From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumorsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

2008 ◽  
Vol 86 (2) ◽  
pp. 81-91 ◽  
Author(s):  
Olena Morozova ◽  
Marco A. Marra
Keyword(s):  
Next Generation Sequencing ◽  
Review Process ◽  
Peer Review Process ◽  
Genome Rearrangements ◽  
Next Generation ◽  
Special Issue ◽  
Sequencing Technologies ◽  
Cancer Genomes ◽  
Generation Sequencing ◽  
Selection Of

Genome rearrangements have long been recognized as hallmarks of human tumors and have been used to diagnose cancer. Techniques used to detect genome rearrangements have evolved from microscopic examinations of chromosomes to the more recent microarray-based approaches. The availability of next-generation sequencing technologies may provide a means for scrutinizing entire cancer genomes and transcriptomes at unparalleled resolution. Here we review the methods that have been used to detect genome rearrangements and discuss the scope and limitations of each approach. We end with a discussion of the potential that next-generation sequencing technologies may offer to the field.

scholarly journals Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 505
Author(s):  
Manfred Grabherr ◽  
Bozena Kaminska ◽  
Jan Komorowski
Keyword(s):  
Machine Learning ◽  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Computational Power ◽  
Next Generation ◽  
Special Issue ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Sequencing Technologies ◽  
Generation Sequencing

The massive increase in computational power over the recent years and wider applicationsof machine learning methods, coincidental or not, were paralleled by remarkable advances inhigh-throughput DNA sequencing technologies.[...]

scholarly journals RumimiR: a detailed microRNA database focused on ruminant species

2019 ◽  
Author(s):  
Bourdon Céline ◽  
Bardou Philippe ◽  
Aujean Etienne ◽  
Le Guillou Sandrine ◽  
Tosser-Klopp Gwenola ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Easy Access ◽  
Data Filtering ◽  
Next Generation ◽  
Experimental Conditions ◽  
Sequencing Technologies ◽  
Ruminant Species ◽  
Tissue Origin ◽  
Generation Sequencing ◽  
Selection Of

ABSTRACTIn recent years, the increasing use of Next Generation Sequencing technologies to explore the genome has generated large quantities of data. For microRNAs, more and more publications have described several thousand sequences, all species included. In order to obtain a detailed description of microRNAs from the literature for three ruminant species (bovine, caprine and ovine), a new database has been created: RumimiR. To date, 2,887, 2,733 and 5,095 unique microRNAs of bovine, caprine and ovine species, respectively, have been included. In addition to the most recent reference genomic position and sequence of each microRNA, this database contains details on the animals, tissue origins and experimental conditions available from the publications. Identity with human or mouse microRNA is mentioned. The RumimiR database enables data filtering, the selection of microRNAs being based on defined criteria such as animal status or tissue origin. For ruminant studies, RumimiR supplements the widely used miRBase database by browsing and filtering using complementary criteria, and the integration of all published sequences described as novel. The principal goal of this database is to provide easy access to all ruminant microRNAs described in the literature.

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 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.

scholarly journals Immortalization and Functional Screening of Natively Paired Human T Cell Receptor Repertoires

2021 ◽  
Author(s):  
Ahmed S Fahad ◽  
Cheng Yu Chung ◽  
Sheila N. Lopez Acevedo ◽  
Nicoleen Boyle ◽  
Bharat Madan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
T Cell ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Functional Screening ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Human T Cell ◽  
Screening Platform ◽  
Generation Sequencing

Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. Here we developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs. In particular, we leveraged the immortalized nature of physically linked TCRα:β amplicon libraries to analyze binding against multiple recombinant pMHCs on a repertoire scale. To exemplify the utility of this approach, we also performed affinity-based functional mapping in conjunction with quantitative next-generation sequencing to track antigen- specific TCRs. These data successfully validated a new immortalization and screening platform to facilitate detailed molecular analyses of human TCRs against diverse antigen targets associated with health, vaccination, or disease.

scholarly journals Investigation of methods for extraction of bacterial DNA metagenome from goat rumen

2018 ◽  
Vol 15 (2) ◽  
pp. 367-372
Author(s):  
Lê Ngọc Giang ◽  
Lưu Hàn Ly ◽  
Nguyễn Mai Phương ◽  
Lê Tùng Lâm ◽  
Đỗ Thị Huyền ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Rumen Fluid ◽  
Next Generation ◽  
Taq Polymerase ◽  
Bead Beating ◽  
Sequencing Technologies ◽  
Polymerase Inhibitor ◽  
Stool Dna ◽  
Generation Sequencing ◽  
Goat Rumen

Microorganisms, particularly bacteria, in the ruminant's rumen are valuable genetic resources that many scientists interested in. In recent years, the application of next-generation sequencing technologies allows direct decoding an extracted DNA metagenome in each ecological community without culture, increasing the efficiency of exploiting interested genes. Notably, the quantity and quality of extracted DNA play an important role in getting a reliable metagenome database. In this study, DNA metagenome from goat rumen fluid was extracted by five different methods RBB (repeated bead beating plus column), RBBC (repeated bead beating), PSP1, PSP2 (PSP®Spin Stool DNA Kit, protocol 1, 2, Germany) và QIA (QIAamp® DNA Stool Mini Kit, Germany). The results showed that DNA metagenome obtained by all methods had A260/280 greater than 1.8. DNA extracted by the RBB method had high DNA concentration but low A260/230 values (less than 1.4) and still contained Taq polymerase inhibitor. After purifying by QIA column, A260/230 values of RBB-extracted DNA significantly increased up to 2.0 and Taq polymerase inhibitor in samples were removed. However, the concentrations decreased by 57% that nearly equivalent to concentration of DNA metagenome obtained by QIA. The method using PSP®Spin Stool DNA kit produced the highest DNA concentrations (from 149.7 to 195.5 ng/µl) with A260/280 ratios of 1.9 and A260/230 ratios of 1.8 to 1.9. Morever, this method was able to remove polymerase inhibitor and be performed on short time. Therefore, the PSP®Spin Stool DNA kit is a suitable method for DNA metagenome extraction of bacteria from goat rumen. DNA obtained by this method fulfilled all criteria about quality and concentration for sequencing by next-generation sequencing Illumina.

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