), secreted by ruminant embryonic trophoblast cells, has multiple functions with low cytotoxicity. Here, we examined the effects of IFNT on human trophoblast cell functions. First, we performed next-generation sequencing and demonstrated that IFNT-dependent changes in the human Sw.71 trophoblast cell line are partly mediated by proinflammatory as well as IFN signaling...
October 2017: Journal of Interferon & Cytokine Research
https://www.readbyqxmd.com/read/29028368/a-window-into-clinical-next-generation-sequencing-based-oncology-testing-practices
#9
Rakesh Nagarajan, Angela N Bartley, Julia A Bridge, Lawrence J Jennings, Suzanne Kamel-Reid, Annette Kim, Alexander J Lazar, Neal I Lindeman, Joel Moncur, Alex J Rai, Mark J Routbort, Patricia Vasalos, Jason D Merker
CONTEXT: - Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. OBJECTIVE: - To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. DESIGN: - College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing...
October 13, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29027916/a-next-generation-sequencing-approach-uncovers-viral-transcripts-incorporated-in-poxvirus-virions
#10
Marica Grossegesse, Joerg Doellinger, Berit Haldemann, Lars Schaade, Andreas Nitsche
Transcripts are known to be incorporated in particles of DNA viruses belonging to the families of Herpesviridae and Mimiviridae, but the presence of transcripts in other DNA viruses, such as poxviruses, has not been analyzed yet. Therefore, we first established a next-generation-sequencing (NGS)-based protocol, enabling the unbiased identification of transcripts in virus particles. Subsequently, we applied our protocol to analyze RNA in an emerging zoonotic member of the Poxviridae family, namely Cowpox virus...
October 13, 2017: Viruses
https://www.readbyqxmd.com/read/29027628/the-prognostic-significance-of-measurable-minimal-residual-disease-in-acute-myeloid-leukemia
#11
REVIEW
Francesco Buccisano, Christopher S Hourigan, Roland B Walter
PURPOSE OF REVIEW: The purpose of this review was to evaluate recent literature on detection methodologies for, and prognostic significance of, measurable ("minimal") residual disease (MRD) in acute myeloid leukemia (AML). RECENT FINDINGS: There is no "one-fits-all" approach to MRD testing in AML. Most exploited to date are methods relying on immunophenotypic aberrancies (identified via multiparameter flow cytometry) or genetic abnormalities (identified via PCR-based assays)...
October 13, 2017: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/29027617/zebrafish-as-a-model-to-study-neuroblastoma-development
#12
REVIEW
Mattie J Casey, Rodney A Stewart
Neuroblastoma is a pediatric solid tumor arising from embryonic neural crest progenitor cells that normally generate the peripheral sympathetic nervous system. As such, the location of neuroblastoma tumors is correlated with the distribution of major post-ganglionic clusters throughout the sympathetic chain, with the highest incidence in the adrenal medulla or lumbar sympathetic ganglia (~65%). Neuroblastoma is an enigmatic tumor that can spontaneously regress with minimal treatment or become highly metastatic and develop resistance to aggressive treatments, including radiation and high-dose chemotherapy...
October 13, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/29027537/optimal-detection-of-clinically-relevant-mutations-in-colorectal-carcinoma-sample-pooling-overcomes-intra-tumoral-heterogeneity
#13
Andrew C Nelson, Jamie Boone, David Cartwright, Bharat Thyagarajan, Robyn Kincaid, Aaron P Lambert, Kylene Karnuth, Christine Henzler, Sophia Yohe
Intra-tumoral genomic heterogeneity is a well-established biologic property of human malignancies with emerging roles in cancer progression and therapy resistance. However, its impact on the clinical utility of genomic testing in patient management remains unclear. Furthermore, best practices to account for heterogeneity in the provision of highly accurate, clinically valid molecular testing have yet to be firmly established. Genomic biomarkers for the management of colorectal carcinoma are both well-established (ie, KRAS, NRAS) and emerging (BRAF, PIK3CA, and others) in respect to therapy selection and clinical trial eligibility...
October 13, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29027482/structural-genomics-of-pndm-btr-harboring-in191-and-tn6360-and-other-bla-ndm-carrying-incn1-plasmids
#14
Yachao Zhao, Lijun Wang, Zhiyi Zhang, Jiao Feng, Huaixing Kang, Liqun Fang, Xiaoyuan Jiang, Defu Zhang, Zhe Zhan, Dongsheng Zhou, Yigang Tong
AIM: To characterize a conjugative bla NDM-1-carrying plasmid pNDM-BTR from a clinical Escherichia coli isolate. MATERIALS & METHODS: The complete nucleotide sequence of pNDM-BTR was determined using next-generation sequencing technology. Comparative genomic analysis of bla NDM-carrying IncN1 plasmids, including pNDM-BTR, was performed, and the antimicrobial resistance phenotypes were determined. RESULTS: pNDM-BTR contained three accessory modules, namely IS26, a novel Tn3-family transposon Tn6360 and the dfrA14 region composed of In191, ecoRII-ecoRIImet and ΔIS1X2...
October 13, 2017: Future Microbiology
https://www.readbyqxmd.com/read/29027470/next-generation-sequencing-applications-for-cardiovascular-disease
#15
Samira Kalayinia, Hamidreza Goodarzynejad, Majid Maleki, Nejat Mahdieh
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs)...
October 13, 2017: Annals of Medicine
https://www.readbyqxmd.com/read/29027173/native-chromatin-immunoprecipitation-sequencing-chip-seq-from-low-cell-numbers
#16
Teodora Ribarska, Gregor D Gilfillan
ChIP-seq is the current method of choice for genome-wide protein location analysis. Here, we present a native (non-cross-linked) ChIP procedure suitable for histone proteins, coupled with an efficient library preparation technique for subsequent next-generation sequencing. The method enables ChIP-seq starting with 50,000 or more cells.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027167/characterization-of-the-nucleosome-landscape-by-micrococcal-nuclease-sequencing-mnase-seq
#17
Wieteke Anna Maria Hoeijmakers, Richárd Bártfai
MNase-seq allows the genome-wide examination of the nucleosome landscape by determination of nucleosome positioning and occupancy. Typically, native or formaldehyde fixed chromatin is subjected to digestion by micrococcal nuclease (MNase), which degrades linker DNA and yields mainly mono-nucleosomes. The resulting material can be processed directly or can be subjected to an optional chromatin immunoprecipitation step (MNase-ChIP-seq). De-crosslinked and purified DNA is then subjected to next-generation sequencing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027164/chromatin-immunoprecipitation-from-mouse-embryonic-tissue-or-adherent-cells-in-culture-followed-by-next-generation-sequencing
#18
Mário A F Soares, Diogo S Castro
Chromatin immunoprecipitation (ChIP) is considered the method of choice for characterizing interactions between a protein of interest and specific genomic regions. It is of paramount importance in gene-regulation studies, as it can be used to map the target regions of sequence-specific transcription factors and cofactors, or histone marks that characterize distinct chromatin states. ChIP can be used directly to probe interactions with candidate regions (ChIP-PCR), or coupled to Next-Generation Sequencing (ChIP-seq) to generate genome-wide information...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29026837/binding-site-analysis-of-the-caenorhabditis-elegans-nr4a-nuclear-receptor-nhr-6-during-development
#19
Brandon Praslicka, Jeremy S Harmson, Joohyun Kim, Vittobai Rashika Rangaraj, Aikseng Ooi, Chris R Gissendanner
Members of the NR4A subfamily of nuclear receptors make up a highly conserved, functionally diverse group of transcription factors implicated in a multitude of cellular processes such as proliferation, differentiation, apoptosis, metabolism and DNA repair. The gene nhr-6, which encodes the sole C. elegans NR4A nuclear receptor homolog, has a critical role in organogenesis and regulates the development of the spermatheca organ system. Our previous work revealed that nhr-6 is required for spermatheca cell divisions in late L3 and early L4 and spermatheca cell differentiation during the mid L4 stage...
2017: Nuclear Receptor Research
https://www.readbyqxmd.com/read/29026660/comparison-of-classical-multi-locus-sequence-typing-software-for-next-generation-sequencing-data
#20
REVIEW
Andrew J Page, Nabil-Fareed Alikhan, Heather A Carleton, Torsten Seemann, Jacqueline A Keane, Lee S Katz
Multi-locus sequence typing (MLST) is a widely used method for categorizing bacteria. Increasingly, MLST is being performed using next-generation sequencing (NGS) data by reference laboratories and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have compared eight of these applications against real and simulated data, and present results on: (1) the accuracy of each method against traditional typing methods, (2) the performance on real outbreak datasets, (3) the impact of contamination and varying depth of coverage, and (4) the computational resource requirements...
August 2017: Microbial Genomics
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