Application Of Sequencing Technologies Research Articles

A Comprehensive Review of Performance of Next-Generation Sequencing Platforms.

Background Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now. Results The proposed study, based on previous studies and manufacturers' descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position. Conclusion The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory- and time-saving algorithms and databases need to be developed to analyze data produced by the 3rd- and 4th-generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.

High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings.

The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next‐generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third‐generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS‐related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.

Benchmarking of computational error-correction methods for next-generation sequencing data

BackgroundRecent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequencing technologies in clinical tools. Computational error correction promises to eliminate sequencing errors, but the relative accuracy of error correction algorithms remains unknown.ResultsIn this paper, we evaluate the ability of error correction algorithms to fix errors across different types of datasets that contain various levels of heterogeneity. We highlight the advantages and limitations of computational error correction techniques across different domains of biology, including immunogenomics and virology. To demonstrate the efficacy of our technique, we apply the UMI-based high-fidelity sequencing protocol to eliminate sequencing errors from both simulated data and the raw reads. We then perform a realistic evaluation of error-correction methods.ConclusionsIn terms of accuracy, we find that method performance varies substantially across different types of datasets with no single method performing best on all types of examined data. Finally, we also identify the techniques that offer a good balance between precision and sensitivity.

The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges.

Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.

Applications of sequencing technology in clinical microbial infection.

Infectious diseases are a type of disease caused by pathogenic microorganisms. Although the discovery of antibiotics changed the treatment of infectious diseases and reduced the mortality of bacterial infections, resistant bacterial strains have emerged. Anti‐infective therapy based on aetiological evidence is the gold standard for clinical treatment, but the time lag and low positive culture rate of traditional methods of pathogen diagnosis leads to relative difficulty in obtaining the evidence of pathogens. Compared with traditional methods of pathogenic diagnosis, next‐generation and third‐generation sequencing technologies have many advantages in the detection of pathogenic microorganisms. In this review, we mainly introduce recent progress in research on pathogenic diagnostic technology and the applications of sequencing technology in the diagnosis of pathogenic microorganisms. This review provides new insights into the application of sequencing technology in the clinical diagnosis of microorganisms.

The research progress of application of sequencing technology to analyze the genetic information of malignant tumor, especially drug resistant recurrent ovarian cancer

The research progress of application of sequencing technology to analyze the genetic information of malignant tumor, especially drug resistant recurrent ovarian cancer

Applications of genotyping by sequencing in aquaculture breeding and genetics.

Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

Revisiting the Cutaneous Epithelium: Insights from a Nontraditional Model System

In the last 10 years, biology has made revolutionary advances from century-old debates about the relative importance of non-pathogenic bacteria. New applications of sequencing technologies are transforming our understanding of the biology of the skin. Similar to all other epithelia, the skin is colonized by an assemblage of microorganisms which, for the most part, peacefully coexist with their hosts. Alterations to microbial communities are associated with, and likely contribute to, a number of cutaneous disorders. This review focuses on the host factors that shape and maintain skin microbial communities, and the reciprocal role of microbes in pathogen defense and tissue homeostasis. We highlight how work in the nontraditional model system Hydra is uncovering new mechanisms to old cell biological problems that provide a foundation for understanding, preventing and in the long-term even treating skin diseases. We demonstrate that the cutaneous epithelium is an ecosystem hosting a complex microbiome and that components of the innate immune system as well as transcriptional regulators of stem cells are involved in maintaining homeostasis between epithelia and their resident microbiota. We conclude that beneficial bacterial-host interactions should be considered an integral part of skin biology and that nontraditional model systems can provide a holistic understanding of the cutaneous epithelium.

Myelodysplastic Syndromes – The Epigenetic Model for Drug Development?

Application of sequencing technology has advanced our understanding of the molecular landscape of myelodysplastic syndromes (MDS). Recurrent driver mutations in genes implicated in epigenetic regulation, and functional modelling of the disease has proven the importance of epigenetic dysregulation in MDS pathogenesis. Although available therapies such as azacitidine and decitabine are thought to exert their effect by epigenetic modulation, deep understanding of disease biology and development of specific epigenetically targeted therapies is still an area under active research. In this editorial we will focus on the molecular basis of MDS with particular focus on epigenetic dysregulation and new agents under development targeting this group of biological processes.

Genomic screening of the general adult population: key concepts for assessing net benefit with systematic evidence reviews.

Genomic screening of the general adult population: key concepts for assessing net benefit with systematic evidence reviews

Quality assessment and control of high-throughput sequencing data.

Second- and third-generation sequencing technologies are driving a revolution in biology and medicine, with ultra-high throughput sequencers now able to produce 200 human genomes every 3 days at a cost of $1000 per genome (Watson, 2014). Meanwhile, in our lab at Edinburgh Genomics and in other labs throughout the World, researchers are generating their first single-molecule reads from a hand-held, USB-powered sequencer as part of Oxford Nanopore’s MinION access programme (MinION Access Programme, 2014 1 ). Whilst the revolution in biology is recognized, the associated revolution in bioinformatics often goes unmentioned. This Frontiers “Research Topic” is about that revolution; it is about data, and data-driven discovery. The sequencers mentioned above, and others from Pacific Biosciences and Ion Torrent, produce either huge amounts of data, data that are very complex, or both. Bioinformaticians throughouttheworldarecreatingnovelpipelines,algorithmsand tools to be able to cope with the huge amount of diverse data types that can be produced. The very first step in many of those pipelines and tools is quality assessment, quality control and artifact removal. These issues all involve data-driven research—what can we learn from the data? What are the data telling us about quality and artifacts? The first group of papers in the research topic deal with quality assessment and reveal pipelines that are in use in sequencing facilities today. The second set of papers deal with applications of sequencing technologies to particular domains, and how we can improve those applications through effective control of quality and artifacts. The final set of papers deal with very specific biological questions, and what we can learn from the raw data to improve our analyses and help us to better answer those questions. A series of bioinformatics pipelines are applied to sequencing data by the data generating facility, and it is important that those who work with sequencing data understand these. Leggett et al. (2013) reveal many of the pipelines and tools used at The Genome Analysis Centre (TGAC), a genomics institute based in Norwich, UK, which has access to every major sequencing platform. Their paper describes every step in the data generation pipeline, from their Laboratory Information Management System (LIMS) to data-specific pipelines for matepair and RAD-Seq libraries. Similarly, Paszkiewicz et al. (2014)

Whole-Genome Sequencing and Infectious Disease: A Novel Application of Sequencing Technology

Whole-Genome Sequencing and Infectious Disease: A Novel Application of Sequencing Technology

GWAS of Diabetic Nephropathy: Is the GENIE out of the Bottle?

GWAS of Diabetic Nephropathy: Is the GENIE out of the Bottle?