scholarly journals Screening of Bacteriophage Encoded Toxic Proteins with a Next Generation Sequencing-Based Assay

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 750
Author(s):  
Jutta Kasurinen ◽  
Cindy M. Spruit ◽  
Anu Wicklund ◽  
Maria I. Pajunen ◽  
Mikael Skurnik
Keyword(s):  
Next Generation Sequencing ◽  
Genomic Sequence ◽  
Plating Efficiency ◽  
Sewage Sample ◽  
Next Generation ◽  
Screening Assay ◽  
Genes Encoding ◽  
Culture Isolate ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Bacteriophage vB_EcoM_fHy-Eco03 (fHy-Eco03 for short) was isolated from a sewage sample based on its ability to infect an Escherichia coli clinical blood culture isolate. Altogether, 32 genes encoding hypothetical proteins of unknown function (HPUFs) were identified from the genomic sequence of fHy-Eco03. The HPUFs were screened for toxic properties (toxHPUFs) with a novel, Next Generation Sequencing (NGS)-based approach. This approach identifies toxHPUF-encoding genes through comparison of gene-specific read coverages in DNA from pooled ligation mixtures before electroporation and pooled transformants after electroporation. The performance and reliability of the NGS screening assay was compared with a plating efficiency-based method, and both methods identified the fHy-Eco03 gene g05 product as toxic. While the outcomes of the two screenings were highly similar, the NGS screening assay outperformed the plating efficiency assay in both reliability and efficiency. The NGS screening assay can be used as a high throughput method in the search for new phage-inspired antimicrobial molecules.

scholarly journals Comparison of Next-Generation Sequencing Systems

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Lin Liu ◽  
Yinhu Li ◽  
Siliang Li ◽  
Ni Hu ◽  
Yimin He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genomic Sequence ◽  
Sequence Information ◽  
Ion Torrent ◽  
Next Generation ◽  
Extensive Experience ◽  
Ion Torrent Pgm ◽  
Fast Development ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world’s biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

scholarly journals Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

2020 ◽  
Author(s):  
Matteo Chiara ◽  
Anna Maria D’Erchia ◽  
Carmela Gissi ◽  
Caterina Manzari ◽  
Antonio Parisi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genomic Sequence ◽  
Molecular Diagnostic ◽  
Next Generation ◽  
Sequencing Data ◽  
Related Data ◽  
Molecular Tests ◽  
Methodological Approaches ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our ‘vademecum’ for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.

Initial Next-Generation Sequencing (NGS) Results of Alport Syndrome

2019 ◽  
Author(s):  
Altuğ Koç ◽  
Elçin Bora ◽  
Tayfun Cinleti ◽  
Gizem Yıldız ◽  
Meral Torun Bayram ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Alport Syndrome ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The applications of next-generation sequencing (NGS) in drug development for cancer therapy

2020 ◽  
Vol 16 ◽  
Author(s):  
Pelin Telkoparan-Akillilar ◽  
Dilek Cevik
Keyword(s):  
Next Generation Sequencing ◽  
Drug Discovery ◽  
Cancer Therapy ◽  
Target Identification ◽  
Rapid Development ◽  
Next Generation ◽  
Biomedical Sciences ◽  
Dna And Rna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Background: Numerous sequencing techniques have been progressed since the 1960s with the rapid development of molecular biology studies focusing on DNA and RNA. Methods: a great number of articles, book chapters, websites are reviewed, and the studies covering NGS history, technology and applications to cancer therapy are included in the present article. Results: High throughput next-generation sequencing (NGS) technologies offer many advantages over classical Sanger sequencing with decreasing cost per base and increasing sequencing efficiency. NGS technologies are combined with bioinformatics software to sequence genomes to be used in diagnostics, transcriptomics, epidemiologic and clinical trials in biomedical sciences. The NGS technology has also been successfully used in drug discovery for the treatment of different cancer types. Conclusion: This review focuses on current and potential applications of NGS in various stages of drug discovery process, from target identification through to personalized medicine.

scholarly journals Next-Generation Sequencing in Tumor Diagnosis and Treatment

Diagnostics ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 962
Author(s):  
Dario de Biase ◽  
Matteo Fassan ◽  
Umberto Malapelle
Keyword(s):  
Next Generation Sequencing ◽  
Tumor Diagnosis ◽  
Diagnosis And Treatment ◽  
Next Generation ◽  
Multiple Genes ◽  
Next Generation Sequencing Ngs ◽  
Very High ◽  
Generation Sequencing ◽  
High Depth

Next-Generation Sequencing (NGS) allows for the sequencing of multiple genes at a very high depth of coverage [...]

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