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Revue Scientifique Et Technique... Apr 2016Natural virus reservoirs such as wild bats, birds, rodents and non-human primates are generally non-model organisms that have, until recently, presented limited... (Review)
Review
Natural virus reservoirs such as wild bats, birds, rodents and non-human primates are generally non-model organisms that have, until recently, presented limited opportunities for in-depth study. Next-generation sequencing provides a way to partially circumvent this limitation, since the methods required for data acquisition and analysis are largely species-independent. Comparative genomics and other 'omics' provide new opportunities to study the structure and function of various biological systems of wild species that are otherwise out of reach. Genomes of natural reservoir hosts can help to identify dominant pathways of virus-host interaction and to reveal differences between susceptible and resistant organisms, populations and species. This is of great scientific interest and may also provide a resource for the rational design of treatments for viral diseases in humans and livestock. In this way, we will 'learn from nature' and one day apply this knowledge to create disease-resistant livestock or develop novel therapeutic and prevention strategies. Reservoir host genomics will also open up possibilities for developing novel vaccines for wildlife, aid in the development of new diagnostic platforms, and have broad implications for developmental and evolutionary biology. In this review, the authors focus on natural reservoir hosts of viral pathogens, although most of the discussion points should be equally applicable to natural reservoirs of pathogenic bacteria, fungi or other parasites.
Topics: Animals; Communicable Diseases; Disease Reservoirs; Genomics; High-Throughput Nucleotide Sequencing
PubMed: 27217176
DOI: 10.20506/rst.35.1.2425 -
The Journal of Molecular Diagnostics :... Aug 2020Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential.... (Review)
Review
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridization methods, for routine molecular testing of tumors. However, one limitation of routinely used NGS technologies is the inability to detect low-level genomic variants with high accuracy. This can be attributed to the frequent occurrence of low-level sequencing errors and artifacts in NGS workflow that need specialized approaches to be identified and eliminated. This review focuses on the origins and nature of these artifacts and recent improvements in the NGS technologies to overcome them to facilitate accurate high-sensitive detection of low-level mutations. Potential applications of high-sensitive NGS in oncology and comparisons with non-NGS technologies of similar capabilities are also summarized.
Topics: Data Accuracy; Genetic Variation; High-Throughput Nucleotide Sequencing; Humans; In Situ Hybridization, Fluorescence; Limit of Detection; Mutation; Neoplasms; Real-Time Polymerase Chain Reaction; Reproducibility of Results; Sensitivity and Specificity
PubMed: 32480002
DOI: 10.1016/j.jmoldx.2020.04.213 -
Human Heredity 2011
Topics: Genetic Linkage; High-Throughput Nucleotide Sequencing; Humans
PubMed: 22189464
DOI: 10.1159/000334421 -
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 -
Medecine Sciences : M/S Feb 2012
Topics: Databases, Genetic; Disease; Europe; Genetics, Medical; Genome, Human; Genotype; High-Throughput Nucleotide Sequencing; Human Genome Project; Humans; Phenotype; Sequence Analysis, DNA
PubMed: 22377291
DOI: 10.1051/medsci/2012282001 -
Genomics 2014In the last decades, molecular biology has moved from gene-by-gene analysis to more complex studies using a genome-wide scale. Thanks to high-throughput genomic... (Review)
Review
In the last decades, molecular biology has moved from gene-by-gene analysis to more complex studies using a genome-wide scale. Thanks to high-throughput genomic technologies, such as microarrays and next-generation sequencing, a huge amount of information has been generated, expanding our knowledge on the genetic basis of various diseases. Although some of this information could be transferred to clinical diagnostics, the technologies available are not suitable for this purpose. In this review, we will discuss the drawbacks associated with the use of traditional DNA microarrays in diagnostics, pointing out emerging platforms that could overcome these obstacles and offer a more reproducible, qualitative and quantitative multigenic analysis. New miniaturized and automated devices, called Lab-on-Chip, begin to integrate PCR and microarray on the same platform, offering integrated sample-to-result systems. The introduction of this kind of innovative devices may facilitate the transition of genome-based tests into clinical routine.
Topics: Animals; Genomics; High-Throughput Nucleotide Sequencing; Humans; Lab-On-A-Chip Devices; Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction
PubMed: 24560816
DOI: 10.1016/j.ygeno.2014.02.003 -
Medecine Sciences : M/S Apr 2016
Topics: France; Genetic Testing; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Inventions; Knowledge; Rare Diseases; Social Change; Therapies, Investigational
PubMed: 27137856
DOI: 10.1051/medsci/201632s105 -
Annals of Oncology : Official Journal... Aug 2016
Precision medicine and oncology: an overview of the opportunities presented by next-generation sequencing and big data and the challenges posed to conventional drug development and regulatory approval pathways.
Topics: Data Interpretation, Statistical; Drug Approval; Drug Discovery; High-Throughput Nucleotide Sequencing; Humans; Medical Oncology; Neoplasms; Precision Medicine
PubMed: 27117532
DOI: 10.1093/annonc/mdw165 -
Cell Host & Microbe May 2016The development of next-generation sequencing as a cost-effective technology has facilitated the analysis of bacterial population structure at a whole-genome level and... (Review)
Review
The development of next-generation sequencing as a cost-effective technology has facilitated the analysis of bacterial population structure at a whole-genome level and at scale. From these data, phylogenic trees have been constructed that define population structures at a local, national, and global level, providing a framework for genetic analysis. Although still at an early stage, these approaches have yielded progress in several areas, including pathogen transmission mapping, the genetics of niche colonization and host adaptation, as well as gene-to-phenotype association studies. Antibiotic resistance has proven to be a major challenge in the early 21(st) century, and phylogenetic analyses have uncovered the dramatic effect that the use of antibiotics has had on shaping bacterial population structures. An update on insights into bacterial evolution from comparative genomics is provided in this review.
Topics: Animals; Bacteria; DNA, Bacterial; Evolution, Molecular; Genome, Bacterial; Genome-Wide Association Study; High-Throughput Nucleotide Sequencing; Humans; Phylogeny
PubMed: 27173928
DOI: 10.1016/j.chom.2016.04.015 -
Genome Biology Jun 2013The sequencing of large and complex genomes of crop species, facilitated by new sequencing technologies and bioinformatic approaches, has provided new opportunities for... (Review)
Review
The sequencing of large and complex genomes of crop species, facilitated by new sequencing technologies and bioinformatic approaches, has provided new opportunities for crop improvement. Current challenges include understanding how genetic variation translates into phenotypic performance in the field.
Topics: Breeding; Crops, Agricultural; Genetic Variation; Genome, Plant; Genomics; High-Throughput Nucleotide Sequencing; History, 21st Century; Phenotype
PubMed: 23796126
DOI: 10.1186/gb-2013-14-6-206