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Current Issues in Molecular Biology 2018Next-generation sequencing technologies are revolutionizing biology by permitting, transcriptome sequencing, whole-genome sequencing and resequencing, and genome-wide... (Review)
Review
Next-generation sequencing technologies are revolutionizing biology by permitting, transcriptome sequencing, whole-genome sequencing and resequencing, and genome-wide single nucleotide polymorphism profiling. Orchid research has benefited from this breakthrough, and a few orchid genomes are now available; new biological questions can be approached and new breeding strategies can be designed. The first part of this review describes the unique features of orchid biology. The second part provides an overview of the current next-generation sequencing platforms, many of which are already used in plant laboratories. The third part summarizes the state of orchid transcriptome and genome sequencing and illustrates current achievements. The genetic sequences currently obtained will not only provide a broad scope for the study of orchid biology, but also serves as a starting point for uncovering the mystery of orchid evolution.
Topics: Biological Evolution; Chromosome Mapping; DNA, Plant; Gene Expression Profiling; Genome, Plant; High-Throughput Nucleotide Sequencing; Orchidaceae; Plant Breeding; Polymorphism, Single Nucleotide; Sequence Analysis, DNA; Transcriptome
PubMed: 28885174
DOI: 10.21775/cimb.027.051 -
British Journal of Cancer Feb 2017In the context of solid tumours, the evolution of cancer therapies to more targeted and nuanced approaches has led to the impetus for personalised medicine. The targets... (Review)
Review
In the context of solid tumours, the evolution of cancer therapies to more targeted and nuanced approaches has led to the impetus for personalised medicine. The targets for these therapies are largely based on the driving genetic mutations of the tumours. To track these multiple driving mutations the use of next generation sequencing (NGS) coupled with a morphomolecular approach to tumours, has the potential to deliver on the promises of personalised medicine. A review of NGS and its application in a universal healthcare (UHC) setting is undertaken as the technology has a wide appeal and utility in diagnostic, clinical trial and research paradigms. Furthermore, we suggest that these can be accommodated with a unified integromic approach. Challenges remain in bringing NGS to routine clinical use and these include validation, handling of the large amounts of information flow and production of a clinically useful report. These challenges are particularly acute in the setting of UHC where tests are not reimbursed and there are finite resources available. It is our opinion that the challenges faced in applying NGS in a UHC setting are surmountable and we outline our approach for its routine application in diagnostic, clinical trial and research paradigms.
Topics: Clinical Trials as Topic; High-Throughput Nucleotide Sequencing; Humans; Insurance, Health; Mutation; Neoplasms; Precision Medicine; Sequence Analysis, DNA
PubMed: 28103613
DOI: 10.1038/bjc.2016.452 -
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 -
Genome Medicine Nov 2015High-throughput sequencing of B-cell immunoglobulin repertoires is increasingly being applied to gain insights into the adaptive immune response in healthy individuals... (Review)
Review
High-throughput sequencing of B-cell immunoglobulin repertoires is increasingly being applied to gain insights into the adaptive immune response in healthy individuals and in those with a wide range of diseases. Recent applications include the study of autoimmunity, infection, allergy, cancer and aging. As sequencing technologies continue to improve, these repertoire sequencing experiments are producing ever larger datasets, with tens- to hundreds-of-millions of sequences. These data require specialized bioinformatics pipelines to be analyzed effectively. Numerous methods and tools have been developed to handle different steps of the analysis, and integrated software suites have recently been made available. However, the field has yet to converge on a standard pipeline for data processing and analysis. Common file formats for data sharing are also lacking. Here we provide a set of practical guidelines for B-cell receptor repertoire sequencing analysis, starting from raw sequencing reads and proceeding through pre-processing, determination of population structure, and analysis of repertoire properties. These include methods for unique molecular identifiers and sequencing error correction, V(D)J assignment and detection of novel alleles, clonal assignment, lineage tree construction, somatic hypermutation modeling, selection analysis, and analysis of stereotyped or convergent responses. The guidelines presented here highlight the major steps involved in the analysis of B-cell repertoire sequencing data, along with recommendations on how to avoid common pitfalls.
Topics: Computational Biology; Guidelines as Topic; High-Throughput Nucleotide Sequencing; Humans; Receptors, Antigen, B-Cell; Sequence Analysis
PubMed: 26589402
DOI: 10.1186/s13073-015-0243-2 -
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 -
Research in Veterinary Science Oct 2017Production disease in pigs is caused by a variety of different pathogens, mainly enteric and respiratory and can result in significant economic loss. Other factors such... (Review)
Review
Production disease in pigs is caused by a variety of different pathogens, mainly enteric and respiratory and can result in significant economic loss. Other factors such as stress, poor husbandry and nutrition can also contribute to an animal's susceptibility to disease. Molecular biomarkers of production disease could be of immense value by improving diagnosis and risk analysis to determine best practice with an impact on increased economic output and animal welfare. In addition to the use of multiplex PCR or microarrays to detect individual or mixed pathogens during infection, these technologies can also be used to monitor the host response to infection via gene expression. The patterns of gene expression associated with cellular damage or initiation of the early immune response may indicate the type of pathology and, by extension the types of pathogen involved. Molecular methods can therefore be used to monitor both the presence of a pathogen and the host response to it during production disease. The field of biomarker discovery and implementation is expanding as technologies such as microarrays and next generation sequencing become more common. Whilst a large number of studies have been carried out in human medicine, further work is needed to identify molecular biomarkers in veterinary medicine and in particular those associated with production disease in the pig industry. The pig transcriptome is highly complex and still not fully understood. Further gene expression studies are needed to identify molecular biomarkers which may have predictive value in identifying the environmental, nutritional and other risk factors which are associated with production diseases in pigs.
Topics: Animal Husbandry; Animals; Biomarkers; High-Throughput Nucleotide Sequencing; Sus scrofa; Swine; Swine Diseases
PubMed: 28535467
DOI: 10.1016/j.rvsc.2017.05.016 -
Genomics Sep 2021Discovering copy number variation (CNV) in bacteria is not in the spotlight compared to the attention focused on CNV detection in eukaryotes. However, challenges arising...
Discovering copy number variation (CNV) in bacteria is not in the spotlight compared to the attention focused on CNV detection in eukaryotes. However, challenges arising from bacterial drug resistance bring further interest to the topic of CNV and its role in drug resistance. General CNV detection methods do not consider bacteria's features and there is space to improve detection accuracy. Here, we present a CNV detection method called CNproScan focused on bacterial genomes. CNproScan implements a hybrid approach and other bacteria-focused features and depends only on NGS data. We benchmarked our method and compared it to the previously published methods and we can resolve to achieve a higher detection rate together with providing other beneficial features, such as CNV classification. Compared with other methods, CNproScan can detect much shorter CNV events.
Topics: DNA Copy Number Variations; Eukaryota; Genome, Bacterial; High-Throughput Nucleotide Sequencing
PubMed: 34224809
DOI: 10.1016/j.ygeno.2021.06.040 -
Revue Scientifique Et Technique... Apr 2016Next-generation sequencing (NGS) technologies have reshaped genome research. The resulting increase in sequencing depth and resolution has led to an unprecedented level... (Review)
Review
Next-generation sequencing (NGS) technologies have reshaped genome research. The resulting increase in sequencing depth and resolution has led to an unprecedented level of genomic detail and thus an increasing awareness of the complexity of animal, human and pathogen genomes. This has resulted in new approaches to vaccine research. On the one hand, the increase in genome complexity challenges our ability to study and understand pathogen biology and pathogen-host interactions. On the other hand, the increase in genomic data also provides key information for developing and designing improved vaccines against pathogens that were previously extremely difficult to deal with, such as rapidly mutating RNA viruses or bacteria that have complex interactions with the host immune system. This review describes how the broad application of NGS technologies to genome research is affecting vaccine research. It focuses on implications for the field of viral genomics, and includes recent animal and human studies.
Topics: Animals; Drug Design; Genome, Viral; High-Throughput Nucleotide Sequencing; Mutation; Vaccines; Virus Diseases
PubMed: 27217168
DOI: 10.20506/rst.35.1.2417 -
Current Issues in Molecular Biology 2018The history of DNA sequencing dates back to 1970s. During this period the two first generation nucleotide sequencing techniques were developed. Subsequently the Sanger's... (Review)
Review
The history of DNA sequencing dates back to 1970s. During this period the two first generation nucleotide sequencing techniques were developed. Subsequently the Sanger's dideoxy method of sequencing gained popularity over Maxam and Gilbert's chemical method of sequencing. However, in the last decade, we have observed revolutionary changes in DNA sequencing technologies leading to the emergence of next-generation sequencing (NGS) techniques. NGS technologies have enhanced the throughput and speed of sequencing combined with bringing down the overall cost of the process over a time. The major applications of NGS technologies being genome sequencing and resequencing, transcriptomics, metagenomics in relation to plant-microbe interactions, exon and genome capturing, development of molecular markers and evolutionary studies. In this review, we present a broader picture of evolution of NGS tools, its various applications in crop plants, and future prospects of the technology for crop improvement.
Topics: Chromosome Mapping; Chromosomes, Plant; Crops, Agricultural; DNA, Plant; Genetic Markers; Genome, Plant; Genomics; High-Throughput Nucleotide Sequencing; History, 20th Century; History, 21st Century; Metagenomics; Plant Roots; Plants; Rhizosphere; Symbiosis; Transcriptome
PubMed: 28885172
DOI: 10.21775/cimb.027.001 -
Viruses Jan 2014Next-generation high throughput sequencing technologies became available at the onset of the 21st century. They provide a highly efficient, rapid, and low cost DNA... (Review)
Review
Next-generation high throughput sequencing technologies became available at the onset of the 21st century. They provide a highly efficient, rapid, and low cost DNA sequencing platform beyond the reach of the standard and traditional DNA sequencing technologies developed in the late 1970s. They are continually improved to become faster, more efficient and cheaper. They have been used in many fields of biology since 2004. In 2009, next-generation sequencing (NGS) technologies began to be applied to several areas of plant virology including virus/viroid genome sequencing, discovery and detection, ecology and epidemiology, replication and transcription. Identification and characterization of known and unknown viruses and/or viroids in infected plants are currently among the most successful applications of these technologies. It is expected that NGS will play very significant roles in many research and non-research areas of plant virology.
Topics: High-Throughput Nucleotide Sequencing; History, 20th Century; History, 21st Century; Plant Pathology; Plant Viruses; Plants; Virology
PubMed: 24399207
DOI: 10.3390/v6010106