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Lindsey E Minion, Krishnansu S Tewari
Introduction 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 August 14, 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...
October 17, 2016: Expert Review of Anticancer Therapy
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...
October 12, 2016: International Journal of Surgery
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
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...
September 25, 2016: Journal of Antimicrobial Chemotherapy
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...
2016: BMJ Open
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)...
September 17, 2016: Genomics, Proteomics & Bioinformatics
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 (, 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...
September 10, 2016: Bioinformatics
Mónika Szabó, Tibor Nagy, Tímea Wilk, Tibor Farkas, Anna Hegyi, Ferenc Olasz, János Kiss
Two IncA/C family plasmids from the 1960s have been sequenced and classified into A/C2 Type 1 group. R16a and IP40a contain novel antibiotic resistance islands and a complete GIsul2 island not previously found in the family. In the 173.1 kb R16a the 29.9 kb ARI is located in a unique backbone position not utilized by ARIs. ARIR16a consists of Tn1, Tn6020, Tn6333 harboring the resistance genes blaTEM-1D, aphA1b and a mer module, respectively, a truncated Tn5393 copy and a gene cluster with unknown function. Plasmid IP40a is 170...
September 6, 2016: Antimicrobial Agents and Chemotherapy
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
Alberto Magi, Betti Giusti, Lorenzo Tattini
The Oxford Nanopore Technologies MinION is a new device, based on nanopore sequencing that is able to generate reads of tens of kilobases in length with faster sequencing time with respect to other platforms. To evaluate the capability of nanopore data to be exploited for resequencing analyses we used the largest MinION data set to date and we compared with Illumina and Pacific Biosciences technologies. By using five different mapping approaches we estimated that the global sequencing error rate of MinION reads, mainly caused by inserted and deleted bases, is around 11%...
August 24, 2016: Briefings in Bioinformatics
Yesesri Cherukuri, Sarath Chandra Janga
BACKGROUND: Improved DNA sequencing methods have transformed the field of genomics over the last decade. This has become possible due to the development of inexpensive short read sequencing technologies which have now resulted in three generations of sequencing platforms. More recently, a new fourth generation of Nanopore based single molecule sequencing technology, was developed based on MinION(®) sequencer which is portable, inexpensive and fast. It is capable of generating reads of length greater than 100 kb...
2016: BMC Genomics
Spyros Oikonomopoulos, Yu Chang Wang, Haig Djambazian, Dunarel Badescu, Jiannis Ragoussis
To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length...
2016: Scientific Reports
Andrew C Petersen, David C Oneal, Janice R Seibel, Kylie Poel, Courtney L Daum, Steven P Djordjevic, F Chris Minion
Mycoplasmas are cell wall-less bacteria that infect a variety of animals in a species-specific manner. In swine, Mycoplasma hyopneumoniae is the most virulent and presents the most disease and economic problems to the swine industry. Serological assays are commonly used to assess colonization and disease, but antigenic cross-reactivity between M. hyopneumoniae and other mycoplasma species, most notably Mycoplasma hyorhinis, Mycoplasma hyosynoviae and Mycoplasma flocculare, is a concern. The extent of cross-reactivity has not been thoroughly investigated...
August 30, 2016: Veterinary Microbiology
Chenhao Li, Kern Rei Chng, Esther Jia Hui Boey, Amanda Hui Qi Ng, Andreas Wilm, Niranjan Nagarajan
BACKGROUND: Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relatively high single-read error rates (>10 %), including RNA-seq, haplotype sequencing and 16S sequencing. RESULTS: We developed the Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) as a strategy for obtaining long and accurate nanopore reads, starting with low input DNA...
2016: GigaScience
Minh Duc Cao, Devika Ganesamoorthy, Alysha G Elliott, Huihui Zhang, Matthew A Cooper, Lachlan J M Coin
The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance. However, there are few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, strain typing and antibiotic resistance profile identification...
2016: GigaScience
Matthew Loose, Sunir Malla, Michael Stout
The Oxford Nanopore Technologies MinION sequencer enables the selection of specific DNA molecules for sequencing by reversing the driving voltage across individual nanopores. To directly select molecules for sequencing, we used dynamic time warping to match reads to reference sequences. We demonstrate our open-source Read Until software in real-time selective sequencing of regions within small genomes, individual amplicon enrichment and normalization of an amplicon set.
September 2016: Nature Methods
Eng Wee Chua, Pei Yuen Ng
The launch of the MinION Access Program has caused much activity within the scientific community. MinION represents a keenly anticipated, novel addition to the current melange of commercial sequencers. Driven by the nanopore sequencing mechanism that requires minimal sample manipulation, the device is capable of generating long sequence reads in sizes (up to or exceeding 50 kb) that surpass those of all other platforms. One notable advantage of this feature is that long-range haplotypes can be more accurately resolved; such advantage is particularly pertinent to the genotyping of complex loci such as genes encoding the human leukocyte antigens, which are pivotal determinants of drug hypersensitivity...
2016: Frontiers in Pharmacology
Rebecca C Wilson, Oliver W Butters, Tom Clark, Joel Minion, Andrew Turner, Madeleine J Murtagh
ECOUTER (Employing COnceptUal schema for policy and Translation Engagement in Research) - French for 'to listen' - is a new stakeholder engagement method incorporating existing evidence to help participants draw upon their own knowledge of cognate issues and interact on a topic of shared concern. The results of an ECOUTER can form the basis of recommendations for research, governance, practice and/or policy. This paper describes the development of a digital methodology for the ECOUTER engagement process based on currently available mind mapping freeware software...
2016: F1000Research
Stéphane Deschamps, Joann Mudge, Connor Cameron, Thiruvarangan Ramaraj, Ajith Anand, Kevin Fengler, Kevin Hayes, Victor Llaca, Todd J Jones, Gregory May
The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores. While MinION long reads have an error rate substantially higher than the ones produced by short-read sequencing technologies, they can generate de novo assemblies of microbial genomes, after an initial correction step that includes alignment of Illumina sequencing data or detection of overlaps between Oxford Nanopore reads to improve accuracy...
2016: Scientific Reports
Timokratis Karamitros, Ian Harrison, Renata Piorkowska, Aris Katzourakis, Gkikas Magiorkinis, Jean Lutamyo Mbisa
Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy...
2016: PloS One
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