Transposon Insertion Site Sequencing (TIS‐Seq): An Efficient and High‐Throughput Method for Determining Transposon Insertion Site(s) and Their Relative Abundances in a PiggyBac Transposon Mutant Pool by Next‐Generation Sequencing

2017 ◽  
Vol 120 (1) ◽  
Author(s):  
Yaligara Veeranagouda ◽  
Michel Didier
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Insertion Site ◽  
Next Generation ◽  
Piggybac Transposon ◽  
Transposon Insertion ◽  
Mutant Pool ◽  
High Throughput Method ◽  
Relative Abundances ◽  
Generation Sequencing

Next-Generation Sequencing: An Emerging Tool for Drug Designing

2019 ◽  
Vol 25 (31) ◽  
pp. 3350-3357 ◽  
Author(s):  
Pooja Tripathi ◽  
Jyotsna Singh ◽  
Jonathan A. Lal ◽  
Vijay Tripathi
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genomic Research ◽  
Biological Research ◽  
Next Generation ◽  
Human Welfare ◽  
Drug Designing ◽  
Generation Sequencing

Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

scholarly journals Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies

2012 ◽  
Vol 37 (5) ◽  
pp. 811-820 ◽  
Author(s):  
Rajeev K Varshney ◽  
Himabindu Kudapa ◽  
Manish Roorkiwal ◽  
Mahendar Thudi ◽  
Manish K Pandey ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Molecular Breeding ◽  
Next Generation ◽  
Legume Crops ◽  
Generation Sequencing ◽  
Semi Arid

scholarly journals Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Wells W. Wu ◽  
Je-Nie Phue ◽  
Chun-Ting Lee ◽  
Changyi Lin ◽  
Lai Xu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Library Preparation ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Evaluation of TypeSeq, a Novel High-Throughput, Low-Cost, Next-Generation Sequencing-Based Assay for Detection of 51 Human Papillomavirus Genotypes

2019 ◽  
Vol 220 (10) ◽  
pp. 1609-1619 ◽  
Author(s):  
Sarah Wagner ◽  
David Roberson ◽  
Joseph Boland ◽  
Aimée R Kreimer ◽  
Meredith Yeager ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
High Throughput ◽  
Vaccine Efficacy ◽  
Linear Array ◽  
Human Papillomaviruses ◽  
Next Generation ◽  
Hpv Genotyping ◽  
Positive Agreement ◽  
Generation Sequencing

AbstractBackgroundHuman papillomaviruses (HPV) cause over 500 000 cervical cancers each year, most of which occur in low-resource settings. Human papillomavirus genotyping is important to study natural history and vaccine efficacy. We evaluated TypeSeq, a novel, next-generation, sequencing-based assay that detects 51 HPV genotypes, in 2 large international epidemiologic studies.MethodsTypeSeq was evaluated in 2804 cervical specimens from the Study to Understand Cervical Cancer Endpoints and Early Determinants (SUCCEED) and in 2357 specimens from the Costa Rica Vaccine Trial (CVT). Positive agreement and risks of precancer for individual genotypes were calculated for TypeSeq in comparison to Linear Array (SUCCEED). In CVT, positive agreement and vaccine efficacy were calculated for TypeSeq and SPF10-LiPA.ResultsWe observed high overall and positive agreement for most genotypes between TypeSeq and Linear Array in SUCCEED and SPF10-LiPA in CVT. There was no significant difference in risk of precancer between TypeSeq and Linear Array in SUCCEED or in estimates of vaccine efficacy between TypeSeq and SPF10-LiPA in CVT.ConclusionsThe agreement of TypeSeq with Linear Array and SPF10-LiPA, 2 well established standards for HPV genotyping, demonstrates its high accuracy. TypeSeq provides high-throughput, affordable HPV genotyping for world-wide studies of cervical precancer risk and of HPV vaccine efficacy.

scholarly journals High-Throughput Microdissection for Next-Generation Sequencing

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0151775 ◽  
Author(s):  
Avi Z. Rosenberg ◽  
Michael D. Armani ◽  
Patricia A. Fetsch ◽  
Liqiang Xi ◽  
Tina Thu Pham ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Rapid, high-throughput library preparation for next-generation sequencing

2010 ◽  
Vol 7 (8) ◽  
pp. iii-iv ◽  
Author(s):  
Haiying Grunenwald ◽  
Brad Baas ◽  
Nicholas Caruccio ◽  
Fraz Syed
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Library Preparation ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals High-Throughput Next-Generation Sequencing of Polioviruses

2016 ◽  
Vol 55 (2) ◽  
pp. 606-615 ◽  
Author(s):  
Anna M. Montmayeur ◽  
Terry Fei Fan Ng ◽  
Alexander Schmidt ◽  
Kun Zhao ◽  
Laura Magaña ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Acid Extraction ◽  
Whole Genome ◽  
Next Generation ◽  
Diverse Range ◽  
Fta Cards ◽  
Reference Length ◽  
Dnase Treatment ◽  
Generation Sequencing

ABSTRACTThe poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcription (RT), amplification, and the use of the Nextera XT DNA library preparation kit produced significantly better results than other preparations. The average viral reads per total reads, a measurement of efficiency, was as high as 84.2% ± 15.6%. PV genomes covering >99 to 100% of the reference length were obtained and validated with Sanger sequencing. A total of 52 PV genomes were generated, multiplexing as many as 64 samples in a single Illumina MiSeq run. This high-throughput, sequence-independent NGS approach facilitated the detection of a diverse range of PVs, especially for those in vaccine-derived polioviruses (VDPV), circulating VDPV, or immunodeficiency-related VDPV. In contrast to results from previous studies on other viruses, our results showed that filtration and nuclease treatment did not discernibly increase the sequencing efficiency of PV isolates. However, DNase treatment after nucleic acid extraction to remove host DNA significantly improved the sequencing results. This NGS method has been successfully implemented to generate PV genomes for molecular epidemiology of the most recent PV isolates. Additionally, the ability to obtain full PV genomes from FTA cards will aid in facilitating global poliovirus surveillance.

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