Review on Mechanism of DNA Sequencing Technologies in Crop Improvement

The introduction of DNA microarrays and DNA sequencing technologies in medical genetics and diagnostics has been a challenge that has significantly transformed medical practice and patient management. Because of the great advancements in molecular genetics and the development of simple laboratory technology to identify the mutations in the causative genes, also the diagnostic approach to epilepsy has significantly changed. However, the clinical use of molecular cytogenetics and high-throughput DNA sequencing technologies, which are able to test an entire genome for genetic variants that are associated with the disease, is preparing a further revolution in the near future. Molecular Karyotype and Next-Generation Sequencing have the potential to identify causative genes or loci also in sporadic or non-familial epilepsy cases and may well represent the transition from a genetic to a genomic approach to epilepsy.

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Test genetici e consenso informato

SALUTE E SOCIETÀ ◽

10.3280/ses2012-003005 ◽

2012 ◽

pp. 68-95

Author(s):

Marco Seri ◽

Claudio Graziano ◽

Daniela Turchetti ◽

Juri Monducci

Keyword(s):

Dna Sequencing ◽

Human Genetics ◽

Ethical Issues ◽

Clinical Care ◽

Genomic Medicine ◽

Genome Project ◽

Ethical Challenges ◽

Sequencing Technologies ◽

The Human Genome Project

The pace of discovery in the field of human genetics has increased exponentially in the last 30 years. We have witnessed the completion of the Human Genome Project, the identification of hundreds of disease-causing genes, and the dawn of genomic medicine (clinical care based on genomic information). Reduction of DNA sequencing costs, thanks to the so-called "next generation sequencing" technologies, is driving a shift towards the era of "personal genomes", but scientific as well as ethical challenges ahead are countless. We provide an overview on the classification of genetic tests, on informed consent procedures in the context of genetic counseling, and on specific ethical issues raised by the implementation of new DNA sequencing technologies.

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Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data

PeerJ ◽

10.7717/peerj.1419 ◽

2015 ◽

Vol 3 ◽

pp. e1419 ◽

Cited By ~ 6

Author(s):

Jose E. Kroll ◽

Jihoon Kim ◽

Lucila Ohno-Machado ◽

Sandro J. de Souza

Keyword(s):

Alternative Splicing ◽

Dna Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Software Suite ◽

Next Generation Dna Sequencing ◽

Sequencing Technologies ◽

Body Map ◽

Sequencing Platforms

Motivation.Alternative splicing events (ASEs) are prevalent in the transcriptome of eukaryotic species and are known to influence many biological phenomena. The identification and quantification of these events are crucial for a better understanding of biological processes. Next-generation DNA sequencing technologies have allowed deep characterization of transcriptomes and made it possible to address these issues. ASEs analysis, however, represents a challenging task especially when many different samples need to be compared. Some popular tools for the analysis of ASEs are known to report thousands of events without annotations and/or graphical representations. A new tool for the identification and visualization of ASEs is here described, which can be used by biologists without a solid bioinformatics background.Results.A software suite namedSplicing Expresswas created to perform ASEs analysis from transcriptome sequencing data derived from next-generation DNA sequencing platforms. Its major goal is to serve the needs of biomedical researchers who do not have bioinformatics skills.Splicing Expressperforms automatic annotation of transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the analysis of data from all available species. The identification of ASEs is done by a known algorithm previously implemented in another tool namedSplooce. As a final result,Splicing Expresscreates a set of HTML files composed of graphics and tables designed to describe the expression profile of ASEs among all analyzed samples. By using RNA-Seq data from the Illumina Human Body Map and the Rat Body Map, we show thatSplicing Expressis able to perform all tasks in a straightforward way, identifying well-known specific events.Availability and Implementation.Splicing Expressis written in Perl and is suitable to run only in UNIX-like systems. More details can be found at:http://www.bioinformatics-brazil.org/splicingexpress.

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Frontiers in DNA Sequencing: the (R)Evolution of Sequencing Technologies

Encyclopedia of Analytical Chemistry ◽

10.1002/9780470027318.a9183 ◽

2011 ◽

Author(s):

Shirley Horn-Saban ◽

Daniela Amann-Zalcenstein

Keyword(s):

Dna Sequencing ◽

Sequencing Technologies

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Reaping the Benefits of Next-generation Sequencing Technologies for Crop Improvement — Solanaceae

Next Generation Sequencing - Advances, Applications and Challenges ◽

10.5772/61656 ◽

2016 ◽

Author(s):

Sushil Satish Chhapekar ◽

Rashmi Gaur ◽

Ajay Kumar ◽

Nirala Ramchiary

Keyword(s):

Next Generation Sequencing ◽

Crop Improvement ◽

Next Generation ◽

Sequencing Technologies ◽

Generation Sequencing

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Evolution of DNA Sequencing Technologies

Next-Generation Sequencing and Sequence Data Analysis ◽

10.2174/9781681080925115010006 ◽

2015 ◽

pp. 17-24

Keyword(s):

Dna Sequencing ◽

Sequencing Technologies

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Improved Compression of DNA Sequencing Data with Cascading Bloom Filters

International Journal of Foundations of Computer Science ◽

10.1142/s0129054118430013 ◽

2018 ◽

Vol 29 (08) ◽

pp. 1249-1255

Author(s):

Kamil Salikhov

Keyword(s):

Dna Sequencing ◽

Sequence Data ◽

Real Data ◽

Compression Algorithm ◽

Computational Experiments ◽

Bloom Filters ◽

Dna Fragments ◽

Sequencing Data ◽

Sequencing Technologies ◽

Memory Reduction

Modern DNA sequencing technologies generate prodigious volumes of sequence data consisting of short DNA fragments (reads). Storing and transferring this data is often challenging. With this motivation, several specialized compression methods have been developed. In this paper, we present an improvement of the lossless reference-free compression algorithm, suggested by Rozov et al., based on the technique of cascading Bloom filters. Through computational experiments on real data, we demonstrate that our method results in a significant associated memory reduction in practice.

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Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

Genes ◽

10.3390/genes10110858 ◽

2019 ◽

Vol 10 (11) ◽

pp. 858 ◽

Cited By ~ 18

Author(s):

Krehenwinkel ◽

Pomerantz ◽

Prost

Keyword(s):

Dna Sequencing ◽

Biodiversity Loss ◽

Taxonomic Composition ◽

Great Promise ◽

Sequencing Platform ◽

Biological Communities ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Sequencing Studies ◽

High Throughput Dna Sequencing

We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology’s MinION portable sequencing platform, as well as summarize areas of recent development.

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