Au, Chun Hang Ho, Dona N Ip, Beca B K Wan, Thomas S K Ng, Margaret H L Chiu, Edmond K W Chan, Tsun Leung Ma, Edmond S K
Published in
Cancer genetics
Detection of chromosomal translocation is a key component in diagnosis and management of acute myeloid leukemia (AML). Targeted RNA next-generation sequencing (NGS) is emerging as a powerful and clinically practical tool, but it depends on expression of RNA transcript from the underlying DNA translocation. Here, we show the clinical utility of nano...
Radhakrishnan, Guru V. Cook, Nicola M. Bueno-Sancho, Vanessa Lewis, Clare M. Persoons, Antoine Mitiku, Abel Debebe Heaton, Matthew Davey, Phoebe E. Abeyo, Bekele Alemayehu, Yoseph
...
Published in
BMC Biology
BackgroundEffective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics re...
Bialasiewicz, Seweryn Duarte, Tania P. S. Nguyen, Son H. Sukumaran, Vichitra Stewart, Alexandra Appleton, Sally Pitt, Miranda E. Bainomugisa, Arnold Jennison, Amy V. Graham, Rikki
...
Published in
BMC Infectious Diseases
BackgroundRapid diagnosis and appropriate treatment is imperative in bacterial sepsis due increasing risk of mortality with every hour without appropriate antibiotic therapy. Atypical infections with fastidious organisms may take more than 4 days to diagnose leading to calls for improved methods for rapidly diagnosing sepsis. Capnocytophaga canimor...
Grünberger, Felix Reichelt, Robert Bunk, Boyke Spröer, Cathrin Overmann, Jörg Rachel, Reinhard Grohmann, Dina Hausner, Winfried
Published in
Frontiers in microbiology
Pyrococcus furiosus DSM 3638 is a model organism for hyperthermophilic archaea with an optimal growth temperature near 100°C. The genome was sequenced about 18 years ago. However, some publications suggest that in contrast to other Pyrococcus species, the genome of P. furiosus DSM 3638 is prone to genomic rearrangements. Therefore, we re-sequenced ...
Prabakar, Rishvanth K. Xu, Liya Hicks, James Smith, Andrew D.
Published in
Genome Biology
We present SMURF-seq, a protocol to efficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form long molecules. Applying SMURF-seq using the Oxford Nanopore MinION yields up to 30 fragments per read, providing an average of 6.2 and up to 7.5 million mappable fragments per run, increasing information throughpu...
Arango-Argoty, G. A. Dai, D. Pruden, A. Vikesland, P. Heath, L. S. Zhang, L.
Published in
Microbiome
BackgroundDirect and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic el...
Rodríguez-Pérez, Héctor Hernández-Beeftink, Tamara Lorenzo-Salazar, José M. Roda-García, José L. Pérez-González, Carlos J. Colebrook, Marcos Flores, Carlos
Published in
BMC Bioinformatics
BackgroundThe Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.ResultsWe present NanoDJ, a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices. It integrates basecalling, ...
Che, You Xia, Yu Liu, Lei Li, An-Dong Yang, Yu Zhang, Tong
Published in
Microbiome
BackgroundWastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown.ResultsIn this study, we combined Oxford Nanopore and I...
Kraft, Florian Wesseler, Katharina Begemann, Matthias Kurth, Ingo Elbracht, Miriam Eggermann, Thomas
Published in
Clinical Epigenetics
BackgroundDeletions of the imprinting centre 1 (IC1) in 11p15.5 are rare and their clinical significance is not only influenced by their parental origin but also by their exact genomic localization. In case the maternal IC1 allele is affected, the deletion is associated with the overgrowth disorder Beckwith-Wiedemann syndrome (BWS) and a gain of me...
Boldogkői, Zsolt Tombácz, Dóra Balázs, Zsolt
Published in
Virus Genes
The temporal coordination of viral gene expression is imperative for the regulation of the herpesvirus replication cycle. While the main factors of this transcriptional coordination are known, the subtler control mechanisms of gene expression remain elusive. Recent long read sequencing-based approached have revealed an intricate meshwork of overlap...
