scholarly journals A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 1002 ◽  
Author(s):  
Charles C Bell ◽  
Graham W Magor ◽  
Kevin R Gillinder ◽  
Andrew C Perkins
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
High Throughput Screening ◽  
Screening Strategy ◽  
Next Generation ◽  
Induced Mutations ◽  
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 Molecular interactions of nanomaterials and organisms: defining biomarkers for toxicity and high-throughput screening using traditional and next-generation sequencing approaches

The Analyst ◽  
2014 ◽  
Vol 139 (5) ◽  
pp. 882-895 ◽  
Author(s):  
Rebecca Klaper ◽  
Devrah Arndt ◽  
Jared Bozich ◽  
Gustavo Dominguez
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput ◽  
Molecular Interactions ◽  
High Throughput Screening ◽  
Molecular Pathways ◽  
Next Generation ◽  
Generation Sequencing

The expression of molecular pathways in an organism provides a clue as to the potential impacts of exposure to nanomaterials.

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
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