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https://www.readbyqxmd.com/read/29238890/real-time-detection-of-braf-v600e-mutation-from-archival-hairy-cell-leukemia-ffpe-tissue-by-nanopore-sequencing
#1
Davide Vacca, Valeria Cancila, Alessandro Gulino, Giosuè Lo Bosco, Beatrice Belmonte, Arianna Di Napoli, Ada Maria Florena, Claudio Tripodo, Walter Arancio
The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixation protocols. In order to investigate the suitability of MinION sequencing on formalin-fixed paraffin-embedded samples, the presence and frequency of BRAF c.1799T > A mutation was investigated in two archival tissue specimens of Hairy cell leukemia and Hairy cell leukemia Variant...
December 13, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/29237003/illumina-short-read-and-minion-long-read-wgs-to-characterize-the-molecular-epidemiology-of-an-ndm-1-serratia-marcescens-outbreak-in-romania
#2
H T T Phan, N Stoesser, I E Maciuca, F Toma, E Szekely, M Flonta, A T M Hubbard, L Pankhurst, T Do, T E A Peto, A S Walker, D W Crook, D Timofte
Background and Objectives: Serratia marcescens is an emerging nosocomial pathogen, and the carbapenemase blaNDM has been reported in several surveys in Romania. We aimed to investigate the molecular epidemiology of S. marcescens in two Romanian hospitals over 2010-15, including a neonatal NDM-1 S. marcescens outbreak. Methods: Isolates were sequenced using Illumina technology together with carbapenem-non-susceptible NDM-1-positive and NDM-1-negative Klebsiella pneumoniae and Enterobacter cloacae to provide genomic context...
December 8, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29224067/multiplexed-targeted-sequencing-for-oxford-nanopore-minion-a-detailed-library-preparation-procedure
#3
Timokratis Karamitros, Gkikas Magiorkinis
MinION is a small form factor sequencer recently retailed by Oxford Nanopore technologies. This lighter-sized USB3.0-interfaced device uses innovative nanotechnology to generate extra-long reads from libraries prepared using only standard molecular biology lab equipment. The flexibility and the portability of the platform makes it ideal for point-of-interest and real-time surveillance applications. However, MinION's limited capacity is not enough for the study of specific targets within larger genomes. Apart from just PCR-amplifying regions of interest, the capture of long reads spanning the edges of known-unknown genomic regions is of great importance for structural studies, such as the identification of mobile elements' integrations sites, bridging over low complexity repetitive regions etc...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29221894/efficacy-of-an-inactivated-mycoplasma-hyorhinis-vaccine-in-pigs
#4
Brian Martinson, Whitney Zoghby, Kenneth Barrett, Lawrence Bryson, Rodney Christmas, F C Minion, Jeremy Kroll
Lameness and polyserositis in pigs caused by Mycoplasma hyorhinis are generally treated with antibiotics and may require multiple doses. The costs of these antibiotics combined with economic losses from culling and reduced feed conversion due to lameness are hardships to the swine producer. In this study we have demonstrated efficacy of an inactivated M. hyorhinis vaccine administered to three-week old caesarian-derived colostrum-deprived piglets. Three doses of vaccine (high, medium, and low) were evaluated and compared to a placebo control...
December 5, 2017: Vaccine
https://www.readbyqxmd.com/read/29186559/phyloscanner-inferring-transmission-from-within-and-between-host-pathogen-genetic-diversity
#5
Chris Wymant, Matthew Hall, Oliver Ratmann, David Bonsall, Tanya Golubchik, Mariateresa de Cesare, Astrid Gall, Marion Cornelissen, Christophe Fraser
A central feature of pathogen genomics is that different infectious particles (virions, bacterial cells, etc.) within an infected individual may be genetically distinct, with patterns of relatedness amongst infectious particles being the result of both within-host evolution and transmission from one host to the next. Here we present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone...
November 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29183387/nanopore-sequencing-of-full-length-brca1-mrna-transcripts-reveals-co-occurrence-of-known-exon-skipping-events
#6
Lucy C de Jong, Simone Cree, Vanessa Lattimore, George A R Wiggins, Amanda B Spurdle, Allison Miller, Martin A Kennedy, Logan C Walker
BACKGROUND: Laboratory assays evaluating the effect of DNA sequence variants on BRCA1 mRNA splicing may contribute to classification by providing molecular evidence. However, our knowledge of normal and aberrant BRCA1 splicing events to date has been limited to data derived from assays targeting partial transcript sequences. This study explored the utility of nanopore sequencing to examine whole BRCA1 mRNA transcripts and to provide accurate categorisation of in-frame and out-of-frame splicing events...
November 28, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29182147/rapid-re-identification-of-human-samples-using-portable-dna-sequencing
#7
Sophie Zaaijer, Assaf Gordon, Daniel Speyer, Robert Piccone, Simon Cornelis Groen, Yaniv Erlich
DNA re-identification is used for a broad suite of applications, ranging from cell line authentication to forensics. However, current re-identification schemes suffer from high latency and limited access. Here, we describe a rapid, inexpensive, and portable strategy to robustly re-identify human DNA called 'MinION sketching'. MinION sketching requires as few as 3 min of sequencing and 60-300 random SNPs to re-identify a sample enabling near real-time applications of DNA re-identification. Our method capitalizes on the rapidly growing availability of genomic reference data for cell lines, tissues in biobanks, and individuals...
November 28, 2017: ELife
https://www.readbyqxmd.com/read/29177090/completing-bacterial-genome-assemblies-with-multiplex-minion-sequencing
#8
Ryan R Wick, Louise M Judd, Claire L Gorrie, Kathryn E Holt
Illumina sequencing platforms have enabled widespread bacterial whole genome sequencing. While Illumina data is appropriate for many analyses, its short read length limits its ability to resolve genomic structure. This has major implications for tracking the spread of mobile genetic elements, including those which carry antimicrobial resistance determinants. Fully resolving a bacterial genome requires long-read sequencing such as those generated by Oxford Nanopore Technologies (ONT) platforms. Here we describe our use of the ONT MinION to sequence 12 isolates of Klebsiella pneumoniae on a single flow cell...
October 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29163399/minion-nanopore-sequencing-enables-correlation-between-resistome-phenotype-and-genotype-of-coliform-bacteria-in-municipal-sewage
#9
Yu Xia, An-Dong Li, Yu Deng, Xiao-Tao Jiang, Li-Guan Li, Tong Zhang
Wastewater treatment plants (WWTPs) functioned as the intersection between the human society and nature environment, are receiving increasingly more attention on risk assessment of the acquisition of environmental antibiotic resistance genes (ARGs) by pathogenetic populations during treatment. However, because of the general lack of robust resistome profiling methods, genotype, and resistance phenotype is still poorly correlated in human pathogens of sewage samples. Here we applied MinION sequencing to quantify the resistance genes of multiple antibiotic resistant (MAR) coliform bacteria, a common indicator for human enteric pathogens in sewage samples...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29136087/the-utility-and-perspectives-of-ngs-based-methods-in-bsl-3-and-bsl-4-laboratory-sequencing-and-analysis-strategies
#10
Tomasz Wolkowicz
Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e...
November 10, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29122881/whole-genome-sequencing-of-a-human-clinical-isolate-of-emm28-streptococcus-pyogenes-causing-necrotizing-fasciitis-acquired-contemporaneously-with-hurricane-harvey
#11
S Wesley Long, Priyanka Kachroo, James M Musser, Randall J Olsen
We discovered an emm28 Streptococcus pyogenes isolate causing necrotizing fasciitis in a patient exposed to the floodwaters of Hurricane Harvey in the Houston, TX, metropolitan area in August 2017. The Oxford Nanopore MinION instrument provided sufficient genome sequence data within 1 h of beginning sequencing to close the genome.
November 9, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29122092/rapid-and-accurate-sequencing-of-enterovirus-genomes-using-minion-nanopore-sequencer
#12
Ji Wang, Yue Hua Ke, Yong Zhang, Ke Qiang Huang, Lei Wang, Xin Xin Shen, Xiao Ping Dong, Wen Bo Xu, Xue Jun Ma
OBJECTIVE: Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. METHODS: In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION...
October 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/29117310/sequencing-and-phasing-cancer-mutations-in-lung-cancers-using-a-long-read-portable-sequencer
#13
Ayako Suzuki, Mizuto Suzuki, Junko Mizushima-Sugano, Martin C Frith, Wojciech Makalowski, Takashi Kohno, Sumio Sugano, Katsuya Tsuchihara, Yutaka Suzuki
Here, we employed cDNA amplicon sequencing using a long-read portable sequencer, MinION, to characterize various types of mutations in cancer-related genes, namely, EGFR, KRAS, NRAS and NF1. For homozygous SNVs, the precision and recall rates were 87.5% and 91.3%, respectively. For previously reported hotspot mutations, the precision and recall rates reached 100%. The precise junctions of EML4-ALK, CCDC6-RET and five other gene fusions were also detected. Taking advantages of long-read sequencing, we conducted phasing of EGFR mutations and elucidated the mutational allelic backgrounds of anti-tumor drug-sensitive and resistant mutations, which could provide useful information for selecting therapeutic approaches...
June 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29109544/mapping-and-phasing-of-structural-variation-in-patient-genomes-using-nanopore-sequencing
#14
Mircea Cretu Stancu, Markus J van Roosmalen, Ivo Renkens, Marleen M Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan, Jerome Korzelius, Ewart de Bruijn, Edwin Cuppen, Michael E Talkowski, Tobias Marschall, Jeroen de Ridder, Wigard P Kloosterman
Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements...
November 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/29103684/age-susceptibility-of-caesarian-derived-colostrum-deprived-pigs-to-mycoplasma-hyorhinis-challenge
#15
Brian Martinson, F C Minion, Jeremy Kroll, Joseph Hermann
Mycoplasma hyorhinis (MHR) is a major cause of lameness, arthritis, and polyserositis among growing pigs. Reduced performance and culling due to MHR infection result in economic losses in swine production. We have previously developed an MHR challenge model in seven week-old CDCD pigs using cell-associated challenge material which results in both severe pericarditis and lameness. In this study we sequentially challenged CDCD pigs at seven, ten, thirteen, and sixteen weeks of age. Lameness was observed in >60% of the animals in the first three age groups but only 33% in the oldest age group...
October 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/29102105/cholesterol-exacerbates-mycoplasma-hyopneumoniae-induced-apoptosis-via-stimulating-proliferation-and-adhesion-to-porcine-alveolar-macrophages
#16
Maojun Liu, Gaimei Du, Beibei Liu, Yun Hu, Jie Liu, Yimin Jia, F Chris Minion, Guoqing Shao, Ruqian Zhao
Mycoplasma hyopneumoniae (M. hyo) is the agent of porcine enzootic pneumonia, a disease that causes considerable economic losses in the swine industry. Induction of apoptosis in porcine alveolar macrophages is an important pathogenic mechanism of M. hyo. Cholesterol has been reported to influence cell adherence and cell invasion of Mycoplasma gallisepticum and Mycoplasma fermentans leading to apoptosis, but the role of cholesterol on the apoptotic inducing activity of M. hyo remains unknown. In this study, we found a positive correlation between cholesterol level and M...
November 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/29099796/genome-analysis-and-genetic-stability-of-the-cryptophlebia-leucotreta-granulovirus-crlegv-sa-after-15-years-of-commercial-use-as-a-biopesticide
#17
Marcel van der Merwe, Michael D Jukes, Lukasz Rabalski, Caroline Knox, John K Opoku-Debrah, Sean D Moore, Martyna Krejmer-Rabalska, Boguslaw Szewczyk, Martin P Hill
Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae) is an indigenous pest in southern Africa which attacks citrus fruits and other crops. To control T. leucotreta in South Africa, an integrated pest management (IPM) programme incorporating the baculovirus Cryptophlebialeucotreta granulovirus (CrleGV-SA) as a biopesticide has been implemented. This study investigated the genetic stability of a commercially produced CrleGV-SA product that has been applied in the field since 2000. Seven representative full-genome sequences of the CrleGV-SA isolate spanning a 15-year period were generated and compared with one another...
November 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29089590/campylobacter-fetus-meningitis-confirmed-by-a-16s-rrna-gene-analysis-using-the-minion-nanopore-sequencer-south-korea-2016
#18
Jangsup Moon, Narae Kim, Han Sang Lee, Hye-Rim Shin, Soon-Tae Lee, Keun-Hwa Jung, Kyung-Il Park, Sang Kun Lee, Kon Chu
No abstract text is available yet for this article.
November 1, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/29078748/whole-genome-assembly-of-babesia-ovata-and-comparative-genomics-between-closely-related-pathogens
#19
Junya Yamagishi, Masahito Asada, Hassan Hakimi, Takeshi Q Tanaka, Chihiro Sugimoto, Shin-Ichiro Kawazu
BACKGROUND: Babesia ovata, belonging to the phylum Apicomplexa, is an infectious parasite of bovids. It is not associated with the manifestation of severe symptoms, in contrast to other types of bovine babesiosis caused by B. bovis and B. bigemina; however, upon co-infection with Theileria orientalis, it occasionally induces exacerbated symptoms. Asymptomatic chronic infection in bovines is usually observed only for B. ovata. Comparative genomic analysis could potentially reveal factors involved in these distinguishing characteristics; however, the genomic and molecular basis of these phenotypes remains elusive, especially in B...
October 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29074664/complete-genome-sequence-of-kluyvera-intestini-sp-nov-isolated-from-the-stomach-of-a-patient-with-gastric-cancer
#20
George Tetz, Maria Vecherkovskaya, Paul Zappile, Igor Dolgalev, Aristotelis Tsirigos, Adriana Heguy, Victor Tetz
We report here an update to the draft genome sequence of Kluyvera intestini sp. nov. strain GT-16, generated using MinION long-read sequencing technology. The complete genome sequence of the human-derived strain GT-16 measured 5,768,848 bp. An improved high-quality complete genome sequence provides insights into the mobility potential of resistance genes in this species.
October 26, 2017: Genome Announcements
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