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https://www.readbyqxmd.com/read/29678912/characterizing-the-ecology-of-vibrio-in-the-neuse-river-estuary-north-carolina-using-heat-shock-protein-60-hsp60-next-generation-amplicon-sequencing
#1
Kelsey J Jesser, Rachel T Noble
Of marine eubacteria, the genus Vibrio is intriguing because member species are relevant to both marine ecology and human health. Many have touted the relationships of Vibrio to environmental factors, especially temperature and salinity, to predict total Vibrio abundance, but these studies lacked the taxonomic resolution to identify relationships among species and key drivers of Vibrio dynamics. In order to improve NGS surveys of Vibrio, we have conducted both 16S small subunit ribosomal RNA (rRNA) and heat shock protein 60 ( hsp60 ) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29673906/interest-of-next-generation-sequencing-in-bcg-treated-high-risk-bladder-cancer
#2
C Jungels, N Martinez Chanza, S Albisinni, M Mercier, N d'Haene, S Rorive, T Roumeguère
OBJECTIVES: There are only few predictive factors for response of non-musculo-invasive bladder cancer (NMIBC) to Bacillus Calmette-Guérin (BCG) therapy. Our study analyzed the results of the sequencing of new generation (NGS) targeted on 50 genes of oncological interest obtained on bladder resection parts in high-risk NMIBC patients treated with BCG, to describe this population from a molecular point of view and try to correlate these results in patients who present or not recurrence after BCG...
April 16, 2018: Progrès en Urologie
https://www.readbyqxmd.com/read/29673316/a-study-on-fast-calling-variants-from-next-generation-sequencing-data-using-decision-tree
#3
Zhentang Li, Yi Wang, Fei Wang
BACKGROUND: The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging. RESULTS: We proposed a decision-tree based variant calling algorithm. Experiments on a set of real data indicate that our algorithm achieves high accuracy and sensitivity for SNVs and indels and shows good adaptability on low-coverage data...
April 19, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29672674/trumicount-correctly-counting-absolute-numbers-of-molecules-using-unique-molecular-identifiers
#4
Florian G Pflug, Arndt von Haeseler
Motivation: Counting molecules using next-generation sequencing (NGS) suffers from PCR amplification bias, which reduces the accuracy of many quantitative NGS-based experimental methods such as RNASeq. This is true even if molecules are made distinguishable using unique molecular identifiers (UMIs) before PCR amplification, and distinct UMIs are counted instead of reads: Molecules that are lost entirely during the sequencing process will still cause underestimation of the molecule count, and amplification artifacts like PCR chimeras create phantom UMIs and thus cause over-estimation...
April 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29671148/identification-of-a-cold-tolerant-locus-in-rice-oryza-sativa-l-using-bulked-segregant-analysis-with-a-next-generation-sequencing-strategy
#5
Jian Sun, Luomiao Yang, Jingguo Wang, Hualong Liu, Hongliang Zheng, Dongwei Xie, Minghui Zhang, Mingfang Feng, Yan Jia, Hongwei Zhao, Detang Zou
BACKGROUND: Cold stress can cause serious abiotic damage that limits the growth, development and yield of rice. Cold tolerance during the booting stage of rice is a key factor that can guarantee a high and stable yield under cold stress. The cold tolerance of rice is controlled by quantitative trait loci (QTLs). Based on the complex genetic basis of cold tolerance in rice, additional efforts are needed to detect reliable QTLs and identify candidate genes. In this study, recombinant inbred lines (RILs) derived from a cross between a cold sensitive variety, Dongnong422, and strongly cold-tolerant variety, Kongyu131, were used to screen for cold-tolerant loci at the booting stage of rice...
April 18, 2018: Rice
https://www.readbyqxmd.com/read/29668842/garfield-ngs-genomic-variants-filtering-by-deep-learning-models-in-ngs
#6
Viola Ravasio, Marco Ritelli, Andrea Legati, Edoardo Giacopuzzi
Summary: Exome sequencing approach is extensively used in research and diagnostic laboratories to discover pathological variants and study genetic architecture of human diseases. However, a significant proportion of identified genetic variants are actually false positive calls, and this pose serious challenges for variants interpretation. Here, we propose a new tool named GARFIELD-NGS (Genomic vARiants FIltering by dEep Learning moDels in NGS), which rely on deep learning models to dissect false and true variants in exome sequencing experiments performed with Illumina or ION platforms...
April 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29666883/snp-based-pool-genotyping-and-haplotype-analysis-accelerate-fine-mapping-of-the-wheat-genomic-region-containing-stripe-rust-resistance-gene-yr26
#7
Jianhui Wu, Qingdong Zeng, Qilin Wang, Shengjie Liu, Shizhou Yu, Jingmei Mu, Shuo Huang, Hanan Sela, Assaf Distelfeld, Lili Huang, Dejun Han, Zhensheng Kang
NGS-assisted super pooling emerging as powerful tool to accelerate gene mapping and haplotype association analysis within target region uncovering specific linkage SNPs or alleles for marker-assisted gene pyramiding. Conventional gene mapping methods to identify genes associated with important agronomic traits require significant amounts of financial support and time. Here, a single nucleotide polymorphism (SNP)-based mapping approach, RNA-Seq and SNP array assisted super pooling analysis, was used for rapid mining of a candidate genomic region for stripe rust resistance gene Yr26 that has been widely used in wheat breeding programs in China...
April 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29666441/using-biology-to-guide-the-treatment-of-sarcomas-and-aggressive-connective-tissue-tumours
#8
REVIEW
Armelle Dufresne, Mehdi Brahmi, Marie Karanian, Jean-Yves Blay
Sarcomas are a heterogeneous group of malignancies that arise from cells of a mesenchymal origin. Surgery forms the mainstay of the treatment of most patients with localized sarcoma and might be followed or preceded by chemotherapy and/or radiotherapy. In the metastatic setting, systemic treatments tend to improve survival and control symptoms. However, the adverse events and sometimes disappointing outcomes associated with these empirical approaches to treatment indicate a need for new approaches. The advent of next-generation sequencing (NGS) has enabled more targeted treatment of many malignancies based on the presence of specific alterations...
April 17, 2018: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/29666117/novel-insights-into-the-pathogenesis-of-t-cell-lymphomas
#9
John S Van Arnam, Megan S Lim, Kojo S J Elenitoba-Johnson
T-cell lymphomas are a heterogeneous group of rare malignancies with overlapping clinical, immunologic and histologic features. Recent advances in our understanding of T-cell differentiation based on gene expression profiling, next-generation sequencing (NGS) and transgenic mouse modeling studies have better elucidated the pathogenetic mechanisms underlying the diverse biology of T-cell lymphomas. These studies show that while genetic alterations in epigenetic modifiers are implicated in all subtypes of T-cell lymphomas, specific subtypes demonstrate enrichment for particular recurrent alterations targeting specific genes...
April 17, 2018: Blood
https://www.readbyqxmd.com/read/29665853/microsatellite-instability-in-prostate-cancer-by-pcr-or-next-generation-sequencing
#10
Jennifer A Hempelmann, Christina M Lockwood, Eric Q Konnick, Michael T Schweizer, Emmanuel S Antonarakis, Tamara L Lotan, Bruce Montgomery, Peter S Nelson, Nola Klemfuss, Stephen J Salipante, Colin C Pritchard
BACKGROUND: Microsatellite instability (MSI) is now being used as a sole biomarker to guide immunotherapy treatment for men with advanced prostate cancer. Yet current molecular diagnostic tests for MSI have not been evaluated for use in prostate cancer. METHODS: We evaluated two next-generation sequencing (NGS) MSI-detection methods, MSIplus (18 markers) and MSI by Large Panel NGS (> 60 markers), and compared the performance of each NGS method to the most widely used 5-marker MSI-PCR detection system...
April 17, 2018: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/29665779/a-machine-learning-model-to-determine-the-accuracy-of-variant-calls-in-capture-based-next-generation-sequencing
#11
Jeroen van den Akker, Gilad Mishne, Anjali D Zimmer, Alicia Y Zhou
BACKGROUND: Next generation sequencing (NGS) has become a common technology for clinical genetic tests. The quality of NGS calls varies widely and is influenced by features like reference sequence characteristics, read depth, and mapping accuracy. With recent advances in NGS technology and software tools, the majority of variants called using NGS alone are in fact accurate and reliable. However, a small subset of difficult-to-call variants that still do require orthogonal confirmation exist...
April 17, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29664687/distinctiveness-and-similarities-between-extended-spectrum-%C3%AE-lactamase-producing-escherichia-coli-isolated-from-cattle-and-the-community-in-israel
#12
Ziv Lifshitz, Na'ama Sturlesi, Miriam Parizade, Shlomo E Blum, Michal Gordon, Diana Taran, Amos Adler
The goal of this study was to compare the molecular features of bovine- and human community-acquired extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Israel. Bovine ESBL-producing E. coli were isolated during a point-prevalence study from the main farming locations throughout Israel. Human ESBL-producing E. coli isolates were collected from community-acquired urinary tract infection cases. Molecular typing was done initially by repetitive extragenic palindromic-PCR. Representative isolates were subjected to next-generation sequencing (NGS) and analyzed for multilocus sequence typing (MLST), core genome MLST (cgMLST), blaCTX-M gene allele, and mobile genetic elements (MGEs) surrounding it...
April 17, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29664468/unifying-cancer-and-normal-rna-sequencing-data-from-different-sources
#13
Qingguo Wang, Joshua Armenia, Chao Zhang, Alexander V Penson, Ed Reznik, Liguo Zhang, Thais Minet, Angelica Ochoa, Benjamin E Gross, Christine A Iacobuzio-Donahue, Doron Betel, Barry S Taylor, Jianjiong Gao, Nikolaus Schultz
Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing...
April 17, 2018: Scientific Data
https://www.readbyqxmd.com/read/29661874/characterization-of-extensively-or-pandrug-resistant-st147-and-st101-oxa-48-producing-klebsiella-pneumoniae-isolates-causing-bloodstream-infections-in-icu-patients
#14
Kalliope Avgoulea, Vincenzo Di Pilato, Olympia Zarkotou, Samanta Sennati, Leda Politi, Antonio Cannatelli, Katerina Themeli-Digalaki, Tommaso Giani, Athanassios Tsakris, Gian Maria Rossolini, Spyros Pournaras
Carbapenem-resistant Klebsiella pneumoniae cause important healthcare-associated infections worldwide. An outbreak of ST11 OXA-48-producing K. pneumoniae isolates (OXA-48-Kp) occurred in Tzaneio Hospital in 2012 and was contained until 2014, when OXA-48-Kp reemerged. The present study involved 19 bloodstream infection (BSI) OXA-48-Kp recovered from 19 ICU patients hospitalized between August 2014 and July 2016. MICs were determined by broth microdilution. β-lactamase genes were detected by PCR. All isolates were typed by PFGE/MLST and 10 representative isolates by next generation sequencing (NGS)...
April 16, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29661793/cell-free-plasma-dna-for-disease-stratification-and-prognosis-in-head-and-neck-cancer
#15
Markus A Schirmer, Julia Beck, Martin Leu, Michael Oellerich, Margret Rave-Fränk, Philip D Walson, Ekkehard Schütz, Martin Canis
BACKGROUND: Clinicians face many challenges in disease stratification and outcome prediction in head and neck squamous cancer cell (HNSCC) patients. Given the limitations of currently used clinical scoring, repetitive biopsies, and imaging techniques, liquid biopsy approaches may provide valuable additional diagnostic and prognostic information. METHODS: A noninterventional, single-center observational study was performed with clinical data and plasma samples from HNSCC patients...
April 16, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29659903/feasibility-study-of-cancer-genome-alterations-identified-by-next-generation-sequencing-abc-study
#16
Yoichi Naito, Hideaki Takahashi, Kohei Shitara, Wataru Okamoto, Hideaki Bando, Takeshi Kuwata, Yasutoshi Kuboki, Shingo Matsumoto, Izumi Miki, Takeharu Yamanaka, Atsushi Watanabe, Motohiro Kojima
Background: To confirm the feasibility and explore the clinical applicability of amplicon sequencing by next generation sequencing (NGS) of biopsy samples from patients with advanced solid tumors, we conducted a prospective study. Methods: Patients with unresectable, advanced, or recurrent solid tumors were included. Key eligibility criteria were as follows: 20 years or older, any planned systemic therapy, adequate lesion for biopsy, and written informed consent...
April 12, 2018: Japanese Journal of Clinical Oncology
https://www.readbyqxmd.com/read/29659792/tracking-the-ngs-revolution-managing-life-science-research-on-shared-high-performance-computing-clusters
#17
Martin Dahlö, Douglas G Scofield, Wesley Schaal, Ola Spjuth
Background: Next-Generation Sequencing (NGS) has transformed the life sciences and many research groups are newly dependent upon computer clusters to store and analyse large datasets. This creates challenges for e-infrastructures accustomed to hosting computationally mature research in other sciences. Using data gathered from our own clusters at UPPMAX computing centre at Uppsala University, Sweden, where core hours usage by ∼800 NGS and ∼200 non-NGS projects is now similar, we compare and contrast the growth, administrative burden and cluster usage of NGS projects with projects from other sciences...
April 5, 2018: GigaScience
https://www.readbyqxmd.com/read/29659569/targeted-next-generation-sequencing-identifies-functionally-deleterious-germline-mutations-in-novel-genes-in-early-onset-familial-prostate-cancer
#18
Paula Paulo, Sofia Maia, Carla Pinto, Pedro Pinto, Augusta Monteiro, Ana Peixoto, Manuel R Teixeira
Considering that mutations in known prostate cancer (PrCa) predisposition genes, including those responsible for hereditary breast/ovarian cancer and Lynch syndromes, explain less than 5% of early-onset/familial PrCa, we have sequenced 94 genes associated with cancer predisposition using next generation sequencing (NGS) in a series of 121 PrCa patients. We found monoallelic truncating/functionally deleterious mutations in seven genes, including ATM and CHEK2, which have previously been associated with PrCa predisposition, and five new candidate PrCa associated genes involved in cancer predisposing recessive disorders, namely RAD51C, FANCD2, FANCI, CEP57 and RECQL4...
April 16, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29658778/shrangesim-simulation-of-single-nucleotide-polymorphism-clusters-in-next-generation-sequencing-data
#19
Markus Boenn
Genomic variations are in the focus of research to uncover mechanisms of host-pathogen interactions and diseases such as cancer. Nowadays, next-generation sequencing (NGS) data are analyzed through dedicated pipelines to detect them. Surrogate NGS data in conjunction with genomic variations help to evaluate pipelines and validate their outcomes, fostering selection of proper tools for a given scientific question. I describe how existing approaches for simulating NGS data in conjunction with genomic variations fail to model local enrichments of single nucleotide polymorphisms (SNPs), so called SNP clusters...
April 16, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29657308/characteristics-of-the-gut-microbiota-in-adult-patients-with-type-1-and-2-diabetes-based-on-the-analysis-of-a-fragment-of-16s-rrna-gene-using-next-generation-sequencing
#20
Dominika Salamon, Agnieszka Sroka-Oleksiak, Przemysław Kapusta, Magdalena Szopa, Sandra Mrozińska, Agnieszka H Ludwig-Słomczyńska, Paweł P Wołkow, Małgorzata Bulanda, Tomasz Klupa, Maciej T Małecki, Tomasz Gosiewski
INTRODUCTION    Scientific data indicate  a possible influence of the gastrointestinal tract microbiota on the development of type 1 (T1DM) and 2 (T2DM) diabetes. Sequence analysis of 16S rRNA identified several hundred bacterial species of the intestinal ecosystem, most of which cannot be cultured. OBJECTIVES    We aimed at evaluating the composition of the gut microbiota in adult patients with T1DM and T2DM and establishing a link between data obtained from microbiological testing and the patients' clinical data...
April 15, 2018: Polish Archives of Internal Medicine
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