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Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets.
Annika Brinkmann, Andreas Andrusch, Ariane Belka, Claudia Wylezich, Dirk Höper, Anne Pohlmann, Thomas Nordahl Petersen, Pierrick Lucas, Yannick Blanchard, Anna Papa, Angeliki Melidou, Bas B Oude Munnink, Jelle Matthijnssens, Ward Deboutte, Richard J Ellis, Florian Hansmann, Wolfgang Baumgärtner, Erhard van der Vries, Albert Osterhaus, Cesare Camma, Iolanda Mangone, Alessio Lorusso, Maurilia Marcacci, Alexandra Nunes, Miguel Pinto, Vítor Borges, Annelies Kroneman, Dennis Schmitz, Victor Max Corman, Christian Drosten, Terry C Jones, Rene S Hendriksen, Frank M Aarestrup, Marion Koopmans, Martin Beer, Andreas Nitsche
Jan 09, 2020
Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral...
external quality assessment high-throughput sequencing next-generation sequencing proficiency testing virus diagnostics Computational Biology Computer Simulation Data analysis Europe Genome Viral High-Throughput Nucleotide Sequencing Humans Intersectoral Collaboration Laboratory Proficiency Testing Reproducibility of Results Sequence Analysis DNA viruses
Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia
Samuel C. B. Stubbs, Barbara A. Blacklaws, Benediktus Yohan, Frilasita A. Yudhaputri, Rahma F. Hayati, Brian Schwem, Edsel M. Salvaña, Raul V. Destura, James S. Lester, Khin S. Myint, R. Tedjo Sasmono, Simon D. W. Frost
Jun 06, 2020
Abstract: Background: Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances...
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.
Armando Arias, Simon J Watson, Danny Asogun, Ekaete Alice Tobin, Jia Lu, My VT Phan, Umaru Jah, Raoul Emeric Guetiya Wadoum, Luke Meredith, Lucy Thorne, Sarah Caddy, Alimamy Tarawalie, Pinky Langat, Gytis Dudas, Nuno R Faria, Simon Dellicour, Abdul Kamara, Brima Kargbo, Brima Osaio Kamara, Sahr Gevao, Daniel Cooper, Matthew Newport, Peter Horby, Jake Dunning, Foday Sahr, Tim Brooks, Andrew JH Simpson, Elisabetta Groppelli, Guoying Liu, Nisha Mulakken, Kate Rhodes, James Akpablie, Zabulon Yoti, Margaret Lamunu, Esther Vitto, Patrick Otim, Collins Owilli, Isaac Boateng, Lawrence Okoror, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Ighodalo Yemisis, Donatus Adomeh, Solomon Ehikhiametalor, Patience Akhilomen, Chris Aire, Andreas Kurth, Nicola Cook, Jan Baumann, Martin Gabriel, Roman Wölfel, Antonino Di Caro, Miles W Carroll, Stephan Günther, John Redd, Dhamari Naidoo, Oliver G Pybus, Andrew Rambaut, Paul Kellam, Ian Goodfellow, Matthew Cotten
Jun 13, 2018
To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources...
Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia
Samuel C. B. Stubbs, Barbara A. Blacklaws, Benediktus Yohan, Frilasita A. Yudhaputri, Rahma F. Hayati, Brian Schwem, Edsel M. Salvaña, Raul V. Destura, James S. Lester, Khin S. Myint, R. Tedjo Sasmono, Simon D. W. Frost
Feb 12, 2021
Abstract: Background: Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances...
Cross-phenotype analysis of Immunochip data identifies KDM4C as a relevant locus for the development of systemic vasculitis.
Lourdes Ortiz-Fernández, Francisco David Carmona, Raquel López-Mejías, Maria Francisca González-Escribano, Paul A Lyons, Ann W Morgan, Amr H Sawalha, Peter A Merkel, Kenneth GC Smith, Miguel A González-Gay, Javier Martín, UK GCA Consortium, Turkish Takayasu Study Group, Vasculitis Clinical Research Consortium, IgAV Study Group, AAV Study group Spanish GCA Study Group
Apr 18, 2018
OBJETIVE: Systemic vasculitides represent a heterogeneous group of rare complex diseases of the blood vessels with a poorly understood aetiology. To investigate the shared genetic component underlying their predisposition, we...
Autoantibodies outcomes research systemic sclerosis Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis Case-Control Studies Epigenesis Genetic Female Genetic Loci Genetic Predisposition to Disease Giant Cell Arteritis HLA-DQ Antigens HLA-DQ beta-Chains Humans Jumonji Domain-Containing Histone Demethylases Linkage Disequilibrium Male Phenotype Polymorphism Single Nucleotide Protein Array Analysis Systemic Vasculitis Takayasu arteritis
Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia.
Samuel C B Stubbs, Barbara A Blacklaws, Benediktus Yohan, Frilasita A Yudhaputri, Rahma F Hayati, Brian Schwem, Edsel M Salvaña, Raul V Destura, James S Lester, Khin S Myint, R Tedjo Sasmono, Simon D W Frost
Mar 16, 2020
BACKGROUND:Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably...
Published by: Virology journal
Research with variola virus after smallpox eradication
In this issue of PLOS Pathogens, Hutson and coworkers at the Centers for Disease Control
and Prevention (CDC) in Atlanta, USA describe a study with infectious variola virus that was
approved by the World Health Organization...
Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity.
Alistair B Russell, Elizaveta Elshina, Jacob R Kowalsky, Aartjan JW Te Velthuis, Jesse D Bloom
May 03, 2019
Influenza virus-infected cells vary widely in their expression of viral genes and only occasionally activate innate immunity. Here, we develop a new method to assess how the genetic variation in viral populations contributes to...
Book Review: Youssef Cassis, Richard S. Grossman & Catherine R. Schenk eds., The Oxford handbook of banking and financial history (Oxford
SA-MI Schneider
Jan 25, 2017
The Oxford Handbook of Banking and Financial History is a timely work of synthesis that consolidates the recent resurgence of scholarly interest in the long-term evolution of the global financial system. Its editors have...
Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum.
Mary Dias, Chitra Pattabiraman, Shilpa Siddappa, Malali Gowda, Anita Shet, Derek Smith, Barbara Muehlemann, Krishnapriya Tamma, Tom Solomon, Terry Jones, Sudhir Krishna
Apr 09, 2019
Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA...
Cemented versus cementless Oxford unicompartmental knee arthroplasty using radiostereometric analysis
B J L Kendrick, B L Kaptein, E R Valstar, H S Gill, W F M Jackson, C A F Dodd, A J Price, D W Murray
Feb 01, 2015
The most common reasons for revision of unicompartmental knee arthroplasty (UKA) are loosening and pain. Cementless components may reduce the revision rate. The aim of this study was to compare the fixation and clinical...
Cemented versus cementless Oxford unicompartmental knee arthroplasty using radiostereometric analysis
B J L Kendrick, B L Kaptein, E R Valstar, H S Gill, W F M Jackson, C A F Dodd, A J Price, D W Murray
Feb 01, 2015
The most common reasons for revision of unicompartmental knee arthroplasty (UKA) are loosening and pain. Cementless components may reduce the revision rate. The aim of this study was to compare the fixation and clinical...
Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.
Kirstyn Brunker, Gurdeep Jaswant, S M Thumbi, Kennedy Lushasi, Ahmed Lugelo, Anna M Czupryna, Fred Ade, Gati Wambura, Veronicah Chuchu, Rachel Steenson, Chanasa Ngeleja, Criselda Bautista, Daria L Manalo, Ma Ricci R Gomez, Maria Yna Joyce V Chu, Mary Elizabeth Miranda, Maya Kamat, Kristyna Rysava, Jason Espineda, Eva Angelica V Silo, Ariane Mae Aringo, Rona P Bernales, Florencio F Adonay, Michael J Tildesley, Denise A Marston, Daisy L Jennings, Anthony R Fooks, Wenlong Zhu, Luke W Meredith, Sarah C Hill, Radoslaw Poplawski, Robert J Gifford, Joshua B Singer, Mathew Maturi, Athman Mwatondo, Roman Biek, Katie Hampson
Mar 26, 2020
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost...
Rabies virus SURVEILLANCE phylogenetic Zoonoses nanopore Lyssavirus Neglected tropical diseases whole genome sequencing MinION Dog-mediated Rabies Field Sequencing
Published by: Wellcome open research
SARS-CoV-2 within-host diversity and transmission.
Katrina A Lythgoe, Matthew Hall, Luca Ferretti, Mariateresa de Cesare, George MacIntyre-Cockett, Amy Trebes, Monique Andersson, Newton Otecko, Emma L Wise, Nathan Moore, Jessica Lynch, Stephen Kidd, Nicholas Cortes, Matilde Mori, Rebecca Williams, Gabrielle Vernet, Anita Justice, Angie Green, Samuel M Nicholls, M Azim Ansari, Lucie Abeler-Dörner, Catrin E Moore, Timothy EA Peto, David W Eyre, Robert Shaw, Peter Simmonds, David Buck, John A Todd, Oxford Virus Sequencing Analysis Group (OVSG), Thomas R Connor, Shirin Ashraf, Ana da Silva Filipe, James Shepherd, Emma C Thomson, COVID-19 Genomics UK (COG-UK) Consortium, David Bonsall, Christophe Fraser, Tanya Golubchik
Mar 10, 2021
Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.
Kirstyn Brunker, Gurdeep Jaswant, SM Thumbi, Kennedy Lushasi, Ahmed Lugelo, Anna M Czupryna, Fred Ade, Gati Wambura, Veronicah Chuchu, Rachel Steenson, Chanasa Ngeleja, Criselda Bautista, Daria L Manalo, Ma Ricci R Gomez, Maria Yna Joyce V Chu, Mary Elizabeth Miranda, Maya Kamat, Kristyna Rysava, Jason Espineda, Eva Angelica V Silo, Ariane Mae Aringo, Rona P Bernales, Florencio F Adonay, Michael J Tildesley, Denise A Marston, Daisy L Jennings, Anthony R Fooks, Wenlong Zhu, Luke W Meredith, Sarah C Hill, Radoslaw Poplawski, Robert J Gifford, Joshua B Singer, Mathew Maturi, Athman Mwatondo, Roman Biek, Katie Hampson
Mar 20, 2020
Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost...
Pan-cancer analysis of whole genomes.
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of...
Cell Proliferation Cellular Senescence Chromothripsis Cloud Computing DNA Mutational Analysis evolution Molecular Female Genome Human Genomics Germ-Line Mutation High-Throughput Nucleotide Sequencing Humans Information Dissemination Male Mutagenesis Mutation Neoplasms Oncogenes Promoter Regions Genetic RNA Splicing Reproducibility of Results Telomerase Telomere
HPG pore
BACKGROUND: The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer available, the...
A Path Analysis of Online Group Buying
Online group buying has emerged as a new bargaining power for many shoppers and become more so as a result of increasingly growing popularity of social networking and community-based web sites. Aside from significant quantity...
Published by: IGI Global Scientific Publishing
The Structure and Replication of Semliki Forest Virus, A Mosquito-Borne Animal Virus
Nicholas Hill Acheson
Jan 01, 0001
Semliki Forest virus is a group A arthropod-borne virus which contains RNA and possesses a lipoprotein envelope. It can be transmitted among animals by mosquitoes in which it multiplies, but its natural host is not known. The...
Published by: Rockefeller University
Meta-analysis and multidisciplinary consensus statement
Siddharth Srivastava, Jamie A Love-Nichols, Kira A Dies, David H Ledbetter, Christa L Martin, Wendy K Chung, Helen V Firth, Thomas Frazier, Robin L Hansen, Lisa Prock, Han Brunner, Ny Hoang, Stephen W Scherer, Mustafa Sahin, David T Miller, NDD Exome Scoping Review Work
Group
Feb 12, 2021
PURPOSE: For neurodevelopmental disorders (NDDs), etiological evaluation can be a diagnostic odyssey involving numerous genetic tests, underscoring the need to develop a streamlined algorithm maximizing molecular diagnostic...
The Max-Min Group Contest
We investigate a group all-pay auction in which each group's effort is represented by the minimum among the effort levels exerted by the group members and the prize is a group-specific public good. We fully characterize the...
DNAscent v2
Michael A Boemo
Jul 28, 2021
Background
Measuring DNA replication dynamics with high throughput and single-molecule resolution is critical for understanding both the basic biology behind how cells replicate their DNA and how DNA replication can be...
DNA Replication budding yeast Replication origins Replication forks Oxford nanopore Residual neural networks DNAscent Sequence Analysis DNA Software Nanopores High-Throughput Nucleotide Sequencing Deep learning nanopore sequencing
Published by: BMC genomics
The Max-Min Group Contest
We investigate a group all-pay auction in which each group's effort is represented by the minimum among the effort levels exerted by the group members and the prize is a group-specific public good. We fully characterize the...
DNAscent v2
Michael A. Boemo
Jun 09, 2021
Abstract: Background: Measuring DNA replication dynamics with high throughput and single-molecule resolution is critical for understanding both the basic biology behind how cells replicate their DNA and how DNA replication can...
Genetic and Biochemical Analysis of the Bryan Strain of Rous Sarcoma Virus
Teena Louise Lerner
Jan 01, 0001
Integration of Rous sarcoma virus DNA into its host genome was analyzed under conditions where secondary integration via virus spread was inhibited. This was accomplished by using the noninfectious pol- ,env- alpha variant of...
Published by: Rockefeller University
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