SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

One of the most important achievements of Next Generation Sequencing (NGS) is to produce millions of sequences reads in a short period of time, and to produce large sequences of deoxyribonucleic acid (DNA) in fragments of any size. Libraries can be generated from whole genomes or any DNA or RNA region of interest without the need to know its sequence beforehand. In the forensic field, one of the main problems is the limited amount of sample available, as well as its degraded state samples. Next-generation sequencing (NGS) technology, with its high-throughput capacity and low cost, has developed rapidly in recent years and become an important analytical tool for many genomics researchers. New opportunities in the research domain of the forensic studies emerge by using the power of next generation sequencing technology, which can be applied to simultaneously analyzing multiple loci of forensic interest in different genetic materials. Furthermore, next-generation sequencing (NGS) technology can also have potential applications in many other aspects of forensic science such as achieving the simultaneous analysis of the standard autosomal DNA (STRs and SNPs), deoxyribonucleic acid (DNA) database construction, ancestry and phenotypic inferences, monozygotic twin studies, body fluid and species identification, forensic animal, plant and microbiological analyses, mitochondrial DNA, microbiological analysis, epigenetics analysis, MicroRNA analysis, animal and plant DNA analysis and X and Y chromosomal markers. In this study, we review the application of next generation sequencing (NGS) technology in the field of forensic science with the aim of providing a reference for future forensic studies and practice.

Collection and storage of HLA NGS genotyping data for the 17th International HLA and Immunogenetics Workshop

Applications of next-generation sequencing in fisheries research: A review

Next generation sequencing(NGS)has made great progress, applied from science technology to clinical diagnosis in the past several years. With a simple, fast, high-throughput, and high-resolution feature, it has been believed to be one of the most potential technology in clinical tests, especially in individual tumor diagnosis and treatment, noninvasive prenatal screening, genetic disorders screening field. This paper will briefly review the application of next generation sequencing in the field of infection disease.(Chin J Lab Med, 2017, 40: 492-494) Key words: High-throughput nucleotide sequencing; Infection; Mutation

Gene fusions are important genomic events in human cancer because their fusion gene products can drive the development of cancer and thus are potential prognostic tools or therapeutic targets in anti-cancer treatment. Major advancements have been made in computational approaches for fusion gene discovery over the past 3 years due to improvements and widespread applications of high-throughput next generation sequencing (NGS) technologies. To identify fusions from NGS data, existing methods typically leverage the strengths of both sequencing technologies and computational strategies. In this article, we review the NGS and computational features of existing methods for fusion gene detection and suggest directions for future development.

Next-generation sequencing (NGS) technologies are enabling breakthroughs in how the biomedical community is developing and evaluating medical products. One example is the potential application of this method to the detection and identification of microbial contaminants in biologic products. In order for the U.S. Food and Drug Administration (FDA) to be able to evaluate the utility of this technology, we need to have the information technology infrastructure and bioinformatics tools to be able to store and analyze large amounts of data. To address this need, we have developed the High-performance Integrated Virtual Environment, or HIVE. HIVE uses a combination of distributed cloud storage and distributed cloud computations to provide a platform that is both rapid and responsive to support the growing and increasingly diverse scientific and regulatory needs of FDA scientists in their evaluation of NGS in research and ultimately for evaluation of NGS data in regulatory submissions.

Advancements in genomic (DNA and RNA) sequencing have dramatically accelerated research in the domain of host microbiome during current decade. Extensive application of next generation sequencing (NGS) technologies has identified the core microbiome of the human gut that is being used for improving health. Microbial communities of plant host have been recognized as a potential biological factor essential for shaping, acclimation, growth and health of the host. Nevertheless, we are far away to understand precise composition of the microbial communities and their function in the plant host. The purpose of this article is to highlight specific area of microbial - plant association that can be deeply analysed by using NGS and spectral technologies.

Next-generation sequencing (NGS) technology has revolutionized cancer research and treatment by enabling comprehensive analysis of genetic mutations, alterations, and expression profiles. It allows for the identification of cancer-driving mutations, helping in the development of targeted therapies. NGS provides detailed insights into tumor heterogeneity, resistance mechanisms, and clonal evolution. Its high-throughput capacity facilitates large-scale studies, improving our understanding of cancer genomics. By enabling personalized treatment plans based on individual genetic profiles, NGS holds promise for more effective and tailored cancer therapies. Early reviews on cancer genomics often lacked comprehensive coverage of emerging technologies. They missed in-depth analysis of NGS advancements, their impact on cancer research, and clinical applications. The review addresses this gap by reviving a thorough examination of NGS methods, their role in identifying genetic mutations, and their potential in personalized cancer treatment, thus providing essential insights into the evolving landscape of cancer genomics. The article covers the advancements in technology and bioinformatic approaches for NGS data analysis. It delves into NGS applications in research and diagnostics, particularly for solid cancer diagnosis. The review highlights specific cancer types, including hereditary breast cancer, melanoma, prostate cancer, thyroid cancer, lung cancer, and colorectal cancer. It explores NGS contribution in understanding the genetic basis of these cancers and its potential for enhancing personalized diagnosis and treatment strategies. This review rectifies early lacunas by providing a comprehensive and updated examination of NGS technology, addressing gaps in previous analyses and emphasizes bioinformatic approaches for NGS data analysis, crucial for interpreting vast genomic data accurately. The review meets the current need for a thorough understanding of NGS’s role in personalized cancer treatment and research.

The advances in next generation sequencing (NGS) technologies have tremendous impacts on the studies of structural and functional genomics. Sequencing‐based approaches like ChIP‐Seq and RNA‐Seq have started taking the place of microarray experiments to study protein–DNA ( deoxyribonucleic acid ) interactions and transcriptomic profiling, respectively. The arrival of NGS technologies has also enabled several whole human genome resequencing studies to be completed efficiently at an affordable price. The major strengths of NGS technologies are their ultra high‐throughput production, characterized by their ability to generate several hundred megabases to tens of gigabases of sequencing data per instrument run, and more importantly, the steep reduction in cost compared to the traditional Sanger sequencing method. Hence, NGS technologies have rapidly become the primary choice for large scale as well as genome‐wide sequencing studies. The new sequencing‐based approaches to explore structural and functional genomics have produced important information and significantly expanded our knowledge in these areas. Key concepts The rapid developments in sequencing technologies have transformed the approaches in the studies of structural and functional genomics. The arrival of next generation sequencing (NGS) technologies has started substituting traditional Sanger sequencing method in many large‐scale or genome‐wide sequencing studies. Shortly after the first next generation sequencer was introduced by Roche® 454 Life Science, the Genome Sequencer 20 (GS 20) System (it was subsequently replaced by GS FLX System), another two biotechnology companies also marketed their sequencing platforms: Illumina® Genome Analyzer (GA) and Applied Biosystems® (ABI) Supported Oligonucleotide Ligation Detection System (SOLiD). The major attractions of NGS technologies are their ultra high‐throughput production, characterized by their ability to produce gigabases of sequencing data per instrument run, and more importantly, the steep reduction in cost compared to the traditional sequencing method. Previously, the molecular genomics studies mainly relied on microarray technologies such as gene expression microarrays and the ChIP‐chip method (i.e. chromatin immunoprecipitation coupled with microarray) for genome‐wide interrogation. The NGS technologies have been used in various research areas besides the standard sequencing applications such as whole genome sequencing; they have also been increasingly applied in detecting structural variations (paired‐end mapping), studies of protein–DNA interactions and histone modifications (ChIP‐Seq) and transcriptomic profiling of messenger RNAs (mRNAs) and noncoding RNAs (RNA‐Seq). Sequencing‐based approaches have already yielded numerous novel and important findings in research areas like genome‐wide mapping of histone modifications and protein–DNA interactions, discovery of genetic variations and transcriptomics studies even though the approaches are still new and maturing. The NGS technologies have shown their potential of being dominant in future genomics studies. This is evident from several international projects using NGS technologies like the ENCODE Project, 1000 Genomes Project and cancers sequencing project by the International Cancer Genome Consortium. It is only a matter of time before achieving the goal of $1000 per whole genome sequencing. This should not be too far from now given the progresses in the development of third generation sequencing technologies. Although the $1000 genome will technically make sequencing of thousands of human genomes a reality, the substantial cost that will be incurred for data storage, powerful computational packages and analytical softwares has to be borne in mind. However, beyond affordability, what are left behind are the bioinformatics challenges in processing and analysing the huge amount of sequencing data.

The application of next-generation sequencing (NGS) technologies for the development of simple sequence repeat (SSR) or microsatellite loci for genetic research in the botanical sciences is described. Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been a difficult and costly process. NGS technologies allow the efficient identification of large numbers of microsatellites at a fraction of the cost and effort of traditional approaches. The major advantage of NGS methods is their ability to produce large amounts of sequence data from which to isolate and develop numerous genome-wide and gene-based microsatellite loci. The two major NGS technologies with emergent application in SSR isolation are 454 and Illumina. A review is provided of several recent studies demonstrating the efficient use of 454 and Illumina technologies for the discovery of microsatellites in plants. Additionally, important aspects during NGS isolation and development of microsatellites are discussed, including the use of computational tools and high-throughput genotyping methods. A data set of microsatellite loci in the plastome and mitochondriome of cranberry (Vaccinium macrocarpon Ait.) is provided to illustrate a successful application of 454 sequencing for SSR discovery. In the future, NGS technologies will massively increase the number of SSRs and other genetic markers available to conduct genetic research in understudied but economically important crops such as cranberry.

Thanks to recent advances in next-generation sequencing (NGS) technology, diverse livestock species have been dissected at the genome-wide sequence level. As for cattle, there are currently four Korean indigenous breeds registered with the Domestic Animal Diversity Information System of the Food and Agricultural Organization of the United Nations: Hanwoo, Chikso, Heugu, and Jeju Heugu. These native genetic resources were recently whole-genome resequenced using various NGS technologies, providing enormous single nucleotide polymorphism information across the genomes. The NGS application further provided biological such that Korean native cattle are genetically distant from some cattle breeds of European origins. In addition, the NGS technology was successfully applied to detect structural variations, particularly copy number variations that were usually difficult to identify at the genome-wide level with reasonable accuracy. Despite the success, those recent studies also showed an inherent limitation in sequencing only a representative individual of each breed. To elucidate the biological implications of the sequenced data, further confirmatory studies should be followed by sequencing or validating the population of each breed. Because NGS sequencing prices have consistently dropped, various population genomic theories can now be applied to the sequencing data obtained from the population of each breed of interest. There are still few such population studies available for the Korean native cattle breeds, but this situation will soon be improved with the recent initiative for NGS sequencing of diverse native livestock resources, including the Korean native cattle breeds.

to explore the cutting-edge research on oral health and systemic diseases. 13Our first volume collated 17 insightful papers exploring the use of microbial meta-omics data to 14 better understand the complex biological context of health and disease. These contributions 15 provided a comprehensive overview of the current state of knowledge and future directions in the 16 field of oral microbiome research using NGS technologies. NGS technologies hold immense 17 potential for developing strategies to modulate the oral microbiome for improved overall health. A 18 key theme emerging from these studies is the significant impact of systemic conditions, such as 19 hypertension and hyperglycemia, and dysbiosis in distant body sites, like the gut, on the oral 20 microbiota via the oral-gut axis. This intricate connection between the oral cavity and the gut 21 warrants significant attention. In this volume, Lin et al investigated the presence of oral bacteria 22 in the gut of patients without any history of intestinal disorders. Their research give compelling 23 evidence for the transmission of oral taxa, commonly residing on the tongue dorsum, to the 24 rectum. Notably, they discovered that the translocation of oral bacteria to the rectum was 25 significantly more prevalent in participants with advanced age, hypertension, and those utilizing 26 proton pump inhibitors. 27This volume also features an interesting perspective by Filardo et al that explores the human 28 microbiome as a "hidden organ", with important contribution to host functions and significant 29 influence on human health. The review provides insights into human microbiome profiling, 30 describing various metagenomic methods, including 16S rRNA gene sequencing and its 31 associated biases (partial or full-length of the 16S rRNA gene) for the accurate identification of 32 bacteria to the species level, as well as biases associated with different sequencing platforms, 33 that may lead to the underestimation of the biodiversity of the microbiota being studied. 34For a more comprehensive picture, shotgun metagenomics offers a deeper taxonomic and 35 functional characterisation of the microbiome (de Cena et al., 2021, Kifle et al., 2024). While first 36 and second-generation sequencing technologies revolutionised the field by enabling higher-resolution analyses, further advancements have brought about third-generation platforms like 38 PacBio and Oxford Nanopore Technologies. These platforms offer long-read sequencing, which, 39 when combined with short-read methods (although admittedly more expensive), can significantly 40 improve coverage and assembly performance, facilitating the detection of low-abundance 41 species. This combined approach would provide a more thorough characterisation of the 42 microbiota and offer a clearer picture of microbial interactions during the transition to dysbiosis 43 (de Cena et al., 2021). However, the high cost of combining these sequencing approaches 44 remains a significant obstacle. This cost disparity leads to a major limitation in the current data which facilitates collaboration, enables new discoveries, and saves time and resources. However, 76 challenges such as incomplete metadata, incompatible software, and lack of standardisation 77 hinder data reuse. Implementing "FAIR" principles can address these issues by ensuring data is 78 "findable, accessible, interoperable, and reusable". This can lead to more efficient data handling, 79 faster insights, and reduced research costs, through the deployment of a user-friendly framework 80 that promotes inter-disciplinary collaboration. Furthermore, we argue that future studies require 81 much more detailed metadata. Research on the oral microbiome and systemic health should 82 include comprehensive data on the donor's oral health, including periodontal disease and caries, 83 as well as well-characterised and reproducible disease diagnoses. However, there are some 84 concerns regarding General Data Protection Regulation (GDPR) for data privacy with regards to 85 patients' data information, which may limit such implementation in healthcare research. 86In conclusion, the oral microbiome undeniably impacts overall human health. A deeper 87 understanding of host-microbe interactions can inform targeted strategies for disease prevention 88 and treatment. This knowledge can guide the development of novel preventive strategies through 89 microbiome modulation. Moreover, achieving predictive health and disease models for 90 personalised therapies focused on restoring a healthy microbiome will necessitate collaboration 91 between microbiologists and clinicians to strengthen the connection between biological and 92 clinical characteristics. 93 94 95

The advent of next-generation sequencing (NGS) technology has opened up a plethora of possibilities in cancer research by allowing for an unprecedented characterization of the cancer genome. The sensitivity, broad dynamic range, speed, and reduced cost per sample make the NGS technology a highly attractive platform in biomedical research compared to other sequencing and expression profiling techniques. NGS is being currently employed in several malignancies for both quantitative and qualitative profiling of nucleic acids and has already uncovered novel genetic determinants that play an important role during tumor development. In particular, the use of NGS technology for profiling the transcriptome from tumor tissues and body fluids has led to the identification of novel molecular targets that could potentially be translated in the clinic as diagnostic, prognostic, and therapeutic biomarkers. Currently, efforts are also being undertaken in the clinic to characterize an individual’s cancer genome for guiding evidence-based molecular therapies tailored for individual patients. In this chapter, we review recent advances in the use of NGS technology for RNA-based biomarker studies in cancer and its potential implications in the overall management of the disease.

Background: Numerous sequencing techniques have been progressed since the 1960s with the rapid development of molecular biology studies focusing on DNA and RNA. Methods: A great number of articles, book chapters, websites are reviewed, and the studies covering NGS history, technology and applications to cancer therapy are included in the present article. Results: High throughput next-generation sequencing (NGS) technologies offer many advantages over classical Sanger sequencing with decreasing cost per base and increasing sequencing efficiency. NGS technologies are combined with bioinformatics software to sequence genomes to be used in diagnostics, transcriptomics, epidemiologic and clinical trials in biomedical sciences. NGS technology has also been successfully used in drug discovery for the treatment of different cancers. Conclusion: This review focuses on current and potential applications of NGS in various stages of drug discovery process, from target identification through to personalized medicine.

The mammalian brain is an evolutionary marvel in which engraving and re-engraving of cellular states enable complex information processing and lifelong maintenance. Understanding the mechanisms by which neurons alter and maintain their molecular signatures during information processing is a fundamental goal of neuroscience. Next-generation sequencing (NGS) technology is rapidly transforming the ability to probe the molecular basis of neuronal function. NGS can define not only the complete molecular signatures of cells by transcriptome analyses but also the cascade of events that induce or maintain such signatures by epigenetic analyses. Here we offer some general and practical information to demystify NGS technology and highlight its potential to the neuroscience field. We start with discussion of the complexity of the nervous system, then introduce various applications of NGS with practical considerations and describe basic principles underlying various NGS technologies. Finally, we discuss emerging NGS-related technologies for the neuroscience field.