• We defined a core genome multilocus sequence typing scheme comprising 2,038 loci and demonstrated its congruence with whole-genome single-nucleotide polymorphism variation. (cdc.gov)
  • Whole-genome sequencing (WGS) provides the highest possible resolution of genetic differences among individual isolates. (cdc.gov)
  • Even the best short read whole genome sequences aren't whole. (jax.org)
  • Whole-genome sequencing (WGS) is a laboratory procedure that determines the order of all or most of the nucleotides in the genome of these disease-causing microbes, enabling public health officials to better understand how microorganisms move through populations and change over time. (cdc.gov)
  • How does whole-genome sequencing work? (cdc.gov)
  • Why is whole-genome sequencing important to public health? (cdc.gov)
  • Whole-genome sequencing provides detailed genetic information about pathogens, which are microbes that cause illnesses. (cdc.gov)
  • DeepVariant is designed for use as a germline variant caller that can apply different models trained for specific sample types (such as whole genome and whole exome samples) to yield higher accuracy results. (nvidia.com)
  • So, scientists use single-cell whole-genome sequencing to identify copy number variations and single-nucleotide variations within single cells, [2] . (wearecellix.com)
  • Current efforts to understand antibiotic resistance on the whole genome scale tend to focus on known genes even as high throughput sequencing strategies uncover novel mechanisms. (datadryad.org)
  • Trust and the ethical challenges in the use of whole genome sequencing for tuberculosis surveillance: a qualitative study of stakeholder perspectives. (cdc.gov)
  • Should pretest genetic counselling be required for patients pursuing genomic sequencing? (nih.gov)
  • We assessed the decision-making of individuals pursuing genomic sequencing without a requirement for pretest genetic counselling. (nih.gov)
  • We sought to describe the extent to which individuals who decline genetic counselling reported decisional conflict or struggled to make a decision to pursue genomic testing. (nih.gov)
  • As genomic sequencing is used more widely, genetic counselling resources may not be sufficient to meet demand. (nih.gov)
  • Our results challenge the notion that all individuals need genetic counselling in order to make an informed decision about genomic sequencing. (nih.gov)
  • The genome, or genetic material, of an organism is made up of a unique DNA or RNA sequence. (cdc.gov)
  • Next-generation sequencing (NGS) refers to sequencing technologies that can process a large quantity of genetic material at a time. (cdc.gov)
  • Via genome sequencing of both lung transplant recipients and donors, we examine genetic ancestral markers that are associated with graft rejection and dysfunction. (nih.gov)
  • Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
  • Linkage maps are valuable tools in genetic and genomic studies. (rosaceae.org)
  • To understand the genetic epidemiology of C. auris infection both within this hospital and within a global context, we sequenced the outbreak isolate genomes using Oxford Nanopore Technologies and Illumina platforms to detect antifungal resistance alleles and reannotate the C. auris genome. (ox.ac.uk)
  • Genetic diversity, population structure, and relationships of apricot (Prunus) based on restriction site-associated DNA sequencing. (the-mwg.com)
  • A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds. (animbiosci.org)
  • Contrastingly, the other five breeds (Yantai, Licha, Yimeng, Wulain, and Heigai) displayed high genetic diversity within breed and had some extent of mixture pattern with the Western commercial breeds, especially Duroc and Landrace ( F ST values from 0.1043 to 0.2536). (animbiosci.org)
  • Because these approaches will rely on novel data types such as DNA sequences and high-throughput phenotyping images, Breeding 4 will call for analyses that are complementary to traditional quantitative genetic studies, being based on machine learning techniques which make efficient use of sequence and image data. (springer.com)
  • GCS also uses expertise to identify specific genes and studies, as well as extensive sequencing genomics to explore how the variants may genetic profiles that contribute to the work. (who.int)
  • High genetic diversity of Plasmodium falciparum in the low transmission setting of the Kingdom of Eswatini. (cdc.gov)
  • Using targeted next-generation sequencing to characterize genetic differences associated with insecticide resistance in Culex quinquefasciatus populations from the southern U.S. (cdc.gov)
  • Our understanding of the landscape of pediatric cancer genomics has improved markedly in the past 20 years with the advent of next generation sequencing and other high throughput genetic sequencing. (medscape.com)
  • Transposable elements (TEs) are mobile genetic sequences that comprise around 50% of our genomic DNA. (lu.se)
  • Core genome MLST (cgMLST), using the set of genes conserved among isolates of a given bacterial group, represents an approach that combines the high resolution of genome-level variation and the high reproducibility and portability of MLST ( 14 ). (cdc.gov)
  • WormBase offers many ways of searching and retrieving data from the database: WormMart, Wiki - was a tool for retrieving varied information on many genes (or the sequences of those genes). (wikipedia.org)
  • Genome Browser - browse the genes of C. elegans (and other species) in their genomic context Textpresso - a search tool that queries published C. elegans literature (including meeting abstracts) and a subset of nematode literature. (wikipedia.org)
  • No exome-sequenced TMD/AMKL sample had other recurrently mutated genes. (unige.ch)
  • Furthermore, we discuss recent findings on EBV associated gastric carcinogenesis by focusing on the roles of latent genes, epigenetic abnormalities, genomic alterations, and post-transcriptional regulation by cellular and viral microRNAs (miRNAs). (spandidos-publications.com)
  • When applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq demonstrated a 12- to 32-fold increase in the discovery of differentially spliced genes. (nature.com)
  • The wide availability of vectors and sticky ends allows enough versatility to combine more than four different promoters, genes of interest, and terminator sequences. (bvsalud.org)
  • These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species. (rosaceae.org)
  • Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark (H3K4me2) in brain. (gsea-msigdb.org)
  • Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. (peerj.com)
  • Alleles of the latter three genes are tightly linked among most sequenced E. coli genomes, and had not been implicated in antibiotic resistance previously. (datadryad.org)
  • Our experimental strategy shows that long-range genomic PCR followed by UHTs provides an excellent system to perform a thorough screening of candidate genes for hereditary retinal degeneration. (molvis.org)
  • A common approach to the mutational screening of candidate genes consists of sequencing their exons and immediate intron boundaries. (molvis.org)
  • However, since pathogenic mutations can sometimes be located deep within introns, as was recently shown for retinal degeneration genes as well [ 7 , 8 ], we decided to analyze the full MDH1 sequence. (molvis.org)
  • SNPs or single nucleotide polymorphisms are on many scientist's wish list in experimental studies of genomic DNA sequences. (bitesizebio.com)
  • Now with the availability of high throughput sequencing methods, also known as next generation sequencing (NGS), SNPs can be identified in the large amounts of DNA sequence that is generated. (bitesizebio.com)
  • Hinrichsen P. Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). (rosaceae.org)
  • Guajardo V, Solís S, Sagredo B, Gainza F, Muñoz C, Gasic K, Hinrichsen P. Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). (rosaceae.org)
  • For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. (rosaceae.org)
  • Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. (rosaceae.org)
  • A total of 8,476 high quality SNPs were selected for mapping. (rosaceae.org)
  • Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphism and is widely used in population genetics research. (the-mwg.com)
  • we sequenced genomic DNA from pools of E. coli clinical isolates with similar antibiotic resistance phenotypes using SOLiD technology to uncover SNPs unanimously conserved in each pool. (datadryad.org)
  • Single nucleotide polymorphisms (SNPs) that result in non-synonymous changes in gyrA (encoding the well-known S83L allele associated with fluoroquinolone resistance), mutM, ligB, and recG were unanimously conserved in every fluoroquinolone-resistant pool. (datadryad.org)
  • Discrimination of RNA editing sites from genome-encoded single-nucleotide polymorphism (SNPs) is known to be one of the main challenges in identifying RNA editing sites. (um.edu.my)
  • When we filtered the putative RNA editing sites identified through genome sequence-independent and sequence-dependent approaches with the Single Nucleotide Polymorphism Database (dbSNP), 71% and 10% of known SNPs were found, respectively. (um.edu.my)
  • Hence, suggesting that DNA-Seq information from the same individual may possibly reduce the chances of novel and rare genomic variants (SNPs) being interpreted as RNA editing events. (um.edu.my)
  • We review traditional survival methods and regularization methods, with various penalty functions, for the analysis of high-dimensional genomics, and describe machine learning techniques that have been adapted to survival analysis. (genominfo.org)
  • PFGE achieves some level of resolution given the high structural dynamics of B. pertussis genomes, driven by insertion sequence elements dynamics ( 12 ), and is more discriminatory than MLVA or MLST. (cdc.gov)
  • Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota , the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum . (nature.com)
  • Agricultural biotechnology involves the handling of complex plant genomes and this needs complex instrumentation especially as several projects are underway to sequence the genomes of wheat, banana and beans. (biotecharticles.com)
  • Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
  • The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. (peerj.com)
  • We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013-2014 by ARSP. (who.int)
  • Recently, high-depth transcriptome sequencing approach (RNA-Seq) has enabled the identification of editing events without depending on the genomic sequences. (um.edu.my)
  • Until now, strain genotyping for surveillance and epidemiology has been based mostly on pulsed-field gel electrophoresis (PFGE), antigen and virulence factor genotyping, 7-gene multilocus sequence typing (MLST), or multilocus variable-number tandem-repeat analysis (MLVA) ( 9 - 11 ). (cdc.gov)
  • Since 2014, the Advanced Molecular Detection (AMD) program has worked to integrate the latest next-generation sequencing technology with bioinformatics and epidemiology expertise to improve public health. (cdc.gov)
  • Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris. (ox.ac.uk)
  • Epidemiology Group (GEP) is to including in silico, expression, and work over the 2016-2017 biennium are contribute to understanding the causes sequencing studies, which are often described here. (who.int)
  • ARSP) has been capturing information on resistant gonorrhoea since 1996, but genomic epidemiology studies on this pathogen are lacking in the Philippines. (who.int)
  • On the other hand, using low coverage sequencing might provide a better picture of the population's variation, but then again, it will have much higher uncertainties and errors. (bitesizebio.com)
  • It works by taking aligned sequencing reads in BAM/CRAM format and utilizes a convolutional neural network (CNN) to classify the locus into true underlying genomic variation or sequencing error. (nvidia.com)
  • With the development of high throughput technologies such as tandem mass spectrometry (MS/MS) and next generation sequencing, more and more nonsynonymous single-nucleotide variations (nsSNVs) that cause variation of amino acids have been identified, some of which result in the damage of PTMs. (hindawi.com)
  • Among the pools of clinical isolates, genomic variation was concentrated adjacent to previously reported inversion and duplication differences between the SMS-3-5 isolate and the drug-susceptible laboratory strain, DH10B. (datadryad.org)
  • Sequence curation at WormBase refers to the maintenance and annotation of the primary genomic sequence and a consensus gene set. (wikipedia.org)
  • this helps in the confirmation and evidence for the gene model as WormBase routinely retrieve sequence data from these public databases. (wikipedia.org)
  • With the development of high-throughput sequencing technology, gene mutation detection has become another important resource to investigate regulatory mechanisms and cellular processes. (hindawi.com)
  • Either at genomic or at proteomic level, mutations have significant impact on normal gene or protein function, and human diseases could be associated with mutations like nonsynonymous single-nucleotide variations (nsSNVs) on amino acids. (hindawi.com)
  • It requires both a Fasta file containing the nucleotide sequences of the genome and GTF file providing information about gene annotation and genomic features. (constellab.community)
  • Because of their role in genomic instability and gene amplification in some human cancers, it is important to develop systematic approaches to detect and characterize DNA palindromes. (biomedcentral.com)
  • Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. (peerj.com)
  • RNA editing is an enzyme-mediated transcriptional alteration mechanism in eukaryotic cells that changes the sequences of primary RNA transcripts through nucleotide modification, insertion or deletion which leads to the diversification of gene products. (um.edu.my)
  • As a proof of concept for candidate gene screening to be routinely performed by ultra high throughput sequencing (UHTs), we analyzed MDH1 in a patient from each of the two families described so far to show linkage between arRP and RP28 . (molvis.org)
  • With genomic long-range PCR, we amplified all introns and exons of the MDH1 gene (23.4 kb). (molvis.org)
  • GEN also tries in driving cancer incidence, and also to provides a facility for high-throughput to identify individuals who are at high facilitate accurate assessment of gene- genomic techniques and the related enough risk that they are likely to benefit environment interactions. (who.int)
  • [ 16 ] More commonly, a low gene copy number of C4 is seen as a risk factor for SLE, whereas a high copy number of C4 is protective against SLE. (medscape.com)
  • Full-length RNA-sequencing methods using long-read technologies can capture complete transcript isoforms, but their throughput is limited. (nature.com)
  • On the other hand, if you are dealing with medium and low coverage sequencing data, you might want to use probabilistic or Bayesian methods to avoid undercalling of heterozygous genotypes. (bitesizebio.com)
  • Residual amounts of amplified genomic DNA are minimized and do not interfere with mitochondrial-specific downstream methods such as qPCR or direct Sanger sequencing. (qiagen.com)
  • Due to its high processivity and strand displacement activity, REPLI-g DNA Polymerase is capable of amplifying up to 100 kb without dissociating from the DNA template and minimizes unequal sequence and locus representation compared with PCR-based amplification methods. (qiagen.com)
  • Existing methods for measuring transcript levels in single cells include RT-qPCR (1), single molecule counting using digital PCR (2) or hybridization probes (3, 4), and next generation sequencing (5). (justia.com)
  • However, with the development of high-throughput technologies for producing "omics" data, more advanced statistical methods, such as regularization, should be required to construct the predictive survival model with high-dimensional genomic data. (genominfo.org)
  • DNA quality underpins success of GBS methods as the DNA must be amenable to restriction enzyme digestion and sequencing. (pacb.com)
  • A barrier to implementing GBS technologies is access to inexpensive, high-throughput extraction methods that yield sequencing-quality genomic DNA (gDNA) from plants. (pacb.com)
  • Several high-throughput DNA extraction methods are available, but typically provide low yield or poor quality gDNA, or are costly (US$6-$9/sample) for consumables.We modified a non-organic solvent protocol to extract microgram quantities (1-13 µg) of sequencing-quality high molecular weight gDNA inexpensively in 96-well plates from either fresh, freeze-dried or silica gel-dried plant tissue. (pacb.com)
  • However, these studies would not detect palindromes due to the instability of palindromes in BAC clones and the inability of the methods used to directly sequence palindromes. (biomedcentral.com)
  • The work presented in this thesis focuses on the bioinformatic methods for a TE-centric analysis of next- and third-generation sequencing technologies. (lu.se)
  • Relatively fast, inexpensive and accurate, short read sequencing (technically known as high throughput massively parallel sequencing) requires breaking the genome into millions of short-250 bases, plus or minus-segments for sequencing and then reassembling them to generate the full sequence. (jax.org)
  • Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. (memberclicks.net)
  • Single-molecule reads that span the entire genome can capture species without an existing reference sequence as well as detect variants within a particular species. (jax.org)
  • The more frequently a base is sequenced, the higher the coverage of the reads, and the higher the reliability as well. (bitesizebio.com)
  • I almost forgot to mention that you could also get your hands on data with high sensitivity and high specificity, by combining information from the initial alignment with the local short reads you have generated from scratch ( de novo assembly). (bitesizebio.com)
  • By combining these files, STAR constructs an index that allows for rapid identification of potential alignments between the sequencing reads and the reference genome. (constellab.community)
  • Contrasting with other extraction protocols we assessed, Illumina-based sequencing of GBS libraries developed from this gDNA had very uniform high quality base-calls to the end of sequence reads. (pacb.com)
  • Despite the intrinsic complexity of human genome sequences, reads were easily mapped and analyzed, and all algorithms used provided the same results. (molvis.org)
  • This enables poorly resourced or "orphan" crops/species access to high-density, high-throughput marker platforms which have revolutionised population genetics studies and plant breeding. (pacb.com)
  • We set up a publicly accessible core genome multilocus sequence typing database to enable global comparisons of B. pertussis isolates, opening the way for internationally coordinated surveillance. (cdc.gov)
  • The multilocus sequence type, multiantigen sequence type, presence of determinants of antimicrobial resistance and relatedness among the isolates were all derived from the sequence data. (who.int)
  • Despite the small number of isolates studied, they were genetically diverse, as shown by the sequence types, the N. gonorrhoeae multiantigen sequence typing types and the tree. (who.int)
  • This first genomic survey of N. gonorrhoeae isolates collected by ARSP will be used to contextualize prospective surveillance. (who.int)
  • ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. (lu.se)
  • Exome sequencing identifies putat. (unige.ch)
  • We performed exome sequencing in 7 TMD/AMKL cases and copy-number analysis in these and 10 additional cases. (unige.ch)
  • Other improvements have come from comparing genomic DNA to cDNA sequences and analysis of RNASeq high-throughput data. (wikipedia.org)
  • When differences between the genomic sequence and transcripts are identified, re-analysis of the original genomic data often leads to modifications of the genomic sequence. (wikipedia.org)
  • Genomic analysis indicates that SARS-CoV-2 is most related to RaTG13, a beta corona virus derived from bats by 96% 1 . (preprints.org)
  • Here, we develop a specialized target‐capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. (researchgate.net)
  • Unfortunately, such devices do not allow for high throughput analysis due to the manual effort involved in operating the valving mechanisms. (justia.com)
  • Although these systems provide a high-throughput qPCR readout, they do not address the front end sample preparation and require single cell isolation by FACS or micropipette followed by off-chip processing and pre-amplification of starting template prior to analysis. (justia.com)
  • Analysis of mutated target sequences and human genomic DNA reveal that Cascade recognizes an extended protospacer adjacent motif (PAM). (finkelsteinlab.org)
  • CHAMP provides a framework for high-throughput, quantitative analysis of protein-DNA interactions on synthetic and genomic DNA. (finkelsteinlab.org)
  • Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. (gsea-msigdb.org)
  • He has made a significant impact on bioinformatics and biological interpretation of research involving analysis of DnaseI hypersensitive sites, digital genomic footprinting, and comparative enrichment analysis. (cancer.gov)
  • Recently, I have developed a highly sophisticated algorithm for identifying short genomic regions (footprints) which enable analysis of transcriptional activities at the nucleotide resolution. (cancer.gov)
  • The algorithm has been implemented in Dnase2TF, a public domain software platform used by many biology groups for high-throughput analysis of digital genomic footprinting. (cancer.gov)
  • His Ph.D. studies focused on statistical analysis of high-dimensional data. (cancer.gov)
  • Also, sequence analysis requires systems for handling fluids and mixing the reagents introduced onto the chip. (wearecellix.com)
  • Microfluidic devices can potentially increase DNA analysis throughput since they handle fluid volumes quickly and precisely. (wearecellix.com)
  • Droplet generation offers a cost-effective and high-throughput analysis. (wearecellix.com)
  • Conventionally, both genomic and transcriptomic sequences are required for analysis. (um.edu.my)
  • From the analysis, more editing events were detected using the genomic sequence-independent method (based on RNA sequences alone). (um.edu.my)
  • Aluru S. High throughput ANI analysis of 90K prokaryotic cases. (cdc.gov)
  • We administered a 100-item survey to 3037 individuals who consented to the Return of Actionable Variants Empirical study, a genomic medicine implementation study supported by the National Institutes of Health (USA) eMERGE consortium. (nih.gov)
  • SIRVs: spike-in RNA variants as external isoform controls in RNA-sequencing. (nature.com)
  • We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. (nature.com)
  • DeepVariant can therefore call single nucleotide variants (SNVs) and insertions/deletions (InDels) from sequencing data at high accuracy in germline samples. (nvidia.com)
  • It offers several advantages over similar tools, including its ability to detect a wide range of variants with high accuracy, its scalability for analyzing large datasets, and its open source availability. (nvidia.com)
  • The T2T (telomere-to-telomere) consortium announced in late March 2022 that it had generated the first complete, gapless sequence of a human genome. (jax.org)
  • The first "complete" human genome sequence was actually complete only in terms of what researchers could achieve with the technology available at that time. (jax.org)
  • Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. (nature.com)
  • See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)
  • Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature. (peerj.com)
  • In this study, both genomic sequence-dependent and genomic sequence-independent approaches were used to identify RNA editing sites present in human primary monocytes from a healthy individual. (um.edu.my)
  • As far as we know, this is the first study that utilized both genomic-dependent and genomic-independent sequence approaches to identify RNA editing sites using high-depth genomic and transcriptomics datasets. (um.edu.my)
  • The original reference genome sequence, as well as my own, was generated using short read sequencing technology. (jax.org)
  • They vary depending on whether you are interested in germline or somatic mutations, However, they generally align sequences back to a reference genome and make calls depending on the probability parameters you set. (bitesizebio.com)
  • STAR facilitates efficient and accurate mapping of high-throughput sequencing data to a reference genome. (constellab.community)
  • Of these, single cell RT-qPCR provides combined advantages of sensitivity, specificity, and dynamic range, but is limited by low throughput, high reagent cost, and difficulties in accurately measuring low abundance transcripts (6). (justia.com)
  • Further assessing nuclei acid quality of these FFPE samples through gDNA/RNA amplifiability by qPCR and artifactual mutation occurring during FFPE tissue preparation by NGS library sequencing. (memberclicks.net)
  • What can you do with Next Generation Sequencing? (utmb.edu)
  • Some next-generation sequencing devices read fluorescent signals. (cdc.gov)
  • In this Review, we discuss the issue of sequencing depth in the design of next-generation sequencing experiments. (ox.ac.uk)
  • Here, we describe a chip-hybridized association-mapping platform (CHAMP) that repurposes next-generation sequencing chips to simultaneously measure the interactions between proteins and ∼10^7 unique DNA sequences. (finkelsteinlab.org)
  • The recent development of next-generation sequencing DNA marker technologies, such as genotyping-by-sequencing (GBS), generates thousands of informative single nucleotide polymorphism markers in almost any species, regardless of genomic resources. (pacb.com)
  • The protocol is scalable, readily automated without requirement for fume hoods, requires approximately three hours to process 192 samples (384-576 samples/day), and is inexpensive at US$0.62/sample for consumables.This versatile, scalable and simple protocol yields high molecular weight genomic DNA suitable for restriction enzyme digestion and next-generation sequencing applications including GBS and long-read sequencing platforms such as PacBio. (pacb.com)
  • Newer sequencing platforms have revolutionized this field, by generating larger volumes of data and dramatically lowering the cost of sequencing. (cdc.gov)
  • Additionally, its deep learning-based approach allows it to provide better support for different sequencing platforms, as it can be retrained to provide higher accuracy for specific protocols or research areas. (nvidia.com)
  • At another level the LEADS computational biology platform or other similar platforms are used for enabling semantic integration of protein sequences. (biotecharticles.com)
  • Here we report genome sequences and analyses of 44 diploid potatoes, as well as 2 species in the Etuberosum section. (nature.com)
  • Sequencing depth and coverage: key considerations in genomic analyses. (ox.ac.uk)
  • Sequencing technologies have placed a wide range of genomic analyses within the capabilities of many laboratories. (ox.ac.uk)
  • After 4 weeks of conversion, we performed global analyses of RNA and protein levels by RNA-sequencing and mass spectrometry. (lu.se)
  • Many of these changes were single nucleotide insertions or deletions, however several large mis-assemblies have been uncovered. (wikipedia.org)
  • This method allowed identifying cells with pathogenic mutations during complete remission and revealed complex clonal evolution within acute myeloid leukemia (AML) tumours that were not observable with traditional sequencing, [3] . (wearecellix.com)
  • Therefore, we reasoned that MDH1 could correspond to the RP28 locus, and mutations in its sequence could be responsible for the disease in a manner similar to that of pathogenic changes in IDH3B . (molvis.org)
  • We show that human and chimpanzee cells differentiate in a similar man¬ner and that the difference in interspecies protein abundance is higher than transcript-level differences, suggesting that post-transcriptional mechanisms play a role in the difference between human and chim¬panzee brain development. (lu.se)
  • Analytical programs compare the new sequence data to the reference sequence and identify variations in the sample that allow scientists to infer an ancestral relationship, much like a family tree. (cdc.gov)
  • Traditional sequencing is often unable to point out minor variations in the genome. (wearecellix.com)
  • Genome scans using dense single-nucleotide polymorphism (SNP) data have recently become a reality. (harvard.edu)
  • The consortium has assembled a premier group of scientists that focus their activities on the molecular mechanisms that underlie ageing, with an emphasis on how maintenance of genomic integrity in self-renewing tissues is preserved under different metabolic rates. (umcg.nl)
  • Long read sequencing technologies haven't pushed aside short read sequencing or Illumina, the largest company in the field, as some predicted back then, but they are now being applied to a wider range of research applications. (jax.org)
  • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible seventh pandemic El Tor sublineage AFR15, indicating trimmer for Illumina sequence data. (cdc.gov)
  • Fig. 2: Single-cell isoform-resolved sequencing of primary human CD8 + T cells with MAS-ISO-seq. (nature.com)
  • Human tumor-infiltrating CD8 + T cells single-cell RNA-sequencing data are available from dbGAP with accession number phs003200.v1.p1 . (nature.com)
  • Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. (nature.com)
  • Sequencing coverage refers to the average number of times a single base is read during a sequencing experiment. (bitesizebio.com)
  • High-throughput single cell measurement technologies are therefore of interest and have broad applications in clinical and research settings. (justia.com)
  • Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. (gsea-msigdb.org)
  • Researchers can use the microfluidics approach to obtain high throughput and scalable single-cell sequencing. (wearecellix.com)
  • SPAdes: a new genome ing 1970, and the related cholera strain, Vibrio choler- assembly algorithm and its applications to single-cell ae O1 biotype El Tor (7PET), has since become endemic sequencing. (cdc.gov)
  • In these studies, upwards of a million single-nucleotide polymorphisms are typed in each individual. (medscape.com)
  • With high coverage sequencing data, you could simply ignore the low-quality alleles and count only the high-quality alleles that you come across. (bitesizebio.com)
  • These technologies have been available since 2004, and they have largely replaced the previous method ("Sanger sequencing") and make high-throughput WGS possible. (cdc.gov)
  • An overview of bioinstrumentation including its application in diverse areas such as agriculture, botany, and cellular and molecular biology especially with reference to microarrays, sequencing technologies, and lab automation technologies. (biotecharticles.com)
  • In this article we intend to discuss mostly about bioinstrumentation as applicable to agriculture, botany, and cellular and molecular biology especially with reference to microarrays, sequencing technologies, and lab automation technologies. (biotecharticles.com)
  • The process of plant tissue culture involves making plants or clones of plants under sterile conditions and this needs refined and higher resolution technologies. (biotecharticles.com)
  • The advancements of high-throughput sequencing technologies have resulted in the identification of significant numbers of RNA editing sites. (um.edu.my)
  • Evaluate equivalence of routine and difficult Sanger Sequencing templates using a variety of legacy and new-to-market reagents. (memberclicks.net)
  • 2) Provide guidance to ABRF Sanger Sequencing facilities with regard to feasibility of modifying existing dye terminator chemistry protocols to further cost-savings potential. (memberclicks.net)
  • The changes in the genomic sequence pose difficulties when comparing chromosomal coordinates of data derived from different releases of WormBase. (wikipedia.org)
  • The sequencer produces data-millions of long strings of letters-which are then assembled together or aligned with a reference sequence. (cdc.gov)
  • This means that you have to get high quality NGS data, which requires careful library preparation (including DNA size selection ) to obtain. (bitesizebio.com)
  • Then again, you are not going to let that stop you from getting your hands on the high-quality data sets, are you? (bitesizebio.com)
  • By using high coverage sequence data, you will get more specific variant calls and genotype estimations. (bitesizebio.com)
  • DeepVariant is a deep learning based variant caller developed by Google for germline variant calling of high-throughput sequencing data. (nvidia.com)
  • Here, the high-throughput sequencing is used to test the genome-level diversity, population structure, and relationships apricots, which are important for the conservation of germplasm and molecular breeding. (the-mwg.com)
  • HIV-1 DNA sequence diversity and evolution during acute subtype C infection. (cdc.gov)
  • It will be even more vital should a variant with high virulence and/or non-responsiveness to current vaccines arise. (jax.org)
  • The extracted DNA was of high molecular weight and digested readily with restriction enzymes. (pacb.com)
  • The key aim of this training program is the elucidation of the molecular pathway by which intrinsic genomic integrity can be modified by the extrinsic rate of metabolism. (umcg.nl)
  • RNA (total, poly A+ and miRNA), chromatin immunoprecipitated DNA (ChIP-Seq) and DNA (genomic and amplicon-derived). (utmb.edu)
  • The higher risk of SLE in women and men with Klinefelter syndrome may be associated with enhanced expression of toll-like receptor 7 (TLR7), a key pathogenic factor in SLE that is encoded on an X chromosome locus. (medscape.com)
  • It highlights the importance of genomic surveillance in the Western Pacific and other endemic regions for understanding the spread of drug-resistant gonorrhoea worldwide. (who.int)
  • The new "spider‐specific" probes were used to sequence UCE loci in 51 specimens. (researchgate.net)
  • More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine. (gsea-msigdb.org)
  • ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. (peerj.com)
  • It enables researchers to generate and manipulate droplets using microfluidic pumps producing tiny droplets at high speed, [3] . (wearecellix.com)
  • New pathogens can be identified by comparing their sequence to a database of all known pathogens and finding related species. (cdc.gov)
  • We developed a new protocol to identify palindromes that couples the S1 nuclease treated Cot0 DNA (GAPF) with high-throughput sequencing (GAP-Seq). (biomedcentral.com)
  • Costs are reduced by indexing ("bar coding") individual template libraries, allowing multiple libraries to be sequenced in each of the flow cell lanes. (utmb.edu)
  • Palindromes are also underrepresented in high-throughput sequencing results generated from libraries constructed by PCR amplification or sequencing steps that involve emulsion PCR amplification (Yang H. et al. (biomedcentral.com)
  • Long read sequencing has long been important for sequencing microbes. (jax.org)
  • an early onset and a high frequency of bilateral disease characterize these cases. (medscape.com)
  • However, due to limited research budgets…*looks at the wallet* *sigh*, forcing yourself to obtain high coverage will result in sequencing fewer samples. (bitesizebio.com)
  • The REPLI-g Mitochondrial DNA Kit overcomes this limitation by enriching for mitochondrial DNA sequences in total DNA samples. (qiagen.com)