scholarly journals Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum ) population

2017 ◽  
Vol 92 (3) ◽  
pp. 495-508 ◽  
Author(s):  
Prateek Gupta ◽  
Bodanapu Reddaiah ◽  
Hymavathi Salava ◽  
Pallawi Upadhyaya ◽  
Kamal Tyagi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Solanum Lycopersicum ◽  
Next Generation ◽  
Induced Mutations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Discovery of mutations in Chenopodium quinoa Willd through EMS mutagenesis and mutation screening using pre-selection phenotypic data and next-generation sequencing

2018 ◽  
Vol 156 (10) ◽  
pp. 1196-1204 ◽  
Author(s):  
Camilo Mestanza ◽  
Ricardo Riegel ◽  
Santiago C. Vásquez ◽  
Diana Veliz ◽  
Nicolás Cruz-Rosero ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mutation Screening ◽  
Chenopodium Quinoa ◽  
Acetolactate Synthase ◽  
Screening Strategy ◽  
Next Generation ◽  
Induced Mutations ◽  
Phenotypic Data ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractQuinoa (Chenopodium quinoaWilld) is a dicotyledonous annual species belonging to the family Amaranthaceae, which is nutritionally well balanced in terms of its oil, protein and carbohydrate content. Targeting-induced local lesions in genomes (the TILLING strategy) was employed to find mutations in acetolactate synthase (AHAS) genes in a mutant quinoa population. TheAHASgenes were targeted because they are common enzyme target sites for five herbicide groups. Ethyl methane sulfonate (EMS) was used to induce mutations in theAHASgenes; it was found that 2% EMS allowed a mutation frequency of one mutation every 203 kilobases to be established. In the mutant population created, a screening strategy using pre-selection phenotypic data and next-generation sequencing (NGS) allowed identification of a mutation that alters the amino acid composition of this species (nucleotide 1231 codon GTT→ATT, Val→Ile); however, this mutation did not result in herbicide resistance. The current work shows that TILLING combined with the high-throughput of NGS technologies and an overlapping pool design provides an efficient and economical method for detecting induced mutations in pools of individuals.

scholarly journals Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing

2018 ◽  
Author(s):  
Daniel H. Goldhill ◽  
Pinky Langat ◽  
Hongyao Xie ◽  
Monica Galiano ◽  
Shahjahan Miah ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Broad Spectrum ◽  
Influenza Pandemic ◽  
Antiviral Drug ◽  
Sequence Information ◽  
Next Generation ◽  
Induced Mutations ◽  
Mutation Bias ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractFavipiravir is a broad spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible through Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole genome sequencing of virus.ImportanceNew antiviral drugs are needed as a first line of defence in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic.

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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