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Revue Scientifique Et Technique... Apr 2016Viral genome sequencing has become the cornerstone of almost all aspects of virology. In particular, high-throughput, next-generation viral genome sequencing has become... (Review)
Review
Viral genome sequencing has become the cornerstone of almost all aspects of virology. In particular, high-throughput, next-generation viral genome sequencing has become an integral part of molecular epidemiological investigations into outbreaks of viral disease, such as the recent outbreaks of Middle Eastern respiratory syndrome, Ebola virus disease and Zika virus infection. Multiple institutes have acquired the expertise and necessary infrastructure to perform such investigations, as evidenced by the accumulation of thousands of novel viral sequences over progressively shorter time periods. The authors recently proposed a nomenclature comprised of five high-throughput sequencing standard categories to describe the quality of determined viral genome sequences. These five categories (standard draft, high quality, coding complete, complete and finished) cover all levels of viral genome finishing and can be applied to sequences determined by any technology platform or assembly technique.
Topics: Animals; Genome, Viral; High-Throughput Nucleotide Sequencing; Molecular Epidemiology; Terminology as Topic; Virus Diseases; Viruses
PubMed: 27217167
DOI: 10.20506/rst.35.1.2416 -
Food Chemistry Jul 2014A portable bioluminescence analyser for detecting the DNA sequence of genetically modified organisms (GMOs) was developed by using a photodiode (PD) array....
A portable bioluminescence analyser for detecting the DNA sequence of genetically modified organisms (GMOs) was developed by using a photodiode (PD) array. Pyrosequencing on eight genes (zSSIIb, Bt11 and Bt176 gene of genetically modified maize; Lectin, 35S-CTP4, CP4EPSPS, CaMV35S promoter and NOS terminator of the genetically modified Roundup ready soya) was successfully detected with this instrument. The corresponding limit of detection (LOD) was 0.01% with 35 PCR cycles. The maize and soya available from three different provenances in China were detected. The results indicate that pyrosequencing using the small size of the detector is a simple, inexpensive, and reliable way in a farm/field test of GMO analysis.
Topics: DNA, Plant; Food, Genetically Modified; High-Throughput Nucleotide Sequencing; Luminescence; Plants, Genetically Modified; Polymerase Chain Reaction; Glycine max; Zea mays
PubMed: 24518318
DOI: 10.1016/j.foodchem.2014.01.001 -
Human Immunology Dec 2015
Review
Topics: Computational Biology; HLA Antigens; High-Throughput Nucleotide Sequencing; Histocompatibility Testing; Humans; Open Reading Frames; Untranslated Regions
PubMed: 25777625
DOI: 10.1016/j.humimm.2015.03.001 -
Omics : a Journal of Integrative Biology Feb 2014High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In... (Review)
Review
High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.
Topics: Animals; Fishes; Gene Expression Profiling; Gene Library; Genome; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Polymorphism, Single Nucleotide; RNA; Sequence Analysis, RNA; Transcriptome
PubMed: 24380445
DOI: 10.1089/omi.2013.0110 -
Handbook of Clinical Neurology 2016Over the past 5 years, the advent of massively parallel technologies for understanding disease at the molecular level accompanied by simultaneous rapid development of... (Review)
Review
Over the past 5 years, the advent of massively parallel technologies for understanding disease at the molecular level accompanied by simultaneous rapid development of the computational tools needed to analyze and filter such data has revolutionized medical science. These "next-generation" "omics" technologies include next-generation sequencing technology for detection of disease-associated DNA sequence variants, RNA sequencing for transcriptome and noncoding RNA analysis, quantitative detection of epigenomic dynamics, and chromatin immunoprecipitation sequencing analysis for DNA-protein interactions, interactome analysis for networks formed by protein-protein interactions, and metabolome analysis for metabolic systems. The analysis and integration of data derived from massively parallel technologies will significantly deepen our understanding of human disease, will inform functional studies, in vitro and in vivo model generation, and will advance the development of improved, personalized diagnostic tools and more effective therapeutic targets. In this chapter we review the classic genomic approaches for identifying mechanisms underlying human disease, and summarize the emerging "omics" technologies allowing massively parallel interrogation of biologic systems.
Topics: Genomics; High-Throughput Nucleotide Sequencing; Humans; Nervous System Diseases
PubMed: 27637954
DOI: 10.1016/B978-0-12-802973-2.00006-9 -
Oral Diseases Jul 2016Remarkable advances in high-throughput sequencing technologies have fundamentally changed our understanding of the genetic and epigenetic molecular bases underlying... (Review)
Review
Remarkable advances in high-throughput sequencing technologies have fundamentally changed our understanding of the genetic and epigenetic molecular bases underlying human health and diseases. As these technologies continue to revolutionize molecular biology leading to fresh perspectives, it is imperative to thoroughly consider the enormous excitement surrounding the technologies by highlighting the characteristics of platforms and their global trends as well as potential benefits and limitations. To date, with a variety of platforms, the technologies provide an impressive range of applications, including sequencing of whole genomes and transcriptomes, identifying of genome modifications, and profiling of protein interactions. Because these applications produce a flood of data, simultaneous development of bioinformatics tools is required to efficiently deal with the big data and to comprehensively analyze them. This review covers the major achievements and performances of the high-throughput sequencing and further summarizes the characteristics of their applications along with introducing applicable bioinformatics tools. Moreover, a step-by-step procedure for a practical transcriptome analysis is described employing an analytical pipeline. Clinical perspectives with special consideration to human oral health and diseases are also covered.
Topics: Computational Biology; High-Throughput Nucleotide Sequencing; Humans; Mouth Diseases; Oral Health
PubMed: 26602181
DOI: 10.1111/odi.12403 -
Chembiochem : a European Journal of... Jan 2015Next-generation-sequencing (NGS) technologies enable us to obtain extensive information by deciphering millions of individual DNA sequencing reactions simultaneously.... (Review)
Review
Next-generation-sequencing (NGS) technologies enable us to obtain extensive information by deciphering millions of individual DNA sequencing reactions simultaneously. The new DNA-sequencing strategies exceed their precursors in output by many orders of magnitude, resulting in a quantitative increase in valuable sequence information that could be harnessed for qualitative analysis. Sequencing on this scale has facilitated significant advances in diverse disciplines, ranging from the discovery, design, and evaluation of many small molecules and relevant biological mechanisms to maturation of personalized therapies. NGS technologies that have recently become affordable allow us to gain in-depth insight into small-molecule-triggered biological phenomena and empower researchers to develop advanced versions of small molecules. In this review we focus on the overlooked implications of NGS technologies in chemical biology, with a special emphasis on small-molecule development and screening.
Topics: Biochemistry; Computational Biology; Drug Discovery; Genome, Human; High-Throughput Nucleotide Sequencing; High-Throughput Screening Assays; Humans; Nucleic Acid Conformation; Precision Medicine; Small Molecule Libraries
PubMed: 25421391
DOI: 10.1002/cbic.201402556 -
Briefings in Bioinformatics Jan 2021
Topics: Computational Biology; High-Throughput Nucleotide Sequencing
PubMed: 33401308
DOI: 10.1093/bib/bbaa398 -
The Journal of Investigative Dermatology May 2017Like any true conceptual revolution, next-generation sequencing (NGS) has not only radically changed research and clinical practice, it has also modified scientific... (Review)
Review
Like any true conceptual revolution, next-generation sequencing (NGS) has not only radically changed research and clinical practice, it has also modified scientific culture. With the possibility to investigate DNA contents of any organism and in any context, including in somatic disorders or in tissues carrying complex microbial populations, it initially seemed as if the genetic underpinning of any biological phenomenon could now be deciphered in an almost streamlined fashion. However, over the past recent years, we have once again come to understand that there is no such a thing as great opportunities without great challenges. The steadily expanding use of NGS and related applications is now facing biologists and physicians with novel technological obstacles, analytical hurdles and increasingly pressing ethical questions.
Topics: High-Throughput Nucleotide Sequencing; Humans; Molecular Biology; Skin; Skin Diseases
PubMed: 28411851
DOI: 10.1016/j.jid.2016.02.818 -
TheScientificWorldJournal 2014The world has now entered into a new era of genomics because of the continued advancements in the next generation high throughput sequencing technologies, which includes... (Review)
Review
The world has now entered into a new era of genomics because of the continued advancements in the next generation high throughput sequencing technologies, which includes sequencing by synthesis-fluorescent in situ sequencing (FISSEQ), pyrosequencing, sequencing by ligation using polony amplification, supported oligonucleotide detection (SOLiD), sequencing by hybridization along with sequencing by ligation, and nanopore technology. Great impacts of these methods can be seen for solving the genome related problems of plant and animal kingdom that will open the door of a new era of genomics. This may ultimately overcome the Sanger sequencing that ruled for 30 years. NGS is expected to advance and make the drug discovery process more rapid.
Topics: Drug Discovery; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA
PubMed: 24688432
DOI: 10.1155/2014/802437