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Nanopore sequencing

Lev Voskoboinik, Uzi Motro, Ariel Darvasi
Interpretation of complex DNA mixtures is an ongoing challenge in the field of forensic genetics. Commonly used STR markers are quite polymorphic, enabling very high statistical association between a single source DNA profile from a crime scene and a matching suspect. STR typing of low order mixtures with two and three contributors also commonly produces high statistical association for a contributor, using current interpretation software. However higher order mixtures, with four contributors or more, are more challenging...
May 2, 2018: Forensic Science International. Genetics
Sophie M Colston, Gregory A Ellis, Seongwon Kim, Hemantha W Wijesekera, Dagmar H Leary, Baochuan Lin, Benjamin C Kirkup, W Judson Hervey, Gary J Vora
Vibrio campbellii is a pathogen of aquatic animals and has been proposed as a bacterial partner in the formation of bioluminescent milky seas. We present here the complete genome sequences assembled from Illumina and Oxford Nanopore data for two bioluminescent Vibrio campbellii strains (BoB-53 and BoB-90) isolated from biofouled moorings in the Bay of Bengal.
May 17, 2018: Genome Announcements
Mitsunori Yoshida, Hanako Fukano, Yuji Miyamoto, Keigo Shibayama, Masato Suzuki, Yoshihiko Hoshino
Mycobacterium marinum is a slowly growing, broad-host-range mycobacterial species. Here, we report the complete genome sequence of a Mycobacterium marinum type strain that was isolated from tubercles of diseased fish. This sequence will provide essential information for future taxonomic and comparative genome studies of its relatives.
May 17, 2018: Genome Announcements
Anthony Bayega, Yu Chang Wang, Spyros Oikonomopoulos, Haig Djambazian, Somayyeh Fahiminiya, Jiannis Ragoussis
RNA sequencing using next-generation sequencing (NGS, RNA-Seq) technologies is currently the standard approach for gene expression profiling, particularly for large-scale high-throughput studies. NGS technologies comprise short-read RNA-Seq (dominated by Illumina) and long-read RNA-Seq technologies provided by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). Although short-read sequencing technologies are the most widely used, long-read technologies are increasingly becoming the standard approach for de novo transcriptome assembly and isoform expression quantification due to the complex nature of the transcriptome which consists of variable lengths of transcripts and multiple alternatively spliced isoforms for most genes...
2018: Methods in Molecular Biology
Emily Rames, Joanne Macdonald
Enteroviruses (EV) are associated with a range of serious infections, including aseptic meningitis, hand foot and mouth disease, myocarditis, acute flaccid paralysis and encephalitis. Improved methods for assessing EV genotypic diversity could assist molecular epidemiology studies, clinical diagnosis and environmental surveillance. We report new methods for EV genome amplification, and subsequent genotyping using the miniaturised MinION sequencing device. Importantly, this next-generation sequencer enabled correct strain-level assignment of identity for the EV-A71 isolate assessed, where strains with up to 99...
May 12, 2018: Virus Research
Muralikrishna Lella, Radhakrishnan Mahalakshmi
Membrane protein aggregation is associated with neurodegenerative diseases. Despite remarkable advances to map protein aggregation, molecular elements that drive the structural transition from functional to amyloidogenic β-sheet polymers remain elusive. Here, we report a simple and reliable reverse-mapping method to identify the molecular elements. We validate our approach by obtaining molecular details of aggregation loci of human β-barrel nanopore ion channels that are vital for cell survival. By coupling bottom-up synthesis with time-resolved aggregation kinetics and high-resolution imaging, we identify molecular elements that switch folded channels to polymeric β-rich aggregates...
May 15, 2018: Journal of Physical Chemistry Letters
Kim N T Ton, Simone L Cree, Sabine J Gronert-Sum, Tony R Merriman, Lisa K Stamp, Martin A Kennedy
The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been associated with adverse drug reactions (ADRs) and disease susceptibility. The frequency of such HLA-B alleles varies by ethnicity, and therefore it is important to understand the prevalence of such alleles in different population groups. Research into HLA involvement in ADRs would be facilitated by improved methods for genotyping key HLA-B alleles...
2018: Frontiers in Genetics
Sang Won Jung, Han Seul Kim, Art E Cho, Yong-Hoon Kim
Controlling the dynamics of DNA translocation is a central issue in the emerging nanopore-based DNA sequencing. To address the potential of heteroatom doping of carbon nanostructures to achieve this goal, herein we carry out atomistic molecular dynamics simulations for single-stranded DNAs translocating between two pristine or doped carbon nanotube (CNT) electrodes. Specifically, we consider the substitutional nitrogen doping of capped CNT (capCNT) electrodes and perform two types of molecular dynamics simulations for the entrapped and translocating single-stranded DNAs...
May 9, 2018: ACS Applied Materials & Interfaces
Jina Ko, Neha Bhagwat, Taylor Black, Stephanie S Yee, Young-Ji Na, Stephen A Fisher, Junhyong Kim, Erica L Carpenter, Ben Z Stanger, David Issadore
Improved diagnostics for pancreatic ductal adenocarcinoma (PDAC) to detect the disease at earlier, curative stages and to guide treatments is crucial to progress against this disease. The development of a liquid biopsy for PDAC has proven challenging due to the sparsity and variable phenotypic expression of circulating biomarkers. Here we report methods we developed for isolating specific subsets of extracellular vesicles (EV) from plasma using a novel magnetic nanopore capture technique. In addition, we present a workflow for identifying EV miRNA biomarkers using RNA sequencing and machine-learning algorithms, which we used in combination to classify distinct cancer states...
May 7, 2018: Cancer Research
Yuanhai You, Yongjun Kou, Longfei Niu, Qiong Jia, Yahui Liu, Mark R Davies, Mark J Walker, Jiaqiang Zhu, Jianzhong Zhang
The incidence of scarlet fever cases remains high in China. Here, we report the complete genome sequence of a Streptococcus pyogenes isolate of serotype M12, which has been confirmed as the predominant serotype in recent outbreaks. Genome sequencing was achieved by a combination of Oxford Nanopore MinION and Illumina methodologies.
May 3, 2018: Genome Announcements
Liang Gong, Chee-Hong Wong, Wei-Chung Cheng, Harianto Tjong, Francesca Menghi, Chew Yee Ngan, Edison T Liu, Chia-Lin Wei
Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( ), to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation...
April 30, 2018: Nature Methods
Chirag Jain, Alexander Dilthey, Sergey Koren, Srinivas Aluru, Adam M Phillippy
Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long-read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for efficiency. In this article, we combine a fast approximate read mapping algorithm based on minimizers with a novel MinHash identity estimation technique to achieve both scalability and precision...
April 30, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Federico Tondini, Vladimir Jiranek, Paul R Grbin, Cristobal A Onetto
Here, we report the first sequenced genome of an indigenous Australian wine isolate of Torulaspora delbrueckii using the Oxford Nanopore MinION and Illumina HiSeq sequencing platforms. The genome size is 9.4 Mb and contains 4,831 genes.
April 26, 2018: Genome Announcements
Daniel H Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic, Rohan B H Williams
BACKGROUND: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets...
April 20, 2018: Biology Direct
Amrita Srivathsan, Bilgenur Baloğlu, Wendy Wang, Wei Xin Tan, Denis Bertrand, Amanda Hui Qi Ng, Esther Jia Hui Boey, Jayce Jia Yu Koh, Niranjan Nagarajan, Rudolf Meier
DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory, is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and demonstrate that one flowcell can generate barcodes for ~500 specimens despite the high base-call error rates of MinION™ reads. The pipeline overcomes these errors by first summarizing all reads for the same tagged amplicon as a consensus barcode...
April 19, 2018: Molecular Ecology Resources
Mari Tohya, Tsutomu Sekizaki, Tohru Miyoshi-Akiyama
Streptococcus ruminantium sp. nov. of type strain GUT-187T, previously classified as Streptococcus suis serotype 33, is a recently described novel streptococcal species. This study was designed to determine the complete genome sequence of S. ruminantium GUT-187T using a combination of Oxford Nanopore and the Illumina platform, and to compare this sequence with the genomes of 27 S. suis representative strains. The genome of GUT-187T was 2,090,539 bp in size, with a GC content of 40.01%. This genome contained 1,961 predicted protein coding DNA sequences (CDSs); of these, 1,685 (85...
April 1, 2018: Genome Biology and Evolution
Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, Xin Gao
Motivation: Oxford Nanopore sequencing is a rapidly developed sequencing technology in recent years. To keep pace with the explosion of the downstream data analytical tools, a versatile Nanopore sequencing simulator is needed to complement the experimental data as well as to benchmark those newly developed tools. However, all the currently available simulators are based on simple statistics of the produced reads, which have difficulty in capturing the complex nature of the Nanopore sequencing procedure, the main task of which is the generation of raw electrical current signals...
April 6, 2018: Bioinformatics
Christophe Audebert, David Hot, Ségolène Caboche
High throughput sequencing has opened up new clinical opportunities moving towards a medicine of precision. Oncology, infectious diseases or human genomics, many applications have been developed in recent years. The introduction of a third generation of nanopore-based sequencing technology, addressing some of the weaknesses of the previous generation, heralds a new revolution. Portability, real time, long reads and marginal investment costs, these promising new technologies point to a new shift of paradigm...
April 2018: Médecine Sciences: M/S
Cheriyacheruvakkara Owais, Anto James, Chris John, Rama Dhali, Rotti Srinivasamurthy Swathi
Research on the permeation of various species through one-atom-thick nanoporous carbon membranes has gained an unprecedented importance in the last decade, thanks to the development of numerous theoretical design strategies for a plethora of applications ranging from gas separation, water desalination, isotope separation, and chiral separation, to DNA sequencing. Although some of the recent experiments have demonstrated successful performance of such carbon membranes in sieving, many of the suggested applications are yet to be realized in experiments...
April 12, 2018: Journal of Physical Chemistry. B
Rabaab Zahra, Saba Javeed, Bibi Malala, Dmitriy Babenko, Mark A Toleman
Objectives: To discover the Escherichia coli STs and associated resistance mechanisms in the community in Islamabad, Pakistan by analysis of E. coli isolates in sewage. Methods: One hundred and ten E. coli were isolated from sewage across the city of Islamabad without antibiotic bias and confirmed as E. coli by MALDI-TOF MS. Isolates were characterized by fumC/fimH (CH) typing and core-genome MLST. Resistance mechanisms, virulence genes, phylotypes and plasmid incompatibility types were determined in a subset of isolates by in silico analysis...
April 10, 2018: Journal of Antimicrobial Chemotherapy
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