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PubMed Journals Articles About "Illumina Announces TruSeq Sequencing Genome Analyzer" RSS

08:01 EST 18th November 2018 | BioPortfolio

Illumina Announces TruSeq Sequencing Genome Analyzer PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Illumina Announces TruSeq Sequencing Genome Analyzer articles that have been published worldwide.

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Showing "Illumina Announces TruSeq Sequencing Genome Analyzer" PubMed Articles 1–25 of 7,000+

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...


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...

Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient Derived Tumors Clinical Application of Whole-Genome Sequencing for Reporting Targetable Variants in Cancer.

We have developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay which provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, Indels, copy number variants, structural variants, and RNA gene fusions, was analyzed. New York State's Department of Health NGS guidelines were expanded on for establishing performance validation appli...


Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens.

With the emergence of RNA sequencing technologies, metatranscriptomic studies are rapidly gaining attention as they simultaneously provide insight into gene expression profiles and therefore disease association pathways of microbial pathogens and their hosts. This approach, therefore, holds promise for applicability in infectious disease diagnostics. A challenge of this approach in the clinical setting is the low amount and quality of RNA, especially microbial RNA in most clinically-infected specimens. Here...

Kannadigas from South India.

A total of 174 (48 bone marrow and 126 cord blood donors) Kannada speaking individuals (Kannadigas) from Karnataka, Tamilnadu and Telangana were typed for HLA A, B, C, DRB and DQB alleles. Out of 174 samples, 146 samples were typed by Sanger sequencing using SeCore Sequencing IVD® kit user protocol (Invitrogen) and the results detected on an automated ABI 3730xl DNA analyzer instrument. The sequencing data was analyzed using uTYPE® 7.1. The other 28 samples were typed by NGS Illumina MiniSeq Platform usin...

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.

A reliable targeted next-generation sequencing strategy for diagnosis of myopathies and muscular dystrophies, especially for the giant titin and nebulin genes.

Myopathies and muscular dystrophies (M-MDs) are genetically heterogeneous diseases, with more than 100 identified genes, including the giant and complex titin (TTN) and nebulin (NEB) genes. Next-generation sequencing technology revolutionized M-MD diagnosis and revealed high frequency of TTN and NEB variants. We developed a next-generation sequencing diagnostic strategy targeted on the coding sequences of 135 M-MD genes. Comparison of two targeted capture technologies (SeqCap EZ Choice library capture kit (...

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing.

Leptosphaeria maculans and Leptosphaeria biglobosa are ascomycete phytopathogens of Brassica napus (oilseed rape, canola). Here we report the complete sequence of three Leptosphaeria genomes (L. maculans JN3, L. maculans Nz-T4 and L. biglobosa G12-14). Nz-T4 and G12-14 genome assemblies were generated de novo and the reference JN3 genome assembly was improved using Oxford Nanopore MinION reads. The new assembly of L. biglobosa showed the existence of AT rich regions and pointed to a genome compartmentalizat...

Whole Genome Sequencing of NDM-1-Producing ST11 Klebsiella pneumoniae Isolated in a Private Laboratory in Greece.

The emergence and spread of NDM-1-encoding Klebsiella pneumoniae is causing worldwide concern, whereas a second epicenter of their dissemination after the Indian subcontinent is thought to be located in the Balkans. In this study, the complete genome sequencing of an NDM-1-producing ST11 K. pneumoniae isolated in a private laboratory in Greece is presented. The genome sequencing was performed on Illumina MiniSeq. Multilocus Sequence Typing was determined using a BLAST-based approach whereas antimicrobial re...

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.

First whole genome sequencing of Russian isolate of Capnocytophaga canimorsus, opportunistic pathogen causing lethal sepsis.

Capnocytophaga canimorsus is a part of healthy oral flora of dogs and cats. However, when it is transmitted to human subjects via animal bites or scratches, it can cause severe complications like endocarditis or even lethal septic shock, especially in immunocompromised persons. In this study, we performed the first whole-genome sequencing on Illumina HiSeq platform of Russian isolate of C. canimorsus that have caused lethal sepsis in 51-old male from Moscow. We believe that the availability of genomic seque...

BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes.

The use of targeted next-generation sequencing (NGS) provides great new opportunities for molecular and medical genetics. However, in order to take advantage of these opportunities, we need to have reliable tools for extracting the necessary information from the huge amount of data generated by NGS. Here we present our automatic multithreaded workflow for processing NGS data of BRCA1 and BRCA2 genes obtained with NGS technology named BRCA-analyzer. Optimizing it on the sequencing data of 899 samples from 69...

Analysis of Sulfate-Reducing and Sulfur-Oxidizing Prokaryote Community Structures in Marine Sediments with Different Sequencing Technologies.

Sulfate-reducing prokaryotes (SRP) and sulfur-oxidizing prokaryotes (SOP) play vital roles in the sulfur cycle. The SRP community was used to represent a microbial community with high richness and diversity. The 454 pyrosequencing, Illumina high-throughput sequencing, and traditional clone library methods that target the dissimilatory sulfite reductase subunit gene (), which encodes a key enzyme in the sulfate reduction pathway, were used to compare the differences in SRP community characteristics. Compara...

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...

Evaluation of the precision ID mtDNA whole genome panel on two massively parallel sequencing systems.

Sequencing whole mitochondrial genomes by capillary electrophoresis is a costly and time/labor-intensive endeavor. Many of the previous Sanger sequencing-based approaches generated amplicons that were several kilobases in length; lengths that are likely not amenable for most forensic applications. However, with the advent of massively parallel sequencing (MPS) short-amplicon multiplexes covering the entire mitochondrial genome can be sequenced relatively easily and rapidly. Recently, the Precision ID mtDNA ...

Genomic insights of Vibrio harveyi RT-6 strain, from infected "Whiteleg shrimp" (Litopenaeus vannamei) using Illumina Platform.

The pathogenicity of "Vibriosis" in shrimps imposes prominent menace to the sustainable growth of mariculture economy. Often the disease outbreak is associated speciously with Vibrio harveyi and its closely related species. The present study investigated the complete genome of the strain V. harveyi RT-6 to explore the molecular mechanism of pathogenesis. The genome of V. harveyi possesses a single chromosome of 6,374,398 bp in size, G+C content (44.7 %) and 5,730 protein coding genes. The reads of 1.3 Gb we...

Identifying the inserted locus of randomly integrated expression plasmids by whole-genome sequencing of Aspergillus strains.

Whole-genome sequencing was conducted on two Aspergillus oryzae strains used for the manufacturing of food enzymes, Acrylaway® and Shearzyme®, with the aim of identifying the inserted locus of randomly integrated expression plasmid and obtaining flanking sequences for safety assessment. Illumina paired-end sequencing was employed, and the obtained reads were mapped to two references: the public genome sequence of Aspergillus oryzae RIB40 and the in-house sequence of the used expression plasmid. Introducin...

A decade of genome sequencing has revolutionized studies of experimental evolution.

Genome sequencing has revolutionized studies using experimental evolution of microbes because it readily provides comprehensive insight into the genetic bases of adaptation. In this perspective we discuss applications of sequencing-based technologies used to study evolution in microbes, including genomic sequencing of isolated evolved clones and mixed evolved populations, and also the use of sequencing methods to follow the fate of introduced variations, whether neutral barcodes or variants introduced by ge...

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.

Draft genome resource for the potato powdery scab pathogen Spongospora subterranea.

The Plasmodiophorida (Phytomyxea, Rhizaria) are a group of protist that infect plants. Of this group, Spongospora subterranea causes major problems for the potato industry by causing powdery scab and root galling of potatoes and as vector for the Potato mop top virus (PMTV, Pomovirus, Virgaviridae). A single tuber isolate (SSUBK13) of this uncultivable protist was used to generate DNA for Illumina sequencing. The data were assembled to a draft genome of 28.08 Mb consisting of 2340 contigs and an L50 of 280....

High-Throughput Contiguous Full-Length Next-Generation Sequencing of HLA Class I and II Genes from 96 Donors in a Single MiSeq Run.

The human leukocyte antigen (HLA) genes regulate and drive the immune system, and are among the most polymorphic loci in the human genome. HLA diversity is known to play an important role in transplantation and disease association studies. There are multiple approaches to DNA-based HLA genotyping and recent advances in next-generation sequencing (NGS) technologies have facilitated the development of whole gene sequencing methods. We describe an accurate, efficient, scalable, and cost-effective approach to c...

The genome assembly of the fungal pathogen Pyrenochaeta lycopersici from Single-Molecule Real-Time sequencing sheds new light on its biological complexity.

The first draft genome sequencing of the non-model fungal pathogen Pyrenochaeta lycopersici showed an expansion of gene families associated with heterokaryon incompatibility and lacking of mating-type genes, providing insights into the genetic basis of this "imperfect" fungus which lost the ability to produce the sexual stage. However, due to the Illumina short-read technology, the draft genome was too fragmented to allow a comprehensive characterization of the genome, especially of the repetitive sequence ...

A reference genome of the Chinese hamster based on a hybrid assembly strategy.

Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assem...

Whole-genome sequencing identification of a multidrug-resistant Listeria monocytogenes serotype 1/2a isolated from fresh mixed sausage in southern Brazil.

A previous study performed by our group reported the characterization of a multidrug-resistant isolate of Listeria monocytogenes serotype 1/2a, named Lm16 isolate. This foodborne isolate is of particular interest because it is highly resistant to antimicrobials, disinfectants and heavy metals. In this study, we used the whole-genome shotgun method to sequence Lm16 isolate using the Illumina MiSeq platform. By assembling and analysis of the new genome, we were able to identify three efflux pumps (mepA, msrA,...


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