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PubMed Journals Articles About "Rapid Whole Genome Sequencing StatSeq Diseases Diagnoses" RSS

08:27 EST 20th January 2019 | BioPortfolio

Rapid Whole Genome Sequencing StatSeq Diseases Diagnoses PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Rapid Whole Genome Sequencing StatSeq Diseases Diagnoses articles that have been published worldwide.

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We have published hundreds of Rapid Whole Genome Sequencing StatSeq Diseases Diagnoses news stories on BioPortfolio along with dozens of Rapid Whole Genome Sequencing StatSeq Diseases Diagnoses Clinical Trials and PubMed Articles about Rapid Whole Genome Sequencing StatSeq Diseases Diagnoses for you to read. In addition to the medical data, news and clinical trials, BioPortfolio also has a large collection of Rapid Whole Genome Sequencing StatSeq Diseases Diagnoses Companies in our database. You can also find out about relevant Rapid Whole Genome Sequencing StatSeq Diseases Diagnoses Drugs and Medications on this site too.

Showing "Rapid whole genome sequencing StatSeq Diseases Diagnoses" PubMed Articles 1–25 of 22,000+

Enabling genome-wide association testing with multiple diseases and no healthy controls.

While large-scale whole genome sequencing is feasible the high costs compel investigators to focus on disease subjects. As a result large sequencing datasets of samples with different diseases are often readily available, but not healthy controls to contrast them with. While it is possible to perform an association study using only diseases, the associations could be driven by a disease acting as a control and not the focal disease.


An outpatient clinic as a potential site of transmission for an outbreak of NDM-producing Klebsiella pneumoniae ST716: a study using whole-genome sequencing.

The incidence of nosocomial infections due to carbapenem-resistant Klebsiella pneumoniae is increasing worldwide. Whole genome sequencing (WGS) can help elucidate the transmission route of nosocomial pathogens.

Whole Genome Sequencing in Severe Chronic Obstructive Pulmonary Disease.

Genome-wide association studies (GWAS) have identified common variants associated with chronic obstructive pulmonary disease (COPD). Whole-genome sequencing (WGS) offers comprehensive coverage of the entire genome compared with genotyping arrays or exome sequencing.


Complete genome sequencing of Comamonas kerstersii 8943, a causative agent for peritonitis.

Because of poor differentiation among the members of genus Comamonas using phenotypic methods, human infections caused by C. kerstersii are sporadically reported in the literature. Here, we represent the first complete genome sequence of C. kerstersii 8943, which caused peritonitis in a patient with continuous ambulatory peritoneal dialysis (CAPD). The complete genome with no gaps was obtained using third-generation Pacific Biosciences (PacBio) RSII sequencing system with single-molecule real-time (SMRT) an...

Whole-Genome Bisulfite Sequencing for the Methylation Analysis of Insect Genomes.

DNA methylation is a conserved epigenetic modification of animal genomes, but genome methylation patterns appear surprisingly diverse in insects. Whole-genome bisulfite sequencing (WGBS) represents a sensitive and robust method for the characterization of genome-wide methylation patterns at single-base resolution. Here, we describe a step-by-step protocol for the generation and analysis of WGBS datasets using standard Illumina sequencing platforms. In comparison to whole-genome sequencing, WGBS has addition...

AFLP-AFLP in silico-NGS approach reveals polymorphisms in repetitive elements in the malignant genome.

The increasing interest in exploring the human genome and identifying genetic risk factors contributing to the susceptibility to and outcome of diseases has supported the rapid development of genome-wide techniques. However, the large amount of obtained data requires extensive bioinformatics analysis. In this work, we established an approach combining amplified fragment length polymorphism (AFLP), AFLP in silico and next generation sequencing (NGS) methods to map the malignant genome of patients with chroni...

Development of the Knowledge of Genome Sequencing (KOGS) questionnaire.

Whole-genome sequencing is being implemented in research and clinical care, yet tools to assess patients' knowledge are lacking. Our aim was to develop a robust measure of whole-genome sequencing knowledge suitable for patients and other stakeholders including research participants, public, students, and healthcare professionals.

Delay in effective therapy in anidulafungin-resistant Candida tropicalis fungaemia: Potential for rapid prediction of antifungal resistance with whole-genome-sequencing.

The feasibility of using whole-genome-sequencing (WGS) for the prediction of antifungal resistance in anidulafungin-resistant Candida tropicalis candidaemia isolates was investigated.

Sequencing of Treponema pallidum subsp. pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material.

Treponema pallidum subsp. pallidum (TPA) is the infectious agent of syphilis, a disease that infects more than 5 million people annually. Since TPA is an uncultivable bacterium, most of the information on TPA genetics comes from genome sequencing and molecular typing studies. This study presents the first complete TPA genome (without sequencing gaps) of clinical isolate (UZ1974), which was obtained directly from clinical material, without multiplication in rabbits. Whole genome sequencing was performed usin...

Electronic Transport through DNA Nucleotides in Atomically Thin Phosphorene Electrodes for Rapid DNA Sequencing.

Rapid progresses in developing the fast, low-cost, and reliable methods for DNA sequencing are envisaged for development of personalized medicine. In this respect, nanotechnology has paved the role for the development of advanced DNA sequencing techniques including sequencing with solid-state nanopores or nanogaps. Herein, we have explored the application of a black phosphorene based nanogap-device for DNA sequencing. Using density-functional-theory (DFT) based non-equilibrium Green's function (NEGF) approa...

Nontuberculous mycobacteria: Insights on taxonomy and evolution.

Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a rapid pace, while taxonomical relationships are re-defined in large part due to the accessibility of WGS. The evo...

Application of BIG-Annotator in the genome sequencing data functional annotation and genetic diagnosis.

The next generation sequencing (NGS) technology has been playing important roles in genetic diagnosis of diseases in recent years, and serving as a technological basis of precision medicine. In analyzing NGS data, the variant annotation is an important step. In this study, we developed a computationally efficient software (BIG-Annotator) to perform functional annotation for whole-genome single nucleotide polymorphisms. BIG-Annotator integrates the widely used databases and pipelines for variant annotation o...

Why 3D genome alternations play important roles in diseases.

The present issue with enthusiasm overviews technologies to detect 3D genome structures, relationship of 3D genome and diseases, and potential mechanism of regulatory elements to maintain 3D genome stability. Rapid development of biotechnology provides more powerful approach to monitor dynamic changes of genome dimensions and organization as well as function. Disorganization and dysfunction of 3D genome, compartments, TADs, chromosomal loops, and intranuclear microenvironments play central roles in initiati...

Tigmint: correcting assembly errors using linked reads from large molecules.

Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficult due to gaps and errors in the sequencing data, repetitive sequence in the underlying genome, and heterozygosity. As a result, assembly errors are common. In the absence of a reference genome, these misassemblies may be identified by comparing the sequencing data to the assembly and looking for discre...

Genomic epidemiological investigation of a Streptococcus suis outbreak in Guangxi, China, 2016.

In June 2016, a Streptococcus suis outbreak occurred in Guangxi, China. We determined the genetic characteristics of six clinically isolated strains by serotyping, PCR, and whole-genome sequencing, performing genome epidemiology analysis on these and 961 public available S. suis genomes. We also classified the first sequence type ST665 human case. Sporadic and outbreak cases were distinguished by whole-genome sequencing and phylogenomics. This approach could help to prevent and control S. suis epidemics in ...

Genome Size Estimation and Quantitative Cytogenetics in Insects.

With care, it is possible using flow cytometry to create a precise and accurate estimate of the genome size of an insect that is useful for genomics, genetics, molecular/cell biology, or systematics. Genome size estimation is a useful first step in a complete genome sequencing project. The number of sequencing reads required to produce a given level of coverage depends directly upon the 1C amount of DNA per cell, while an even more critical need is an accurate 1C genome size estimate to compare against the ...

A collaborative translational research framework for evaluating and implementing the appropriate use of human genome sequencing to improve health.

In a Policy Forum, Muin Khoury and colleagues discuss research on the clinical application of genome sequencing data.

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based...

Reporting of Clinical Genome Sequencing Results.

High-throughput sequencing and high-performance computing technologies have become powerful tools in clinical genetic diagnosis of hereditary disorders and genetic screening of healthy individuals to provide information for the diagnosis, treatment, and prevention of diseases or impairment and assessment of health. For patients with undiagnosed disorders, including many rare disorders, the whole-genome sequencing (WGS) test may end the diagnostic odyssey, ultimately guiding clinical care for them and their ...

Genome editing in the mammalian brain using the CRISPR-Cas system.

Recent advances in genome editing technologies such as the clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease Cas9 have enabled the rapid and efficient modification of endogenous genomes in a variety of cell types, accelerating biomedical research. In particular, precise genome editing in somatic cells in vivo allows for the rapid generation of genetically modified cells in living animals and holds great promise for the possibility of directly correcting genetic defec...

Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing.

Avian pox is an infectious disease caused by avipoxviruses (APV), resulting in cutaneous and/or tracheal lesions. Poxviruses share large genome sizes (from 130 to 360 kb), featuring repetitions, deletions or insertions as a result of a long-term recombination history. The increasing performances of next-generation sequencing (NGS) opened new opportunities for surveillance of poxviruses, based on timely and affordable workflows. We investigated the application of the 3 generation Oxford Nanopore Minion tec...

Whole genome sequencing reveals Trans-European spread of an epidemic Neisseria meningitidis serogroup W clone.

In June 2018, a French student travelling to Amsterdam from Dijon developed an invasive meningococcal disease. Whole genome sequencing (WGS) typed that the isolate as (W:P1.5,2:F1-1:cc11) that was already involved in a cluster of cases in Dijon. The isolate belonged to a new variant within the UK 2013-sublineage of the South American/UK lineage that is expanding in both the Netherlands and France. WGS is powerful in real-time tracking of international spread of epidemic meningococcal clones.

IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing.

In the past years, the long read (LR) sequencing technologies, such as Pacific Biosciences and Oxford Nanopore Technologies, have been demonstrated to substantially improve the quality of genome assembly and transcriptome characterization. Compared to the high cost of genome assembly by LR sequencing, it is more affordable to generate LRs for transcriptome characterization. That is, when informative transcriptome LR data are available without a high-quality genome, a method for de novo transcriptome assembl...

Comparison of three variant callers for human whole genome sequencing.

Testing of patients with genetics-related disorders is in progress of shifting from single gene assays to gene panel sequencing, whole-exome sequencing (WES) and whole-genome sequencing (WGS). Since WGS is unquestionably becoming a new foundation for molecular analyses, we decided to compare three currently used tools for variant calling of human whole genome sequencing data. We tested DeepVariant, a new TensorFlow machine learning-based variant caller, and compared this tool to GATK 4.0 and SpeedSeq, using...

Rapid, real-time chemiluminescent detection of DNA mutation based on digital microfluidics and pyrosequencing.

To explore genome mutation meaningfully, it is in urgent need to develop an automated and inexpensive platform for DNA mutation analysis. Digital microfluidics is a powerful platform for a broad range of applications due to the advantages of high automatization and low reagent consumption. Pyrosequencing enables DNA sequencing based on non-electrophoresis bioluminescence, which is suitable for rapid and sensitive analysis of short sequences. Herein, we describe a palmtop sequencing platform for automatic, r...


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