Article
Biochemical Research Methods
Kijin Kim, Kyungmin Park, Seonghyeon Lee, Seung-Hwan Baek, Tae-Hun Lim, Jongwoo Kim, Balachandran Manavalan, Jin-Won Song, Won-Keun Kim
Summary: VirPipe is a new pipeline for detecting viral genomes from Nanopore or Illumina sequencing, with streamlined installation and customization.
Article
Plant Sciences
Hyo-Jeong Lee, Sang-Min Kim, Rae-Dong Jeong
Summary: In this study, wheat virome in three different geographical regions of Korea was investigated using ONT and Illumina sequencing. Five viral species, including newly identified SCYLV and WLYaV in Korean wheat samples, were identified. Both ONT and Illumina sequencing were reliable and powerful tools for detecting and identifying wheat viruses.
Article
Biochemistry & Molecular Biology
Amrita Srivathsan, Rebecca Ker Loh, Elliott James Ong, Leshon Lee, Yuchen Ang, Sujatha Narayanan Kutty, Rudolf Meier
Summary: DNA obtained from invertebrates can be used to survey vertebrate communities, but the interaction between the two groups is not well understood. This study found that there was no specialization in the interactions between the dung and carrion fly community and the vertebrate species. However, uncommon fly species can carry the DNA signal for vertebrate species that are difficult to detect using iDNA. The fly community sourced for iDNA was unexpectedly rich and carried DNA for a variety of rare and common vertebrate species.
Article
Microbiology
Meshack Juma, Arun Sankaradoss, Redcliff Ndombi, Patrick Mwaura, Tina Damodar, Junaid Nazir, Awadhesh Pandit, Rupsy Khurana, Moses Masika, Ruth Chirchir, John Gachie, Sudhir Krishna, Ramanathan Sowdhamini, Omu Anzala, Iyer S. Meenakshi
Summary: This study highlights the utility of mobile DNA sequencing technology in producing a consensus genome for sequence typing and detecting genetic determinants of antimicrobial resistance. The workflow used in this study can be applied to any clinical isolate for antimicrobial resistance mutation dataset creation and genome identification, assembly, and analysis. Further research is needed to assess the use of real-time sequencing in outbreak investigations, diagnosis, and infection management, particularly in resource-limited settings.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Sophie A. Simon, Katharina Schmidt, Lea Griesdorn, Andre R. Soares, Till L. V. Bornemann, Alexander J. Probst
Summary: This study evaluated the use of lower-than-recommended DNA quantities for Nanopore library preparation and found that high-quality MAGs could still be recovered when the input level reached 35ng. Furthermore, Nanopore reads from input quantities as low as 1ng improved the quality of hybrid assemblies when combined with short-read data.
Article
Biotechnology & Applied Microbiology
Jidong Lang, Yanju Li, Wenjuan Yang, Ruyi Dong, Yuebin Liang, Jia Liu, Lanyou Chen, Weiwei Wang, Binbin Ji, Geng Tian, Nanying Che, Bo Meng
Summary: This study identified and annotated the genome sequence and ARGs of the newly isolated bacterium A. faecalis PGB1.
Article
Multidisciplinary Sciences
Sudheer Gupta, Ashvini Yadav, Sam Stubbs, Simon Frost, Kudsia Ansari, Ram Kumar Nema, Shashwati Nema, Debasis Biswas
Summary: This study validates the previous findings on the mutations associated with the Chikungunya outbreak and identifies key mutations throughout the entire genome. The analysis shows a close relation between the outbreak strains and the Singapore 2015 strain, and also reveals previously non-existent mutations in the C and E2 genes, as well as in the nsP3 gene.
Article
Biochemical Research Methods
Dylan G. Maghini, Eli L. Moss, Summer E. Vance, Ami S. Bhatt
Summary: Utilizing a combination of short-read metagenomic sequencing and long-read sequencing, high-quality bacterial genomes can be obtained from the complex human gut microbiome, with some challenges to overcome.
Article
Biochemical Research Methods
Hector Rodriguez-Perez, Laura Ciuffreda, Carlos Flores
Summary: NanoCLUST is an analysis pipeline that outperforms other state-of-the-art software in accurately characterizing bacterial identification and abundance profile estimation at the species level, demonstrating its effectiveness with two commercial mock communities.
Article
Biochemistry & Molecular Biology
Filippo Martignano, Uday Munagala, Stefania Crucitta, Alessandra Mingrino, Roberto Semeraro, Marzia Del Re, Iacopo Petrini, Alberto Magi, Silvestro G. Conticello
Summary: Liquid biopsy, particularly analyzing cell-free DNA, is crucial in precision oncology. Nanopore sequencing provides a cost-effective and rapid alternative for detecting copy number variations in plasma DNA, making it accessible for both research and clinical purposes.
Article
Obstetrics & Gynecology
Anna Oberle, Lara Urban, Stefanie Falch-Leis, Chiara Ennemoser, Yoko Nagai, Kyota Ashikawa, Patricia A. Ulm, Markus Hengstschlaeger, Michael Feichtinger
Summary: This study investigated the feasibility of using nanopore technology for full-length 16S rRNA gene sequencing as an alternative approach for endometrial microbiome analysis. Results from experiments on 33 patients seeking infertility treatment showed that nanopore sequencing was reliable and could accurately assess and compare the microbiome composition of different patients.
REPRODUCTIVE BIOMEDICINE ONLINE
(2021)
Article
Multidisciplinary Sciences
Linh Truong, Felipe Ayora, Lloyd D'Orsogna, Patricia Martinez, Dianne De Santis
Summary: Genetic information provides insights into the organism's exome, genome, epigenetics, and structural organization. The development of a cloud-based automated analysis pipeline using Microsoft Azure has been shown to improve the efficiency and cost-effectiveness of HLA genotyping services.
Article
Virology
Kathy K. Li, Betty Lau, Nicolas M. Suarez, Salvatore Camiolo, Rory Gunson, Andrew J. Davison, Richard J. Orton
Summary: Nanopore sequencing is increasingly used in clinical settings due to its portability, cost-effectiveness, and real-time operation. Despite initial challenges, improvements in sequencing hardware and software have mitigated high sequencing error rates. In this study, we evaluated the feasibility of using nanopore sequencing to determine the complete genomes of human cytomegalovirus (HCMV) directly from high-viral-load clinical samples without viral DNA enrichment, PCR amplification, or prior sequence knowledge. Our hybrid bioinformatic approach achieved highly accurate HCMV genomes from urine and lung samples, demonstrating the capability of nanopore sequencing for clinical diagnostics.
Review
Microbiology
Anzaan Dippenaar, Sander N. Goossens, Melanie Grobbelaar, Selien Oostvogels, Bart Cuypers, Kris Laukens, Conor J. Meehan, Robin M. Warren, Annelies van Rie
Summary: The application of portable next-generation sequencing devices is limited in the tuberculosis field, and more research investment is needed to unleash their full potential.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Heon Seok Kim, Susan M. Grimes, Anna C. Hooker, Billy T. Lau, Hanlee P. Ji
Summary: The developed single-cell approach combines long-read and short-read sequencing to detect CRISPR-modified mRNA transcript structures and assess the impact of genetic variants on alternative mRNA isoforms. The method provides targeted genomic edits and transcript isoform structure detection at single-cell resolution.
Article
Biochemical Research Methods
Wouter De Coster, Svenn D'Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Article
Geriatrics & Gerontology
Eline Wauters, Sara Van Mossevelde, Kristel Sleegers, Julie van der Zee, Sebastiaan Engelborghs, Anne Sieben, Rik Vandenberghe, Stephanie Philtjens, Marleen Van den Broeck, Karin Peeters, Ivy Cuijt, Wouter De Coster, Tim Van Langenhove, Patrick Santens, Adrian Ivanoiu, Patrick Cras, Jan L. De Bleecker, Jan Versijpt, Roeland Crols, Nina De Klippel, Jean-Jacques Martin, Peter P. De Deyn, Marc Cruts, Christine Van Broeckhoven
NEUROBIOLOGY OF AGING
(2018)
Article
Clinical Neurology
Rita Cacace, Bavo Heeman, Sara Van Mossevelde, Arne De Roeck, Julie Hoogmartens, Peter De Rijk, Helena Gossye, Kristof De Vos, Wouter De Coster, Mojca Strazisar, Greet De Baets, Joost Schymkowitz, Frederic Rousseau, Nathalie Geerts, Tim De Pooter, Karin Peeters, Anne Sieben, Jean-Jacques Martin, Sebastiaan Engelborghs, Eric Salmon, Patrick Santens, Rik Vandenberghe, Patrick Cras, Peter P. De Deyn, John C. van Swieten, Cornelia M. van Duijn, Julie van der Zee, Kristel Sleegers, Christine Van Broeckhoven, Johan Goeman, Roeland Crols, Dirk Nuytten, Jan L. De Bleecker, Tim Van Langenhove, Adrian Ivanoiu, Olivier Deryck, Bruno Bergmans, Jan Versijpt, Alex Michotte, Jean Delbeck, Christiana Willems, Nina De Klippel
ACTA NEUROPATHOLOGICA
(2019)
Review
Biotechnology & Applied Microbiology
Wouter De Coster, Christine Van Broeckhoven
TRENDS IN BIOTECHNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Wouter De Coster, Peter De Rijk, Arne De Roeck, Tim De Pooter, Svenn D'Hert, Mojca Strazisar, Kristel Sleegers, Christine Van Broeckhoven
Review
Genetics & Heredity
Wouter De Coster, Matthias H. Weissensteiner, Fritz J. Sedlazeck
Summary: Long-read sequencing technologies have advanced to the point where they can be applied to variant detection at a population scale. New computational tools have led to the emergence of population-scale studies in the past two years, with many more expected in the future. The review covers recent developments, challenges, experimental design guidance, as well as strategies for variant validation and genotyping.
NATURE REVIEWS GENETICS
(2021)
Article
Biochemical Research Methods
Wouter De Coster, Rosa Rademakers
Summary: As the cohort size in long-read sequencing projects grows, there is a need for more efficient software to handle and evaluate sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. This article presents novel tools for summarizing experiments, filtering datasets, visualizing phased alignments results, and updates to the NanoPack software suite.
Article
Clinical Neurology
Arne De Roeck, Tobi Van den Bossche, Julie van der Zee, Jan Verheijen, Wouter De Coster, Jasper Van Dongen, Lubina Dillen, Yalda Baradaran-Heravi, Bavo Heeman, Raquel Sanchez-Valle, Albert Llado, Benedetta Nacmias, Sandro Sorbi, Ellen Gelpi, Oriol Grau-Rivera, Estrella Gomez-Tortosa, Pau Pastor, Sara Ortega-Cubero, Maria A. Pastor, Caroline Graff, Hakan Thonberg, Luisa Benussi, Roberta Ghidoni, Giuliano Binetti, Alexandre de Mendonca, Madalena Martins, Barbara Borroni, Alessandro Padovani, Maria Rosario Almeida, Isabel Santana, Janine Diehl-Schmid, Panagiotis Alexopoulos, Jordi Clarimon, Alberto Lleo, Juan Fortea, Magda Tsolaki, Maria Koutroumani, Radoslav Matej, Zdenek Rohan, Peter De Deyn, Sebastiaan Engelborghs, Patrick Cras, Christine Van Broeckhoven, Kristel Sleegers
ACTA NEUROPATHOLOGICA
(2017)
Meeting Abstract
Biochemistry & Molecular Biology
W. De Coster, S. Van Mossevelde, S. Engelborghs, M. Vandenbulcke, L. Mateiu, M. Mattheijssens, K. Peeters, R. Vandenberghe, P. Cras, P. P. De Deyn, M. Cruts, C. Van Broeckhoven
JOURNAL OF NEUROCHEMISTRY
(2016)
Article
Genetics & Heredity
Wouter De Coster, Mojca Strazisar, Peter De Rijk
NAR GENOMICS AND BIOINFORMATICS
(2020)
