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Nanopore sequencing

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https://www.readbyqxmd.com/read/28638988/same-day-genomic-and-epigenomic-diagnosis-of-brain-tumors-using-real-time-nanopore-sequencing
#1
Philipp Euskirchen, Franck Bielle, Karim Labreche, Wigard P Kloosterman, Shai Rosenberg, Mailys Daniau, Charlotte Schmitt, Julien Masliah-Planchon, Franck Bourdeaut, Caroline Dehais, Yannick Marie, Jean-Yves Delattre, Ahmed Idbaih
Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making...
June 21, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28638050/de-novo-yeast-genome-assemblies-from-minion-pacbio-and-miseq-platforms
#2
Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield, Robert M Davies, German Tischler, David K Jackson, Thomas M Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637243/nanopore-sequencing-data-analysis-state-of-the-art-applications-and-challenges
#3
Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data...
June 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28630164/single-molecule-nanopore-enzymology
#4
REVIEW
Kherim Willems, Veerle Van Meervelt, Carsten Wloka, Giovanni Maglia
Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28626560/selective-single-molecule-nanopore-sensing-of-proteins-using-dna-aptamer-functionalised-gold-nanoparticles
#5
Xiaoyan Lin, Aleksandar P Ivanov, Joshua B Edel
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28623312/recovery-of-the-first-full-length-genome-sequence-of-a-parapoxvirus-directly-from-a-clinical-sample
#6
Thomas Günther, Ludwig Haas, Malik Alawi, Peter Wohlsein, Jerzy Marks, Adam Grundhoff, Paul Becher, Nicole Fischer
We recovered the first full-length poxvirus genome, including the terminal hairpin region, directly from complex clinical material using a combination of second generation short read and third generation nanopore sequencing technologies. The complete viral genome sequence was directly recovered from a skin lesion of a grey seal thereby preventing sequence changes due to in vitro passaging of the virus. Subsequent analysis of the proteins encoded by this virus identified genes specific for skin adaptation and pathogenesis of parapoxviruses...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28615658/serotyping-dengue-virus-with-isothermal-amplification-and-a-portable-sequencer
#7
Junya Yamagishi, Lucky R Runtuwene, Kyoko Hayashida, Arthur E Mongan, Lan Anh Nguyen Thi, Linh Nguyen Thuy, Cam Nguyen Nhat, Kriengsak Limkittikul, Chukiat Sirivichayakul, Nuankanya Sathirapongsasuti, Martin Frith, Wojciech Makalowski, Yuki Eshita, Sumio Sugano, Yutaka Suzuki
The recent development of a nanopore-type portable DNA sequencer has changed the way we think about DNA sequencing. We can perform sequencing directly in the field, where we collect the samples. Here, we report the development of a novel method to detect and genotype tropical disease pathogens, using dengue fever as a model. By combining the sequencer with isothermal amplification that only requires a water bath, we were able to amplify and sequence target viral genomes with ease. Starting from a serum sample, the entire procedure could be finished in a single day...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28605506/multi-locus-and-long-amplicon-sequencing-approach-to-study-microbial-diversity-at-species-level-using-the-miniontm-portable-nanopore-sequencer
#8
Alfonso Benítez-Páez, Yolanda Sanz
Background: The miniaturised and portable DNA sequencer MinION TM has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION TM platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. Results: After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67,000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION TM device using R9 and R9...
June 12, 2017: GigaScience
https://www.readbyqxmd.com/read/28605450/a-spectral-algorithm-for-fast-de-novo-layout-of-uncorrected-long-nanopore-reads
#9
Antoine Recanati, Thomas Brüls, Alexandre d'Aspremont
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However, their high error rate significantly complicates assembly and requires expensive correction steps to layout the reads using standard assembly engines. Results: We present an original and efficient spectral algorithm to layout the uncorrected nanopore reads, and its seamless integration into a straightforward overlap/layout/consensus (OLC) assembly scheme...
June 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28594827/unicycler-resolving-bacterial-genome-assemblies-from-short-and-long-sequencing-reads
#10
Ryan R Wick, Louise M Judd, Claire L Gorrie, Kathryn E Holt
The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate "hybrid" assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads...
June 8, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28591605/blocking-of-single-%C3%AE-hemolysin-pore-by-rhodamine-derivatives
#11
Tatyana I Rokitskaya, Pavel A Nazarov, Andrey V Golovin, Yuri N Antonenko
Measurements of ion conductance through α-hemolysin pore in a bilayer lipid membrane revealed blocking of the ion channel by a series of rhodamine 19 and rhodamine B esters. The longest dwell closed time of the blocking was observed with rhodamine 19 butyl ester (C4R1), whereas the octyl ester (C8R1) was of poor effect. Voltage asymmetry in the binding kinetics indicated that rhodamine derivatives bound to the stem part of the aqueous pore lumen. The binding frequency was proportional to a quadratic function of rhodamine concentrations, thereby showing that the dominant binding species were rhodamine dimers...
June 6, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28586766/sem-induced-shrinkage-and-site-selective-modification-of-single-crystal-silicon-nanopores
#12
Qi Chen, Yifan Wang, Tao Deng, Zewen Liu
Solid-state nanopores with feature sizes around 5 nm play a critical role in bio-sensing fields, especially in single molecule detection and sequencing of DNA, RNA, and proteins. In this paper we present a systematically study on shrinkage and site-selective modification of single-crystal silicon (SCS) nanopores with a conventional scanning electron microscope (SEM). Square nanopores with measurable sizes as small as 8 nm × 8 nm and rectangle nanopores with feature sizes (the smaller one of the length and width) down to 5 nm have been obtained by using the SEM-induced shrinkage technique...
June 6, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28582401/deepnano-deep-recurrent-neural-networks-for-base-calling-in-minion-nanopore-reads
#13
Vladimír Boža, Broňa Brejová, Tomáš Vinař
The MinION device by Oxford Nanopore produces very long reads (reads over 100 kBp were reported); however it suffers from high sequencing error rate. We present an open-source DNA base caller based on deep recurrent neural networks and show that the accuracy of base calling is much dependent on the underlying software and can be improved by considering modern machine learning methods. By employing carefully crafted recurrent neural networks, our tool significantly improves base calling accuracy on data from R7...
2017: PloS One
https://www.readbyqxmd.com/read/28558786/lost-in-plasmids-next-generation-sequencing-and-the-complex-genome-of-the-tick-borne-pathogen-borrelia-burgdorferi
#14
G Margos, S Hepner, C Mang, D Marosevic, S E Reynolds, S Krebs, A Sing, M Derdakova, M A Reiter, V Fingerle
BACKGROUND: Borrelia (B.) burgdorferi sensu lato, including the tick-transmitted agents of human Lyme borreliosis, have particularly complex genomes, consisting of a linear main chromosome and numerous linear and circular plasmids. The number and structure of plasmids is variable even in strains within a single genospecies. Genes on these plasmids are known to play essential roles in virulence and pathogenicity as well as host and vector associations. For this reason, it is essential to explore methods for rapid and reliable characterisation of molecular level changes on plasmids...
May 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28546497/complete-genome-sequence-of-the-autotrophic-acetogen-clostridium-formicaceticum-dsm-92-t-using-nanopore-and-illumina-sequencing-data
#15
Michael M Karl, Anja Poehlein, Frank R Bengelsdorf, Rolf Daniel, Peter Dürre
Here, we report the closed genome sequence of Clostridium formicaceticum, an Rnf- and cytochrome-containing autotrophic acetogen that is able to convert carbon monoxide to acetate using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (4.59 Mb).
May 25, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#16
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28538092/discriminating-residue-substitutions-in-a-single-protein-molecule-using-a-sub-nanopore
#17
Zhuxin Dong, Eamonn Kennedy, Mohammad Hokmabadi, Gregory Timp
It is now possible to create, in a thin inorganic membrane, a single, sub-nanometer-diameter pore, i.e. a sub-nanopore, about the size of an amino acid residue. To explore the prospects for sequencing protein with it, measurements of the force and current were performed as two denatured histones, which differed by four amino acid residue substitutions, were impelled systematically through the sub-nanopore one-at-a-time using an atomic force microscope. The force measurements revealed that once the denatured protein, stabilized by sodium dodecyl sulfate (SDS), translocated through the sub-nanopore, a disproportionately large force was required to pull it back...
May 24, 2017: ACS Nano
https://www.readbyqxmd.com/read/28530800/label-free-multiplexed-single-molecule-analysis-of-protein-dna-complexes-with-nanopores
#18
Garbiñe Celaya, Judit Perales-Calvo, Arturo Muga, Fernando Moro, David Rodriguez-Larrea
Protein interactions with specific DNA sequences are crucial in the control of gene expression and the regulation of replication. Single-molecule methods offer excellent capabilities to unravel the mechanism and kinetics of these interactions. Here we develop a nanopore approach where a target DNA sequence is contained in a hairpin followed by a ssDNA. This system allows DNA-protein complexes to be distinguished from bare DNA molecules as they are pulled through a single nanopore detector, providing both equilibrium and kinetic information...
May 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28508050/butterfly-gyroid-nanostructures-as-a-time-frozen-glimpse-of-intracellular-membrane-development
#19
Bodo D Wilts, Benjamin Apeleo Zubiri, Michael A Klatt, Benjamin Butz, Michael G Fischer, Stephen T Kelly, Erdmann Spiecker, Ullrich Steiner, Gerd E Schröder-Turk
The formation of the biophotonic gyroid material in butterfly wing scales is an exceptional feat of evolutionary engineering of functional nanostructures. It is hypothesized that this nanostructure forms by chitin polymerization inside a convoluted membrane of corresponding shape in the endoplasmic reticulum. However, this dynamic formation process, including whether membrane folding and chitin expression are simultaneous or sequential processes, cannot yet be elucidated by in vivo imaging. We report an unusual hierarchical ultrastructure in the butterfly Thecla opisena that, as a solid material, allows high-resolution three-dimensional microscopy...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28503666/robust-long-read-native-dna-sequencing-using-the-ont-csgg-nanopore-system
#20
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
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