Real - time analysis
of nanopore - based metagenomic sequencing from orthopaedic device infection
NanoOK: Multi-reference alignment analysis
of nanopore sequencing data, quality and error profiles
A talk by Stephanie Hao of Johns Hopkins University Applications
of Nanopore Sequencing for Infectious Disease Detection at London Calling 2016.
NanoOk — Flexible, multi-reference software for pre - and post-alignment analysis
of nanopore sequencing data, quality and error profiles
The recent development
of a nanopore - type portable DNA sequencer has changed the way we think about DNA sequencing.
We developed a portable system for metagenomic analyses consisting
of nanopore technology - based sequencer, MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly.
Artist's conception
of a nanopore drilled into a layer of graphene to speed up DNA sequencing.
The goal of this course is to teach the fundamentals
of nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform.
The ability
of Nanopore sequencing to define the complete exonic structure of CACNA1C allows us to identify known and novel gene isoforms, including novel exons and multi-exonic skipping events and their expression across multiple brain regions.
I will review recent advances in the use
of nanopore sequencing for clinical microbiology and human genetics, including our collaborations on viral and bacterial diagnostic sequencing, real - time surveillance, direct RNA and human whole - genome sequencing, and discuss the opportunities and barriers around moving to sequencing as a routine test in the clinic.
CsgG is a relative newcomer to the lineup
of nanopore candidates.
• Oxford Nanopore Technologies Ltd, a U.K. - based developer
of nanopore - based electronic systems for analysis of single molecules, raised $ 100 million pounds ($ 140 million).
This parameter depends on the nature of the oxide nanoparticles and on the existence
of nanopores.
Wang said the remaining hurdles to commercialization include the fabrication of a dense enough crossbar device to address individual bits and a way to control the size
of the nanopores.
Not exact matches
Researchers, including Karnik's group, have developed techniques to fabricate graphene membranes and precisely riddle them with tiny holes, or
nanopores, the size
of which can be tailored to filter out specific molecules.
Now, a team
of chemical engineering researchers based in South Africa has established ways
of accurately simulating methane adsorption and desorption in carbon with
nanopores.
Gundlach and his team, in the process
of investigating
nanopore sequencing, tried out a variety
of molecular motors to move DNA through the pore.
Activated carbon, which is a type
of carbon material containing numerous
nanopores, is often used to adsorb gases in the energy sector.
But when the polymer comes into contact with G - series nerve agents — the family
of toxic chemicals that includes sarin gas — it flattens into a dense sheet that seals over the carbon
nanopores underneath.
Now an upstart technology, called
nanopore sequencing, looks ready to jump to the front
of the pack.
Now, a team led by Jens Gundlach, a physicist at the University
of Washington, Seattle, reports today in Nature Biotechnology that it has incorporated Akeson's phi29 protein into its
nanopore setup, which uses a different pore protein that's more adept at quickly identifying all four chemical bases.
«Oxford
Nanopore was the first announcement, but they've been roundly criticized for not showing much data,» says chemist Geoffrey Barrall, president of Electronic BioSciences in San Diego, California, which is also developing nanopore seq
Nanopore was the first announcement, but they've been roundly criticized for not showing much data,» says chemist Geoffrey Barrall, president
of Electronic BioSciences in San Diego, California, which is also developing
nanopore seq
nanopore sequencing.
Nanopores are miniscule holes (often as small as a few billionths
of a meter) that measure a change in electrical current as molecules pass through them.
«By adjusting for a variety
of parameters we were able to identify a pore size range, a
nanopore, that best suited the purpose
of the textile, one that is highly opaque visibly and at the same time highly transparent in the thermal wavelength range,» said Fan.
At left is a single
nanopore viewed from the side; at right is a diagram
of metabolite exchange across the membrane.
The
nanopores can be filled with specific cytokines, oligonucleotides, large protein antigens, or any variety
of drugs
of interest to allow a vast number
of possible combinations to treat a range
of infections.
In an 8 March letter to the U.S. International Trade Commission, the company denies all charges
of infringement, and claims that Illumina is acting on «unsubstantiated speculation» to block Oxford
Nanopore products and maintain its own monopoly over conventional DNA sequencing.
Oxford
Nanopore holds an exclusive license on the use
of the pore, Brown said today, and has developed more than 700 variations
of it.
Illumina licenses patents on an Msp system from the University
of Washington, Seattle, and the University
of Alabama, Birmingham, and claimed that Oxford
Nanopore's sequencers infringed those patents.
Oxford
Nanopore Technologies, the company that pioneered a new DNA analysis technique called nanopore sequencing, has remained secretive about the microscopic channel at the heart of its p
Nanopore Technologies, the company that pioneered a new DNA analysis technique called
nanopore sequencing, has remained secretive about the microscopic channel at the heart of its p
nanopore sequencing, has remained secretive about the microscopic channel at the heart
of its products.
Drndić and her colleagues tested their silicon nitride
nanopore on homopolymers, or single strands
of DNA with sequences that consist
of only one base repeated several times.
The suit came as distressing news to some researchers, who feared they might lose access to the firm's
nanopore products, or that the battle would stifle the development
of new platforms.
The
nanopore devices closest to being a commercially viable option for sequencing are made out
of protein pores and lipid bilayers.
An illustration
of a single - stranded DNA homopolymer translocating through a silicon nitride
nanopore.
For the
nanopore to be effective at determining a sequence
of bases, its diameter must approach the diameter
of the DNA and its thickness must approach that
of the space between one base and the next, or about 0.3 nanometers.
The differences in base sizes are so small, however, that the proportions
of both the
nanopores and membranes need to be close those
of the DNA strands themselves — a major challenge.
Now, a team led by University
of Pennsylvania physicists has used solid - state
nanopores to differentiate single - stranded DNA molecules containing sequences
of a single repeating base.
As each base
of the strand passes through the pore, it blocks some ions from passing through at the same time; amplifiers attached to the
nanopore chip can register the resulting drop in electrical current.
The NHGRI grant will help fund Drndić's further research into the feasibility
of graphene
nanopore sequencing as a cost - effective alternative to today's methods.
«We have shown that we can make graphene membranes and that we can pass DNA through them, a proof -
of - concept for graphene
nanopores,» Drndić said.
New
nanopore DNA sequencing technology on a device the size
of a USB stick could be used to diagnose infection — according to new research from the University
of East Anglia and Public Health England.
This study aimed to assess the feasibility
of using the Oxford
Nanopore Technologies (ONT) MinION long - read sequencer in reconstructing fully closed plasmid sequences from eight Enterobacteriaceae i...
Sissel Juul joined Oxford
Nanopore in the summer
of 2014 to lead the company's US Applications group, setting up a lab in New York City.
Applying
Nanopore Sequencing and Real - Time Antimicrobial Resistance Gene Analysis to Address the Threat
of Carbapenem - Resistant Gram - Negative Organisms
Moreover, we demonstrated that although the Oxford
Nanopore technology is a relatively new sequencing technology, currently with a high error rate, it is already useful in the generation
of high - quality genome assemblies.
This presentation will review methods for which
Nanopore sequencing and real - time antimicrobial resistance gene analysis can help to address the threat
of CRO as a diagnostic tool in the Medical Microbiology Laboratory.
Here, we describe the results obtained from our current long read sequencing project
of 100 Icelanders with Oxford
Nanopore technology.
The audience fidgeted with eager impatience to hear Clive Brown
of Oxford
Nanopore present an update on their single - molecule, real - time sequencing technology.
Early MinION ™
nanopore single - molecule sequencing technology enables the characterization
of hepatitis B virus genetic complexity in clinical samples — Virginie Sauvage — PLOS ONE
Next steps: The team wants to understand how much farther the activity and stability
of immobilized enzymes can be enhanced by rationally altering the enzymes and the
nanopore sizes and functional groups.