• The Roche GS-FLX will provide an additional level of sequencing service to researchers who want to tackle whole genomes. (biospace.com)
  • Specific applications include de novo sequencing and re-sequencing of genomes, metagenomics, RNA analysis, and targeted sequencing of DNA regions of interest. (pressebox.com)
  • In CPT-seq, the researchers first divided the dilution into 96 copies, adding the indexing sequence with the transposon, and then mixed them to redistribute to 96 compartments, which removed the transposase and introduced a new index sequence by amplification, generating more than 9,200 virtual compartments. (pitchengine.com)
  • On genomic DNA, the single base difference of different individuals is called single nucleotide polymorphism(SNP). (pitchengine.com)
  • The CLF can also help with gap closure and sequence verification, using more traditional sequencing methods. (biospace.com)
  • Characterization of the novel virus confirms the utility of unbiased high-throughput sequencing for pathogen discovery and provides an opportunity for public health efforts to quickly curb emerging viral pandemics in the future. (pressebox.com)
  • Unbiased, high-throughput sequencing with the 454 Sequencing system revealed the presence of a previously undiscovered Old World arenavirus. (pressebox.com)
  • Within 72 hours of the sample arriving at JFK Airport, we identified the novel virus using high throughput sequencing,' said Thomas Briese, Associate Director of the Center for Infection and Immunity at the Mailman School of Public Health of Columbia University. (pressebox.com)
  • The unbiased, high-throughput 454 Sequencing System has been shown to be a powerful pathogen discovery tool in a series of recent studies. (pressebox.com)
  • 454 Life Sciences, a center of excellence of Roche Applied Science, develops and commercializes the innovative 454 Sequencing System for ultra-high-throughput DNA sequencing. (pressebox.com)
  • This includes data storage and analysis capabilities to make sense of the large amounts of data generated by this type of large-scale research project. (biospace.com)
  • Studies had shown that CPT-seq can anchor unpatterned contigs on the reference genome and detect erroneous sequences. (pitchengine.com)
  • For example, beyond genome sequencing we see a significant need for sequencing of transcriptomes, clinical samples, paired-end amplicon sequencing, and other cutting-edge uses of the technology and services. (biospace.com)
  • This dual indexing program takes only three hours and is suitable for small amounts of genomic DNA. (pitchengine.com)
  • The hallmarks of the 454 Sequencing System are its simple, unbiased sample preparation and long, highly accurate sequence reads, including paired-end reads. (pressebox.com)
  • The vast majority of DNA sequencers now generate short sequence reads. (pitchengine.com)
  • Epigenetic modifications of chromatin and DNA are relevant for eukaryotic gene expression. (springer.com)
  • Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. (frontiersin.org)
  • Sequencher has integrated the comprehensive Cufflinks suite for in-depth transcript analysis and differential gene expression of your RNA-Seq data. (genecodes.com)
  • The spectrum of spontaneous mutation of an endogenous mammalian cell gene has been determined at the DNA sequence level. (pnas.org)
  • Sequences toward the ends of the MCMV genome encode tandem arrays of homologous glycoproteins (gps) arranged as two gene families. (asm.org)
  • We examined the bacterial composition of chlorinated drinking water using 16S rRNA gene clone libraries derived from RNA and DNA extracted from twelve water samples collected in three different months (June, August, and September of 2007). (epa.gov)
  • We used three nuclear genes, comprising two noncontiguous fragments of elongation factor 1α (EF-1α 5′ and EF-1α 3′), fragments of the D2 and D10 expansion regions of the large subunit ribosomal DNA gene (28S), and a region of the small subunit ribosomal DNA gene (18S). (wiley.com)
  • The N-terminal amino acid sequence of the purified Ia immunity protein was determined and was found to be in perfect agreement with that predicted from the DNA sequence of its structural gene. (asm.org)
  • In general, DNA sequencing is referred to as a molecular technique that helps in determining the nucleotide sequence of DNA (deoxyribonucleic acid), which is the most fundamental level of knowledge of a gene or genome. (medgadget.com)
  • Targeted gene sequencing panels are important tools for analyzing precise mutations in a specified sample. (express-press-release.net)
  • Moreover, targeted gene sequencing makes the study easier and produces smaller and manageable data set. (express-press-release.net)
  • RNA-based Targeted Sequencing is a technique for sequencing and selecting specific pathways or transcripts of interest of gene expression microarray. (express-press-release.net)
  • A key step in the regulation of gene expression is the sequence-specific binding of transcription factors (TFs) to their DNA recognition sites. (biomedcentral.com)
  • We hypothesized that for human and mouse, many orthologous genes expressed in a similarly tissue-specific manner in both human and mouse gene expression data, are likely to be co-regulated by orthologous TFs that bind to DNA sequence motifs present within noncoding sequence conserved between these genomes. (biomedcentral.com)
  • The yopM gene is longer than previously thought (by a sequence encoding two leucine-rich repeats), the ORF upstream of ypkA-yopJ is discussed as a potential Syc gene, and a previously undescribed ORF downstream of yopE was identified as being potentially significant. (pubmedcentralcanada.ca)
  • RESULTS: Maximum likelihood analysis of sequences data from rbcL, ndhF, and matK gene regions (total aligned length 7323 bp) yielded a phylogenetic tree with high bootstrap values for most branches. (umd.edu)
  • Molecular cloning, expression, and DNA sequence analysis of the gene that encodes the 16-kilodalton outer membrane lipoprotein of Serpulina hyodysenteriae. (asm.org)
  • The gene (smpA) that encodes the 16-kDa outer membrane lipoprotein of Serpulina hyodysenteriae was cloned in Escherichia coli, and its primary structure was determined by nucleotide sequencing. (asm.org)
  • DNA sequence analysis of the gene showed that three regions of the protein likely to be exposed on the cell surface not only differed extensively from the corresponding regions of the E. coli polypeptide but also from all other sequenced OmpA proteins. (epfl.ch)
  • Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. (biomedcentral.com)
  • Conclusions The combined approach of DNA pooling followed by MPR strongly facilitates mutation analysis in broadly heterogeneous single gene disorders. (bmj.com)
  • One clone (lambda YH 8) contained part of pre-S(I) through the entire S gene and the other (lambda YH 16) had the middle section of the S to the end of X gene of HBV DNA. (eurekamag.com)
  • These sequences of D. nodosus fimA gene from NZ were genetically different from previously reported strains in the GenBank (NCBI) and commercial vaccine strains. (lincoln.ac.nz)
  • Cloning and DNA sequence analysis of pepQ, a prolidase gene from Lactobacillus delbrueckii subsp. (semanticscholar.org)
  • lactis (DSM7290) DNA, in the low-copy-number vector pLG339, a recombinant clone was selected, which complemented a mutation in the prolidase gene (pepQ) of Escherichia coli UK173. (semanticscholar.org)
  • Cloning and sequence analysis of the X-Prolyl-dipeptidyl-aminopeptidase gene (pepX) from Lactobacillus delbrückii ssp. (semanticscholar.org)
  • Promoters play a central role in transcription initiation and gene regulation, so it is necessary for these DNA regions to be differentiated from non-promoter sequences. (jbsdonline.com)
  • 3. Makino S, Naoki A, Suzuki M. Visual presentation of complete genomic DNA sequences, and its application to identification of gene-coding regions. (concordia.ca)
  • Analysis of protein sequences and phylogeny of the plant MSH gene family show that these proteins are evolutionarily conserved, and follow the classical model of asymmetric protein evolution. (escholarship.org)
  • Direct cycle DNA sequencing of ~450 bp of the PCR products of four C. trachomatis isolates revealed complete identity of one isolate with the known sequence of serovar F, while the other three isolates harboured three phenotypically silent point mutations at codons 96, 305 and 312 of the EF-Tu gene. (nus.edu.sg)
  • The sequence analyses confirm the authenticity of the target bands, reiterate the conservation and role of the EF-Tu gene in protein biosynthesis, and indicate the utility of the primers for the rapid detection of C. trachomatis. (nus.edu.sg)
  • One reason scientists pay close attention to DNA sequence is that it can help them identify a gene or a mutation that may cause a disease. (ucla.edu)
  • GENTAUR antibody-antibodies.com The Marketplace for Antibodies : Human chromosome 11 DNA sequence and analysis including novel gene identification. (antibody-antibodies.com)
  • Human chromosome 11 DNA sequence and analysis including novel gene identification. (antibody-antibodies.com)
  • Optimize your workflow efficiency with these capillary electrophoresis systems - from the highly sensitive multiplex gene expression capabilities of the GeXP Genetic Analysis System and the high-resolution applications of the PA 800 plus Pharmaceutical Analysis System, to the exceedingly sensitive CESI 8000 High Performance Separation-ESI Module. (sciex.com)
  • Gene Codes is a leading biotech company developing bioinformatics solutions for DNA Sequence Analysis. (biotech-365.com)
  • Molecular sequence and structure data of DNA, RNA, and proteins, gene expression profiles or microarray data, metabolic pathway data are some of the major types of data being analysed in bioinformatics. (wikipedia.org)
  • Since the origin of bioinformatics, sequence analysis has remained the major area of research with wide range of applications in database searching, genome annotation, comparative genomics, molecular phylogeny and gene prediction. (wikipedia.org)
  • Brinkman AB, Simmer F, Ma K et al (2010) Whole-genome DNA methylation profiling using MethylCap-seq. (springer.com)
  • The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications. (frontiersin.org)
  • Whole genome sequencing and its clinical relevance are presented particularly in the context of analysis of nucleotide and structural genomic variants in large population studies and in certain patient cohorts. (frontiersin.org)
  • The complete DNA sequence of the Smith strain of murine cytomegalovirus (MCMV) was determined from virion DNA by using a whole-genome shotgun approach. (asm.org)
  • Whole genome and capture‑based sequencing found that EV mtDNA covered the whole mitochondrial genome. (spandidos-publications.com)
  • The most comprehensive method for determining the methylation status of every nucleotide is whole-genome bisulfite sequencing (WGBS) , however, this approach is not economically viable due to the high cost of whole genome sequencing and the combination of large numbers of samples required in MWAS. (creativebiomart.net)
  • There are few existing visualization methods for raw nucleotide sequences of a whole genome or chromosome. (concordia.ca)
  • We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. (biomedcentral.com)
  • Whole genome sequencing (WGS) at 30× coverage can also be used for CNA and LOH detection, but requires at least 100 ng of high quality input DNA and has challenges associated with cost, bioinformatics processing time, and storage of large datasets. (biomedcentral.com)
  • A method often used to overcome the challenge of a limiting amount of DNA is whole genome amplification (WGA) to increase the amount of starting template DNA [ 9 ]. (biomedcentral.com)
  • Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. (semanticscholar.org)
  • We determined almost complete small-subunit ribosomal DNA sequences of 50 reference strains belonging to the genera Corynebacterium, Rhodococcus, and Gordona and compared these sequences with previously published sequences. (nih.gov)
  • This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics. (sciencemag.org)
  • DNA sequencing in the new technology that has revolutionized molecular biology and genomics research. (medgadget.com)
  • Observed DNA sequence variations were assessed for pathogenicity by review of the scientific literature, and mutation and polymorphism databases, through the use of in silico tools including sorting intolerant from tolerant (SIFT) and polymorphism phenotyping (PolyPhen), and according to the recommendations of the American College of Medical Genetics and Genomics for the interpretation of DNA sequence variations. (bmj.com)
  • MinIT, a rapid analysis and device control accessory for nanopore DNA sequencing, is now arriving with genomics researchers. (sttinfo.fi)
  • The huge reduction in the sequencing cost and increase in sequencing efficiency, the incomparable sequencing throughput, sensitivity, and accuracy all make NGS the most promising laboratory technology for cancer genomics, cancer genetics, early diagnosis and personalized treatment of cancer patients in next decade [ 2 - 4 ]. (jcancer.org)
  • Phylogenetic analysis of 1234 and 1117 RNA-based and DNA-based clone sequences, respectively, showed that unclassified Bacteria were the most abundant sequences, representing on average 57% of all sequences analyzed. (epa.gov)
  • Is the Subject Area "Phylogenetic analysis" applicable to this article? (plos.org)
  • CONCLUSIONS: Phylogenetic analysis supports the monophyly of Agalinis, including species formerly in Tomanthera, and this group is sister to a group formed by the genera Aureolaria, Brachystigma, Dasistoma, and Seymeria. (umd.edu)
  • Sequencher is packed with proprietary algorithms and peer-reviewed favorites that generate results for Sanger , Next-Gen Sequencing (NGS) , and RNA-Seq sequence data. (genecodes.com)
  • Sequencher's extensive Sanger analysis features are the foundation it was built upon. (genecodes.com)
  • Methods Sanger sequencing was performed on DNA isolated from peripheral blood or lymphoblastoid cell lines. (bmj.com)
  • PCR products were then subjected to MPR on an Illumina Genome-Analyser and mutations were subsequently assigned to their respective mutation carrier via CEL I endonuclease based heteroduplex screening and confirmed by Sanger sequencing. (bmj.com)
  • abstract = "Honey contains DNA from many different organisms that are part of hive micro-environmental niches and honey bee pathospheres. (dtu.dk)
  • cDNA clones for a cadherin molecule were isolated from a cDNA library of human hepatocellular carcinoma cells which lacked E- and P-cadherin expression but exhibited cell aggregation activity mediated by an unknown cadherin, and they were subjected to sequence analysis. (aacrjournals.org)
  • By digestion with HindIII restriction enzyme, a human hepatocellular carcinoma was shown to contain only 2 hepatitis B virus (HBV) DNA inserts. (eurekamag.com)
  • Xu H, Zhu X, Xu Z, Hu Y, Bo S, Xing T, Zhu K. Non-invasive Analysis of Genomic Copy Number Variation in Patients with Hepatocellular Carcinoma by Next Generation DNA Sequencing. (jcancer.org)
  • To explore new molecular diagnosis approaches for early detection and differential diagnosis of hepatocellular carcinoma (HCC), we analyzed genomic copy number variations (CNV) using plasma cell-free DNA from patients with HCC by next generation DNA sequencing. (jcancer.org)
  • This method should prove to be a powerful tool for rapid investigations in human genetics and diagnostics, pathogen detection, and DNA molecular recognition. (pnas.org)
  • This webinar will discuss findings from the study, in which molecular residual disease (MRD) was assessed using circulating tumor DNA (ctDNA) without prior mutational knowledge in oligometastatic colorectal cancer (CRC) patients who had received neoadjuvant chemotherapy. (genomeweb.com)
  • Ribosomal DNA (rDNA) has been widely utilized for molecular systematics and the identification of microorganisms. (asm.org)
  • We have previously presented data on ITS sequences for the molecular identification of all members of the genus Trichosporon . (asm.org)
  • 4. SIP is an adaption of a traditional molecular biology technique that can be used to characterize any unknown genomic flanking sequence or to extend any sequence for which only minimal sequence information is available. (mdc-berlin.de)
  • Virus LPV-K38, from the original LPV isolate passaged in BJAB cells, was the first molecular clone of LPV to be fully sequenced ( 11 ). (asm.org)
  • The results of a cladistic analysis based on a combined character matrix consisting of the morphological data set of Meier & Hilger (2000) and the molecular data set of Baker & al. (brillonline.com)
  • Partitioned Bremer Support values reveal that 90% of the tree support is generated by the DNA sequence characters, although the average morphological character contributes twice the support of an average molecular character. (brillonline.com)
  • Molecular analysis of its mutational landscape may enable the identification of novel therapies. (aacrjournals.org)
  • Using molecular techniques, it is possible to detect Yp sequences in the majority of XX males. (ugent.be)
  • Nucleotide sequence analysis revealed an open reading frame of 1104 nucleotides corresponding to a protein of 368 amino acids with a calculated pI of 4.64 and a molecular mass of 41087 Da. (semanticscholar.org)
  • Biochip technology combines two in one: multiparametric molecular analysis and quick identification of genomic material in biological samples. (bats.ch)
  • CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. (biomedcentral.com)
  • One of the most reliable approaches available to date is molecular inversion probe (MIP) technology, which can obtain high-quality CNA and genotype data from FFPE samples with less than 100 ng of input DNA [ 4 ]. (biomedcentral.com)
  • Such molecular phylogeny analyses employing alignment-free approaches are said to be part of next-generation phylogenomics. (wikipedia.org)
  • Availability of the reference human genome sequence enabled the generation of oligonucleotide probes and short sequence markers (SNPs) mapped to specific chromosome positions that could then be used to generate microarray platforms to analyze DNA from specific patients to search for genomic copy number variants and genomic structural variants. (frontiersin.org)
  • Screening the millions of reads that next-generation sequencing produces presents a major challenge when searching for candidate SNPs. (genecodes.com)
  • With GSNAP(2) the SNP analysis takes a different approach looking at both previously reported SNPs as well as new candidates. (genecodes.com)
  • The user must supply a list of known SNPs as well as the reads and a reference sequence. (genecodes.com)
  • Most meQTLs involve CpG-SNPs, while sequence-dependent effects on chromatin binding are also important in regions of active chromatin. (harvard.edu)
  • However, to apply methyl-seq to this kind of dataset you ideally require both DNA sequence data and bisulphite treated sequence data for each wheat accession otherwise C-T SNPS will be incorrectly classified as unmethylated cytosine sites. (biomedcentral.com)
  • After quality control, a total of 185,117 autosomal SNPs were kept for further analysis. (g3journal.org)
  • At present, the 26S rDNA sequences of almost all yeasts, including nonpathogenic species, have been determined ( 3 , 7 , 8 ). (asm.org)
  • DNA coding for rRNA) sequences with rDNA sequences of known phylogeny. (asm.org)
  • it was estimated that 72% of the rDNA sequences from the total population of culturable cells would match these 21 sampled sequences (72% coverage). (asm.org)
  • A preliminary set of 21 Plant Clinic isolates was sequenced at the USDA/ARS Floral and Nursery Plants Research Unit in Beltsville, MD. Partial 16S rDNA sequences from the preliminary analysis were used to identify related database sequences of R. fascians isolated from non-plant environments with a nucleotide blast algorithm through the National Center for Biotechnology Information (NCBI). (oregonstate.edu)
  • Our analysis has focused on nucleotide sequences available from seven humans. (genetics.org)
  • Average nucleotide diversity among the sequences is 1.7%, several-fold higher than estimates from restriction endonuclease site variation in mtDNA from these individuals and previously reported for other humans. (genetics.org)
  • In addition, other results suggest that restriction site (as well as pairwise sequence) comparisons may underestimate the total number of substitutions that have occurred since the divergence of two mtDNA sequences from a common ancestral sequence, even at low levels of divergence. (genetics.org)
  • There is no convincing evidence that recombination has contributed to the mtDNA sequence diversity we have observed. (genetics.org)
  • Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. (arctichealth.org)
  • Emerging evidence has revealed that mitochondrial DNA (mtDNA) is encapsulated in plasma extracellular vesicles (EVs). (spandidos-publications.com)
  • In this study, we recovered and sequenced mite mitochondrial DNA (mtDNA) from honey from different locations around the world (Europe, Asia, Africa, North and South America). (dtu.dk)
  • mtDNA sequence entries available in GenBank and assigned them to different mitotypes. (dtu.dk)
  • Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. (sciencemag.org)
  • Cloning, DNA sequence analysis and partial characterization of pepN, a lysyl aminopeptidase from Lactobacillus delbrückii ssp. (semanticscholar.org)
  • Alternatively, fingerprinting of total PCR products may be carried out by using, for example, amplified ribosomal DNA (rDNA) restriction analysis ( 28 , 34 ), length heterogeneity PCR ( 30 ), single-strand conformation polymorphism ( 19 , 31 ), and terminal restriction fragment length polymorphism ( 20 , 37 ). (asm.org)
  • The cloning approach has provided lists of sequence percentages or restriction fragment length polymorphism classes, along with their relative amounts in libraries. (asm.org)
  • We have developed a method for discriminating between alleles that uses a synthetic nanopore to measure the binding of a restriction enzyme to DNA. (ed.gov)
  • Restriction enzyme mapping analysis for 14.6 kb revealed that the map was in conflict with the report of Meade et al. (ajas.info)
  • DGGE banding profiles obtained from triplicate samples pooled prior to analysis indicated that there was less evenness in improved soils, suggesting that selection for specific bacterial groups occurred. (asm.org)
  • Sequence Analysis of Bacterial DNA in the Colon and Stomach of the Tyr" by Raul J. Cano, Friedrich Tiefenbrunner et al. (calpoly.edu)
  • mA) were amplified from bacterial DNA using polymerase chain reaction (PCR). (lincoln.ac.nz)
  • Genomic sequencing of clinical microbiological specimens expands our capacity to study cultivable, fastidious and uncultivable members of the bacterial community. (semanticscholar.org)
  • The technology, called PANGEA (predictive analysis of noncoding genomic enhancer/promoter alterations), could eventually help researchers and clinicians more accurately classify cancer subtypes to better guide prognoses and treatments. (genomeweb.com)
  • For promoter classification the suitable choices were found to be Principal Component Analysis (PCA) feature extraction and General Regression Neural Network (GRNN) classifier. (psu.edu)
  • An RNA polymerase I promoter located in the CHO and mouse ribosomal DNA spacers: functional analysis and factor and sequence requirements. (asm.org)
  • We report results of experiments in which we demonstrated the existence of a polymerase I promoter within the ribosomal DNA spacer upstream from the rRNA initiation site in Chinese hamsters and mice. (asm.org)
  • Sequence comparisons also revealed a great similarity between the CHO and mouse spacer promoter regions, yet there was much less similarity between the flanking sequences. (asm.org)
  • Two sequences required for activity of the Epstein-Barr virus BART RNA promoter in transfection assays have been identified by site-directed mutagenesis. (microbiologyresearch.org)
  • Candidate sequences were suggested by mapping a region of unmethylated DNA in EBV around the BART promoter followed by in vivo footprinting the promoter in the C666-1 nasopharyngeal carcinoma cell line, which expresses BART RNAs. (microbiologyresearch.org)
  • On the other hand several experimental and computational studies have shown that promoter sequences possess some special properties, which are common across all organisms. (jbsdonline.com)
  • Global DNA next generation sequencing market, based on the product was segmented as, platforms, services and consumables. (openpr.com)
  • We describe a method to generate ultra-long sequences by nanopore-based sequencing platforms. (jove.com)
  • 1. There are few available tools to comprehensively and economically identify uncharacterized flanking regions that are not extremely labour intensive and which exploit the advantages of emerging long‐read sequencing platforms. (mdc-berlin.de)
  • The real-time, high-resolution sequence output makes the technology highly suitable for applications including complex mutation analysis, microbial identification, and DNA methylation quantification. (qiagen.com)
  • Ultra-low-cost DNA sequencing and tumor biopsy analysis, in which morphology and mutation analysis are combined, can substantially decrease diagnostic costs and make it more widely accessible," Kühnemund said. (ucla.edu)
  • Through this we can model the effect of stutter in STR analysis and gain better understanding of the mutation process that naturally occurs in STRs. (ojp.gov)
  • The global DNA next generation sequencing market is expected to reach US$ 22,716.9 Mn in 2025 from US$ 4,898.5 Mn in 2017. (openpr.com)
  • The market for DNA next generation sequencing is expected to grow significantly due to factors such as, declining price of sequencing, technological advancements in sequencing and increasing prevalence of cancer. (openpr.com)
  • In addition, usage of NSG in biomarker discovery & precision medicine is anticipated to have a positive impact on the growth of the DNA next generation sequencing market in the coming years. (openpr.com)
  • These product innovations and launches are expected to propel the growth of the DNA next generation sequencing market during the forecast period. (openpr.com)
  • The objective of the study is to describe, define, and forecast the DNA next generation sequencing market by product, application, end user, and region. (openpr.com)
  • The utility of analyzing cell-free circulating tumor DNA (ctDNA) by next-generation sequencing (NGS) is not established. (aacrjournals.org)
  • We use next-generation sequencing to assay blood DNA methylation at approximately 4.5 million loci, each comprising 2.9 CpGs on average, in 697 normal subjects. (harvard.edu)
  • Like the principle of methyl-DNA immunoprecipitation sequencing (MeDIP-Seq) , methyl-CpG-binding domain sequencing (MBD-Seq) is essentially a combination of affinity-based capture approach and next-generation sequencing (NGS). (creativebiomart.net)
  • Next generation DNA sequencing (NGS) has brought genome sequencing to clinical laboratories. (jcancer.org)
  • Both efficient lysis of the microbiota and the quality of the obtained fecal DNA are important for allowing the downstream next-generation sequencing to cover the phylogenetic diversity of both Gram-negative and Gram-positive bacteria living in the mouse gut. (bio-protocol.org)
  • Advancements in Next-Generation Sequencing (NGS) have progressed to the stage of forensic validation and development of interpretation guidelines, however newer sequencing technologies are rapidly evolving that may better serve forensic needs. (ojp.gov)
  • All mutations identified by oligonucleotide microarray and all disagreements with conventional gel-based DNA sequence analysis were confirmed by re-analysis with manual and automated dideoxy DNA sequencing. (aacrjournals.org)
  • A total of 77 ovarian cancers were identified as having TP53 mutations by one of the two approaches, 71 by microarray and 63 by gel-based DNA sequence analysis. (aacrjournals.org)
  • If you would like to use the methyl-CpG binding domain (MBD)-based capture method to enrich hypermethylated DNA fragments for other downstream applications, such as DNA methylation microarray testing , our flexible services will meet your research needs. (creativebiomart.net)
  • a reference sequence of the human genome was derived. (frontiersin.org)
  • Easily use consensus sequences from the Project Window as a reference sequence for NGS alignments for hybrid sequencing projects. (genecodes.com)
  • Sequencher's Reference Sequence is a powerful feature controlling numbering, features and much more. (genecodes.com)
  • Other significant factors that are continually driving the global DNA sequencing market are a rise in technological advancements in DNA sequencing, growth in collaborations & partnerships, and increase in genome mapping programs globally. (medgadget.com)
  • These probe arrays, or DNA chips, can then be applied to parallel DNA hybridization analysis, directly yielding sequence information. (pnas.org)
  • The fluorescence signals from complementary probes were 5-35 times stronger than those with single or double base-pair hybridization mismatches, demonstrating specificity in the identification of complementary sequences. (pnas.org)
  • sequence capture, the capture and sequencing of DNA fragments by the hybridization of genomic DNA with synthesized probes. (biomedcentral.com)
  • Due to limited sample availability, few PCR assays were possible, so analyses were designed to detect viral regulatory region sequences. (asm.org)
  • Our experience in the development of quantitative assays for DNA and fixation were to our advantage in the optimisation of the DNA probe hybridisation thereby obtaining assays with good sensitivity and reproducibility. (bats.ch)
  • Although the high success rate of CNA by MIP assays in FFPE-derived DNA makes it arguably the best currently used method, its application remains limited since in many research and clinical settings, obtaining 100 ng of input DNA is often unachievable, particularly for small biopsy samples and pre-cancerous lesions. (biomedcentral.com)
  • High-throughput sequencing allows interrogating the status of methylated DNA at nucleotide resolution and genome-wide, bringing unprecedented views on the distribution and dynamics of this relevant modification in healthy and diseased tissues. (springer.com)
  • Akalin A, Kormaksson M, Li S et al (2012b) methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. (springer.com)
  • The unmethylated fraction is removed, and finally the methylation-enriched portion of the genome is eluted and sequenced to detect genome-wide methylation sites. (creativebiomart.net)
  • Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication. (arctichealth.org)
  • Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC-AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. (arctichealth.org)
  • Conventional DNA sequence analysis demonstrated an 87% accuracy rate, 82% sensitivity, and a 100% specificity. (aacrjournals.org)
  • The sensitivity analysis also reveals a remarkable stability of the preferred tree with 25 of the 36 tree nodes supported under 16 different analysis conditions. (brillonline.com)
  • In this study, we have compared the sensitivity and specificity of READSCAN to a manually constructed analysis workflow in a common, commercial NGS web application. (aacrjournals.org)
  • The sequencing techniques currently available for the detection of known or "hotspot" mutations, however, offer incredibly high levels of sensitivity. (ascopost.com)
  • Results For proof of principle, DNA from patients with known mutations was used and detection of 22 out of 24 different alleles (92% sensitivity) was demonstrated. (bmj.com)
  • Moreover, we can make it easy to capture fragments with a small number of methylated sites by using a low-salinity elution buffer, and further enhance the sensitivity by using the shortest possible DNA fragments. (creativebiomart.net)
  • Each method has both common and unique issues related to the required starting DNA amount, specificity, sensitivity, genome coverage, and accuracy as well as cost. (biomedcentral.com)
  • Fluorescence detection in automated DNA sequence analysis. (nih.gov)
  • Fluorescence detection of the DNA fragments is accomplished by means of a fluorophore covalently attached to the oligonucleotide primer used in enzymatic DNA sequence analysis. (nih.gov)
  • Our study suggested that non-invasive genomic CNV analysis using plasma samples could be a valuable tool for early detection and differential diagnosis of HCC. (jcancer.org)
  • Although CNV analysis itself cannot establish the diagnosis, it can help identify patients at high risk for HCC among patients with chronic liver diseases, which would prompt closer and more frequent surveillance for early tumor detection and intervention. (jcancer.org)
  • Phylogeny of R. fascians isolates obtained from Plant Clinic submissions was determined with 16S ribosomal DNA (16S rDNA) sequence analysis with sequence primers designed to amplify specific regions of R. fascians 16S rDNA. (oregonstate.edu)
  • Applications involving analysis of cell free DNA in maternal blood for prenatal diagnosis of specific autosomal trisomies are reviewed. (frontiersin.org)
  • The variability of chemotaxonomic characteristics within the genus Corynebacterium suggests that small-subunit ribosomal DNA sequence analysis is probably the most straightforward method for confirming that a bacterium belongs to this genus. (nih.gov)
  • The wild type ebg operon has been sequenced, and the sequence differences of the mutant enzymes and repressors have been determined. (genetics.org)
  • Although three varieties within a single species can be distinguished for each varietal level by ITS sequence analysis, the distinction is based on differences of only three or four nucleotides ( 20 ). (asm.org)
  • 2017). This study identified differences in the DNA extraction method as the biggest influence on the downstream gut microbiota analysis results. (bio-protocol.org)
  • At most, six nucleotide differences were observed among the sequences of the F. tularensis strains. (microbiologyresearch.org)
  • Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations. (biomedcentral.com)
  • We have developed a method for the partial automation of DNA sequence analysis. (nih.gov)
  • The associated software (RepeatFinder), should prove helpful in the analysis of repeat structure for both complete and partial genome sequences. (jcvi.org)
  • The other LCR-related ORFs are interspersed among three intact insertion sequence (IS) elements (IS 100 and two new IS elements, IS 1616 and IS 1617 ) and numerous defective or partial transposable elements. (pubmedcentralcanada.ca)
  • Our results suggest that analysis of IGS regions provides a powerful method to distinguish between phylogenetically closely related species and that a geographic substructure may exist among T . asahii clinical isolates. (asm.org)
  • we accept a wide range of biological and clinical samples including genomic DNA, cells, tissues, formalin-fixed and paraffin-embedded samples. (creativebiomart.net)
  • Whether performing reference-guided alignments, de novo assembly, variant calling, or SNP analyses, Sequencher has the tools you need to get results. (genecodes.com)
  • On the basis of PCR and DNA sequencing, 6 new D. nodosus isolates were identified and characterized from NZ. (lincoln.ac.nz)
  • Send primer pair sequences from Primer-BLAST runs in Sequencher Connections to your Sequencher project. (genecodes.com)
  • You won't see the first section of sequence, but if it is short enough, you can see both ends by sequencing twice, once with each primer. (protocol-online.org)
  • Primer pairs LPR1/LPR2 and LPR3/LPR4 designed to detect LPV regulatory region sequences are given in Table 1 . (asm.org)
  • PCR analysis of PBMC DNA with primer pair LPR3/LPR4 yielded a robust PCR-amplified band that was estimated to be about 550 bp in size from the K661 lane A sample, but not from the other samples (Fig. 2 ). (asm.org)
  • We also identified five genotypes of T . asahii , which is a major causative agent of deep-seated trichosporonosis, based on the IGS 1 sequences of 43 strains. (asm.org)
  • The 16S ribosomal DNAs (rDNAs) of two strains of Francisella tularensis and one strain of Francisella philomiragia were sequenced. (microbiologyresearch.org)
  • Two variable regions, comprising 390 to 450 nucleotides of the 16S rDNA molecules of 17 additional Francisella strains, including members of the species F. tularensis and F. philomiragia , were also sequenced. (microbiologyresearch.org)
  • The sequence of Francisella novicida was virtually identical to the sequences of the F. tularensis strains, thereby supporting the hypothesis that these organisms are members of the same species. (microbiologyresearch.org)
  • Alignment-based approaches generally give excellent results when the sequences under study are closely related and can be reliably aligned, but when the sequences are divergent, a reliable alignment cannot be obtained and hence the applications of sequence alignment are limited. (wikipedia.org)
  • Evidence suggests that massively parallel sequencing analysis of ctDNA from patients with advanced disease allows for the identification of the entire constellation of somatic mutations found in cancer cells, either from the primary tumor or from metastatic lesions. (ascopost.com)
  • Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus . (peerj.com)
  • Circulating tumor DNA (ctDNA) in plasma comprises a fraction of cfDNA, and is believed to be shed in the bloodstream by cancer cells through apoptosis, necroptosis, or secretion (eg, exosomes) not only from the primary tumor, but also metastatic lesions and minimal residual disease. (ascopost.com)
  • As the amount of ctDNA in cfDNA varies (and is often low in patients with low tumor burden), de novo discovery of mutations by plasma DNA analysis is not trivial. (ascopost.com)
  • Whether sequencing of ctDNA will render tumor biopsies redundant remains to be determined, particularly because of the strong association between ctDNA yield and disease burden and the technologic and bioinformatic developments required for de novo discovery of mutations based solely on ctDNA analysis. (ascopost.com)