scholarly journals Broad‐spectrum next‐generation sequencing‐based diagnosis of a case of Nager syndrome

2020 ◽  
Vol 34 (9) ◽  
Author(s):  
Jue Zhao ◽  
Liwei Yang
Keyword(s):  
Next Generation Sequencing ◽  
Broad Spectrum ◽  
Next Generation ◽  
Nager Syndrome ◽  
Generation Sequencing

scholarly journals Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome

BIO-PROTOCOL ◽  
2021 ◽  
Vol 11 (5) ◽  
Author(s):  
Shuntai Zhou ◽  
Collin Hill ◽  
Michael Clark ◽  
Timothy Sheahan ◽  
Ralph Baric ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Broad Spectrum ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Novel PCR-Based Methods Enhance Characterization of Vaginal Microbiota in a Bacterial Vaginosis Patient before and after Treatment

2013 ◽  
Vol 79 (13) ◽  
pp. 4181-4185 ◽  
Author(s):  
Janet A. Lambert ◽  
Apoorv Kalra ◽  
Cristina T. Dodge ◽  
Susan John ◽  
Jack D. Sobel ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Vaginosis ◽  
Quantitative Pcr ◽  
Broad Spectrum ◽  
Vaginal Microbiota ◽  
Next Generation ◽  
Healthy Women ◽  
Before And After ◽  
Generation Sequencing

ABSTRACTDeep characterization, even by next-generation sequencing, of the vaginal microbiota in healthy women or posttreatment bacterial vaginosis patients is limited by the dominance of lactobacilli. To improve detection, we offer two approaches: quantitative PCR (qPCR) using phylogenetic branch-inclusive primers and sequencing of broad-spectrum amplicons generated with oligomers that block amplification of lactobacilli.

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

2018 ◽  
Vol 93 (2) ◽  
Author(s):  
Daniel H. Goldhill ◽  
Pinky Langat ◽  
Hongyao Xie ◽  
Monica Galiano ◽  
Shahjahan Miah ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Next Generation Sequencing ◽  
Broad Spectrum ◽  
Influenza Pandemic ◽  
Antiviral Drug ◽  
Sequence Information ◽  
Next Generation ◽  
Mutation Bias ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ABSTRACT Favipiravir 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. IMPORTANCE New antiviral drugs are needed as a first line of defense 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.

Broad spectrum mutational analysis of chromophobe renal cell carcinoma using next-generation sequencing

2021 ◽  
Vol 219 ◽  
pp. 153350
Author(s):  
Veronica Mollica ◽  
Tania Franceschini ◽  
Elisa Gruppioni ◽  
Alessandro Rizzo ◽  
Costantino Ricci ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Next Generation Sequencing ◽  
Cell Carcinoma ◽  
Broad Spectrum ◽  
Renal Cell ◽  
Mutational Analysis ◽  
Chromophobe Renal Cell Carcinoma ◽  
Next Generation ◽  
Generation Sequencing

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.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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