Nanopores to sequence. Medical search. Frequent questions

Whole genome sequencing (Oxford Nanopore R9.4) of Escherichia coli UT. (nih.gov)
To help solve these cases, the program will perform whole-genome sequencing and methylation analysis using Oxford Nanopore's highest-throughput sequencing device for rapid results, the company said. (genomeweb.com)
However, compared to other flaviviruses, USUV has received less research attention and there is therefore limited access to whole-genome sequences and also to in-depth phylogenetic and phylodynamic analyses. (frontiersin.org)
Mycobacterium tuberculosis whole-genome sequencing (WGS) has been widely used for genotypic drug susceptibility testing (DST) and outbreak investigation. (ox.ac.uk)
Dadurch können über Multiplexing Protokolle viele Proben auf einmal bearbeitet werden, wodurch die Kosten deutlich geringer sind als bei Whole Genome Sequencing Protokollen. (hhu.de)
They were able to sequence the whole genome and confirm that the bacteria did not carry genetic markers for antibiotic resistance or evidence of genetic engineering in only 8.5 hours. (cdc.gov)
Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. (lu.se)
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. (cdc.gov)
Analysis of Treponema pallidum strains from China using improved methods for whole-genome sequencing from primary syphilis chancres. (cdc.gov)
SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission. (cdc.gov)

2 dozen ventional next-generation sequencing platform (Illumina, diagnostic laboratories, has been equally unprecedented. (cdc.gov)
To ease future molecular studies, this study compares first- (partial sequencing via Sanger), second- (Illumina), and third-generation (MinION Nanopore) sequencing platforms for USUV. (frontiersin.org)
We concluded that depending on the focus of a research project, amplicon-based MinION Nanopore sequencing can be an ideal cost- and time-effective alternative to Illumina in producing optimal genome coverage. (frontiersin.org)
Illumina sequencers) is necessary to evaluate nanopore data and understand its benefits and limitations. (gla.ac.uk)
The aim of this study was to determine whether Nanopore sequencing data can provide equivalent information to Illumina for transmission clustering and genotypic DST for M tuberculosis. (ox.ac.uk)
In this genomic analysis, we analysed 151 M tuberculosis isolates from Madagascar, South Africa, and England, which were collected between 2011 and 2018, using phenotypic DST and matched Illumina and Nanopore data. (ox.ac.uk)
Illumina sequencing was done with the MiSeq, HiSeq 2500, or NextSeq500 platforms and Nanopore sequencing was done on the MinION or GridION platforms. (ox.ac.uk)
We then used those SNPs to compare transmission clusters identified by Nanopore with the currently used UK Health Security Agency Illumina pipeline (COMPASS). (ox.ac.uk)
We compared Illumina and Nanopore WGS-based DST predictions using the Mykrobe software and mutation catalogue. (ox.ac.uk)
The Nanopore BCFtools pipeline identified SNPs with a median precision of 99·3% (IQR 99·1-99·6) and recall of 90·2% (88·1-94·2) compared with a precision of 99·6% (99·4-99·7) and recall of 91·9% (87·6-98·6) using the Illumina COMPASS pipeline. (ox.ac.uk)
Illumina-based clusters were also closely replicated using a five SNP threshold and clustering accuracy was maintained using mixed Illumina and Nanopore datasets. (ox.ac.uk)
Genotyping resistance variants with Nanopore was highly concordant with Illumina, having zero discordant SNPs across more than 3000 SNPs and four insertions or deletions (indels), across 60 000 indels. (ox.ac.uk)
Illumina and Nanopore technologies can be used independently or together by public health laboratories performing M tuberculosis genotypic DST and outbreak investigations. (ox.ac.uk)
Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiological diagnostic techniques. (ox.ac.uk)
Here, we report a real-time analytical pathway for Nanopore sequence data, designed for detecting bacterial composition of prosthetic joint infections but potentially useful for any microbial sequencing, and compare detection by direct-from-clinical-sample metagenomic nanopore sequencing with Illumina sequencing and standard microbiological diagnostic techniques. (ox.ac.uk)

Daniel Branton , Harvard's Higgins Professor of Biology, Emeritus, and his collaborators David Deamer and Mark Akeson at the University of California, Santa Cruz, are among the 2023 Golden Goose Award winners for their invention and research developing Nanopore Sequencing . (harvard.edu)
To share about the workflows and (foodborne) pathogen detection in general, we organize a 1-day hybrid (F2F at FHNW Muttenz, Switzerland and online), free and practical workshop on February 2nd, 2023 to learn how to detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy, an open-source platform for FAIR data analysis . (galaxyproject.org)

They applied their approach to individual bacteria and the mouse gut genome, as well as demonstrate a method for nanopore sequencing-based methylation binning of metagenomic contigs, associating mobile genetic elements with their host genomes, and identifying misassembled metagenomic contigs. (genomeweb.com)
We believe that nanopore metagenomic sequencing can have a significant impact as a diagnostic tool in patients with suspected bacterial RTI. (ersjournals.com)
Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices. (ox.ac.uk)
CONCLUSIONS: We demonstrate a novel, scalable pipeline for real-time analysis of MinION sequence data and use of this pipeline to show initial proof of concept that metagenomic MinION sequencing can provide rapid, accurate diagnosis for prosthetic joint infections. (ox.ac.uk)
For example, rapid metagenomic identification of viral pathogens in clinical samples can be accomplished by real-time nanopore sequencing analysis. (cdc.gov)
The training focused on utilizing the Oxford Nanopore Technology sequencing - a platform for metagenomic sequencing of acute watery diarrhoea. (who.int)
During the 2018 Lassa fever outbreak in Nigeria, samples from patients with suspected Lassa fever but negative Lassa virus PCR results were processed through custom gene expression array cards and metagenomic sequencing. (cdc.gov)

A quarter of all the world's SARS-CoV-2 viral genomes have now been sequenced with nanopore devices. (wikipedia.org)
Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. (nih.gov)
Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. (nih.gov)
Nanopore sequencing has been used, for example, throughout the COVID-19 pandemic to sequence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes [ 5 ]. (ersjournals.com)
In this course, the participants will learn to use the Oxford Nanopore MinION DNA sequencer combined with metagenome binning techniques in order to recover individual genomes from complex metagenomes. (aau.dk)
With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
During this period, tremendous success has been achieved in the fields of decoding of human genome, technological advancement of new era of human genome applications, toward personalized genomes and discovery of rare variants, leveraging genome sequencing to impact on cancer researches and mammalian evolution and population structure. (springer.com)
We investigated if Nanopore sequencing can detect sufficient N. gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. (ox.ac.uk)
Using Nanopore sequencing of urine samples from men with urethral gonorrhoea sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture. (ox.ac.uk)
There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance.MethodsWe investigated if Nanopore sequencing can detect sufficient N. gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. (ox.ac.uk)
N. gonorrhoeae could also be detected from urine in cobas PCR Media tubes and from urethral swabs, and in the presence of simulated Chlamydia co-infection.ConclusionUsing Nanopore sequencing of urine samples from men with urethral gonorrhoea sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture. (ox.ac.uk)

Evaluation of nanopore-based sequencing technology for gene marker based analysis of complex microbial communities. (gla.ac.uk)
The focus of this study is on the evaluation of nanopore sequencing data: read quality, sequencing errors, alignment quality but also bacterial community structure. (gla.ac.uk)
Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis. (ox.ac.uk)

This article lays out recent developments and applications of nanopore sequencing technologies and their potential application in forensic analysis, addressing current and potential techniques in mitochondrial DNA analysis, SNP and STR typing, and microbial identification, as well as recent developments in library preparation and data analysis tools. (ojp.gov)
Herein, the authors outline recent developments and applications of nanopore sequencing technologies and their potential application in forensic analysis. (ojp.gov)
This method adds to the toolbox for nanopore-based STR analysis and expands the applications of nanopore sequencing in scientific research and clinical scenarios. (researchsquare.com)

Such a direct method for reading a sequence could be faster and more accurate than current approaches. (scienceblogs.com)
Using these approaches, nanopores may be used as nanoscale reactor for single-molecule enzymology studies, or sensors for sequencing individual proteins as they translocate across the nanopore. (videolectures.net)
With emphasis on MinION Nanopore sequencing, cDNA-direct and target-enrichment (amplicon-based) sequencing approaches were validated in parallel. (frontiersin.org)
Expansion of high-throughput sequencing (HTS) technologies and reduction in analysis costs has allowed for detailed exploration of various habitats with use of amplicon, metagenomics, and metatranscriptomics approaches. (gla.ac.uk)
For this reason, mock bacterial community samples were generated, sequenced and analysed with use of multiple bioinformatics approaches. (gla.ac.uk)
2003 ). The NHGRI has categorized new sequencing approaches into those that offer near-term and revolutionary benefits with a 100-fold cost reduction per base pair (bp) within the next five years. (springer.com)
Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches. (lu.se)

At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. (nih.gov)
The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. (nanoporetech.com)
And in the field or in the lab, nanopore sequencing produces direct, real-time sequence reads as soon as the sequencing process begins yielding up to 100 kb long reads or longer. (harvard.edu)
In contrast, a sub-nanopore, which is about the size of an amino acid residue, reads the primary structure of a single whole protein molecule, although imperfectly, and is embedded in a microfluidic device about the size of a flash-drive. (openphilanthropy.org)
When will nanopore sequencing push short-reads (i.e. (enseqlopedia.com)
Using long sequencing reads from the Oxford Nanopore Technologies platform, we phased SNVs within large gene copy arrays for the first time. (elifesciences.org)
HLA reads were aligned to donor -specific reference sequences based on the known type of each donor . (bvsalud.org)
We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. (uea.ac.uk)
We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. (edu.sa)
Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. (lu.se)

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have of identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. (nist.gov)
These nanopore systems are emerging as prominent tool for protein identification, detection, and analysis, suggesting realistic prospects in novel protein sequencing. (nist.gov)
This review summarizes the recent advances in nanopore sensors for protein sequencing from identification of individual amino acids to control translocation rates. (nist.gov)
Specifically, from an engineering perspective, the review aims to provides an opinion for future developments to realize nanopore-based protein sequencing by emphasizing joint efforts from various fields including chemical conjugation, protein engineering, molecular simulation, machine learning-assisted identification, and electronic device fabrication that are necessary for real-world translation. (nist.gov)
Our approach enables native proteins to be transported enzymatically and non-enzymatically in the absence of denaturant and electrophoretic tags, with potential applications for protein sequencing. (nature.com)

Consecutive patients with suspected sepsis admitted to ICU will undergo MinION nanopore pathogen sequencing integrated with personalised antibiotic therapy using a combination of Bayesian dosing software (ID-ODSTM) and measured antibiotic plasma concentrations. (who.int)
Time to pathogen identification and susceptibility testing using MinION nanopore pathogen sequencing direct from whole blood. (who.int)

In 1989 he sketched out a plan to drive a single-strand of DNA through a protein nanopore embedded into a thin membrane as part his work to synthesize RNA from scratch. (wikipedia.org)
The biological or solid-state membrane, where the nanopore is found, is surrounded by electrolyte solution. (wikipedia.org)
Biological nanopores are a class of membrane proteins that form nanometer-size apertures on lipid membranes. (videolectures.net)
Nanopore sequencing involves drawing many single strands of DNA through a two-nanometer diameter pore in an otherwise tightly sealed lipid membrane separating two small liquid filled containers. (harvard.edu)
As the DNA strand is drawn through the nanopore from the container on the first side of membrane to the container on the second side, the different nucleotide bases (known as A, C, G, T or U) trigger different electrical responses allowing researchers to identify the order or sequence of the bases. (harvard.edu)
Nanopore sequencing utilises a membrane protein pore as a biosensor to sequence RNA or DNA molecules as they pass through the pore [ 4 ]. (ersjournals.com)
Using our funding, Dr. Timp and his collaborators will experiment with new sub-nanopore topographies, membrane materials and electrolyte conditions to improve the read fidelity and translocation kinetics, as well as explore new algorithms to discriminate between proteins and identify all twenty proteogenic amino acids and their post-translational modifications. (openphilanthropy.org)

Publications on the method outline its use in rapid identification of viral pathogens, monitoring ebola, environmental monitoring, food safety monitoring, human genome sequencing, plant genome sequencing, monitoring of antibiotic resistance, haplotyping and other applications. (wikipedia.org)
The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. (galaxyproject.org)
In one cohort, for example, nanopore sequencing identified pathogens in almost 40% of culture-negative samples [ 8 ]. (ersjournals.com)
Optimising treatment outcomes for children and adults through rapid genome sequencing of sepsis pathogens. (who.int)

How much does Nanopore cDNA Sequencing Cost? (stackexchange.com)
Nanopore sequencing also offers, for the first time, direct RNA sequencing , as well as PCR or PCR-free cDNA sequencing. (lifeboat.com)
The recent development of long-read direct RNA (dRNA) sequencing has the potential to overcome many limitations of short and long-read sequencing methods that require RNA fragmentation, cDNA synthesis or PCR. (ox.ac.uk)
cDNA libraries were prepared from peripheral blood lymphocytes from 12 donors and sequenced by nanopore long-read sequencing. (bvsalud.org)

Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
Loman's lab started doing its own gene sequencing in 2009, with an instrument called the Genome Sequencer FLX. (thetwittertagproject.com)
Turnaround time, for example, is much shorter: nanopore-based methods have been shown to report pathogen and acquired resistance gene identification within 8 h of receiving a sample, compared to 48-72 h or more for culture-based methods [ 7 ]. (ersjournals.com)
Our results establish the ability of dRNA sequencing to identify biologically relevant differences in gene and isoform expression and perform the key capabilities of expression profiling methodologies. (ox.ac.uk)
Sequencing-by-synthesis (SBS) technology currently dominates the gene sequencing market. (ieee.org)
Following duplication events, the resulting stretches of homologous sequence can promote recombination between gene copies. (elifesciences.org)
or the transmembrane protein gene cassettes of some pathogenic bacteria ( Santoyo and Romero, 2005 ), gene conversion can also generate sequence diversity. (elifesciences.org)
Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. (edu.sa)
All 10x Genomic services include a final report containing a Cell Ranger web summary file for quality control (QC) of the sequencing outcome, as well as FASTQ, BAM, gene count matrix containing all single cells or nuclei passing QC, basic visualization and clustering. (lu.se)
Usage of reporter genes need to be specified in iLab before project start and the exact sequence information and gene co-ordinates need to be submitted to be included during sequencing read alignment. (lu.se)

Under an applied potential the ionic current through nanopores is used to identify molecules or to follow reactions at the single-molecule level. (videolectures.net)

They also find that nanopore sequencing signals display complex heterogeneity across methylation events of the same type, which suggests that detection methods are best developed using a diverse collection of species. (genomeweb.com)
However, there are few methods for STR detection based on nanopore sequencing due to the challenges posed by the sequencing principles and the data characteristics of nanopore sequencing. (researchsquare.com)
NanoSTR can be used for STR detection and genotyping based on long-read data from nanopore sequencing with improved accuracy and efficiency compared with other existing methods, such as Tandem-Genotypes and TRiCoLOR. (researchsquare.com)
Although NanoSTR needs further optimization and development, it is useful as an analytical method for the detection of STR loci by nanopore sequencing. (researchsquare.com)
Nanopore sequencing is an evolving third/fourth generation sequencing technology for direct detection of nucleotide sequences with kb or even Mb base pairs (7)(8) . (researchsquare.com)
In terms of data characteristics, NanoSTR effectively avoids the non-random sequencing errors and unexpected insertions-deletions (indels) associated with nanopore sequencing (8)(9) and thus improves the efficiency of sequencing data utilization, the detection rate of STR genotypes, and the accuracy of STR profiling. (researchsquare.com)
We also demonstrate that our method has performance comparable to existing techniques without limiting the detection of repeats, or the length of the input sequence. (elsevierpure.com)
Nanopore sequencing offers advantages in speed of detection over MiSeq. (ox.ac.uk)
The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)

The investigators note that existing methods for detecting DNA modification from nanopore sequencing data cannot effectively characterize unknown bacterial methylomes without previous knowledge. (genomeweb.com)
To enable nanopore sequencing for broad methylation discovery, they generated a training dataset from an assortment of bacterial species and develop a technique that combines the identification and fine mapping of the three forms of methylation into a multi-label classification framework. (genomeweb.com)

Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing. (nih.gov)

My sequencing raw data was a result of a metagenomics analysis (16s and 18s). (stackexchange.com)
Eine besondere Anwendung von Amplicon Sequenzierungen ist das 16S Sequencing zur Bestimmung mikrobieller Spezies aus natürlichen Populationen (Mikrobiom Metagenomics). (hhu.de)

Findings from this study will inform future plans for implementing long-read sequencing in clinical settings in this part of the world. (genomeweb.com)
This study suggests that Nanopore adaptive sampling is an efficient technique for investigating structural variants suitable for clinical setting. (bmj.com)
But nanopore sequencing is not yet a routine clinical practice as part of RTI diagnostic panels, despite the fact that nanopore sequencing has several clinical advantages over culture, which remains the gold standard diagnostic tool for RTIs [ 6 ]. (ersjournals.com)
While the initial applications of this tool are expected in research settings, we believe it is possible that it could eventually be commercialized and lead to inexpensive methods for protein identification and sequencing in clinical settings. (openphilanthropy.org)
As a result, clinical and public health institutions making decisions on which sequencing technology to adopt for tuberculosis can base the choice on cost (which varies by country), batching, and turnaround time. (ox.ac.uk)

I was proud to stand with my international colleagues in a celebration at the Library of Congress on April 14, 2003 (which happens to be my birthday), to announce that we had stitched together the very first reference sequence of the human genome at a total cost of about $400 million. (nih.gov)
That first reference human genome was sequenced using automated machines that were the size of small phone booths. (nih.gov)
Now, a report in Nature Biotechnology highlights the latest advance: the sequencing and assembly of a human genome using a pocket-sized device [1]. (nih.gov)
The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.com)
Year 2011 is celebrated as the 10th anniversary since the human genome was first sequenced ( www.nature.com/natureconferences/hg10years/index.html ). (springer.com)

An approach for using nanopore sequencing to discover different types of DNA methylation from bacteria and the microbiome is described by a Mount Sinai-led team in this week's Nature Methods . (genomeweb.com)
However, there is currently no complete software for detecting SNPs, phasing haplotypes and mapping methylation to these from nanopore sequence data. (nanoporetech.com)
Together, these tools can accurately detect allele-specific methylation genome-wide using nanopore sequence data with coverage as low as ten-fold redundancy. (nanoporetech.com)
We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m 6 A). Here we show that m 6 A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. (uea.ac.uk)
We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). (uea.ac.uk)

In our study, we resolved a germline tandem duplication of exon 18 to 20 of BRCA1 using Nanopore sequencing with adaptive sampling enrichment, classifying the variant as pathogenic within ten days. (bmj.com)

Capital outlay for the MinION (Oxford Nanopore Technologies, Oxford, UK), the smallest nanopore sequencing device (smaller than the average mobile phone), is very low relative to other sequencing platforms, with starting prices advertised from USD 1000 per device. (ersjournals.com)

The pediatric samples involved in the project have previously been interrogated by other sequencing methods that can detect single-base changes but not larger disease-causing variants, Oxford Nanopore said. (genomeweb.com)
In the recent years, Oxford Nanopore long-read sequencing has proved its relevance to accurately and rapidly provide genetic diagnoses of these types of variants. (bmj.com)

The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. (springer.com)
Many experts thought the key to cheaper DNA sequencers was going to be performing the SBS process in nanopore-based DNA sequencers . (ieee.org)
Now researchers at Wyss Institute for Biologically Inspired Engineering at Harvard University believe that they have developed a way to make these nanopore-SBS DNA sequencers fast, accurate, and, most importantly, cheaper than what is currently on the market. (ieee.org)
One big obstacle to overcome in nanopore-SBS sequencers: The DNA strands are synthesized so close to the nanopores that they interfere with the electrical signal of those strands passing through the pore. (ieee.org)

The first commercial system for nanopore sequencing ( Oxford Nanopore Technologies Ltd ) required 20 years of scientific trial and error. (scienceblogs.com)
DNA sequencing was dominated by Sanger's chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. (nih.gov)
Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. (nih.gov)
NEW YORK - Oxford Nanopore Technologies said on Tuesday that it has launched a pilot program with Al Jalila Children's Specialty Hospital (AJCH) in the United Arab Emirates to explore the utility of nanopore sequencing in unresolved rare disease cases. (genomeweb.com)
Advancements in DNA sequencing technologies are occurring at a rapid rate. (ojp.gov)
Oxford Nanopore Technologies (ONT) has developed a portable, nanopore-based sequencing instrument that has already been utilized for on-site identification of Zika and Ebola viruses, full genome sequencing, evaluation of DNA and RNA base modifications, and enrichment-free mitochondrial DNA analysis. (ojp.gov)
The black boxes from Oxford Nanopore Technologies arrive in the mail in FedEx envelopes, looking a bit like individually packaged bars of soap. (thetwittertagproject.com)
After years of work and publications, Harvard and UC Santa Cruz licensed patents to Oxford Nanopore Technologies (ONT). (harvard.edu)
Since then, breathtaking progress has been made in developing innovative technologies that have made DNA sequencing far easier, faster, and more affordable. (nih.gov)
This research project investigated the potential of a novel nanopore-based sequencing platform from Oxford Nanopore Technologies (ONT) for rapid and accurate analysis of various environmentally complex samples. (gla.ac.uk)
however, Nanopore technology developed by Oxford Nanopore Technologies has not been thoroughly evaluated. (ox.ac.uk)
RESULTS: DNA was extracted from the sonication fluids of seven explanted orthopaedic devices, and additionally from two culture negative controls, and was sequenced on the Oxford Nanopore Technologies MinION platform. (ox.ac.uk)
This study reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems. (elifesciences.org)

Research,CharlesVille,RepublicofLiberia(F.K.Bolay);Centers pore sequencing is being developed as a rapid diagnostic forDiseaseControlandPrevention,Atlanta,Georgia,USA tool for management of outbreaks of various diseases ( 7 , 8 ). (cdc.gov)
The Open Philanthropy Project recommended a grant of $2,054,142 over three years to the University of Notre Dame to support the development of an instrument that uses a sub-nanometer-diameter pore (i.e. a sub-nanopore) to read the amino acid sequence of whole protein molecules. (openphilanthropy.org)

Biological nanopore sequencing relies on the use of transmembrane proteins, called protein nanopores, in particular, formed by protein toxins, that are embedded in lipid membranes so as to create size dependent porous surfaces - with nanometer scale "holes" distributed across the membranes. (wikipedia.org)

Sequencing libraries were prepared from purified genomic DNA using the Ligation sequencing kit 1D R9 version (SQK-LSK108) according to the manufacturer's protocol. (nih.gov)

These proteins can be used as an alternative to the nanopores in silicon. (scienceblogs.com)
Here we show that the transport of proteins and peptides across nanopores can be finely controlled. (videolectures.net)
Folded proteins can trapped inside nanopores by exploiting electrophoretic forces, while small peptides can be stretched and unfolded by engineering strong electroosmotic flows through the nanopore. (videolectures.net)
An engineered nanopore translocates untagged full-length proteins by electroosmotic force. (nature.com)

Nanopore sequencing has the potential to offer relatively low-cost genotyping, high mobility for testing, and rapid processing of samples with the ability to display results in real-time. (wikipedia.org)
The rapid development of this technology creates possibilities relevant to standard DNA sequencing, direct analysis of forensic samples, including blood, semen, and buccal swabs, mitochondrial DNA analysis, SNP and STR analysis, familial identification, and microbial identification for bioterrorism and geolocation. (ojp.gov)
Reducing time to appropriate antibiotics by integrating rapid pathogen genome sequencing with personalised antimicrobial dosing in children and adults with sepsis. (who.int)
The DIRECT study is a pilot prospective, non-randomised multicentre trial of an integrated diagnostic and therapeutic algorithm combining rapid direct pathogen sequencing and software-guided, personalised antibiotic dosing in children and adults with sepsis on ICU. (who.int)

Using a combination of next-generation sequencing, bioinformatics, and molecular cloning, CDC can identify the functions of the individual antibodies and what part of the influenza virus they target. (cdc.gov)

Using a mixture of synthetic controls and human SH-SY5Y cell differentiation into neuron-like cells, we show that dRNA sequencing accurately quantifies RNA expression and identifies differential expression of genes and isoforms. (ox.ac.uk)
Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing. (bvsalud.org)

By 2005 Bayley had made substantial progress with the method to sequence DNA and co-founded Oxford Nanopore to help push the technology further. (wikipedia.org)
Consequently, we must rely on technology to tell us what the sequence of bases must be. (scienceblogs.com)
The greatest challenge in getting this technology to work is that DNA is small and nanopores, while sounding small, are really big relative to DNA. (scienceblogs.com)
The partnership aims to solve challenging rare disease cases by leveraging new technology with "greater visibility to a range of genetic variation," according to Oxford Nanopore. (genomeweb.com)
The technology provides real-time information on DNA sequence and is currently being used around the world in both large research laboratories and in field work situations. (harvard.edu)
Clive Brown presented a webinar on Tuesday with multiple updates on Oxford Nanopore technology, Keith Robison covered them all over at OmicsOmics, but I'll just be focussing on the launch of GridION X5. (enseqlopedia.com)
If they can further develop the technology, they could enable doctors to quickly discern changes in your specific DNA sequence signaling a disease. (ieee.org)

Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. (nist.gov)
Additionally, the relatively large nanopore they were able to use should allow the DNA molecules to more easily pass through, allowing for easier and faster reading of the sequence. (medgadget.com)
The notion of sequencing nucleic acids by drawing single molecules of DNA or RNA through a nanopore was initially considered quite impossible by most people, including most of the expert scientists who reviewed our grant proposals at NIH. (harvard.edu)

Another foundation for nanopore sequencing was laid by the work of a team led by Hagan Bayley who from the 1990s began to independently develop stochastic sensing, a technique that measures the change in an ionic current passing through a nanopore to determine the concentration and identity of a substance. (wikipedia.org)

The current methods for determining a DNA sequence rely on mimicking the processes used in nature to replicate DNA and copy chromosomes before cells divide. (scienceblogs.com)
Nanopore sequencing methods were not easy to develop. (scienceblogs.com)
Raw sequencing data as generated by the five different methods used are provided for each of the three samples used in the comparison. (usgs.gov)
Nucleic acid sequencing can provide a detailed overview of microbial communities in comparison with standard plate-culture methods. (gla.ac.uk)
Furthermore, this study developed sophisticated library preparation and data analyses methods to enable high-accuracy analysis of amplicon libraries from complex microbial communities for sequencing on the nanopore platform. (gla.ac.uk)
In practice, however, the high error rate and special data characteristics of long-read sequencing have limited the efficient identification of STR polymorphisms, and therefore, further evaluation of the analytical methods is required (9)(10) . (researchsquare.com)
There are a few methods for STR identification based on nanopore sequencing, and the representative software are Tandem-Genotypes (11) , NanoSatellite (12) , STRique (13) ， etc. (researchsquare.com)
It was thought initially that the much shorter turnaround time would mean that nanopore sequencing is a less accurate method of pathogen identification than traditional culture methods. (ersjournals.com)
Findings such as these verify the accuracy of nanopore sequencing-based methods and indicate that there are clear advantages over culture-based methods in identifying RTIs. (ersjournals.com)
We used N. gonorrhoeae spiked urine samples and samples from gonorrhoea infections to determine optimal DNA extraction methods that maximize the amount of N. gonorrhoeae DNA sequenced whilst minimizing contaminating host DNA. (ox.ac.uk)
We used N. gonorrhoeae spiked urine samples and samples from gonorrhoea infections to determine optimal DNA extraction methods that maximize the amount of N. gonorrhoeae DNA sequenced whilst minimizing contaminating host DNA.ResultsIn simulated infections the Qiagen UCP Pathogen Mini kit provided the highest ratio N. gonorrhoeae to human DNA and the most consistent results. (ox.ac.uk)

Bei dem Amplicon Sequencing werden ein bzw. (hhu.de)

Once inside the nanopore, the molecule translocates through via a combination of electro-phoretic, electro-osmotic and sometimes thermo-phoretic forces. (wikipedia.org)

Additionally, they discuss recent developments in library preparation and data analysis tools further streamlining the sequencing process that integrate workflows in laboratories or in remote field scenarios. (ojp.gov)
For example, NanoSatellite directly analyzes STRs based on electric current distribution, and the accuracy of analysis depends heavily on the stability of the sequencing current and the precision of the basecalling model. (researchsquare.com)
For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)
The nine samples sequenced in this pilot study have shown a proof of concept for sequencing and analysis that will enable us to investigate further sequencing to improve specificity and sensitivity. (ox.ac.uk)

Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the need for PCR amplification or chemical labeling of the sample. (wikipedia.org)

By using fixed charges to engineer a strong electroosmotic flow, we achieve the unidirectional transport of natural polypeptides across nanopores. (nature.com)

Nanopore sequencing offers advantages in all areas of research. (nanoporetech.com)

Using Molecule World™ we can examine the structures of these nanopores and learn about some of their properties. (scienceblogs.com)
A promising approach that many have been trying to implement in order to speed up and reduce the cost of DNA sequencing is pushing the molecule through a tiny hole and using nearby electrodes to detect the unique change in the electric field as each nucleotide comes through. (medgadget.com)
In the field of forensics, one particular single-molecule sequencing platform shows promise for becoming a viable solution for small to midsize forensic laboratories. (ojp.gov)

Oxford Nanopore systems offer real-time, scalable, direct DNA sequencing. (lifeboat.com)

The trick was to biologically engineer the nanopore structure. (ieee.org)

We have highlighted the potential impact of nanopore sequencing as a feasible method of pathogen identification in RTI and we believe it has multiple advantages over traditional culture, particularly time to result (including antibiotic resistance markers). (ersjournals.com)

The decades-long collaboration began in the early 1990s when Deamer and Branton began discussing their similar ideas for expediting the sequencing of DNA by drawing single nucleic acid strands through an interface. (harvard.edu)

Oxford Nanopore sequencing: new opportunities for plant genomics? (nih.gov)
In addition, Oxford Nanopore said it will collaborate with AJCH on optimizing the workflow and informatics to support the clinicians involved in this work. (genomeweb.com)
It's that Oxford Nanopore specifically looked a little dubious. (thetwittertagproject.com)
MAP participants have to test their devices on a pre-specified sample, and can't share any data with the public until they certify to Oxford Nanopore that the instrument is "acceptable. (thetwittertagproject.com)
The UK biotech sector was in the news yesterday morning with two companies and their COVID tests making headlines: Oxford Nanopore and DNANudge. (enseqlopedia.com)

It's not just that dealing with the data they produce is a job for dedicated experts, who use gigabytes of memory and days of compute time to wring useful information out of their raw DNA sequence. (thetwittertagproject.com)
I am wondering if exists a program easy to use that can bring me Basic Statistics of Quality Control from raw data made by MinION device (nanopore). (stackexchange.com)
I assume raw data is in Fastq format, but ideally you should also use the sequencing_summary.txt file generated by the basecaller. (stackexchange.com)
How can I generate ASV file from nanopore sequencing data? (stackexchange.com)
Nanopore ##Assembly-Data-END## FEATURES Location/Qualifiers source 1. (cdc.gov)

The small size of the platform, its low cost, and its requirement of only basic laboratory equipment makes this platform well suited for small laboratories wishing to begin developing expertise in sequence-based forensic analyses. (ojp.gov)
ONT is an emerging company that developed the first-ever portable nanopore-based sequencing platform called MinIONTM. (gla.ac.uk)
Besides, NanoSTR also showed 86.36% and 73.48% concordance using the standard samples 9948 and 2800M with MinION sequencing platform, respectively. (researchsquare.com)
Meanwhile, the concordance with Qnome-3841 sequencing platform were 71.97% and 53.03%, respectively. (researchsquare.com)
The course includes hands-on library preparation and sequencing using the MinION platform. (aau.dk)
Established in 2019, CTG offers a dynamic, state-of-the-art platform for single-cell sequencing to users. (lu.se)

In spite of the strong evidence we published in our 1996 PNAS paper, many readers initially doubted that we had in fact electrophoretically drawn a single polymer of nucleic acid through a nanopore. (harvard.edu)

The magnitude of the electric current density across a nanopore surface depends on the nanopore's dimensions and the composition of DNA or RNA that is occupying the nanopore. (wikipedia.org)

A common method for creating a nanopore involves using lasers to drill holes in silicon wafers. (scienceblogs.com)

In fact, this new genome sequence-completed in a matter of weeks-includes some notoriously hard-to-sequence stretches of DNA, filling several key gaps in our original reference genome. (nih.gov)
Nanopore sequencing has introduced the ability to sequence long stretches of DNA, enabling the resolution of repeating segments, or paired SNPs across long stretches of DNA. (elsevierpure.com)

As part of the collaboration, the company will provide sequencing systems and reagents, as well as facilitate knowledge sharing. (genomeweb.com)
That's a big change from conventional sequencing procedures that require expensive reagents and machines. (ieee.org)

The resulting device can analyze multiple DNA sequences electronically on the same chip simultaneously. (ieee.org)

In this study, we sought to determine if long-read sequencing could be used to accurately quantify allele -specific HLA transcripts in primary human lymphocytes . (bvsalud.org)

Chemicals and Drugs11

Analytical, Diagnostic and Therapeutic Techniques and Equipment9

Phenomena and Processes10

Disciplines and Occupations1

Technology, Industry, Agriculture6

Information Science2

Health Care1

Whole-genome10

Illumina15

20232

Metagenomic7

Genomes11

Evaluation of nanopore3

Applications of nanopore3

Approaches7

Reads10

Protein Sequencing5

MinION Nanopore2

Membrane7

Pathogens4

CDNA4

Gene10

Single-molecule level1

Detection9

Bacterial2

Plant genome1

Metagenomics2

Clinical5

Human genome5

Methylation5

Adaptive1

Platforms1

Variants2

Sequencers4

Technologies13

Pore2

Biological1

Genomic1

Proteins4

Rapid4

Bioinformatics1

Isoforms2

Technology7

Molecules3

Ionic current1

Methods11

Amplicon1

Translocates1

Analysis4

Amplification1

Strong electroosmotic1

Offers advantages1

Molecule3

Direct1

Biologically1

Pathogen identification1

Strands1

OXFORD5

Data5

Platform6

Nucleic1

Nanopore's1

Involves1

Stretches2

Reagents2

Analyze1

Accurately1