scholarly journals A 'Variant Viewer' for investigating population-level variation in Arabidopsis thaliana

2021 ◽  
Author(s):  
Matthew Cumming ◽  
Eddi Esteban ◽  
Vincent Lau ◽  
Asher Pasha ◽  
Nicholas J. Provart
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
High Throughput ◽  
Web Application ◽  
High Throughput Sequencing ◽  
Population Level ◽  
Gene Families ◽  
Level Variation ◽  
Splice Isoforms ◽  
Large Populations

High throughput sequencing has opened the doors for investigators to probe genetic variation present in large populations of organisms. In plants, the 1001 Genomes Project (1001genomes.org) is one such effort that sought to characterize the extant worldwide variation in Arabidopsis thaliana for future analyses to compare and draw upon. We developed a web application that accesses the 1001 Genomes database called The Variant Viewer, for investigators to view variants in any A. thaliana gene and within gene families. These variants may be visualized in the context of alignments of queried genes, across splice isoforms of these genes and in relation to conserved domains.

scholarly journals INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. eabe5054
Author(s):  
Qianxin Wu ◽  
Chenqu Suo ◽  
Tom Brown ◽  
Tengyao Wang ◽  
Sarah A. Teichmann ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Limit Of Detection ◽  
Point Of Care ◽  
Population Level ◽  
Reaction Products ◽  
Testing Strategy ◽  
Asymptomatic Patients ◽  
Testing Stage ◽  
Population Scale

We present INSIGHT [isothermal NASBA (nucleic acid sequence–based amplification) sequencing–based high-throughput test], a two-stage coronavirus disease 2019 testing strategy, using a barcoded isothermal NASBA reaction. It combines point-of-care diagnosis with next-generation sequencing, aiming to achieve population-scale testing. Stage 1 allows a quick decentralized readout for early isolation of presymptomatic or asymptomatic patients. It gives results within 1 to 2 hours, using either fluorescence detection or a lateral flow readout, while simultaneously incorporating sample-specific barcodes. The same reaction products from potentially hundreds of thousands of samples can then be pooled and used in a highly multiplexed sequencing–based assay in stage 2. This second stage confirms the near-patient testing results and facilitates centralized data collection. The 95% limit of detection is <50 copies of viral RNA per reaction. INSIGHT is suitable for further development into a rapid home-based, point-of-care assay and is potentially scalable to the population level.

Profiling population-level diversity and dynamics of Accumulibacter via high throughput sequencing of ppk1

2019 ◽  
Vol 103 (23-24) ◽  
pp. 9711-9722 ◽  
Author(s):  
Wei Song ◽  
Min Jia Zheng ◽  
Hao Li ◽  
Wei Zheng ◽  
Feng Guo
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Population Level

scholarly journals HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e85879 ◽  
Author(s):  
Fabrice P. A. David ◽  
Julien Delafontaine ◽  
Solenne Carat ◽  
Frederick J. Ross ◽  
Gregory Lefebvre ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Access ◽  
High Throughput ◽  
Web Application ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Sequencing Data Analysis

scholarly journals Alu elements: at the crossroads between disease and evolution

2013 ◽  
Vol 41 (6) ◽  
pp. 1532-1535 ◽  
Author(s):  
Jernej Ule
Keyword(s):  
Genetic Variation ◽  
Personalized Medicine ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rapid Progress ◽  
Functional Elements ◽  
Alu Elements ◽  
Gradual Evolution ◽  
Major Increase ◽  
The Cost

The cost of DNA sequencing is decreasing year by year, and the era of personalized medicine and the $1000 genome seems to be just around the corner. In order to link genetic variation to gene function, however, we need to learn more about the function of the non-coding genomic elements. The advance of high-throughput sequencing enabled rapid progress in mapping the functional elements in our genome. In the present article, I discuss how intronic mutations acting at Alu elements enable formation of new exons. I review the mutations that cause disease when promoting a major increase in the inclusion of Alu exon into mature transcripts. Moreover, I present the mechanism that represses such a major inclusion of Alu exons and instead enables a gradual evolution of Alu elements into new exons.

scholarly journals Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data

2016 ◽  
Author(s):  
Guillaume Devailly ◽  
Anna Mantsoki ◽  
Anagha Joshi
Keyword(s):  
High Throughput ◽  
Web Application ◽  
High Throughput Sequencing ◽  
Single Gene ◽  
Public Domain ◽  
Web Tool ◽  
The Public ◽  
Link Type ◽  
A Genome ◽  
Public Data

SummaryBetter protocols and decreasing costs have made high-throughput sequencing experiments now accessible even to small experimental laboratories. However, comparing one or few experiments generated by an individual lab to the vast amount of relevant data freely available in the public domain might be limited due to lack of bioinformatics expertise. Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments (ChIP-seq, RNA-seq and CAGE) provided by a user, to the data in the public domain. Heat*seq currently contains over 12,000 experiments across diverse tissue and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualise user experiments. High quality figures and tables are produced and can be downloaded in multiple formats.AvailabilityWeb application:www.heatstarseq.roslin.ed.ac.uk/. Source code:https://github.com/[email protected];[email protected]

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