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Circulation Research Sep 2015
Topics: Cost-Benefit Analysis; Heart Diseases; High-Throughput Nucleotide Sequencing; Humans
PubMed: 26358106
DOI: 10.1161/CIRCRESAHA.115.307344 -
Annual Review of Genomics and Human... Aug 2016The term next-generation sequencing is almost a decade old, but it remains the colloquial way to describe highly parallel or high-output sequencing methods that produce... (Review)
Review
The term next-generation sequencing is almost a decade old, but it remains the colloquial way to describe highly parallel or high-output sequencing methods that produce data at or beyond the genome scale. Since the introduction of these technologies, the number of applications and methods that leverage the power of genome-scale sequencing has increased at an exponential pace. This review highlights recent concepts, technologies, and methods from next-generation sequencing to illustrate the breadth and depth of the applications and research areas that are driving progress in genomics.
Topics: Genome, Human; Genomics; High-Throughput Nucleotide Sequencing; Humans; Sequence Analysis, DNA
PubMed: 27362342
DOI: 10.1146/annurev-genom-083115-022413 -
Journal of Microbiology and... Sep 2015Wolbachia is an obligate symbiotic bacteria that is ubiquitous in arthropods, with 25-70% of insect species estimated to be infected. Wolbachia species can interact with...
Wolbachia is an obligate symbiotic bacteria that is ubiquitous in arthropods, with 25-70% of insect species estimated to be infected. Wolbachia species can interact with their insect hosts in a mutualistic or parasitic manner. Sequence types (ST) of Wolbachia are determined by multilocus sequence typing (MLST) of housekeeping genes. However, there are some limitations to MLST with respect to the generation of clone libraries and the Sanger sequencing method when a host is infected with multiple STs of Wolbachia. To assess the feasibility of massive parallel sequencing, also known as next-generation sequencing, we used pyrosequencing for sequence typing of Wolbachia in butterflies. We collected three species of butterflies (Eurema hecabe, Eurema laeta, and Tongeia fischeri) common to Korea and screened them for Wolbachia STs. We found that T. fischeri was infected with a single ST of Wolbachia, ST41. In contrast, E. hecabe and E. laeta were each infected with two STs of Wolbachia, ST41 and ST40. Our results clearly demonstrate that pyrosequencing-based MLST has a higher sensitivity than cloning and Sanger sequencing methods for the detection of minor alleles. Considering the high prevalence of infection with multiple Wolbachia STs, next-generation sequencing with improved analysis would assist with scaling up approaches to Wolbachia MLST.
Topics: Animals; Butterflies; High-Throughput Nucleotide Sequencing; Korea; Multilocus Sequence Typing; Wolbachia
PubMed: 26139612
DOI: 10.4014/jmb.1503.03097 -
Pathobiology : Journal of... 2017Interrogation of tissue informs on patient management through delivery of a diagnosis together with associated clinically relevant data. The diagnostic pathologist will... (Review)
Review
Interrogation of tissue informs on patient management through delivery of a diagnosis together with associated clinically relevant data. The diagnostic pathologist will usually evaluate the morphological appearances of a tissue sample and, occasionally, the pattern of expression of a limited number of biomarkers. Recent developments in sequencing technology mean that DNA and RNA from tissue samples can now be interrogated in great detail. These new technologies, collectively known as next-generation sequencing (NGS), generate huge amounts of data which can be used to support patient management. In order to maximize the utility of tissue interrogation, the molecular data need to be interpreted and integrated with the morphological data. However, in order to interpret the molecular data, the pathologist must understand the utility and the limitations of NGS data. In this review, the principles behind NGS technologies are described. In addition, the caveats in the interpretation of the data are discussed, and a scheme is presented to "classify" the types of data which are generated. Finally, a glossary of new terminology is included to help pathologists become familiar with the lexicon of NGS-derived molecular data.
Topics: Gene Library; High-Throughput Nucleotide Sequencing; Histological Techniques; Humans; Pathology, Molecular; Sequence Analysis, DNA; Statistics as Topic
PubMed: 29131018
DOI: 10.1159/000480089 -
Seminars in Diagnostic Pathology Sep 2019From a technical perspective, specimen identity determination in surgical pathology over the last several decades has primarily focused on analysis of repetitive DNA... (Review)
Review
From a technical perspective, specimen identity determination in surgical pathology over the last several decades has primarily focused on analysis of repetitive DNA sequences, specifically microsatellite repeats. However, a number of techniques have recently been developed that have similar, if not greater, utility in surgical pathology, most notably analysis of single nucleotide polymorphism (SNPs) and gene panels by next generation sequencing (NGS). For cases with an extremely limited sample or a degraded sample, sequence analysis of mitochondrial DNA continues to be the method of choice. From a diagnostic perspective, interest in identity determination in surgical pathology is usually centered on resolving issues of specimen provenance due to specimen labeling/accessioning deficiencies and possible contamination, but is also frequently performed in cases for which the patient's clinical course following definitive therapy is remarkably atypical, in cases of an unexpected diagnosis, and by patient request for "peace of mind". However, the methods used for identity determination have a much broader range of applications in surgical pathology beyond tissue provenance analysis. The methods can be used to provide ancillary information for cases in which the histomorphology is not definitively diagnostic, as for example for tumors that have a virtually identical microscopic appearance but for which the differential diagnosis includes synchronous/metachronous tumors versus a metastasis, and for the diagnosis of hydropic early gestations versus hydatidiform molar pregnancies. The methods also have utility in several other clinical settings, for example to rule out a donor-transmitted malignancy in a transplant recipient, to monitor bone marrow transplant engraftment, and to evaluate natural chimerism.
Topics: High-Throughput Nucleotide Sequencing; Humans; Pathology, Surgical
PubMed: 31196743
DOI: 10.1053/j.semdp.2019.06.001 -
Combinatorial Chemistry & High... May 2014
Topics: Academies and Institutes; Animals; Australia; Drosophila; Germany; High-Throughput Nucleotide Sequencing; Humans; MicroRNAs; RNA Interference; RNA, Small Interfering
PubMed: 24807562
DOI: 10.2174/138620731704140416113418 -
PLoS Computational Biology Feb 2021
Topics: Computational Biology; High-Throughput Nucleotide Sequencing; Humans; Software; Terminology as Topic; Whole Genome Sequencing; Writing
PubMed: 33600404
DOI: 10.1371/journal.pcbi.1008645 -
Journal of Mathematical Biology Jul 2014Pyrosequencing is one of the important next-generation sequencing technologies. We derive the distribution of the number of positive signals in pyrograms of this...
Pyrosequencing is one of the important next-generation sequencing technologies. We derive the distribution of the number of positive signals in pyrograms of this sequencing technology as a function of flow cycle numbers and nucleotide probabilities of the target sequences. As for the distribution of sequence length, we also derive the distribution of positive signals for the fixed flow cycle model. Explicit formulas are derived for the mean and variance of the distributions. A simple result for the mean of the distribution is that the mean number of positive signals in a pyrogram is approximately twice the number of flow cycles, regardless of nucleotide probabilities. The statistical distributions will be useful for instrument and software development for pyrosequencing and other related platforms.
Topics: Computer Simulation; High-Throughput Nucleotide Sequencing; Models, Genetic; Nucleotides; Sequence Analysis, DNA
PubMed: 23722629
DOI: 10.1007/s00285-013-0691-5 -
Mitochondrion Jul 2014Next-generation sequencing, also known as high-throughput sequencing, has greatly enhanced researchers' ability to conduct biomedical research on all levels.... (Review)
Review
Next-generation sequencing, also known as high-throughput sequencing, has greatly enhanced researchers' ability to conduct biomedical research on all levels. Mitochondrial research has also benefitted greatly from high-throughput sequencing; sequencing technology now allows for screening of all 16,569 base pairs of the mitochondrial genome simultaneously for SNPs and low level heteroplasmy and, in some cases, the estimation of mitochondrial DNA copy number. It is important to realize the full potential of high-throughput sequencing for the advancement of mitochondrial research. To this end, we review how high-throughput sequencing has impacted mitochondrial research in the categories of SNPs, low level heteroplasmy, copy number, and structural variants. We also discuss the different types of mitochondrial DNA sequencing and their pros and cons. Based on previous studies conducted by various groups, we provide strategies for processing mitochondrial DNA sequencing data, including assembly, variant calling, and quality control.
Topics: DNA Copy Number Variations; DNA, Mitochondrial; Genetic Variation; High-Throughput Nucleotide Sequencing; Humans; Mitochondrial Diseases; Polymorphism, Single Nucleotide
PubMed: 24859348
DOI: 10.1016/j.mito.2014.05.004 -
FEMS Microbiology Letters Aug 2018Industrial biotechnology develops and applies microorganisms for the production of bioproducts and enzymes with applications ranging from food and feed ingredients and... (Review)
Review
Industrial biotechnology develops and applies microorganisms for the production of bioproducts and enzymes with applications ranging from food and feed ingredients and processing to bio-based chemicals, biofuels and pharmaceutical products. Next generation DNA sequencing technologies play an increasingly important role in improving and accelerating microbial strain development for existing and novel bio-products via screening, gene and pathway discovery, metabolic engineering and additional optimization and understanding of large-scale manufacturing. In this mini-review, we describe novel DNA sequencing and analysis technologies with a focus on applications to industrial strain development, enzyme discovery and microbial community analysis.
Topics: Bacteria; High-Throughput Nucleotide Sequencing; Industrial Microbiology
PubMed: 30010862
DOI: 10.1093/femsle/fny103