scholarly journals Identification and complete genome sequencing of paramyxoviruses in mallard ducks (Anas platyrhynchos) using random access amplification and next generation sequencing technologies

2011 ◽  
Vol 8 (1) ◽  
pp. 463 ◽  
Author(s):  
Toon Rosseel ◽  
Bénédicte Lambrecht ◽  
Frank Vandenbussche ◽  
Thierry van den Berg ◽  
Steven Van Borm
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Anas Platyrhynchos ◽  
Random Access ◽  
Next Generation ◽  
Complete Genome Sequencing ◽  
Sequencing Technologies ◽  
Generation Sequencing

scholarly journals SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Anna Maria Rachiglio ◽  
Luca De Sabato ◽  
Cristin Roma ◽  
Michele Cennamo ◽  
Mariano Fiorenza ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Automated System ◽  
Next Generation ◽  
Campania Region ◽  
Complete Genome Sequencing ◽  
Two Samples ◽  
Different Response ◽  
Generation Sequencing

Abstract Background Since the first complete genome sequencing of SARS-CoV-2 in December 2019, more than 550,000 genomes have been submitted into the GISAID database. Sequencing of the SARS-CoV-2 genome might allow identification of variants with increased contagiousness, different clinical patterns and/or different response to vaccines. A highly automated next generation sequencing (NGS)-based method might facilitate an active genomic surveillance of the virus. Methods RNA was extracted from 27 nasopharyngeal swabs obtained from citizens of the Italian Campania region in March–April 2020 who tested positive for SARS-CoV-2. Following viral RNA quantification, sequencing was performed using the Ion AmpliSeq SARS-CoV-2 Research Panel on the Genexus Integrated Sequencer, an automated technology for library preparation and sequencing. The SARS-CoV-2 complete genomes were built using the pipeline SARS-CoV-2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) and analysed by IQ-TREE software. Results The complete genome (100%) of SARS-CoV-2 was successfully obtained for 21/27 samples. In particular, the complete genome was fully sequenced for all 15 samples with high viral titer (> 200 copies/µl), for the two samples with a viral genome copy number < 200 but greater than 20, and for 4/10 samples with a viral load < 20 viral copies. The complete genome sequences classified into the B.1 and B.1.1 SARS-CoV-2 lineages. In comparison to the reference strain Wuhan-Hu-1, 48 total nucleotide variants were observed with 26 non-synonymous substitutions, 18 synonymous and 4 reported in untranslated regions (UTRs). Ten of the 26 non-synonymous variants were observed in ORF1ab, 7 in S, 1 in ORF3a, 2 in M and 6 in N genes. Conclusions The Genexus system resulted successful for SARS-CoV-2 complete genome sequencing, also in cases with low viral copies. The use of this highly automated system might facilitate the standardization of SARS-CoV-2 sequencing protocols and make faster the identification of novel variants during the pandemic.

scholarly journals Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing

Viruses ◽  
2016 ◽  
Vol 8 (1) ◽  
pp. 12 ◽  
Author(s):  
Bram Vrancken ◽  
Nídia Trovão ◽  
Guy Baele ◽  
Eric van Wijngaerden ◽  
Anne-Mieke Vandamme ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Next Generation ◽  
Complete Genome Sequencing ◽  
Processing Bias ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals Complete Genome Sequence of the Model Oleaginous Alga Nannochloropsis gaditana CCMP1894

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Ariel S. Schwartz ◽  
Rob Brown ◽  
Imad Ajjawi ◽  
Jay McCarren ◽  
Suzan Atilla ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Optical Mapping ◽  
Next Generation ◽  
Nannochloropsis Gaditana ◽  
Sequencing Technologies ◽  
Eukaryotic Genomes ◽  
Generation Sequencing

ABSTRACT The model oleaginous alga Nannochloropsis gaditana was completely sequenced using a combination of optical mapping and next-generation sequencing technologies to generate one of the most complete eukaryotic genomes published to date. The assembled genome is 30.7 Mb long.

scholarly journals Rapid whole-genome mutational profiling using next-generation sequencing technologies

2008 ◽  
Vol 18 (10) ◽  
pp. 1638-1642 ◽  
Author(s):  
D. R. Smith ◽  
A. R. Quinlan ◽  
H. E. Peckham ◽  
K. Makowsky ◽  
W. Tao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Mutational Profiling ◽  
Generation Sequencing

The application of next-generation sequencing technologies to drug discovery and development

2011 ◽  
Vol 16 (11-12) ◽  
pp. 512-519 ◽  
Author(s):  
Peter M. Woollard ◽  
Nalini A.L. Mehta ◽  
Jessica J. Vamathevan ◽  
Stephanie Van Horn ◽  
Bhushan K. Bonde ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Drug Discovery ◽  
Next Generation ◽  
Drug Discovery And Development ◽  
Sequencing Technologies ◽  
Generation Sequencing

scholarly journals Next-generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates reveals a high frequency of M segment reassortment

2014 ◽  
Vol 142 (9) ◽  
pp. 1952-1962 ◽  
Author(s):  
D. GOEDHALS ◽  
P. A. BESTER ◽  
J. T. PAWESKA ◽  
R. SWANEPOEL ◽  
F. J. BURT
Keyword(s):  
Next Generation Sequencing ◽  
High Frequency ◽  
Complete Genome ◽  
Fever Virus ◽  
Likelihood Method ◽  
Haemorrhagic Fever ◽  
Next Generation ◽  
Genome Sequences ◽  
Crimean Congo Haemorrhagic Fever ◽  
Generation Sequencing

SUMMARYCrimean Congo haemorrhagic fever virus (CCHFV) is a bunyavirus with a single-stranded RNA genome consisting of three segments (S, M, L), coding for the nucleocapsid protein, envelope glycoproteins and RNA polymerase, respectively. To date only five complete genome sequences are available from southern African isolates. Complete genome sequences were generated for 10 southern African CCHFV isolates using next-generation sequencing techniques. The maximum-likelihood method was used to generate tree topologies for 15 southern African plus 26 geographically distinct complete sequences from GenBank. M segment reassortment was identified in 10/15 southern African isolates by incongruencies in grouping compared to the S and L segments. These reassortant M segments cluster with isolates from Asia/Middle East, while the S and L segments cluster with strains from South/West Africa. The CCHFV M segment shows a high level of genetic diversity, while the S and L segments appear to co-evolve. The reason for the high frequency of M segment reassortment is not known. It has previously been suggested that M segment reassortment results in a virus with high fitness but a clear role in increased pathogenicity has yet to be shown.

scholarly journals Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 429 ◽  
Author(s):  
Daniela Barros-Silva ◽  
C. Marques ◽  
Rui Henrique ◽  
Carmen Jerónimo
Keyword(s):  
Dna Methylation ◽  
Next Generation Sequencing ◽  
High Throughput Sequencing ◽  
Epigenetic Modification ◽  
Response To Therapy ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Prognosis And Prediction ◽  
Novel Biomarkers ◽  
Generation Sequencing

DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.

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