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https://www.readbyqxmd.com/read/28503666/robust-long-read-native-dna-sequencing-using-the-ont-csgg-nanopore-system
#1
Jean-Michel Carter, Shobbir Hussain
Background: The ability to obtain long read lengths during DNA sequencing has several potentially important practical applications. Especially long read lengths have been reported using the Nanopore sequencing method, currently commercially available from Oxford Nanopore Technologies (ONT). However, early reports have demonstrated only limited levels of combined throughput and sequence accuracy. Recently, ONT released a new CsgG pore sequencing system as well as a 250b/s translocation chemistry with potential for improvements...
April 6, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28491281/annotated-mitochondrial-genome-with-nanopore-r9-signal-for-nippostrongylus-brasiliensis
#2
Jodie Chandler, Mali Camberis, Tiffany Bouchery, Mark Blaxter, Graham Le Gros, David A Eccles
Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We de-novo assembled a single contig mitochondrial genome from N. brasiliensis using MinION R9 nanopore data...
2017: F1000Research
https://www.readbyqxmd.com/read/28488487/too-much-direction
#3
Malcolm Harrison
So NHS England is to employ two more directors of nursing (news, 26 April). Presumably this will require the employment of at least two more admin staff and minions. Total cost? About £200,000 a year? Or about six or seven nurses, just the amount most wards seem to be short of.
May 10, 2017: Nursing Standard
https://www.readbyqxmd.com/read/28475646/parallel-clickseq-and-nanopore-sequencing-elucidates-the-rapid-evolution-of-defective-interfering-rnas-in-flock-house-virus
#4
Elizabeth Jaworski, Andrew Routh
Defective-Interfering RNAs (DI-RNAs) have long been known to play an important role in virus replication and transmission. DI-RNAs emerge during virus passaging in both cell-culture and their hosts as a result of non-homologous RNA recombination. However, the principles of DI-RNA emergence and their subsequent evolution have remained elusive. Using a combination of long- and short-read Next-Generation Sequencing, we have characterized the formation of DI-RNAs during serial passaging of Flock House virus (FHV) in cell-culture over a period of 30 days in order to elucidate the pathways and potential mechanisms of DI-RNA emergence and evolution...
May 5, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28447221/deleterious-abca7-mutations-and-transcript-rescue-mechanisms-in-early-onset-alzheimer-s-disease
#5
Arne De Roeck, Tobi Van den Bossche, Julie van der Zee, Jan Verheijen, Wouter De Coster, Jasper Van Dongen, Lubina Dillen, Yalda Baradaran-Heravi, Bavo Heeman, Raquel Sanchez-Valle, Albert Lladó, Benedetta Nacmias, Sandro Sorbi, Ellen Gelpi, Oriol Grau-Rivera, Estrella Gómez-Tortosa, Pau Pastor, Sara Ortega-Cubero, Maria A Pastor, Caroline Graff, Håkan Thonberg, Luisa Benussi, Roberta Ghidoni, Giuliano Binetti, Alexandre de Mendonça, Madalena Martins, Barbara Borroni, Alessandro Padovani, Maria Rosário Almeida, Isabel Santana, Janine Diehl-Schmid, Panagiotis Alexopoulos, Jordi Clarimon, Alberto Lleó, Juan Fortea, Magda Tsolaki, Maria Koutroumani, Radoslav Matěj, Zdenek Rohan, Peter De Deyn, Sebastiaan Engelborghs, Patrick Cras, Christine Van Broeckhoven, Kristel Sleegers
Premature termination codon (PTC) mutations in the ATP-Binding Cassette, Sub-Family A, Member 7 gene (ABCA7) have recently been identified as intermediate-to-high penetrant risk factor for late-onset Alzheimer's disease (LOAD). High variability, however, is observed in downstream ABCA7 mRNA and protein expression, disease penetrance, and onset age, indicative of unknown modifying factors. Here, we investigated the prevalence and disease penetrance of ABCA7 PTC mutations in a large early onset AD (EOAD)-control cohort, and examined the effect on transcript level with comprehensive third-generation long-read sequencing...
April 27, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28433722/high-precision-genome-sequencing-of-engineered-gluconobacter-oxydans-621h-by-combining-long-nanopore-and-short-accurate-illumina-reads
#6
Angela Kranz, Alexander Vogel, Ursula Degner, Ines Kiefler, Michael Bott, Björn Usadel, Tino Polen
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28413619/picopore-a-tool-for-reducing-the-storage-size-of-oxford-nanopore-technologies-datasets-without-loss-of-functionality
#7
Scott Gigante
Oxford Nanopore Technologies' (ONT) MinION and PromethION long-read sequencing technologies are emerging as genuine alternatives to established Next-Generation Sequencing technologies. A combination of the highly redundant file format and a rapid increase in data generation have created a significant problem both for immediate data storage on MinION-capable laptops, and for long-term storage on lab data servers.  We developed Picopore, a software suite offering three methods of compression. Picopore's lossless and deep lossless methods provide a 25% and 44% average reduction in size, respectively, without removing any data from the files...
2017: F1000Research
https://www.readbyqxmd.com/read/28399700/reply-to-another-pattern-of-chimney-evar-related-type-i-endoleak
#8
Konstantinos P Donas, Frank J Criado, Giovanni Torsello, Frank J Veith, David J Minion
No abstract text is available yet for this article.
April 1, 2017: Journal of Endovascular Therapy
https://www.readbyqxmd.com/read/28376776/the-ecouter-methodology-for-stakeholder-engagement-in-translational-research
#9
Madeleine J Murtagh, Joel T Minion, Andrew Turner, Rebecca C Wilson, Mwenza Blell, Cynthia Ochieng, Barnaby Murtagh, Stephanie Roberts, Oliver W Butters, Paul R Burton
BACKGROUND: Because no single person or group holds knowledge about all aspects of research, mechanisms are needed to support knowledge exchange and engagement. Expertise in the research setting necessarily includes scientific and methodological expertise, but also expertise gained through the experience of participating in research and/or being a recipient of research outcomes (as a patient or member of the public). Engagement is, by its nature, reciprocal and relational: the process of engaging research participants, patients, citizens and others (the many 'publics' of engagement) brings them closer to the research but also brings the research closer to them...
April 4, 2017: BMC Medical Ethics
https://www.readbyqxmd.com/read/28369459/de-novo-assembly-and-population-genomic-survey-of-natural-yeast-isolates-with-the-oxford-nanopore-minion-sequencer
#10
Benjamin Istace, Anne Friedrich, Léo d'Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury
BACKGROUND: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease of use compared with existing long reads sequencing technologies. The MinION sequencer enables the rapid sequencing of small eukaryotic genomes, such as the yeast genome...
February 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28348876/comparison-of-bacterial-genome-assembly-software-for-minion-data-and-their-applicability-to-medical-microbiology
#11
Kim Judge, Martin Hunt, Sandra Reuter, Alan Tracey, Michael A Quail, Julian Parkhill, Sharon J Peacock
Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software. Here, we use a multidrug-resistant Enterobacter kobei isolate as a model organism to compare open source software for the assembly of genome data, and relate this to the time taken to generate actionable information. Three software tools (PBcR, Canu and miniasm) were used to assemble MinION data and a fourth (SPAdes) was used to combine MinION and Illumina data to produce a hybrid assembly...
September 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28337073/real-time-dna-sequencing-in-the-antarctic-dry-valleys-using-the-oxford-nanopore-sequencer
#12
Sarah S Johnson, Elena Zaikova, David S Goerlitz, Yu Bai, Scott W Tighe
The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity...
April 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28334395/pore-guis-for-parallel-and-real-time-processing-of-minion-sequence-data
#13
Robert Stewart, Mick Watson
Motivation: Oxford Nanopore's MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs. Results: We have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets...
March 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#14
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327957/nanosim-nanopore-sequence-read-simulator-based-on-statistical-characterization
#15
Chen Yang, Justin Chu, René L Warren, Inanç Birol
Background: The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing - valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, output of which could be used to benchmark analysis tools. Findings: Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327913/the-use-of-oxford-nanopore-native-barcoding-for-complete-genome-assembly
#16
Sion C Bayliss, Vicky L Hunt, Maho Yokoyama, Harry A Thorpe, Edward J Feil
Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28298449/real-time-sequencing-of-mycobacterium-tuberculosis-are-we-there-yet
#17
Robyn S Lee, Madhukar Pai
Whole-genome sequencing has taken a leading role in epidemiologic studies of tuberculosis, but thus far, its real-time clinical utility has been low, in part because of the requirement for culture. In their report in this issue, Votintseva et al. (A. A. Votintseva, P. Bradley, L. Pankhurst, C. del Ojo Elias, M. Loose, K. Nilgiriwala, A. Chatterjee, E. G. Smith, N. Sanderson, T. M. Walker, M. R. Morgan, D. H. Wyllie, A. S. Walker, T. E. A. Peto, D. W. Crook, and Z. Iqbal, J Clin Microbiol 55:1285-1298, 2017, https://doi...
May 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28288843/non-invasive-diagnosis-of-cutaneous-leishmaniasis-by-the-direct-boil-loop-mediated-isothermal-amplification-method-and-minion%C3%A2-nanopore-sequencing
#18
Kazuo Imai, Norihito Tarumoto, Kiyoko Amo, Makoto Takahashi, Naoya Sakamoto, Atsushi Kosaka, Yasuyuki Kato, Kei Mikita, Jun Sakai, Takashi Murakami, Yutaka Suzuki, Shigefumi Maesaki, Takuya Maeda
Cutaneous leishmaniasis (CL) is gaining attention as a public health problem. We present two cases of CL imported from Syria and Venezuela in Japan. We diagnosed them as CL non-invasively by the direct boil loop-mediated isothermal amplification method and an innovative sequencing method using the MinION™ sequencer. This report demonstrates that our procedure could be useful for the diagnosis of CL in both clinical and epidemiological settings.
March 11, 2017: Parasitology International
https://www.readbyqxmd.com/read/28284606/use-of-signature-tagged-mutagenesis-to-identify-genes-associated-with-colonization-of-sheep-by-e-coli-o157-h7
#19
Nancy A Cornick, Josh Pitzer, Amy F Helgerson, Melissa L Madsen, Kathy T Kurth, Qianjun Xiao, F Chris Minion
Outbreaks of Escherichia coli O157:H7 in the United States due to contaminated foods are a public health issue and a continuing problem. The major reservoir for these organisms is the gastrointestinal tract of ruminants where they are a member of the resident microbiota. Several factors that contribute to the colonization of cattle have been identified, but a systematic screen of genes that might contribute to the colonization and persistence phenotype in mature ruminants has not been reported. Using a sheep model of persistence, signature tagged mutagenesis (STM) was used to screen 1326 mutants for a persistence-negative phenotype of E...
March 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28275074/same-day-diagnostic-and-surveillance-data-for-tuberculosis-via-whole-genome-sequencing-of-direct-respiratory-samples
#20
Antonina A Votintseva, Phelim Bradley, Louise Pankhurst, Carlos Del Ojo Elias, Matthew Loose, Kayzad Nilgiriwala, Anirvan Chatterjee, E Grace Smith, Nicolas Sanderson, Timothy M Walker, Marcus R Morgan, David H Wyllie, A Sarah Walker, Tim E A Peto, Derrick W Crook, Zamin Iqbal
Routine full characterization of Mycobacterium tuberculosis is culture based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near the point of care. We demonstrate a low-cost method of DNA extraction directly from patient samples for M. tuberculosis WGS. We initially evaluated the method by using the Illumina MiSeq sequencer (40 smear-positive respiratory samples obtained after routine clinical testing and 27 matched liquid cultures)...
May 2017: Journal of Clinical Microbiology
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