Full genomic sequence of the HLA‐DQB1 *04:51 allele identified by next generation sequencing

HLA ◽  
2021 ◽  
Author(s):  
Hamid Liacini ◽  
Thomas Morris ◽  
Saber Alzahrani ◽  
Leena Mathew ◽  
Steven Geier
Keyword(s):  
Next Generation Sequencing ◽  
Genomic Sequence ◽  
Next Generation ◽  
Full Genomic Sequence ◽  
Generation Sequencing

scholarly journals Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections

2016 ◽  
Vol 55 (1) ◽  
pp. 177-182 ◽  
Author(s):  
Alexander L. Greninger ◽  
Danielle M. Zerr ◽  
Xuan Qin ◽  
Amanda L. Adler ◽  
Reigran Sampoleo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Infection Prevention ◽  
Genomic Sequence ◽  
Clinical Samples ◽  
Whole Genome ◽  
Next Generation ◽  
Sequence Coverage ◽  
Medical Unit ◽  
Hospital Acquired ◽  
Generation Sequencing

ABSTRACT Metagenomic next-generation sequencing (mNGS) is increasingly used for the unbiased detection of viruses, bacteria, fungi, and eukaryotic parasites in clinical samples. Whole-genome sequencing (WGS) of clinical bacterial isolates has been shown to inform hospital infection prevention practices, but this technology has not been utilized during potential respiratory virus outbreaks. Here, we report on the use of mNGS to inform the real-time infection prevention response to a cluster of hospital-acquired human parainfluenza 3 virus (HPIV3) infections at a children's hospital. Samples from 3 patients with hospital-acquired HPIV3 identified over a 12-day period on a general medical unit and 10 temporally associated samples from patients with community-acquired HPIV3 were analyzed. Our sample-to-sequencer time was <24 h, while our sample-to-answer turnaround time was <60 h with a hands-on time of approximately 6 h. Eight (2 cases and 6 controls) of 13 samples had sufficient sequencing coverage to yield the whole genome for HPIV3, while 10 (2 cases and 8 controls) of 13 samples gave partial genomes and all 13 samples had >1 read for HPIV3. Phylogenetic clustering revealed the presence of identical HPIV3 genomic sequence in the two of the cases with hospital-acquired infection, consistent with the concern for recent transmission within the medical unit. Adequate sequence coverage was not recovered for the third case. This work demonstrates the promise of mNGS for providing rapid information for infection prevention in addition to microbial detection.

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.

Complete genomic sequence of barley (Hordeum vulgare) endornavirus (HvEV) determined by next-generation sequencing

2015 ◽  
Vol 161 (3) ◽  
pp. 741-743 ◽  
Author(s):  
Thierry Candresse ◽  
Armelle Marais ◽  
Roberto Sorrentino ◽  
Chantal Faure ◽  
Sébastien Theil ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hordeum Vulgare ◽  
Genomic Sequence ◽  
Complete Genomic Sequence ◽  
Next Generation ◽  
Generation Sequencing ◽  
Complete Genomic

scholarly journals Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections

2016 ◽  
Author(s):  
Alexander L. Greninger ◽  
Danielle M Zerr ◽  
Xuan Qin ◽  
Amanda L. Adler ◽  
Janet A. Englund ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Infection Prevention ◽  
Genomic Sequence ◽  
Clinical Samples ◽  
Next Generation ◽  
Sequence Coverage ◽  
Medical Unit ◽  
Recent Transmission ◽  
Hospital Acquired ◽  
Generation Sequencing

AbstractMetagenomic next-generation sequencing (mNGS) is increasingly used for the unbiased detection of viruses, bacteria, fungi, and eukaryotic parasites in clinical samples. Whole genome sequencing (WGS) of clinical bacterial isolates has been shown to inform hospital infection prevention practices, but the use of this technology during potential respiratory virus outbreaks has not been taken advantage of. Here, we report on the use of mNGS to inform the real-time infection prevention response to a cluster of hospital-acquired human parainfluenza 3 virus (HPIV3) infections at a children’s hospital. Isolates from 3 patients with hospital-acquired HPIV3 identified over a 12-day period on a general medical unit and 10 temporally-associated isolates from patients with community-acquired of HPIV3 were analyzed. Our sample-to-sequencer time was <24 hours while our sample-to-answer turn-around time was <60 hours with a hands-on time of approximately 6 hours. Eight (2 case isolates and 6 control isolates) of 13 samples had sufficient sequencing coverage to yield whole genomes for HPIV3, while 10 (2 cases and 8 controls) of 13 samples gave partial genomes and all 13 samples had >1 read to HPIV3. Phylogenetic clustering revealed the presence of identical HPIV3 genomic sequence in the two of the cases with hospital-acquired infection, consistent with the concern for recent transmission within the medical unit. Adequate sequence coverage was not recovered for the third case. This work demonstrates the promise of mNGS to provide actionable information for infection control in addition to microbial detection.

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 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.

Next-Generation Sequencing

2012 ◽  
Vol 42 (9) ◽  
pp. 8
Author(s):  
PETER HULICK
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

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.

Sign in / Sign up

Export Citation Format

Share Document