Personal Diagnostics Using DNA-Sequencing

2015 ◽  
pp. 202-217 ◽  
Author(s):  
Udayaraja GK
Keyword(s):  
Dna Sequencing ◽  
Oil Emulsion ◽  
Sequencing Technologies ◽  
Emulsion Pcr ◽  
Genomic Tools ◽  
Template Library ◽  
Water In Oil Emulsion ◽  
Generation Sequencing ◽  
Physician Scientists

DNA sequencing is the process to identification of nucleotides order in genome which developed from very broad history, also it is derived from version of the Sanger biochemistry. SOLiD, 454 and Polonator sequencing based on emulsion PCR to amplify clonal sequencing with in-vitro construction of adaptor-flanked shotgun library, PCR amplified in the context of a water-in-oil emulsion. Solexa technology relies on bridge PCR to amplify clonal sequencing features. At the conclusion of the PCR, each clonal cluster contains ~1,000 copies of a single member of the template library. This chapter focused on next-generation sequencing technologies methods, capabilities and clinical applications of DNA sequencing technologies for researchers in molecular biology and physician scientists. This will also provide the power of these novel genomic tools and methods to use personal diagnostic at molecular level.

scholarly journals Next generation sequencing technologies (NGST) development and applications

2011 ◽  
Vol 152 (2) ◽  
pp. 55-62 ◽  
Author(s):  
Zsuzsanna Mihály ◽  
Balázs Győrffy
Keyword(s):  
Next Generation Sequencing ◽  
Dna Sequencing ◽  
New Technology ◽  
Objective Assessment ◽  
Basic Research ◽  
Next Generation ◽  
New Era ◽  
Sequencing Technologies ◽  
Meta Analyses ◽  
Generation Sequencing

In the past ten years the development of next generation sequencing technologies brought a new era in the field of quick and efficient DNA sequencing. In our study we give an overview of the methodological achievements from Sanger’s chain-termination sequencing in 1975 to those allowing real-time DNA sequencing today. Sequencing methods that utilize clonal amplicons for parallel multistrand sequencing comprise the basics of currently available next generation sequencing techniques. Nowadays next generation sequencing is mainly used for basic research in functional genomics, providing quintessential information in the meta-analyses of data from signal transduction pathways, onthologies, proteomics and metabolomics. Although next generation sequencing is yet sparsely used in clinical practice, cardiology, oncology and epidemiology already show an immense need for the additional knowledge obtained by this new technology. The main barrier of its spread is the lack of standardization of analysis evaluation methods, which obscure objective assessment of the results. Orv. Hetil., 2011, 152, 55–62.

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.[...]

Fat crystal-stabilized water-in-oil emulsion breakdown and marker release during in vitro digestion

LWT ◽  
2021 ◽  
pp. 111802
Author(s):  
Vivekkumar Patel ◽  
Jonathan Andrade ◽  
Dérick Rousseau
Keyword(s):  
In Vitro Digestion ◽  
Oil Emulsion ◽  
Water In Oil Emulsion

scholarly journals In-vitro and in-vivo Characterization of a Multi-Stage Enzyme-Responsive Nanoparticle-in-Microgel Pulmonary Drug Delivery System

2019 ◽  
Author(s):  
Joscelyn C. Mejías ◽  
Krishnendu Roy
Keyword(s):  
Drug Delivery ◽  
Pulmonary Drug Delivery ◽  
Oil Emulsion ◽  
Multi Stage ◽  
Macrophage Phagocytosis ◽  
Efficient Delivery ◽  
Water In Oil Emulsion ◽  
In Vivo Characterization

AbstractAlthough the lung is an obvious target for site-specific delivery of many therapeutics for respiratory airway diseases such as asthma, COPD, and cystic fibrosis, novel strategies are needed to avoid key physiologic barriers for efficient delivery and controlled release of therapeutics to the lungs. Specifically, deposition into the deep lung requires particles with a 1-5 µm aerodynamic diameter; however, particles with a geometric diameter less than 6 µm are rapidly cleared by alveolar macrophages. Additionally, epithelial, endothelial, and fibroblast cells prefer smaller (< 300 nm) nanoparticles for efficient endocytosis. Here we address these contradictory design requirements by using a nanoparticle-inside-microgel system (Nano-in-Microgel). Using an improved maleimide-thiol based Michael Addition during (water-in-oil) Emulsion (MADE) method, we fabricated both trypsin-responsive and neutrophil elastase-responsive polymeric Nano-in-Microgel to show the versatility of the system in easily exchanging enzyme-responsive crosslinkers for disease-specific proteases. By varying the initial macromer concentration, from 20-50 % w/v, the size distribution means ranged from 4-8 µm, enzymatic degradation of the microgels is within 30 minutes, and in vitro macrophage phagocytosis is lower for the higher % w/v. We further demonstrated that in vivo lung delivery of the multi-stage carriers through the pulmonary route yields particle retention up to several hours and followed by clearance within in naïve mice. Our results provide a further understanding of how enzymatically-degradable multi-stage polymeric carriers can be used for pulmonary drug delivery.Graphical Abstract

scholarly journals A highly sensitive method for the detection of recombinant PERV-A/C env RNA using next generation sequencing technologies

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ken Kono ◽  
Kiyoko Kataoka ◽  
Yuzhe Yuan ◽  
Keisuke Yusa ◽  
Kazuhisa Uchida ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Endogenous Retrovirus ◽  
High Titre ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Porcine Islet ◽  
Highly Sensitive ◽  
Generation Sequencing ◽  
Sensitive Method

AbstractSeveral xenogenic cell-based therapeutic products are currently under development around the world for the treatment of human diseases. Porcine islet cell products for treating human diabetes are a typical example. Since porcine cells possess endogenous retrovirus (PERV), which can replicate in human cells in vitro, the potential transmission of PERV has raised concerns in the development of these products. Four subgroups of infectious PERV have been identified, namely PERV-A, -B, -C, and recombinant PERV-A/C. Among them, PERV-A/C shows a high titre and there was a paper reported that an incidence of PERV-A/C viremia was increased in diseased pigs; thus, it would be important to monitor the emergence of PERV-A/C after transplantation of porcine products. In this study, we developed a highly sensitive method for the detection of PERV-A/C using next generation sequencing (NGS) technologies. A model PERV-C spiked with various doses of PERV-A/C were amplified by RT-PCR and the amplicons were analysed by NGS. We found that the NGS analysis allowed the detection of PERV-A/C at the abundance ratios of 1% and 0.1% with true positive rates of 100% and 57%, respectively, indicating that it would be useful for the rapid detection of PERV-A/C emergence after transplantation of porcine products.

scholarly journals Sequencing of Nucleic Acids: from the First Human Genome to Next Generation Sequencing in COVID-19 Pandemic

2021 ◽  
Vol 68 (2) ◽  
pp. 268-278
Author(s):  
Borut Furlani ◽  
Katarina Kouter ◽  
Damjana Rozman ◽  
Alja Videtič Paska
Keyword(s):  
Dna Sequencing ◽  
Human Genome ◽  
New Technologies ◽  
Clinical Medicine ◽  
Clinical Care ◽  
Basic Knowledge ◽  
Clinical Utilization ◽  
Sequencing Technologies ◽  
Clinical Laboratories ◽  
Generation Sequencing

Despite being around for more than 40 years, DNA sequencing is regarded as young technology in clinical medicine. As sequencing is becoming cheaper, faster and more accurate, it is rapidly being incorporated into clinical laboratories. In 2003, the completion of the first human genome opened the door to personalized medicine. Ever since it has been expected for genomics to widely impact clinical care and public health. However, many years can pass for genomic discoveries to reflect back and benefit the patients. DNA sequencing represents a less biased approach to diagnostics. It is not only a diagnostic tool, but can also influence clinical management and therapy. As new technologies rapidly emerge it is important for researchers and health professionals to have basic knowledge about the capabilities and drawbacks of the existing sequencing methods, and their use in clinical setting and research. This review provides an overview of nucleic acid sequencing technologies from historical perspective and later focuses on clinical utilization of sequencing. Some of the most promising areas are presented with selected examples from Slovenian researchers.

scholarly journals GENERATIONS OF DNA SEQUENCING METHODS (REVIEW)

2020 ◽  
Vol 30 (4) ◽  
pp. 3-20
Author(s):  
A. G. Borodinov ◽  
◽  
V. V. Manoilov ◽  
I. V. Zarutsky ◽  
A. I. Petrov ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Methodological Approach ◽  
Time Interval ◽  
Next Generation ◽  
Sequencing Data ◽  
Technical Problems ◽  
Advantages And Disadvantages ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Generation Sequencing

Several decades have passed since the development of the revolutionary DNA sequencing method by Frederick Sanger and his colleagues. After the Human Genome Project, the time interval between sequencing technologies began to shrink, while the volume of scientific knowledge continued to grow exponentially. Following Sanger sequencing, considered as the first generation, new generations of DNA sequencing were consistently introduced into practice. Advances in next generation sequencing (NGS) technologies have contributed significantly to this trend by reducing costs and generating massive sequencing data. To date, there are three generations of sequencing technologies. Second generation se-quencing, which is currently the most commonly used NGS technology, consists of library preparation, amplification and sequencing steps, while in third generation sequencing, individual nucleic acids are sequenced directly to avoid bias and have higher throughput. The development of new generations of sequencing has made it possible to overcome the limitations of traditional DNA sequencing methods and has found application in a wide range of projects in molecular biology. On the other hand, with the development of next generation technologies, many technical problems arise that need to be deeply analyzed and solved. Each generation and sequencing platform, due to its methodological approach, has specific advantages and disadvantages that determine suitability for certain applications. Thus, the assessment of these characteristics, limitations and potential applications helps to shape the directions for further research on sequencing technologies.

In vitro cell delivery by gelatin microspheres prepared in water-in-oil emulsion

2020 ◽  
Vol 31 (3) ◽  
Author(s):  
Nicola Contessi Negrini ◽  
Maria Veronica Lipreri ◽  
Maria Cristina Tanzi ◽  
Silvia Farè
Keyword(s):  
Cell Delivery ◽  
Gelatin Microspheres ◽  
Oil Emulsion ◽  
Water In Oil Emulsion

Application of high-throughput DNA sequencing technology in forensic genetics

2019 ◽  
Vol 304 ◽  
pp. 64-73
Author(s):  
Anna Woźniak ◽  
◽  
Michał Boroń ◽  
Renata Zbieć-Piekarska ◽  
Magdalena Spólnicka ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Cost Reduction ◽  
Forensic Genetics ◽  
Practical Application ◽  
Sequencing Technology ◽  
Sequencing Technologies ◽  
High Throughput Dna Sequencing ◽  
Generation Sequencing ◽  
Forensic Genetic

The turn of the 20th and 21st centuries marks the beginning of high-throughput DNA sequencing methods, which, owing to increasing efficiency and gradual cost reduction, have led to the revolutionization of biomedical research. This article discusses the most popular next generation sequencing technologies and their practical application in forensic genetic analysis.

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