Publisher: University of Delaware. Date Issued: 2015. Abstract: Viral infection and lysis are important processes contributing to the diversification and evolution of microbial communities. In marine ecosystems that cover 70% of the earths surface, there are ~10 million viruses per milliliter of seawater, indicating an incredible diversity of viruses waiting to be explored. An important breakthrough in viral ecology was the application of high-throughput DNA sequencing to entire viral communities. Known as shotgun viral metagenomics, this approach allows access to the majority of viruses that cannot be maintained in culture. Viral metagenomics has revealed surprising insight into ancient associations between viruses and hosts. However, making quantitative inferences from next generation sequencing data requires careful evaluation of viral isolation and DNA library preparation techniques. Many library preparation strategies employ some form of amplification to obtain sufficient DNA for ...
Background Recent high throughput sequencing technology can handle generating plenty of data for bacterial genome sequencing tasks. be utilized to compute a design graph that presents the most appealing contig adjacencies to be able to help biologists in completing the entire genomic series. The design graph shows exclusive contig orderings where feasible and the very best alternatives where required. Conclusions Our brand-new algorithm for contig buying uses series similarity aswell as phylogenetic details to estimation adjacencies of contigs. An assessment of our execution implies that it performs much better than latest approaches while getting much faster at the same time. Today the nucleotide sequences of several genomes are known Background. In the initial genome tasks the procedure of acquiring the DNA series by multi-step clone-by-clone sequencing strategies was pricey and Kenpaullone tedious. Currently the most frequent strategy for de-novo genome sequencing is normally = (data files. ...
Cyanobacteria-dominated blooms in Upper Klamath Lake, Oregon, create poor water quality and produce microcystins that may be detrimental to local wildlife and human health. Genetic tools, including high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR), have been shown to improve the identification and quantification of key groups associated with these blooms over more traditional techniques. We examined the seasonal and interannual variations in nutrient (nitrogen and phosphorus) concentrations between 2013 and 2014 to describe the relations between these factors and the growth dynamics of Aphanizomenon and toxigenic Microcystis as described by DNA sequencing and qPCR. Although total nutrients and chlorophyll a concentrations were similar between years, qPCR results showed the cyanobacterial populations to be 40 times larger in 2014 and indicated a large shift from an Aphanizomenon-dominant, low microcystin-level regime in 2013 to one dominated later in the season by
TY - GEN. T1 - Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. AU - Oesper, Layla. AU - Mahmoody, Ahmad. AU - Raphael, Benjamin J.. PY - 2013/4/3. Y1 - 2013/4/3. N2 - Cancer is a disease driven in part by somatic mutations that accumulate during the lifetime of an individual. The clonal theory [1] posits that the cancerous cells in a tumor are descended from a single founder cell and that descendants of this cell acquired multiple mutations beneficial for tumor growth through rounds of selection and clonal expansion. A tumor is thus a heterogeneous population of cells, with different subpopulations of cells containing both clonal mutations from the founder cell or early rounds of clonal expansion, and subclonal mutations that occurred after the most recent clonal expansion. Most cancer sequencing projects sequence a mixture of cells from a tumor sample including admixture by normal (non-cancerous) cells and different subpopulations of cancerous cells. In addition ...
...Next-generation DNA sequencing (NGS) technology has revolutionized bio......,Essential,informatics,methods,and,tools,for,analyzing,the,explosion,of,NGS,data,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
Next-generation DNA sequencing of image-guided biopsy samples collected by multiple sites reveal predictive biomarkers for cancer treatment.
RNA-Sequencing (RNA-Seq) broadly refers to a family of experimental techniques that give researchers the ability to study the transcriptional landscapes of cells and tissues quantitatively by exploiting high throughput sequencing technology. Currently, the most commonly used sequencing platforms are provided by Illumina, which uses a fluorescence-based paradigm for reading the bases in a nucleotide sequence. One alternative option is provided by Ion Torrent, which is built around the use of pH measurements to read nucleotide sequences. In addition to the distinct sequencing technologies used by these two platforms, there are smaller differences in the types of data they generate. In Illumina data all sequence reads generated during a single experiment have the same lengths, while the lengths of Ion Torrent reads vary. Additionally, the current generation of Illumina instruments can generate sequence reads from both ends of a fragment (paired-end reads), while Ion Torrent cannot.. Prior studies ...
Abstract:. This presentation aims to provide an overview of why we need next generation sequencing platforms and how the different next generation sequencing platforms perform. Moreover, some data on implementation and outcome of the Dutch experience within the Center for Personalized Cancer Treatment will be discussed. One of the challenges of increased targeted treatment for cancer is to select our patients. Novel targeted therapies require an ever-increasing number of predictive biomarker determinations on the limited amount of tissue of patients with metastatic disease. This increasing demand for predictive biomarkers presents us with challenges in the realm of tissue availability, cost-effective use of diagnostics and limiting the time-to-proper diagnosis. Part of this challenge can be resolved by introducing the use of next generation sequencing techniques to multiplex genetic diagnostics. We show that we can validate and implement the Ion Torrent based technology for diagnostic ...
The availability and throughput of next generation sequencing technologies has enabled the rapid and efficient sequencing of transcriptomes for model and non-model species. The majority of de novo transcriptome assemblies in non-model organisms have in the past been produced using the long reads (300-600 bp) generated using Roche 454 [24]. With the recent developments in sequencing technology, short read sequencers (90-400 bp), such as Illumina and Ion Torrent, are starting to be more commonly used for the generation of large next generation sequencing data sets, as the costs are much lower for the same output [25]. Consequently, the use of short read sequencers to generate de novo transcriptome assemblies for non-model organisms may lead to a more complete gene set for these species at a lower cost. The reliability of de novo transcriptome assemblies generated from short read sequencers, however, needs to be validated to ensure that assemblies are accurate and wont compromise the downstream ...
Unlock the full value of your next-generation sequencing (NGS) data sets from Illumina HiSeq/MiSeq/NextSeq/HiSeq X Ten, Roche 454 GS-FLX, LifeTechnologies Solid and Iontorrent /IonProton PGM, and PacBio platforms.. Bespoke NGS data analysis: QFAB provides tailored bioinformatics services to biologists across the spectrum of computational techniques and services applicable to molecular biology and next generation sequencing. QFAB researchers design and implement custom bioinformatics approaches that are developed in consultation with researchers for specific questions in molecular biology.. We can also integrate your genomics data with other -omics, microarrays and clinical datasets.. Our NGS data analysis services include:. Whole genome sequencing data analysis. ...
Next Generation Sequencing Market - (Technology Type - Whole Genome Sequencing, Targeted Resequencing, RNA Sequencing, Whole Exome Sequencing, and De Novo Sequencing); (Application - Oncology, Genetic Screening, Infectious Diseases, Drug and Biomarker Discovery, Agriculture & Animal Research, Idiopathic Diseases and others): Market Growth, Future Prospects and Competitive Analysis, 2017-2025 the market was valued at USD 3.7 Bn in 2017, and is expected to reach USD 20.6 Bn by 2025, expanding at a CAGR of 21.5% from 2017 to 2025.. Browse Full Report Click Here: http://www.acutemarketreports.com/report/next-generation-sequencing-market. Market Insights. Next generation sequencing is a high-throughput sequencing that enables sequencing and assembling of number of short DNA reads at a small period of time and with a better accuracy. The introduction of next generation sequencing technologies has ensured massive changes in the sequencing process by providing better output, higher speed, flexibility ...
DNA nanoball sequencing is a high throughput sequencing technology that is used to determine the entire genomic sequence of an organism. The method uses rolling circle replication to amplify small fragments of genomic DNA into DNA nanoballs. Fluorescent probes bind to complementary DNA and the probes are then ligated to anchor sequences bound to known sequences on the DNA template. The base order is determined via the fluorescence of the ligated and bound probes. This DNA sequencing method allows large numbers of DNA nanoballs to be sequenced per run at lower reagent costs compared to other next generation sequencing platforms. However, a limitation of this method is that it generates only short sequences of DNA, which presents challenges to mapping its reads to a reference genome. The company Complete Genomics uses DNA nanoball sequencing to sequence samples submitted by researchers. DNA Nanoball Sequencing involves isolating DNA that is to be sequenced, shearing it into small 400 - 500 base ...
Applied Maths NV today announces that it has released a new version of its flagship software suite BioNumerics that allows de novo assembly to be performed on next generation sequencing data. This new feature, available in version 6.6, consolidates the development of BioNumerics into a complete and fully integrated suite for preprocessing and analysis of NGS data.
Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU
TY - JOUR. T1 - Genome Detective:. T2 - an automated system for virus identification from high-throughput sequencing data. AU - Michael, Vilsker, AU - Yumna, Moosa,. AU - Sam, Nooij, AU - Vagner S., Fonseca, AU - Yoika, Ghysens, AU - Korneel, Dumon,. AU - Raf, Pauwels, AU - Luiz Carlos, Júnior Alcântara,. AU - Vanden Eynden, Ewout. AU - Vandamme, AM. AU - Deforche, Koen. AU - de Oliveira, Túlio. PY - 2019/3/1. Y1 - 2019/3/1. N2 - Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses. User time is minimal and it is limited to the time required to upload the ...
Roche and Precision System Science, Co., Ltd (PSS) have announced the signing of an exclusive agreement to develop and manufacture a fully automated emulsion PCR instrument for Roches portfolio of next-generation sequencing platforms. It is intended to support Roches GS Junior and GS FLX+ systems as well as the sequencing platforms that Roche is currently developing.
Next-generation sequencing is revolutionising diagnosis and treatment of rare diseases, however its application to understanding common disease aetiology is limited. Rare disease applications binarily attribute genetic change(s) at a single locus to a specific phenotype. In common diseases, where multiple genetic variants within and across genes contribute to disease, binary modelling cannot capture the burden of pathogenicity harboured by an individual across a given gene/pathway. We present GenePy, a novel gene-level scoring system for integration and analysis of next-generation sequencing data on a per-individual basis that transforms NGS data interpretation from variant-level to gene-level. This simple and flexible scoring system is intuitive and amenable to integration for machine learning, network and topological approaches, facilitating the investigation of complex phenotypes. Whole-exome sequencing data from 508 individuals were used to generate GenePy scores. For each variant a score is
Mapping reads to a reference sequence is a common step when analyzing allele effects in high-throughput sequencing data. The choice of reference is critical because its effect on quantitative sequence analysis is non-negligible. Recent studies suggest aligning to a single standard reference sequence, as is common practice, can lead to an underlying bias depending on the genetic distances of the target sequences from the reference. To avoid this bias, researchers have resorted to using modified reference sequences. Even with this improvement, various limitations and problems remain unsolved, which include reduced mapping ratios, shifts in read mappings and the selection of which variants to include to remove biases. To address these issues, we propose a novel and generic multi-alignment pipeline. Our pipeline integrates the genomic variations from known or suspected founders into separate reference sequences and performs alignments to each one. By mapping reads to multiple reference sequences and ...
Author(s): Yang, Yi-Wen | Advisor(s): Jiang, Tao | Abstract: Next-generation sequencing (NGS) technologies are able to sequence DNA or RNA molecules at unprecedented speed and with high accuracy. Recently, NGS technologies have been applied in a variety of contexts, e.g., whole genome sequencing, transcript expression profiling, chromatin immunoprecipitation sequencing, and small RNA sequencing, to accelerate genomic researches. The size of NGS data is usually gigantic such that the data analysis in these applications of NGS largely relies on efficient computational methods. Due to the critical demand for high performance computational algorithms, in the past few years, my research interest was focused on designing novel algorithms to address challenges in NGS data analysis. The main theme of this dissertation includes algorithmic solutions to three crucial problems in NGS data analysis, two arising from differential expression analysis using high-throughput mRNA sequencing (RNA-Seq) and the other from
DNA sequencing is a method to decipher the base sequence in nucleic acids. The elucidation of the DNA sequence is essential for the understanding of virtually all biological processes e.g. human disease biology, inheritance, immunology, oncology, cellular biology. First generation sequencing devices use the capillary electrophoresis-based Sanger sequencing technique. The invention of the Next Generation Sequencing (NGS) technique massively improved the weaknesses of the 1st generation sequencing technique e.g. low throughput, scalability, speed, and resolution. NGS allows massive parallel sequencing which reduces the costs and increases the speed of DNA sequencing. Automated NGS prep ...
DNA sequencing is a method to decipher the base sequence in nucleic acids. The elucidation of the DNA sequence is essential for the understanding of virtually all biological processes e.g. human disease biology, inheritance, immunology, oncology, cellular biology. First generation sequencing devices use the capillary electrophoresis-based Sanger sequencing technique. The invention of the Next Generation Sequencing (NGS) technique massively improved the weaknesses of the 1st generation sequencing technique e.g. low throughput, scalability, speed, and resolution. NGS allows massive parallel sequencing which reduces the costs and increases the speed of DNA sequencing. Automated NGS prep ...
Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel therapeutic strategies against parasitic infections. However, none of transcriptomic studies have extensively covered ES protein prediction for identifying novel therapeutic targets, especially as parasites adopt non-classical secretion pathways. We developed a semi-automated computational approach for prediction and annotation of ES proteins using transcriptomic data from next generation sequencing platforms. For the prediction of non-classically secreted proteins, we have used an improved computational strategy, together with homology matching to a dataset of experimentally determined parasitic helminth ES proteins. We applied this protocol to analyse 454 short reads of parasitic nematode,
Estimation of allele frequency is of fundamental importance in population genetic analyses and in association mapping. In most studies using next-generation sequencing, a cost effective approach is to use medium or low-coverage data (e.g., | 15X). However, SNP calling and allele frequency estimation in such studies is associated with substantial statistical uncertainty because of varying coverage and high error rates. We evaluate a new maximum likelihood method for estimating allele frequencies in low and medium coverage next-generation sequencing data. The method is based on integrating over uncertainty in the data for each individual rather than first calling genotypes. This method can be applied to directly test for associations in case/control studies. We use simulations to compare the likelihood method to methods based on genotype calling, and show that the likelihood method outperforms the genotype calling methods in terms of: (1) accuracy of allele frequency estimation, (2) accuracy of the
htSeqTools is a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies. It includes detection of outliers and biases, inefficient immuno-precipitation and overamplification artifacts, de novo identification of read-rich genomic regions and visualization of the location and coverage of genomic region lists. Availability: Contact: [email protected] Planet E, Stephan-Otto Attolini C, Reina O, Flores O, Rossell D. (2011) htSeqTools: High-Throughput Sequencing Quality Control, Processing and Visualization in R. Bioinformatics .
Next generation sequencing (NGS) platforms give researchers much greater power when profiling tumor samples. However, the use of NGS presents challenges surrounding sample variability, platform bias, and potential failure to detect biomarkers. Horizons standards are appropriate for any NGS library preparation including whole-genome, whole-exome, custom capture and targeted amplicon panels. Horizon has developed this Quality-Seq (Q-Seq) NGS Reference Standard range to support the development and continued validation of Next Generation Sequencing platforms. The Tru-Q DNA Reference Standard portfolio covers multiple endogenous SNPs, insertions and deletions. Tru-Q NGS DNA Reference Standard 1 (5% Tier) covers 10 mutations at 5% allelic frequency in genomic DNA format. These may be diluted to even lower allelic frequencies using our Tru-Q 0 Wild Type standard. Furthermore, because the Tru-Q series has 4 different standards at the 5% alleleic frequency range, you may use rotate these as blinded ...
High throughput sequencing technology has been extensively applied in small RNA research. Thousands of miRNAs and their functions have been identified in higher plants. To date, only a single report detailing transcriptome data in celery has been published, and thus, comprehensive miRNA information is not available for this plant [32]. Moreover, there are no reports concerning miRNAs in other species of Apiaceae. In the present study, miRNAs were identified and characterized from two celery varieties, namely, Jinnan Shiqin and Ventura, which come from different geographical sources but have similar morphology. Till now, this study is the first to identify and investigate small RNAs in celery, and the results provide new information for further research into the functions, biological pathways and evolution of target genes related to temperature stresses in celery.. Over six million reads of 16 to 30 nt were obtained from each library. Based on the sequence conservation of mature miRNAs, 418 ...
Hosted by the International Society for Computational Biology (ISCB) and the Centre for Genomic Regulation (CRG), the Next Generation Sequencing Conference 2014 (NGS 2014) is a dedicated meeting on cutting-edge approaches to the processing and analysis of Next Generation Sequencing data. The goal of this conference is to bring together bioinformatics researchers and biologists facing new high-throughput sequencing challenges. The conference will feature presentations showing how current platforms can be used to address key biological questions and what is the current state of the art for data analysis. Sizeable space will also be dedicated to emerging and future trends in high-throughput sequencing and their associated computational challenges.. see more at http://www.iscb.org/ngs2014. ...
Full genomes of several organisms have been sequenced in the past fifteen years, including the human genome in 2004. These studies were completed using Sanger DNA sequencing, which has a limited throughput and high cost meaning the human genome took fifteen years to sequence and cost nearly three billion dollars
CSHL Press publishes monographs, technical manuals, handbooks, review volumes, conference proceedings, scholarly journals and videotapes. These examine important topics in molecular biology, genetics, development, virology, neurobiology, immunology and cancer biology. Manuscripts for books and for journal publication are invited from scientists world wide.
CSHL Press publishes monographs, technical manuals, handbooks, review volumes, conference proceedings, scholarly journals and videotapes. These examine important topics in molecular biology, genetics, development, virology, neurobiology, immunology and cancer biology. Manuscripts for books and for journal publication are invited from scientists world wide.
A novel smartphone-based microscope could make DNA sequence analysis much easier, faster and more readily accessible in remote locations. The dev
View detailed Table of Content here - https://www.marketsandmarkets.com/Market-Reports/ngs-based-rna-seq-market-102977816.html The expression profiling analysis segment accounted for the largest share of the NGS-based RNA-sequencing market, by application, in 2018. Based on application, the NGS-based RNA sequencing market is segmented into expression profiling analysis, small RNA sequencing, De Novo transcriptome assembly, and variant calling & transcriptome epigenetics. In 2018, the expression profiling analysis segment accounted for the largest share of the NGS-based RNA sequencing market. The dominant market position of this segment is attributed mainly to the increasing prevalence of metabolic disorders, multiple sclerosis, and other diseases. These factors will continue to propel the demand for expression profiling analysis to provide specific treatment options in the market during the forecast period.. The nanopore segment is expected to register the highest growth in the NGS-based ...
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus Matthieu Legendre, Stéphane Audic, Olivier Poirot, Pascal Hingamp, Virginie Seltzer, Deborah Byrne, Audrey Lartigue, Magali Lescot, Alain Bernadac, Julie Poulain, Chantal Abergel and Jean-Michel Claverie Published in Advance April 1, 2010, doi:10.1101/gr.102582.109Mimivirus, a virus infecting Acanthamoeba, is the prototype of the…
BACKGROUND Molecular testing of lung adenocarcinomas (ADCs) is crucial for therapy stratification of patients. Because of the often limited diagnostic material, the authors aimed to explore the suitability of cytology smears for next-generation sequencing (NGS) and compared the results with concurrent histological specimens or cell blocks. METHODS A total of 16 formalin-fixed paraffin-embedded (FFPE) ADCs with known genetic alterations were used as the first cohort for targeted DNA and RNA sequencing. In the second cohort of 8 cases, 8 cytological smears were compared with matching histological specimens or cell blocks for the study. For NGS library amplification, commercially available panels for DNA and RNA sequencing were applied. The Ion Torrent Personal Genome Machine and the Ion Reporter workflow (version 5.0) were used for sequencing. RESULTS All DNA libraries derived from FFPE and non-formalin-fixed cytological smear samples produced acceptable quality metrics, thereby enabling ...
Carbon Black is betting on next-generation antivirus technology by acquiring Confer to extend the capability and appeal of its endpoint protection offerings.
Catalyst Biosciences to Host Key Opinion Leader Meeting on Next-Generation Subcutaneous Factor VIIa Marzeptacog Alfa (Activated) in Patients with Bleeding Disorders on August 15 - - South San Francisco (California)
3 credits. Prerequisites: INFO-I 223; and BIOL-N 322 or BIOL-K 322. This course covers basic concepts of genomic sequencing datasets from several sequencing platforms, including how the data motivates computational needs and methods for analysis. Students learn how to devise approaches for analyzing massive clinical and biomedical sequencing datasets and for developing sound hypotheses and predictions from them.. ...
The Illumina MiSeq uses the same established reversible-terminator sequencing by synthesis chemistry as the HiSeq2000. Researchers have a wide range of sequencing read options ranging from 36 bp singleton to 150 bp paired-end reads. The system is capable of generating over 2 Gb data per run with a high percentage of bases over Q30. The high data yield and superior quality allows scientists to conduct a wide variety of sequencing applications including: highly multiplexed PCR amplicon sequencing, small genome sequencing and de novo sequencing, small RNA sequencing, targeted resequencing and 16S metagenomics.. The addition of numerous Illumina MiSeqs adds another level of sequencing for our clients, said Ardy Arianpour, Vice President of Business Development at Ambry Genetics. Our scientists have spent the last couple months validating sequencing runs and getting amazing results so we can deliver and work with multiple types of samples that fit on the MiSeq.. The MiSeq is a fully integrated ...
Liquid biopsy testing utilising Next Generation Sequencing (NGS) is quickly shifting in direction of medical adoption for personalised oncology. However, earlier than NGS can fulfil its potential any novel testing method should establish methods of lowering errors, permitting separation of true low-frequency mutations from procedural artefacts, and be designed to enhance upon present applied sciences. Popular NGS applied sciences sometimes utilise two DNA seize approaches; PCR and ligation, which have recognized limitations and appear to have reached a improvement plateau with solely small, stepwise enhancements being made.. To maximise the final word utility of liquid biopsy testing we now have developed a extremely versatile method to NGS: Adaptor Template Oligo Mediated Sequencing (ATOM-Seq). ATOM-Seqs strengths and versatility keep away from the foremost limitations of each PCR- and ligation-based approaches. This technology is ligation free, easy, environment friendly, versatile, and ...
Dramatic advances in sequencing technologies have opened new possibilities for whole genome analysis. The increasing read length of next-generation sequencing platforms, as well as the promising perspectives of third generation sequencing platforms, will inevitably lead to better assemblies and represent genomes in large stretches of DNA. Also, third generation technologies (such as the PacBio and IonTorrent systems) will be capable of outputting sequencing reads with large undefined inserts, thus providing valuable paired read information for the assembly and scaffolding process. Concurrently, the development of genome closure software should also receive attention to overcome difficult genomic regions that cannot be covered by draft assemblies.. Our results with GapFiller indicate that gapped genomics regions can be reliably closed through an automatic protocol that uses only short sequencing reads. Costly Sanger sequencing can therefore be limited to a few difficult repeat areas. Also, we ...
High-throughput next-generation sequencing (NGS) technologies continue to provide a wealth of sequence information, resulting in significant advances and new discoveries in a wide range of research areas. To enhance your specific NGS-based research and help you achieve your goals, we provide dedicated NGS target enrichment, library preparation and single cell solutions that eliminate bias and deliver uniform coverage. Our streamlined protocols are easy to use and automate seamlessly integrating workflows to use the full power of next-generation sequencing. Together we are making improvements in life possible.
We seek a bioinformatician with computational and analytical skills to join the University of Minnesota Genomics Center (UMGC). The UMGC provides a wide range of innovative genomic services to UMN and external researchers, with a particular focus on next-generation sequencing (NGS). The UMGC operates a fleet of advanced sequencing instruments, including Illumina HiSeq and MiSeq sequencers, a PacBio Sequel sequencer, the 10X Chromium system, and the Fluidigm C1 single-cell system. Through a partnership with the University of Minnesota Supercomputing Institute (MSI), the UMGCs informatics infrastructure is supported by MSIs HPC compute clusters, high-performance storage platforms, and cloud-computing infrastructure. This position in our Informatics group will support the Operations group in providing genomics services to customers, and work with the R&D group to push the limits of the UMGCs instrumentation and put into production the latest advances in sequencing technology.. Required (Minimum) ...
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Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results
Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non-model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to annotate each predicted contig as either a full-length cDNA, fragment, chimera, allele, paralogue, genomic ...
Deep sequencing analysis of gene expression (DSAGE) measures global gene transcript levels from only 1 to 2 µg total RNA by massively parallel sequencing of cDNA tags
Background: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. Results: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/ human leukocyte antigen (IMGT/HLA) database. The distribution of aligned reads was used to calculate a score function to determine correctly phased alleles by progressively removing false-positive alleles. Comparative HLA typing tests using public datasets from the 1000 Genomes Project and the International HapMap Project demonstrated that HLAscan could perform HLA typing more accurately than previously reported NGS-based methods such as HLAreporter and PHLAT. In addition, the results of HLA-A, ...
The Vironomics Core facilitates research long-read length next generation sequencing. The sequencers in the core are ideal for longer DNA fragment sequencing with instrument run times of only 24 hours. This is accomplished using Ion GeneStudio S5 Prime System, and companion Ion Torrent Chef. The Ion GeneStudio S5 capable of up to 600bp read lengths and has a maximal output of 130 Million 200 bp reads in 12 hours or 4 human exomes per day. Many clients use the longer reads for large genomes, de novo sequencing, 16S sequencing, long amplicons, etc. Customization is available or take advantage of the current expertise in: whole genome sequencing (WGS), de novo assembly, STR cell line verification, targeted amplicon sequencing, plasmid verification, strand-specific RNAseq, and exome sequencing.. ...
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Molecular genetics ; High-Throughput Screening ; Plastic and reconstructive surgery ; Genetics (medical sciences) ; Biology (medical sciences) ; Clinical genetics ; Medical Sciences ; Genetics (life sciences) ; craniosynostosis ; coronal synostosis ; exome sequencing ; high-throughput DNA sequencing ; TCF12-related craniosynostosis ; Saethre-Chotzen syndrome ; genetics ; craniofacial biology ; diagnostic outcomes
Whole genome sequencing (WGS) has become the new gold standard for bacterial outbreak investigation, due to the high resolution available for typing. While sequencing is currently predominantly performed on Illumina devices, the preceding library preparation can be performed using various protocols. Enzymatic fragmentation library preparation protocols are fast, have minimal hands-on time, and work with small quantities of DNA. The aim of our study was to compare three library preparation protocols for molecular typing: Nextera XT (Illumina); Nextera Flex (Illumina); and QIAseq FX (Qiagen). We selected 12 ATCC strains from human Gram-positive and Gram-negative pathogens with %G+C-content ranging from 27% (Fusobacterium nucleatum) to 73% (Micrococcus luteus), each having a high quality complete genome assembly available, to allow in-depth analysis of the resulting Illumina sequence data quality. Additionally, we selected isolates from previously analyzed cases of vancomycin-resistant Enterococcus faecium
FFPE and HOPE fixed specimen were comparable in DNA quality for downstream research purposes. Furthermore, FFPE tumor and fresh frozen tumor exome sequencing data, from the same patient, showed an overlap in the SNV analysis. This led to the central aim which included the analysis of somatic copy number alterations (SCNA) using whole exome sequencing on five CRPC and paired normal FFPE samples by the SOLiD4 next generation sequencing platform. The sequencing data identified two genes, YWHAZ and PTK2. Both genes, located on chromosome 8, were amplified on all five sequenced patients. Furthermore, the amplification frequency of both genes increased depending on the stage of PCa: prostate confined or localized PCa, lymph node metastasized PCa and CRPC. YWHAZ knockdown in the PC-3 cell line impaired proliferation and migration. Similarly, PTK2 inhibition, using a pharmacological inhibitor, TAE226 inhibitor, significantly affected both cell migration and proliferation at a concentration of 10 μM. ...
Although genome sequencing has become widely available with the improvements in next-generation sequencing platforms, even with smaller bacterial genomes (the genome of G. xylinus is approximately 3.5Mbp in size), genome sequencing is still relatively unavailable for small to mid-sized research groups due to high costs. We performed a survey of prices offered by all commercially available service providers using the Illumina MiSeq next-generation sequencing platform (which is the most cost-effective method for bacterial genome sequencing) in Europe, and found that the average costs of fully sequencing a 3.5Mbp genome (which includes library preparation, sequencing, bioinformatics and gap filling) is approximately £500.. In order to be able to sequence the genome with the limited budget available to our group, we decided to purchase the necessary materials for library preparation and sequencing run, and perform the full sequencing cycle ourselves, from preparing the sequencing library, to ...
Although genome sequencing has become widely available with the improvements in next-generation sequencing platforms, even with smaller bacterial genomes (the genome of G. xylinus is approximately 3.5Mbp in size), genome sequencing is still relatively unavailable for small to mid-sized research groups due to high costs. We performed a survey of prices offered by all commercially available service providers using the Illumina MiSeq next-generation sequencing platform (which is the most cost-effective method for bacterial genome sequencing) in Europe, and found that the average costs of fully sequencing a 3.5Mbp genome (which includes library preparation, sequencing, bioinformatics and gap filling) is approximately £500.. In order to be able to sequence the genome with the limited budget available to our group, we decided to purchase the necessary materials for library preparation and sequencing run, and perform the full sequencing cycle ourselves, from preparing the sequencing library, to ...
Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16-20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we
RnRMarketResearch.com adds report Next Generation Sequencing (NGS) Market [Platforms (Illumina HiSeq, MiSeq, Life Technologies Ion Proton/PGM, 454 Roche), Bioinformatics (RNA-Seq, ChIP-Seq), (Pyrosequencing, SBS, SMRT), (Diagnostics, Personalized Medicine)] - Global Forecast to 2017 to its store.. The next generation sequencing market is rapidly evolving with a large number of developments taking place to increase accuracy and speed, and reduce costs of sequencing. It is the fastest-growing and most lucrative segment in the genomics space with an estimated growth of 16.3%. The global NGS market was valued at $1.3 billion in 2012 and is poised to reach $2.7 billion by 2017. By supporting genomics research, various government bodies like NHGRI (National Human Genome Research Institute, U.S.) and Biotechnology and Biological Sciences Research Council (BBSRC, U.K.) are increasing the adoption of high-throughput sequencing platforms.. Inquire a Discount @ ...
The Illumina sequencing platform is very popular among next-generation sequencing platforms. However, the DNA sequencing library construction kit provided by Illumina is considerably expensive. The protocol described here can be used to construct high-quality sequencing libraries from chromatin immunoprecipitated DNA. It uses key reagents from third-party vendors and greatly reduces the cost in library construction for Illumina sequencing.
PUNE, India, August 24, 2017 /PRNewswire/ --. According to a new market research report Next-Generation Sequencing (NGS) Services Market by Type (Targeted, RNA-Seq, Exome, De Novo), Technology (Sequencing by Synthesis, Ion semiconductor, SMRT, Nanopore), & Application (Diagnostics, Oncology, Drug Discovery, Agriculture) - Forecasts to 2022, published by MarketsandMarkets(TM), the global market is projected to reach USD 2,748.6 Million by 2022 from USD 1,059.2 Million in 2017; growing at a CAGR of 21.0%. (Logo: http://photos.prnewswire.com/prnh/20160303/792302 ) Browse 56 Market Data Tables and 38 Figures spread through 157 Pages and in-depth TOC on Next-Generation Sequencing (NGS) Services Market http://www.marketsandmarkets.com/Market-Reports/ngs-services-market-194102241.html [http://www.marketsandmarkets.com/Market-Reports/ngs-services-market-194102241.html?utm_source=prnewswire&utm_medium=Refferal&utm_campaign=PaidPR ] Early buyers will receive 10% customization on this report Factors ...
High-throughput DNA sequencing technology has transformed genetic research and is starting to make an impact on clinical practice. However, analyzing high-throughput sequencing data remains challenging, particularly in clinical settings where accuracy and turnaround times are critical. We present a new approach to this problem, implemented in a software package called Platypus. Platypus achieves high sensitivity and specificity for SNPs, indels and complex polymorphisms by using local de novo assembly to generate candidate variants, followed by local realignment and probabilistic haplotype estimation. It is an order of magnitude faster than existing tools and generates calls from raw aligned read data without preprocessing. We demonstrate the performance of Platypus in clinically relevant experimental designs by comparing with SAMtools and GATK on whole-genome and exome-capture data, by identifying de novo variation in 15 parent-offspring trios with high sensitivity and specificity, and by estimating
Next-generation sequencing (NGS) technologies have been widely used in life sciences. However, several kinds of sequencing artifacts, including low-quality reads and contaminating reads, were found to be quite common in raw sequencing data, which compromise downstream analysis. Therefore, quality control (QC) is essential for raw NGS data. However, although a few NGS data quality control tools are publicly available, there are two limitations: First, the processing speed could not cope with the rapid increase of large data volume. Second, with respect to removing the contaminating reads, none of them could identify contaminating sources de novo, and they rely heavily on prior information of the contaminating species, which is usually not available in advance. Here we report QC-Chain, a fast, accurate and holistic NGS data quality-control method. The tool synergeticly comprised of user-friendly tools for (1) quality assessment and trimming of raw reads using Parallel-QC, a fast read processing tool; (2)
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some next-generation sequencing platforms in order to estimate a population of haplotypes which represent the diversity of the original population. The method proposed here is custom-made to take advantage of the very low error rate and extremely deep coverage per site, which are the main features of some neglected technologies that have not received much attention due to the short length of its reads, which precludes haplotype estimation. This approach allowed us to avoid some hard problems related to haplotype reconstruction (need of
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. Most methods for viral diversity estimation proposed so far are intended to take benefit of the longer reads produced by some next-generation sequencing platforms in order to estimate a population of haplotypes which represent the diversity of the original population. The method proposed here is custom-made to take advantage of the very low error rate and extremely deep coverage per site, which are the main features of some neglected technologies that have not received much attention due to the short length of its reads, which precludes haplotype estimation. This approach allowed us to avoid some hard problems related to haplotype reconstruction (need of
TY - JOUR. T1 - Characterization of endoscopic ultrasound fine-needle aspiration cytology by targeted next-generation sequencing and theranostic potential. AU - Gleeson, Ferga C.. AU - Kipp, Benjamin R.. AU - Kerr, Sarah E.. AU - Voss, Jesse S.. AU - Lazaridis, Konstantinos N.. AU - Katzka, David A.. AU - Levy, Michael J.. PY - 2015/1/1. Y1 - 2015/1/1. N2 - Determination of tumor genetic architecture based on tissue analysis yields important information on signaling pathways involved in cancer pathogenesis and plays a growing role in choosing the optimal medical management of malignancies. Specifically, the advent of next-generation sequencing has led to a rapidly evolving era of relatively inexpensive, high-throughput DNA sequencing of tumors. One such example is multiplexed tumor genotyping (ie, panel testing) of more than 2800 mutations across 50 commonly mutated cancer-associated genes. This resulting mutational landscape shows medically actionable pathogenic alterations to optimize ...
chnology in a metabarcoding approach, to study aphid food-webs using the cabbage aphid as model. We compared the variations in structure and composition of aphid food-webs in the species native range (United Kingdom, UK) and in an invaded range (New Zealand, NZ). We showed that Illumina MiSeq is a well suited technology to study complex aphid food-webs from aphid mummies. We found an unexpectedly high top down pressure in the NZ cabbage aphid food-web, which coupled to a large ratio of consumer species / prey species and a lack of potential inter-specific competition between primary parasitoids, could cause the NZ food-web to be more vulnerable than the UK one. This study also reports for the first time the occurrence of a new hyperparasitoid species in NZ, as well as new associations between hyperparasitoids parasitoids and the cabbage aphid in this country. We conclude that the complexity of aphid food-webs in agricultural systems could often be underestimated, particularly at higher trophic ...
2012.9.25 Copy number variation detection via normalizing high-throughput sequencing data at a nucleotide level Speaker:Ruibin XI (School of Mathematical Sciences, PKU) Time:1:00pm, Se
Read High throughput deep sequencing reveals the important roles of microRNAs during sweetpotato storage at chilling temperature, Scientific Reports on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Molecular profiling with next-generation sequencing (NGS) has been applied in multiple solid cancers to discover potential therapeutic targets. Here, we describe the results of a clinical NGS panel in patients with advanced melanoma. Thirty-six tumor tissues from patients with BRAF wild-type melanoma at Seoul National University Hospital (SNUH; Seoul, Republic of Korea) were collected and deep-sequenced using the SNUH FIRST-Cancer NGS panel to assess single-nucleotide variants, small insertions/deletions, copy number variations, and structural variations to estimate tumor mutation burden (TMB). We discovered 106 oncogenic alterations and most of the patients (n = 33, 92%) harbored at least one oncogenic alteration, including 2 patients who were initially diagnosed as BRAF V600E-negative but were later confirmed to be positive. Altogether, 36 samples were classified into RAS/BRAF/NF1-mutant (n = 14, 39%) or triple wild-type (n = 22, 61%) melanoma subtypes. The estimated median TMB was 8.2 ...
Highlights:. BRCA1 and BRCA2 analysis by Karyo. BRCA1 and BRCA2 are analyzed using CE-IVD kits in our Next Generation Sequencing platform. Full coverage can be obtained by ordering addition large rearrangement analysis of the two genes by means of MLPA analysis.. Human Breast Cancer Panel by Karyo. 19 genes associated with human breast cancer are analyzed using Next Generation Sequencing. The probes are designed to enrich for all the coding exons and splicing sites of these 19 genes. Copy number variation analysis is also included.. The analyzed genes are: AR, ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, DIRAS3, HER2, NBN, PALB2, PTEN, RAD50, RAD51, STK11, TP53, CASP8 και TGFB1.. Exome Analysis - Breast Cancer associated. Hereditary Breast and Ovarian Cancer predominately caused by mutations in genes BRCA1&2 accounts for 5-10% of cases. There is an additional 20-25% with family history present but negative for BRCA1&2 mutations termed Familial Breast Cancer. Modern science has identified ...
Mate Pair Library Sequencing enables the generation of libraries with inserts from 2 to 5 kb in size. These long-insert Paired-End libraries are useful for a number of applications, including De NovoSequencing, genome finishing, and structural variant detection. Combining data generated from Mate Pair library sequencing with that from short-insert paired-end reads provides a powerful combination of read lengths for maximal genomic sequencing coverage across the genome. Following DNA fragmentation, 2-5 Kb fragments are end-repaired with biotin labeled dNTPs. The DNA fragments are circularized, and non-circularized DNA is removed by digestion. Circular DNA is fragmented and fragments biotin labels (corresponding to the ends of the original DNA ligated together) are affinity purified. Purified fragments are end-repaired and ligated to Illumina Paired-End sequencing adapters. Additional sequences complementary to the flow cell oligonucleotides are added to the adapter sequence with tailed PCR ...
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TY - JOUR. T1 - Effective discovery of rare variants by pooled target capture sequencing. T2 - A comparative analysis with individually indexed target capture sequencing. AU - Ryu, Seungjin. AU - Han, Jeehae. AU - Norden-Krichmar, Trina M.. AU - Schork, Nicholas J.. AU - Suh, Yousin. PY - 2018/5/1. Y1 - 2018/5/1. N2 - Identification of all genetic variants associated with complex traits is one of the most important goals in modern human genetics. Genome-wide association studies (GWAS) have been successfully applied to identify common variants, which thus far explain only small portion of heritability. Interests in rare variants have been increasingly growing as an answer for this missing heritability. While next-generation sequencing allows detection of rare variants, its cost is still prohibitively high to sequence a large number of human DNA samples required for rare variant association studies. In this study, we evaluated the sensitivity and specificity of sequencing for pooled DNA samples of ...
Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola ( Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci -QTL- analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 ...
Abstract] Nowadays, the analysis of transcriptome sequencing (RNA-seq) data has become the standard method for quantifying the levels of gene expression. In RNA-seq experiments, the mapping of short reads to a reference genome or transcriptome is considered a crucial step that remains as one of the most time-consuming. With the steady development of Next Generation Sequencing (NGS) technologies, unprecedented amounts of genomic data introduce significant challenges in terms of storage, processing and downstream analysis. As cost and throughput continue to improve, there is a growing need for new software solutions that minimize the impact of increasing data volume on RNA read alignment. In this work we introduce HSRA, a Big Data tool that takes advantage of the MapReduce programming model to extend the multithreading capabilities of a state-of-the-art spliced read aligner for RNA-seq data (HISAT2) to distributed memory systems such as multi-core clusters or cloud platforms. HSRA has been built ...
Several recent studies from the field of epigenetics have combined chromatin-immunoprecipitation (ChIP) with next-generation high-throughput sequencing technologies to describe the locations of histone post-translational modifications (PTM) and DNA methylation genome-wide. While these reports begin to quench the chromatin biologists thirst for visualizing where in the genome epigenetic marks are placed, they also illustrate several advantages of sequencing based genomics compared to microarray analysis. Accordingly, next-generation sequencing (NGS) technologies are now challenging microarrays as the tool of choice for genome analysis. The increased affordability of comprehensive sequence-based genomic analysis will enable new questions to be addressed in many areas of biology. It is inevitable that massively-parallel sequencing platforms will supercede the microarray for many applications, however, there are niches for microarrays to fill and interestingly we may very well witness a symbiotic ...
Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. Alternative methods have been developed in the physical and geological sciences that treat similar data as compositions. Compositional data analysis methods transform the data to relative abundances with the result that the analyses are more robust and reproducible. Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft.title=Next Generation Sequencing of Extracellular RNA&rft.publisher=The University of Melbourne&rft.description=Exosomes are small nanovesicles released by cells. They can be found in bodily fluids such as blood, milk, saliva and cerebrospinal fluid, and be isolated from cell culture supernatants. Exosomes contain protein and genetic material and have been proposed to play a role in cellular communication whereby their contents can be transferred to other cells. We have shown a role for these vesicles in a number of neurodegenerative disorders such as prion, Alzheimers and Parkinsons diseases. In addition, we have developed a next generation sequencing (NGS) platform to sequence the genetic material contained within these vesicles. The collection contains data from our studies sequencing exosomal RNA from a variety of sources including cell cultures, serum, plasma, milk, urine, CSF both to look at ...
low yield in library preparation - posted in ChIP and Next Generation Sequencing: I got a very successful ChIP (DNA sheared to enrichment around 200 bp, more than 2% input at positive controls). Then I used 10 ng ChIPed DNA to make library for sequencing with the NEB kit. But I got a very poor yield (0.4 ng/ul in 30 ul elutes). I repeated twice with the same DNA and the results didnt turn any better. I used the same kit to make another library two months ago and it worked pretty fine....
Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells. Using more sensitive and specific transcriptome deep sequencing, we compared previously published small miRNA and long mRNA of a set of GC B cells and eBL tumors. MiRWalk2.0 was used to identify the validated target genes for the deregulated miRNAs, which would be important for understanding the regulatory networks associated with eBL development. We found 211 differentially expressed
RNA-Seq data analysis.The CLC Genomics Workbench version 10.1.1 was used for bioinformatics analyses in this study. RNA-Seq analysis was done by mapping next-generation sequencing reads and distributing and counting the reads across genes and transcripts. The latest assembly of the A. aegypti genome (GCF_000004015.4) was used as a reference. All libraries were trimmed from sequencing primers and adapter sequences. Low-quality reads (quality score below 0.05) and reads with more than 2 ambiguous nucleotides were discarded. Clean reads were subjected to an RNA-Seq analysis toolbox for mapping reads to the reference genome with mismatch, insertion, and deletion costs of 2, 3, and 3, respectively. Mapping was performed with stringent criteria and allowed a length fraction of 0.8 in mapping parameter, in which at least 80% of nucleotides in a read must be aligned to the reference genome. The minimum similarity between the aligned region of the read and the reference sequence was set at ...
Beckman Coulters SPRIselect is a SPRI-based chemistry that speeds & simplifies nucleic acid size selection for fragment library preparation for next generation sequencing.
SeqOnce Biosciences has launched its RhinoSeq DNA Library Preparation Kit for next-generation sequencing sample preparation. The firm said that the five tube kit contains preformatted master mixes for a simple, fast, and stable workflow. The tool generates a temporary structure that creates sequence-specific single stranded overhangs for sequencing adaptor litigation. When
Barley (Hordeum vulgare L.) is the one of crucial cereal species used as meals and feed crops, in addition to for malting and alcohol manufacturing. At the top of the final century, conventional breeding methods have been complemented by the use of DNA markers. Molecular markers have additionally been used extensively for molecular genetic mapping and QTL evaluation. In 2012, the barley genome sequencing was accomplished, which offered a broad vary of new alternatives - from a extra environment friendly seek for candidate genes controlling economically vital traits to genomic choice.. The evaluate summarizes the outcomes of the research carried out after barley genome sequencing, which found new areas of barley genetics and breeding with excessive throughput screening and genotyping strategies. During this era, intensive research aimed toward identification of barley genomic loci related to economically vital traits have been carried out; on-line databases and instruments for working with barley ...
PURPOSE: To identify biological processes associated with POAG and its subtypes, high-tension (HTG) and normal-tension glaucoma (NTG), by analyzing rare potentially damaging genetic variants.METHODS: A total of 122 and 65 unrelated HTG and NTG participants, respectively, with early onset advanced POAG, 103 non-glaucoma controls and 993 unscreened ethnicity-matched controls were included in this study. Study participants without myocilin disease-causing variants and non-glaucoma controls were subjected to whole exome sequencing on an Illumina HiSeq2000. Exomes of participants were sequenced on an Illumina HiSeq2000. Qualifying variants were rare in the general population (MAF RESULTS: POAG cases showed enrichment of rare variants in camera-type eye development genes (p = 1.40×10-7, corrected p = 3.28×10-4). Implicated eye development genes were related to neuronal or retinal development. HTG cases were significantly enriched for key regulators in the unfolded protein response (UPR) (p = ...
The rapid development of high throughput sequencing (HTS) technologies has made a considerable impact on clinical and genomics research. These technologies offer a time-efficient and cost-effective means for genotyping many pharmaceutical genes affecting the drug response (also known as ADMER genes), which makes HTS a good candidate for assisting the drug treatment and dosage decisions. However, challenges like data storage and transfer, as well as accurate genotype inference in the presence of various structural variations, are still preventing the wider integration of HTS platforms in clinical environments. For these reasons, this thesis presents fast and efficient methods for HTS data compression and accurate ADMER genotyping.First we propose a novel compression technique for reference-aligned HTS data, which utilizes the local assembly technique to assemble the donor genome and eliminate the redundant information about the donor present in the HTS data. Our results show that we can achieve ...
Sequencing genetic material from liquid biopsies promises to be one of the most important recent developments in cancer diagnostics. The relative ease and minimally invasive nature of obtaining liquid biopsies makes it an attractive alternative source of tumor DNA relative to direct tumor biopsies. The importance that
A Survey of Virus Recombination Uncovers Canonical Choices of Artificial Chimeras Generated All through Deep Sequencing Library Preparation. Chimeric reads shall be generated by in vitro recombination all through the preparation of high-throughput sequencing libraries. Our attempt to detect natural recombination between the genomes of dengue virus (DENV; +ssRNA genome) and its mosquito host using the Illumina Nextera sequencing library preparation bundle revealed that almost all, if not all, detected host-virus chimeras had […]. ...