scholarly journals BAQALC: Blockchain Applied Lossless Efficient Transmission of DNA Sequencing Data for Next Generation Medical Informatics

2018 ◽  
Vol 8 (9) ◽  
pp. 1471 ◽  
Author(s):  
Seo-Joon Lee ◽  
Gyoun-Yon Cho ◽  
Fumiaki Ikeno ◽  
Tae-Ro Lee
Keyword(s):  
Dna Sequencing ◽  
Medical Informatics ◽  
Compression Ratio ◽  
Sequence Data ◽  
Lossless Compression ◽  
World Health ◽  
Smart Devices ◽  
Next Generation ◽  
And Storage ◽  
Efficient Transmission

Due to the development of high-throughput DNA sequencing technology, genome-sequencing costs have been significantly reduced, which has led to a number of revolutionary advances in the genetics industry. However, the problem is that compared to the decrease in time and cost needed for DNA sequencing, the management of such large volumes of data is still an issue. Therefore, this research proposes Blockchain Applied FASTQ and FASTA Lossless Compression (BAQALC), a lossless compression algorithm that allows for the efficient transmission and storage of the immense amounts of DNA sequence data that are being generated by Next Generation Sequencing (NGS). Also, security and reliability issues exist in public sequence databases. For methods, compression ratio comparisons were determined for genetic biomarkers corresponding to the five diseases with the highest mortality rates according to the World Health Organization. The results showed an average compression ratio of approximately 12 for all the genetic datasets used. BAQALC performed especially well for lung cancer genetic markers, with a compression ratio of 17.02. BAQALC performed not only comparatively higher than widely used compression algorithms, but also higher than algorithms described in previously published research. The proposed solution is envisioned to contribute to providing an efficient and secure transmission and storage platform for next-generation medical informatics based on smart devices for both researchers and healthcare users.

scholarly journals Next-generation sequencing technologies: breaking the sound barrier of human genetics

Mutagenesis ◽  
2014 ◽  
Vol 29 (5) ◽  
pp. 303-310 ◽  
Author(s):  
El Mustapha Bahassi ◽  
Peter J. Stambrook
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Biological Networks ◽  
New Technologies ◽  
Sequence Data ◽  
Rapid Development ◽  
Relevant Information ◽  
Model Organisms ◽  
Next Generation ◽  
Generation Sequencing

Abstract Demand for new technologies that deliver fast, inexpensive and accurate genome information has never been greater. This challenge has catalysed the rapid development of advances in next-generation sequencing (NGS). The generation of large volumes of sequence data and the speed of data acquisition are the primary advantages over previous, more standard methods. In 2013, the Food and Drug Administration granted marketing authorisation for the first high-throughput NG sequencer, Illumina’s MiSeqDx, which allowed the development and use of a large number of new genome-based tests. Here, we present a review of template preparation, nucleic acid sequencing and imaging, genome assembly and alignment approaches as well as recent advances in current and near-term commercially available NGS instruments. We also outline the broad range of applications for NGS technologies and provide guidelines for platform selection to best address biological questions of interest. DNA sequencing has revolutionised biological and medical research, and is poised to have a similar impact on the practice of medicine. This tool is but one of an increasing arsenal of developing tools that enhance our capabilities to identify, quantify and functionally characterise the components of biological networks that keep us healthy or make us sick. Despite advances in other ‘omic’ technologies, DNA sequencing and analysis, in many respects, have played the leading role to date. The new technologies provide a bridge between genotype and phenotype, both in man and model organisms, and have revolutionised how risk of developing a complex human disease may be assessed. The generation of large DNA sequence data sets is producing a wealth of medically relevant information on a large number of individuals and populations that will potentially form the basis of truly individualised medical care in the future.

ADVANCES IN THE USE OF NEXT-GENERATION SEQUENCE DATA IN PLANT SYSTEMATICS AND EVOLUTION

2010 ◽  
pp. 193-206 ◽  
Author(s):  
D.E. Soltis ◽  
G. Burleigh ◽  
W.B. Barbazuk ◽  
M.J. Moore ◽  
P.S. Soltis
Keyword(s):  
Sequence Data ◽  
Plant Systematics ◽  
Next Generation

scholarly journals Next Generation Sequencing for the Prediction of the Antibiotic Resistance in Helicobacter pylori: A Literature Review

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 437
Author(s):  
Ilaria Maria Saracino ◽  
Matteo Pavoni ◽  
Angelo Zullo ◽  
Giulia Fiorini ◽  
Tiziana Lazzarotto ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Next Generation Sequencing ◽  
Literature Review ◽  
Molecular Mechanisms ◽  
World Health ◽  
Next Generation ◽  
Culture Methods ◽  
Phenotypic Resistance ◽  
H Pylori ◽  
Generation Sequencing

Background and aims: Only a few antimicrobials are effective against H. pylori, and antibiotic resistance is an increasing problem for eradication therapies. In 2017, the World Health Organization categorized clarithromycin resistant H. pylori as a “high-priority” bacterium. Standard antimicrobial susceptibility testing can be used to prescribe appropriate therapies but is currently recommended only after the second therapeutic failure. H. pylori is, in fact, a “fastidious” microorganism; culture methods are time-consuming and technically challenging. The advent of molecular biology techniques has enabled the identification of molecular mechanisms underlying the observed phenotypic resistance to antibiotics in H. pylori. The aim of this literature review is to summarize the results of original articles published in the last ten years, regarding the use of Next Generation Sequencing, in particular of the whole genome, to predict the antibiotic resistance in H. pylori.Methods: a literature research was made on PubMed. The research was focused on II and III generation sequencing of the whole H. pylori genome. Results: Next Generation Sequencing enabled the detection of novel, rare and complex resistance mechanisms. The prediction of resistance to clarithromycin, levofloxacin and amoxicillin is accurate; for other antimicrobials, such as metronidazole, rifabutin and tetracycline, potential genetic determinants of the resistant status need further investigation.

Next-generation DNA sequencing

2008 ◽  
Vol 26 (10) ◽  
pp. 1135-1145 ◽  
Author(s):  
Jay Shendure ◽  
Hanlee Ji
Keyword(s):  
Dna Sequencing ◽  
Next Generation ◽  
Next Generation Dna Sequencing

scholarly journals Next-Generation Sequencing: From Basic Research to Diagnostics

2009 ◽  
Vol 55 (4) ◽  
pp. 641-658 ◽  
Author(s):  
Karl V Voelkerding ◽  
Shale A Dames ◽  
Jacob D Durtschi
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
Single Molecule ◽  
Basic Research ◽  
Clinical Diagnostics ◽  
Massively Parallel ◽  
Next Generation ◽  
New Paradigm ◽  
The Impact ◽  
Generation Sequencing

Abstract Background: For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). Content: This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonally amplified DNA templates or single DNA molecules is performed in a flow cell in a massively parallel manner. Through iterative cycles of polymerase-mediated nucleotide extensions or, in one approach, through successive oligonucleotide ligations, sequence outputs in the range of hundreds of megabases to gigabases are now obtained routinely. Highlighted in this review are the impact of NGS on basic research, bioinformatics considerations, and translation of this technology into clinical diagnostics. Also presented is a view into future technologies, including real-time single-molecule DNA sequencing and nanopore-based sequencing. Summary: In the relatively short time frame since 2005, NGS has fundamentally altered genomics research and allowed investigators to conduct experiments that were previously not technically feasible or affordable. The various technologies that constitute this new paradigm continue to evolve, and further improvements in technology robustness and process streamlining will pave the path for translation into clinical diagnostics.

scholarly journals Detection of a Possible Bioterrorism Agent, Francisella sp., in a Clinical Specimen by Use of Next-Generation Direct DNA Sequencing

2012 ◽  
Vol 50 (5) ◽  
pp. 1810-1812 ◽  
Author(s):  
M. Kuroda ◽  
T. Sekizuka ◽  
F. Shinya ◽  
F. Takeuchi ◽  
T. Kanno ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Clinical Specimen ◽  
Next Generation ◽  
Direct Dna Sequencing ◽  
Bioterrorism Agent

The mycobiome of the oral cavity in healthy dogs and dogs with periodontal disease

2022 ◽  
pp. 1-8
Author(s):  
Brook A. Niemiec ◽  
Jerzy Gawor ◽  
Shuiquan Tang ◽  
Aishani Prem ◽  
Janina A. Krumbeck
Keyword(s):  
Oral Cavity ◽  
Periodontal Disease ◽  
Dna Sequencing ◽  
Fungal Species ◽  
Next Generation ◽  
Data Set ◽  
Next Generation Dna Sequencing ◽  
Sequencing Platform ◽  
The Family ◽  
Healthy Dogs

Abstract OBJECTIVE To investigate the mycobiome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS 51 dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The whole maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the internal transcribed spacer 2 region with a commercial sequencing platform. RESULTS Fungi were detected in all samples, with a total of 320 fungal species from 135 families detected in the data set. No single fungal species was found in all samples. The 3 most frequently found fungal species were Cladosporium sp (46/51 samples), Malassezia restricta (44/51 samples), and Malassezia arunalokei (36/51 samples). Certain fungi, specifically those of the family Didymellaceae, the family Irpicaceae, and the order Pleosporales, were significantly associated with different stages of periodontitis. Mycobial analysis indicated that Cladosporium sp could be considered part of the core oral cavity mycobiome. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that fungi are present in the oral cavity of dogs and are characterized by substantial species diversity, with different fungal communities associated with various stages of periodontal disease. The next-generation DNA sequencing used in the present study revealed substantially more species of fungi than previous culture-based studies.

Adulterants and Contaminants in Psychotropic Herbal Medicines Detected with Mass Spectrometry and Next-Generation DNA Sequencing

2018 ◽  
Vol 32 (6) ◽  
pp. 429-444 ◽  
Author(s):  
Claire L. Hoban ◽  
Ian F. Musgrave ◽  
Megan L. Coghlan ◽  
Matthew W. P. Power ◽  
Roger W. Byard ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Dna Sequencing ◽  
Herbal Medicines ◽  
Next Generation ◽  
Next Generation Dna Sequencing
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