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 ...
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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.
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 ...
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 .
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
Early buyers will receive 10% customization on reports.. This report studies the global NGS-based RNA-seq market over the forecast period of 2017 to 2022. The global NGS-based RNA-seq market is projected to reach USD 2.65 Billion by 2022 from USD 1.05 Billion in 2017, at a CAGR of 20.2%. Factors such as the advantages of RNA-seq over microarray technology, technological advancements in RNA-seq products, increasing number of RNA-seq grants, increasing number of research activities, and rapid growth in precision medicine are driving the growth of the market.. On the basis of product and service, the NGS-based RNA-seq market is categorized into sample preparation, sequencing platforms and consumables, sequencing services, and data analysis, storage, & management. In 2016, the sequencing platforms and consumables segment accounted for the largest share of the market. The data analysis, storage, and management is expected to register the highest CAGR during the forecast period primarily due to ...
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 ...
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)
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 ...
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 ...
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) ...
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 Torrent PGM, Ion Torrent S5, and companion Ion Torrent Chef. The Ion Torrent PGM is capable of 200-400bp read lengths. The Ion Torrent S5 has the ability to increase that to 600bp and increases the number of reads/depth available, 10-90M reads. 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.. ...
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. https://edrn.jpl.nasa.gov/publications/21724842-deep-sequencing-reveals-distinct-patterns https://edrn.jpl.nasa.gov/logo.png ...
Following the completion of the human genome project, the high demand for low-cost sequencing has given rise to a number of high-throughput, next-generation sequencing (NGS) technologies. These new sequencing platforms allow high-throughput sequencing for a wide range of applications such as: |br /> |ul> |li>Whole genome sequencing as de novo or resequencing|/li> |li>Targeted resequencing|/li> |li>Transcriptome profiling|/li> |li>Microbiome research|/li> |li>Gene regulation studies |/li> |/ul>
Following the completion of the human genome project, the high demand for low-cost sequencing has given rise to a number of high-throughput, next-generation sequencing (NGS) technologies. These new sequencing platforms allow high-throughput sequencing for a wide range of applications such as: |br /> |ul> |li>Whole genome sequencing as de novo or resequencing|/li> |li>Targeted resequencing|/li> |li>Transcriptome profiling|/li> |li>Microbiome research|/li> |li>Gene regulation studies |/li> |/ul>
S E M I N A R: "Computational Methods for Detecting Structural Variants in the Next Generation Sequencing data and its applications" by Asst. Prof. Dr. Emre Karakoç, Medipol University. Despite the ease at which genome sequence data can be generated, most studies and standard computational pipelines to date, focus on the detection of single nucleotide variants and small insertions and deletions(indels). The main reason for this situation is that there are no robust methods for detecting larger indels and structural variations. Here I present novel computational methods for detecting these under estimated variants. In addition I developed computational system biology models using this more complete view of the variant landscape, to detect molecular pathways associated with complex diseases and to understand their etiology. Genomic variants especially structural variants, also contribute significantly to the adaptive evolution and introgression across closely related species. I applied ...
Lasergene Genomics allows you to quickly and easily perform and edit de novo genome assemblies from any sequencing platform. Click here to find out more!
Massive parallel sequencing (MPS) technologies have paved the way into new areas of research including individualized medicine. However, sequencing of trace amounts of nucleic acids still rem
This unit presents protocols for construction of next‐generation sequencing (NGS) directional RNA sequencing libraries for the Illumina HiSeq and MiSeq from a wide variety of input RNA sources
Library preparation for next-generation sequencing involves a coordinated series of enzymatic reactions to produce a random, representative collection of adapter modified DNA fragments within a specific range of fragment sizes. The success of next-generation sequencing is contingent on this proper processing of DNA or RNA sample. However as you go from isolating nucleic acid to…
Ion Torrent NGS assays have been retrospectively evaluated on previously characterised positive and negative archival control samples.10 ,13 ,14 ,20 However, in our study, routine clinical samples have been prospectively received by our central laboratory from several local pathology laboratories. Sanger sequencing and Ion Torrent NGS were performed simultaneously, unlike in previous reports where these techniques were performed at different times in different laboratories and on different histological sections.17 ,21 In the diagnostic setting, challenges include the less than optimal DNA quality of some samples due to formalin over-fixation, the low tumour cell content in tumour tissues with abundant inflammatory cells, and insufficient starting material, for example, minimal biopsy fragments. The Ion AmpliSeq Colon and Lung Cancer Panel failed in a small minority of cases (4.4%), in contrast to the 100% success rate of a recent clinical trial whose design included preliminary sample ...
Periannan Senapathy is a molecular biologist, geneticist, author and entrepreneur tenderize steak without mallet. He is the founder, president and chief scientific officer at Genome International Corporation, a biotechnology & bioinformatics firm based in Madison, Wisconsin, which develops next-generation DNA sequencing analysis technologies.. Senapathy is known for his contributions in the biology of RNA splicing and the structure of eukaryotic genes. An algorithm developed by him, known as Shapiro & Senapathy algorithm (S&S) for predicting the splice sites, exons and genes in any animal or plant, has the ability to discover disease-causing mutations in splice junctions in numerous cancers and non-cancer diseases. The Shapiro - Senapathy algorithm has been implemented in many gene-finding and mutation detection tools, and is being used in major research institutions around the world for uncovering mutations in the splicing regions. It is increasingly used in the Next Generation Sequencing era, ...
ROLE SUMMARY:. Roche Sequencing Santa Clara is developing nanopore-sequencing technology to improve the lives of people in a wide variety of applications, including the timely screening of newborns for diseases and the diagnosis of cancers and infectious diseases. Roche is looking for a motivated and team-oriented individual who is passionate about finding new ways to address these urgent needs. As a Principal Scientist, you will be leading scientists that are designing, expressing, purifying, and characterizing biological nanopores for Roche Sequencing Solutions (RSS) next generation sequencing platform. The successful candidate must be excited about single molecule kinetics and learning new concepts from chemistry, physics, algorithm development and electrical engineering and applying them to an interdisciplinary project.. WHO ARE YOU:. Youre someone who wants to influence your own development. Youre looking for a company where you have the opportunity to pursue your interests across ...
EMD Millipore today launched PureGenome™ kits and reagents for rapid and efficient Next Generation Sequencing (NGS) sample preparation. The kits enable NGS library preparation in less than two hours.
Read Bioinformatics for High Throughput Sequencing by with Rakuten Kobo. Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carr...
Next Generation Sequencers have found their way into labs and the global biomedical research community. 2010 has seen a serious uptake of Next Generation Sequencing technology, and today it is perceived as an indispensable tool for researchers.
The accurate microbiological diagnosis of diarrhoea involves numerous laboratory tests and, often, the pathogen is not identified in time to guide clinical management. With next-generation sequencing (NGS) becoming cheaper, it has huge potential in routine diagnostics. The aim of this study was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples. Fifty-eight clinical faecal samples were obtained from patients with diarrhoea as part of the routine diagnostics at Hvidovre University Hospital, Denmark. Ten samples from healthy individuals were also included. DNA was extracted from faecal samples and sequenced on the Illumina MiSeq system. Species distribution was determined with MGmapper and NGS-based diagnostic prediction was performed based on the relative abundance of pathogenic bacteria and Giardia and detection of pathogen-specific virulence genes. NGS-based diagnostic results were compared to conventional findings for 55 of the diarrhoeal samples; 38 ...
Issuu is a digital publishing platform that makes it simple to publish magazines, catalogs, newspapers, books, and more online. Easily share your publications and get them in front of Issuus millions of monthly readers. Title: Next generation sequencing market, Author: dinesh192491, Name: Next generation sequencing market, Length: 3 pages, Page: 1, Published: 2014-03-26
Learn about enabling next-generation sequencing applications with IBM Storwize V7000 Unified and SONAS Gateway solutions. This paper offers recommendations and…
To shed some light on these questions as they arise in clinical practice, Christie Hancock, MD, and colleagues, of Advocate Lutheran General Hospital in Park Ridge, Illinois, reviewed the next-generation sequencing practices and outcomes at their community hospital. A review of 43 cases in which sequencing was obtained showed the most common tumor types for next-generation sequencing to be breast and colorectal.1 Results of sequencing changed management in 12 (28%) of the 43 patients. Two patients were able to enter a clinical trial, and the other 10 had therapeutic changes based on protein or mRNA overexpression.. For the 10 patients undergoing new treatment, this change in management did not translate into lasting responses, compared to patients without a change. Of the 43 patients, 40 died, at a median of 7 months from the time the test was ordered.. Dr. Hancock and her colleagues concluded that although next-generation sequencing yields a lot of information, it may be difficult to interpret ...
This person will conduct bioinformatics and genomic research, and provide her/his expertise to lab members in the collection, management, interpretation, and analysis on biological, pathological, and molecular pathological data, with a focus on, but not limited to, high-throughput technologies with strong emphasis on next-generation sequencing. The main responsibility of this position is on the application of state-of-art bioinformatics technologies to analyze and integrate large scale omics datasets. Require familiarity with existing genomic databases such as, but not limited to, TCGA, ENCODE, CCLE, etc. Proficiency in programming using either R/Perl/Python/Java/C++ is a must. Familiarity with SAS, biostatistics, quantitative analysis, exome and RNA-seq analysis, and NGS laboratory procedures are preferred, but not required. Excellent interpersonal and communication skills are essential, as are the abilities to work both independently and collaboratively and to meet deadlines. Require a BS, MS, ...
Our genomic solutions automate your extraction, quantitation & next generation sequencing library preparation, all to accelerate your NGS workflow.
Although the presence of genetic heterogeneity within the tumors of individual patients is established, it is unclear whether greater heterogeneity predicts a worse outcome. A quantitative measure of genetic heterogeneity based on next-generation sequencing (NGS) data, mutant-allele tumor heterogeneity (MATH), was previously developed and applied to a data set on head and neck squamous cell carcinoma (HNSCC). Whether this measure correlates with clinical outcome was not previously assessed. ...
Along with the improvement of high throughput sequencing technologies, the genetics community is showing marked interest for the rare variants/common diseases hypothesis. While sequencing can still be prohibitive for large studies, commercially available genotyping arrays targeting rare variants prove to be a reasonable alternative. A technical challenge of array based methods is the task of deriving genotype classes (homozygous or heterozygous) by clustering intensity data points.The performance of clustering tools for common polymorphisms is well established, while their performance when conducted with a large proportion of rare variants (where data points are sparse for genotypes containing the rare allele) is less known. We have compared the performance of four clustering tools (GenCall, GenoSNP, optiCall and zCall) for the genotyping of over 10,000 samples using the Illuminas Human Exome BeadChip, which includes 247,870 variants, 90% of which have a minor allele frequency below 5%in a ...
This person will independently lead and conduct bioinformatics and genomic research, and provide her/his expertise to lab members in the collection, management, interpretation, and analysis on biological, pathological, and molecular pathological data, with a focus on, but not limited to, high-throughput technologies with strong emphasis on next-generation sequencing. The main responsibility of this position is on the application of state-of-art bioinformatics technologies to analyze and integrate large scale omics datasets. Require familiarity with existing genomic databases such as, but not limited to, TCGA, ENCODE, CCLE, etc. Proficiency in programming using either R/Perl/Python/Java/C++ is a must. Solid knowledge of biostatistics and strong quantitative skills are also required. Familiarity with SAS, exome and RNA-seq analysis, and NGS laboratory procedures are preferred, but not required. Excellent interpersonal and communication skills are essential, as are the abilities to work both ...
Review papers are beginning to appear based explicitly on next-generation sequencing (NGS), such as those of Lemmon & Lemmon (2013) and McCormack et al. (2013), replacing the earlier work of Philippe et al. (2005), and there are suggestions for how phylogenetics analyses might need to change in response to NGS data (Chan and Ragan 2013). These all treat phylogenomics as being very similar to traditional molecular phylogenetics, in the sense that many people are expecting phylogenomics to provide tree-like resolution of questions that remain unresolved with the current smaller datasets. In the words of Rokas et al. (2003), phylogenomics is intent on "resolving incongruence in molecular phylogenies". That is, incongruent gene trees are seen as the major obstacle to be overcome by phylogenetics data analysis (see also Jeffroy et al. 2006 ...
The presence of detectable MRD in patients with AML who are in remission correlates with an increased risk for relapse and reduced overall survival (OS).3-6 We analyzed bone marrow aspirates collected from patients with FLT3-ITD mutation-positive AML who were treated with the novel oral FLT3 inhibitor, gilteritinib, in a clinical trial (2215-CL-0101; NCT02014558).11 In this trial, adult patients with R/R AML were treated with oral gilteritinib as a single agent in 1 of 7 dose-escalation cohorts.11 Doses of 120 and 200 mg/d resulted in complete inhibition of FLT3 ex vivo, as measured by the plasma-inhibitory assay.22 Of the 137 FLT3-ITD-mutated patients who had received gilteritinib doses of 120 or 200 mg/d, 80 patients who had bone marrow aspirates at baseline and ≥1 additional time point were included in this analysis. Thirty-six of these 80 patients had ,1 ITD. The composite CR rate (CRc; defined as CR plus CRi plus CRp) for these 80 patients was 55% (44 patients). MRD (defined as an ...
Send us your samples and let our Next Generation Sequencing (NGS) experts perform your NGS analysis in state-of-the-art automated laboratories with rigorous quality control and fast turn-around times and superior data analysis and interpretation. Exiqon offers a complete sequencing service including RNA isolation, library preparation, sequencing, data analysis and biological interpretation of the results in a comprehensive and easy-to-read format. ...
Bioinformatics community open to all people. Strong emphasis on open access to biological information as well as Free and Open Source software.
One of the major breakthroughs in modern biology is the development of massively parallel sequencing, also called next generation sequencing (NGS), which enabled the complete delineation of the human genome more than a decade ago. Since then many more species genomes have been sequenced, and the cost per genome has dropped from billions to mere thousands of dollars. New discoveries are being made as a result of the capability many research teams now possess to not only sequence chromosomal DNA, but also to identify which regions a protein of interest specifically binds (Chip-seq), analyze a whole transcriptome of a cell population under investigation (RNA-seq), or find out which RNA regions an RNA binding protein resides (CLIC-seq).. While it is inevitable that many PIs will seriously consider the inclusion of deep sequencing in their next grant proposal, it is not necessarily easy to take the first step and get their feet wet, so to speak. Knowing what format (e.g. 454 for longer reads, ...
NEW] Video collection for the 2013 lectures on Next Generation Sequencing Data Analysis is now available in the course website. The video collections for the 2011 lectures on Next Generation Sequencing Data Analysis are now available at Youtube and Youku. The slides can also be downloaded. Please address all the feedback directly to Dr. Yunlong Liu @ [email protected] ...
Date: 06th - 09th October 2015 and 10th - 13th October, 2015 Time: 9:00 am to 5:00 pm all days Venue: Bioinformatics Lab 2 Coordinator: Mr. Naveen P
Schraga Schwartz, Yuri Motorin. Next-generation sequencing technologies for detection of modified nucleotides in RNAs. RNA Biology, Taylor & Francis, 2016, 14 (9), pp.1124 - 1137. ⟨10.1080/15476286.2016.1251543⟩. ⟨hal-01799254⟩ ...
One of the key elements to a successful Next Generation Sequencing (NGS) project is in the experimental setup. Together with you we can design your NGS project to fit your research interests and budget. TATAA Biocenter will assist you through the whole NGS workflow with library preparation, quality controls, sequencing, and data analysis.. ...
Next-Generation Sequencing. NGS is driving growth and possibilities in scientific research as DNA is sequenced at unprecedented speed. It has opened up new worlds in genomic research, and resulted in novel biological applications in diverse fields of science.. 1st BASE proudly introduces our NGS Service to partner scientists in their NGS pursuits. We offer the latest in NGS technologies, together with cross-platform expertise in choosing the most suitable technology to meet your sequencing needs. Get in touch with us and let us recommend the most suitable NGS platform for your project with no obligations.. 1st BASE is proud to offer NGS platforms from the most trusted names in NGS today:. ...
Next Generation Sequencing (NGS) machines extract from a biological sample a large number of short DNA fragments (reads). These reads are then used for several applications, e.g., sequence reconstruction, DNA assembly, gene expression profiling, mutation analysis. We propose a method to evaluate the similarity between reads. This method does not rely on the alignment of the reads and it is based on the distance between the frequencies of their substrings of fixed dimensions (k-mers). We compare this alignment-free distance with the similarity measures derived from two alignment methods: Needleman-Wunsch and Blast. The comparison is based on a simple assumption: the most correct distance is obtained by knowing in advance the reference sequence. Therefore, we first align the reads on the original DNA sequence, compute the overlap between the aligned reads, and use this overlap as an ideal distance. We then verify how the alignment-free and the alignment-based distances reproduce this ideal distance. The
Over the past 6 years, next generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. All major NGS technology companies providing commercially available instruments (Roche 454, Illumina, Life Technologies) have recently marketed bench top sequencing instruments with lower throughput and shorter run times, thereby broadening the applications of NGS and opening the technology to the potential use for clinical diagnostics. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry and data analysis need to be overcome. To facilitate the implementation of NGS as a routine method in molecular diagnostics, consistent quality standards need to be developed. Here the authors give an overview of ...
Citation. Kirkness, E. F., Venter, J. C., Sealfon, S.C.. Receptor Cloning: High Throughput Sequencing of CDNA Tags for Identification of Novel Genes.. Receptor Molecular Biology. 1995 Mar 01; 25: 126-141.. ...
Breakpoint mapping by next generation sequencing reveals causative gene disruption in patients carrying apparently balanced chromosome rearrangements with intellectual deficiency and/or congenital malformations ...
Rheonix will present data from a user-defined assay for STIs and data that demonstrates new capabilities of its Encompass Optimum™ workstation in NGS
WOBURN, MA-September 10, 2010-Covaris Inc. (a privately-held MA based company) today announced that it has signed a co-marketing agreement with Illumina, Inc. (NASDAQ:ILMN) making Covaris DNA shearing technologies the recommended method of shearing with Illumina next-generation sequencing product lines, including HiSeq, HiScanSQ, and Genome Analyzer. In addition, the proprietary Covaris process enables higher recoveries for nucleic acid extraction, tissue homogenization, chromatin shearing, protein digestion, and cell lysis. The highly controlled Covaris technology is isothermal and non-contact, ensuring molecular stability throughout the sample preparation process. Important for next-generation genetic analysis, the Covaris system allows customers to rapidly and precisely scale up sample processing capability. The Illumina-Covaris partnership will bring industry leading next-generation DNA shearing performance to Illuminas sequencing customers. About Covaris, Inc. ...
University of Missouri-Kansas City School of Law Professor Christopher Holman writes in the most recent issue of Nature Technology that while DNA sequencing technology has spawned a myriad of patent-related lawsuits, "aggressive patent acquisition and enforcement practices" show no signs of abating and may not necessarily be hindering the development of next-generation DNA sequencing and analysis technologies.
The immense amount of biological sequence data available these days requires efficient and sensitive analysis in order to provide e.g. the identification of unknown proteins, or information about the similarity between DNA sequences. Furthermore, new challenges to computational sequence analysis are posed by short sequence reads resulting from modern high throughput sequencing technologies such as 454 or Solexa/Illumina. Viewing biological sequences, such as DNA and proteins, as strings allows their investigation under a generative random string model. That is to say, one can define a probabilistic null model that generates random strings as representatives of a class of sequences. From these, one can deduce general statistical properties. In this thesis, we give a thorough derivation of a probabilistic model, called probabilistic arithmetic automaton (PAA). This models sequences of operations associated to operands depending on chance and provides the computational framework to calculate the ...
DALLAS Dec. 16, 2009 Aided by next-generation DNA sequencing technology, an international team of researchers has gained insights into how more than 60 carcinogens associated with
Over the past 6 years, next-generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry, and data analysis need to be overcome. Each workflow and sequencing platform have their particular problems and caveats, which need to be addressed. Regarding NGS, there is a variety of different enrichment methods, sequencing devices, or technologies as well as a multitude of analyzing software products available. In this manuscript, the authors focus on challenges in data analysis when employing different target enrichment methods and the best applications for each of them ...
A quality assessment package for next-genomics sequencing data. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well.
ASSAY DEVELOPMENT:. Circulating tumor DNA. Tumor-derived DNA fragments in the circulation can be distinguished based on the presence of cancer-specific mutations. However, these mutant DNA copies are often obscured by a relative excess of wild-type background DNA in the plasma. In patients with early stage tumors or minimal residual disease following treatment, the fraction of mutant tumor-derived DNA in plasma can be well below 1 in 1,000. Detection of such low-abundance DNA variants poses a significant technical challenge, especially if one has no prior knowledge of the tumors mutation profile. We have developed methods to enrich mutation-prone regions of plasma DNA by highly multiplexed PCR. We use next-generation DNA sequencing technologies to oversample thousands of copies of these mutation-prone genomic regions, allowing rare sequence variants to be identified and enumerated. However, the sensitivity of this approach is limited by sequencer errors and PCR misincorporations, both of which ...
The CF RDP Genomics Core provides high-throughput DNA sequencing services. The Core also provides informatics support and consultation on whole genome sequencing and transcriptomics by Illumina sequencing. ...
CS 5263 Bioinformatics. Next-generation sequencing technology. Outline. First generation sequencing Next generation sequencing (current) AKA: Second generation sequencing Massively parallel sequencing Ultra high-throughput sequencing Future generation sequencing Analysis challenges....
Next Generation Sequencing applications allow biomedical researchers to examine the expression of tens of thousands of genes at once, giving researchers the opportunity to examine expression across entire genomes. RNA Sequencing applications such as Tag Profiling, Small RNA and Whole Transcriptome Analysis can identify and characterize both known and novel transcripts, splice junctions and non-coding RNAs. These sequencing based-applications also allow for the examination of nucleotide variant. Next Generation Sequencing and these RNA applications allow researchers to examine the cancer transcriptome at an unprecedented level. This presentation will provide an overview of the gene expression data analysis process for these applications with an emphasis on identification of differentially expressed genes, identification of novel transcripts and characterization of alternative splicing as well as variant analysis and small RNA expression. Using data drawn from the GEO data repository and the Short ...
Next Generation Sequencing applications allow biomedical researchers to examine the expression of tens of thousands of genes at once, giving researchers the opportunity to examine expression across entire genomes. RNA Sequencing applications such as Tag Profiling, Small RNA and Whole Transcriptome Analysis can identify and characterize both known and novel transcripts, splice junctions and non-coding RNAs. These sequencing based-applications also allow for the examination of nucleotide variant. Next Generation Sequencing and these RNA applications allow researchers to examine the cancer transcriptome at an unprecedented level. This presentation will provide an overview of the gene expression data analysis process for these applications with an emphasis on identification of differentially expressed genes, identification of novel transcripts and characterization of alternative splicing as well as variant analysis and small RNA expression. Using data drawn from the GEO data repository and the Short ...
High-throughput DNA sequencing has revolutionized the study of cancer genomics with numerous discoveries that are relevant to cancer diagnosis and treatment. The latest sequencing and analysis methods have successfully identified somatic alterations, including single-nucleotide variants, insertions and deletions, copy-number aberrations, structural variants and gene fusions.
Next Generation Sequencing (NGS) technology generates tens of millions of short reads for each DNA/RNA sample. A key step in NGS data analysis is the short read alignment of the generated sequences to a reference genome. Although storing alignment information in the Sequence Alignment/M...read more ...
The use of somatic mutations for predicting clinical outcome is difficult because a mutation can indirectly influence the function of many genes, and also because clinical follow-up is sparse in the relatively young next generation sequencing (NGS) databanks. Here we approach this problem by linking sequence databanks to well annotated gene-chip datasets, using a multigene transcriptomic fingerprint as a link between gene mutations and gene expression in breast cancer patients. The database consists of 763 NGS samples containing mutational status for 22,938 genes and RNA-seq data for 10,987 genes. The gene chip database contains 5,934 patients with 10,987 genes plus clinical characteristics. For the prediction, mutations present in a sample are first translated into a transcriptomic fingerprint by running ROC analysis on mutation and RNA-seq data. Then correlation to survival is assessed by computing Cox regression for both up- and downregulated signatures. According to this approach, the top driver
Next-generation DNA sequencing technologies have turned the vision of precision medicine into a plausible reality, but also threaten to overwhelm computing infrastructures with unprecedented volumes of data. A recent $1.3 million award from the National Institutes of Health will allow researchers at the University of Illinois and Stanford to help address this challenge by developing novel data compression strategies.
en] The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygous sheep receiving the CLPG mutation from their sire. The wild-type phenotype of CLPG/CLPG animals is thought to result from translational inhibition of paternally expressed DLK1 transcripts by maternally expressed miRNAs. To identify the miRNA responsible for this trans effect, we used high-throughput sequencing to exhaustively catalog miRNAs expressed in skeletal muscle of sheep of the four CLPG genotypes. We have identified 747 miRNA species of which 110 map to the DLK1-GTL2 or callipyge domain. We demonstrate that the latter are imprinted and preferentially expressed from the maternal allele. We show that the CLPG mutation affects their level of expression in cis ( approximately 3.2-fold increase) as well as in trans ( approximately 1.8-fold increase). In CLPG/CLPG animals, miRNAs from the DLK1-GTL2 domain account for approximately 20% of miRNAs in skeletal muscle. We show that the CLPG ...
고객의 실험 목적에 따라 맞춤형 패널을 디자인 및 제작하는 서비스를 제공하고 있습니다. 셀레믹스의 Target enrichment 방법은 관심 유전자 영역을 Whole Genome 으로 부터 분리할 수 있으며, 높은 coverage & in-depth Sequencing 데이터를 생성하여 유전자 변이의 검출 감도를 증가 시킵니다 ...
The ThruPLEX DNA-seq Kit generates high quality DNA-seq libraries for Illumina NGS from 50 pg to 50 ng of DNA using a single-tube, 3-step workflow.
The ThruPLEX DNA-seq Kit generates high quality DNA-seq libraries for Illumina NGS from 50 pg to 50 ng of DNA using a single-tube, 3-step workflow.
Molecular and genetic testing is readily available, and genome-scale and high-throughput DNA sequencing technology is increasingly being applied in the clinical diagnostic realm. However, their cost-effectiveness and health outcome benefits need to be carefully examined. Diagnostic genetic testing based on symptoms (eg, testing for fragile X in a boy with mental retardation) differs from predictive genetic testing (eg, evaluating a healthy person with a family history of Huntington disease) and from predisposition genetic testing, which may indicate relative susceptibility to certain conditions or response to certain drug treatment (eg, BRCA1/BRCA2 or HER2 testing for breast cancer). The outcome benefits of many new pharmacogenetic tests have not yet been established by prospective clinical studies; eg, there is insufficient evidence that genotypic testing for warfarin dosing leads to outcomes that are superior to those using conventional dosing algorithms, in terms of reduction of out-of-range ...
...June 23 2011 (Bethesda MD): Today on behalf of the Association for ...The analytical validation requirements for NGS will vary based on the ...While the analytical validity of a NGS instrument may be intrinsically...AMP also pointed out the role of molecular pathology professionals in ...,AMP,comments,at,FDA,meeting,on,next-generation,sequencing,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
The advancement of high-throughput sequencing technologies enables sequencing of human genomes at steadily decreasing costs and increasing quality. Before variants can be analyzed, e.g., in...
Next generation sequencing is defined as a process of DNA sequencing decide the exact order of nucleotides inside a DNA molecule. Next generation sequencin
TY - JOUR. T1 - Haplotype counting by next-generation sequencing for ultrasensitive human DNA detection. AU - Debeljak, Marija. AU - Freed, Donald N.. AU - Welch, Jane A.. AU - Haley, Lisa. AU - Beierl, Katie. AU - Iglehart, Brian S.. AU - Pallavajjalla, Aparna. AU - Gocke, Christopher. AU - Leffell, Mary S.. AU - Lin, Ming-Tseh. AU - Pevsner, Jonathan A.. AU - Wheelan, Sarah. AU - Eshleman, James. PY - 2014. Y1 - 2014. N2 - Human identity testing is critical to the fields of forensics, paternity, and hematopoietic stem cell transplantation. Most bone marrow (BM) engraftment testing currently uses microsatellites or short tandem repeats that are resolved by capillary electrophoresis. Single-nucleotide polymorphisms (SNPs) are theoretically a better choice among polymorphic DNA; however, ultrasensitive detection of SNPs using next-generation sequencing is currently not possible because of its inherently high error rate. We circumvent this problem by analyzing blocks of closely spaced SNPs, or ...
Genetic diversity studies form the basis of many aspects of biodiversity science. High throughput sequencing has the potential to dramatically change how genetic diversity studies are planned and analyzed. Still, although the ratio of the number of reads produced in a single run is truly cost-effective, the relatively high cost of a single run has prevented many academic laboratories from using these innovative technologies. To overcome this limitation, barcoding systems were developed 8), where different oligonucleotides (8 to 10 bp in length) are incorporated in the different DNA samples to be sequenced. After these samples are labelled with the barcodes, they can all be multiplexed and sequenced together in a single sequencing run. Each sample is then sorted using bioinformatics methods, by recognition of its barcode. When coupled with laboratory methods for genome complexity reduction, high throughput sequencing can be a very efficient strategy for providing a massive amount of sequence data ...
Restriction-site associated DNA (RAD) sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis of non-model organisms including genotype-phenotype association mapping, phylogeography, population genetics and scaffolding genome assemblies through linkage mapping. We constructed a RAD library using genomic DNA from a Plutella xylostella (diamondback moth) backcross that segregated for resistance to the insecticide spinosad. Sequencing of 24 individuals was performed on a single Illumina GAIIx lane (51 base paired-end reads). Taking advantage of the lack of crossing over in homologous chromosomes in female Lepidoptera, 3,177 maternally inherited RAD alleles were assigned to the 31 chromosomes, enabling identification of the spinosad resistance and W/Z sex chromosomes. Paired-end reads for each RAD allele were assembled into contigs and compared to the genome of Bombyx mori (n = 28) using BLAST, revealing 28