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https://www.readbyqxmd.com/read/28218898/detecting-dna-cytosine-methylation-using-nanopore-sequencing
#1
Jared T Simpson, Rachael E Workman, P C Zuzarte, Matei David, L J Dursi, Winston Timp
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.
February 20, 2017: Nature Methods
https://www.readbyqxmd.com/read/28218897/mapping-dna-methylation-with-high-throughput-nanopore-sequencing
#2
Arthur C Rand, Miten Jain, Jordan M Eizenga, Audrey Musselman-Brown, Hugh E Olsen, Mark Akeson, Benedict Paten
DNA chemical modifications regulate genomic function. We present a framework for mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION using this nanopore sequencer's ionic current signal. We map three cytosine variants and two adenine variants. The results show that our model is sensitive enough to detect changes in genomic DNA methylation levels as a function of growth phase in Escherichia coli.
February 20, 2017: Nature Methods
https://www.readbyqxmd.com/read/28163813/hematospermia-in-a-returned-traveler
#3
Raynell Lang, Jessica Minion, Alexander Wong
Hematospermia is a common complaint among patients seen in outpatient urology clinics. The differential diagnosis is broad and includes inflammatory, infectious, neoplastic, structural, systemic, and traumatic causes. The most common infectious causes are uropathogens and sexually transmitted infections. However, with increasing global travel, physicians must maintain a high clinical suspicion for pathogens not endemic to their region, including Echinococcus, Mycobacterium tuberculosis, and Schistosoma.1 We present a case of hematospermia in a traveler returning from Eastern Africa with exposure to Lake Malawi...
January 2017: Canadian Urological Association Journal, Journal de L'Association des Urologues du Canada
https://www.readbyqxmd.com/read/28155888/forensic-snp-genotyping-using-nanopore-minion-sequencing
#4
Senne Cornelis, Yannick Gansemans, Lieselot Deleye, Dieter Deforce, Filip Van Nieuwerburgh
One of the latest developments in next generation sequencing is the Oxford Nanopore Technologies' (ONT) MinION nanopore sequencer. We studied the applicability of this system to perform forensic genotyping of the forensic female DNA standard 9947 A using the 52 SNP-plex assay developed by the SNPforID consortium. All but one of the loci were correctly genotyped. Several SNP loci were identified as problematic for correct and robust genotyping using nanopore sequencing. All these loci contained homopolymers in the sequence flanking the forensic SNP and most of them were already reported as problematic in studies using other sequencing technologies...
February 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043580/application-of-highly-portable-minion-nanopore-sequencing-technology-for-the-monitoring-of-nosocomial-tuberculosis-infection
#5
Matthew Bates, Pascal Polepole, Nathan Kapata, Matt Loose, Justin O'Grady
Referral hospitals in sub-Saharan Africa concentrate large numbers of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) patients, failed by community TB services. We have previously shown, from enhanced screening and through autopsy studies, a significant burden of missed TB infections at the University Teaching Hospital, Lusaka, Zambia, with many patients dying or being discharged without treatment. With minimal TB isolation facilities and minimal political will to invest in broader screening and isolation, the risk of nosocomial transmission is likely to be extremely high...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27964738/erratum-to-the-oxford-nanopore-minion-delivery-of-nanopore-sequencing-to-the-genomics-community
#6
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson
No abstract text is available yet for this article.
December 13, 2016: Genome Biology
https://www.readbyqxmd.com/read/27939320/minion-as-part-of-a-biomedical-rapidly-deployable-laboratory
#7
Mathias C Walter, Katrin Zwirglmaier, Philipp Vette, Scott A Holowachuk, Kilian Stoecker, Gelimer H Genzel, Markus H Antwerpen
Fast turnaround times are of utmost importance for biomedical reconnaissance, particularly regarding dangerous pathogens. Recent advances in sequencing technology and its devices allow sequencing within a short time frame outside stationary laboratories close to the epicenter of the outbreak. In our study, we evaluated the portable sequencing device MinION as part of a rapidly deployable laboratory specialized in identification of highly pathogenic agents. We tested the device in the course of a NATO live agent exercise in a deployable field laboratory in hot climate conditions...
December 6, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27936026/a-comparison-and-integration-of-miseq-and-minion-platforms-for-sequencing-single-source-and-mixed-mitochondrial-genomes
#8
Michael R Lindberg, Sarah E Schmedes, F Curtis Hewitt, Jamie L Haas, Krista L Ternus, Dana R Kadavy, Bruce Budowle
Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes...
2016: PloS One
https://www.readbyqxmd.com/read/27903931/comparison-of-perioperative-outcomes-in-endovascular-versus-open-repair-for-juxtarenal-and-pararenal-aortic-aneurysms-a-propensity-matched-analysis
#9
Nathan T Orr, Daniel L Davenport, David J Minion, Eleftherios S Xenos
OBJECTIVE: Endoluminal aortic aneurysm repair is suitable within certain anatomic specifications. This study aims to compare 30-day outcomes of endovascular versus open repairs for juxtarenal and pararenal aortic aneurysms (JAA/PAAs). METHODS: The ACS-NSQIP database was queried from 2012 to 2015 for JAA/PAA repairs. Procedures characterized as emergent were included in the study; however, failed prior repairs and ruptured aneurysms were excluded. The preoperative and perioperative patient characteristics, operative techniques, and outcome variables were compared between the open aortic repair and the endovascular aortic repair groups...
November 30, 2016: Vascular
https://www.readbyqxmd.com/read/27887629/the-oxford-nanopore-minion-delivery-of-nanopore-sequencing-to-the-genomics-community
#10
Miten Jain, Hugh E Olsen, Benedict Paten, Mark Akeson
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
November 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27872319/classification-of-chimney-evar-related-endoleaks-insights-from-the-pericles-registry
#11
EDITORIAL
Konstantinos P Donas, Frank J Criado, Giovanni Torsello, Frank J Veith, David J Minion
No abstract text is available yet for this article.
November 21, 2016: Journal of Endovascular Therapy
https://www.readbyqxmd.com/read/27748633/the-safety-and-efficacy-of-bevacizumab-in-the-treatment-of-patients-with-recurrent-or-metastatic-cervical-cancer
#12
Lindsey E Minion, Krishnansu S Tewari
Bevacizumab is a recombinant humanized monoclonal antibody against vascular endothelial growth factor (VEGF). (Avastin; Genetech, Inc, San Francisco, CA) Angiogenesis is blocked by the binding of bevacizumab to VEGF, inhibiting the binding of this ligand to the VEGF receptor. On 14 August 2014 the Food and Drug Administration (FDA) approved use of bevacizumab in persistent, recurrent, or metastatic cervical cancer. Areas covered: Herein we review pharmacodynamics and kinetics, clinical data and treatment-related toxicities of bevacizumab in the treatment of metastatic, recurrent or persistent cervical cancer...
March 2017: Expert Review of Anticancer Therapy
https://www.readbyqxmd.com/read/27746156/cost-analysis-of-iliac-stenting-performed-in-the-operating-room-and-the-catheterization-lab-a-case-control-study
#13
Sooyeon Kim, Sage P Kramer, Adam J Dugan, David J Minion, John C Gurley, Daniel L Davenport, Victor A Ferraris, Sibu P Saha
BACKGROUND: Iliac arterial stenting is performed both in the operating room (OR) and the catheterization lab (CL). To date, no analysis has compared resource utilization between these locations. METHODS: Consecutive patients (n = 105) treated at a single center were retrospectively analyzed. Patients included adults with chronic, symptomatic iliac artery stenosis with a minimum Rutherford classification (RC) of 3, treated with stents. Exclusion criteria were prior stenting, acute ischemia, or major concomitant procedures...
December 2016: International Journal of Surgery
https://www.readbyqxmd.com/read/27724982/tp53-gene-mutation-analysis-in-chronic-lymphocytic-leukemia-by-nanopore-minion-sequencing
#14
COMPARATIVE STUDY
Crescenzio Francesco Minervini, Cosimo Cumbo, Paola Orsini, Claudia Brunetti, Luisa Anelli, Antonella Zagaria, Angela Minervini, Paola Casieri, Nicoletta Coccaro, Giuseppina Tota, Luciana Impera, Annamaria Giordano, Giorgina Specchia, Francesco Albano
BACKGROUND: The assessment of TP53 mutational status is becoming a routine clinical practice for chronic lymphocytic leukemia patients (CLL). A broad spectrum of molecular techniques has been employed so far, including both direct Sanger sequencing and next generation sequencing. Oxford Nanopore Technologies recently released the MinION an USB-interfaced sequencer. In this paper we report our experience, with the MinION technology for the detection of the TP53 gene mutation in CLL patients...
October 10, 2016: Diagnostic Pathology
https://www.readbyqxmd.com/read/27667325/identification-of-bacterial-pathogens-and-antimicrobial-resistance-directly-from-clinical-urines-by-nanopore-based-metagenomic-sequencing
#15
K Schmidt, S Mwaigwisya, L C Crossman, M Doumith, D Munroe, C Pires, A M Khan, N Woodford, N J Saunders, J Wain, J O'Grady, D M Livermore
OBJECTIVES: The introduction of metagenomic sequencing to diagnostic microbiology has been hampered by slowness, cost and complexity. We explored whether MinION nanopore sequencing could accelerate diagnosis and resistance profiling, using complicated urinary tract infections as an exemplar. METHODS: Bacterial DNA was enriched from clinical urines (n = 10) and from healthy urines 'spiked' with multiresistant Escherichia coli (n = 5), then sequenced by MinION...
January 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/27660317/multimethod-study-of-a-large-scale-programme-to-improve-patient-safety-using-a-harm-free-care-approach
#16
Maxine Power, Liz Brewster, Gareth Parry, Ailsa Brotherton, Joel Minion, Piotr Ozieranski, Sarah McNicol, Abigail Harrison, Mary Dixon-Woods
OBJECTIVES: We aimed to evaluate whether a large-scale two-phase quality improvement programme achieved its aims and to characterise the influences on achievement. SETTING: National Health Service (NHS) in England. PARTICIPANTS: NHS staff. INTERVENTIONS: The programme sought to (1) develop a shared national, regional and locally aligned safety focus for 4 high-cost, high volume harms; (2) establish a new measurement system based on a composite measure of 'harm-free' care and (3) deliver improved outcomes...
September 22, 2016: BMJ Open
https://www.readbyqxmd.com/read/27646134/oxford-nanopore-minion-sequencing-and-genome-assembly
#17
REVIEW
Hengyun Lu, Francesca Giordano, Zemin Ning
The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT)...
October 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27614348/nanocall-an-open-source-basecaller-for-oxford-nanopore-sequencing-data
#18
Matei David, L J Dursi, Delia Yao, Paul C Boutros, Jared T Simpson
MOTIVATION: The highly portable Oxford Nanopore MinION sequencer has enabled new applications of genome sequencing directly in the field. However, the MinION currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls. RESULTS: To allow offline and private analysis of MinION data, we created Nanocall. Nanocall is the first freely available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection...
January 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27600047/characterization-of-two-multidrug-resistant-inca-c-plasmids-from-the-1960s-by-using-the-minion-sequencer-device
#19
Mónika Szabó, Tibor Nagy, Tímea Wilk, Tibor Farkas, Anna Hegyi, Ferenc Olasz, János Kiss
Two A/C incompatibility group (IncA/C family) plasmids from the 1960s have been sequenced and classified into the A/C2 type 1 group. R16a and IP40a contain novel antibiotic resistance islands and a complete GIsul2 genomic island not previously found in the family. In the 173.1-kb R16a, the 29.9-kb antibiotic resistance island (ARI) is located in a unique backbone position not utilized by ARIs. ARIR16a consists of Tn1, Tn6020, and Tn6333, harboring the resistance genes blaTEM-1D and aphA1b and a mer module, respectively; a truncated Tn5393 copy; and a gene cluster with unknown function...
November 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27585964/wgs-for-surveillance-of-antimicrobial-resistance-a-pilot-study-to-detect-the-prevalence-and-mechanism-of-resistance-to-azithromycin-in-a-uk-population-of-non-typhoidal-salmonella
#20
Satheesh Nair, Philip Ashton, Michel Doumith, Steve Connell, Anais Painset, Solomon Mwaigwisya, Gemma Langridge, Elizabeth de Pinna, Gauri Godbole, Martin Day
OBJECTIVES: WGS and phenotypic methods were used to determine the prevalence of azithromycin resistance in Salmonella enterica isolates from the UK and to identify the underlying mechanisms of resistance. METHODS: WGS by Illumina HiSeq was carried out on 683 Salmonella spp. isolates. Known genes associated with azithromycin resistance were detected by WGS using a mapping-based approach. Macrolide resistance determinants were identified and the genomic context of these elements was assessed by various bioinformatics tools...
September 1, 2016: Journal of Antimicrobial Chemotherapy
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