New method helps pocket-sized DNA sequencer achieve near-perfect accuracy 

January 12, 2021

Researchers have found a simple way to eliminate almost all sequencing errors produced by a widely used portable DNA sequencer, potentially enabling scientists working outside the lab to study and track microorganisms like the SARS-CoV-2 virus more efficiently.  

Using special molecular tags, the team was able to reduce the five-to-15 per cent error rate of Oxford Nanopore Technologies' MinION device to less than 0.005 per cent -- even when sequencing many long stretches of DNA at a time.    

"The MinION has revolutionized the field of genomics by freeing DNA sequencing from the confines of large laboratories," says Ryan Ziels, an assistant professor of civil engineering at the University of British Columbia and the co-lead author of the study, which was published this week in Nature Methods. "But until now, researchers haven't been able to rely on the device in many settings because of its fairly high out-of-the-box error rate."

Genome sequences can reveal a great deal about an organism, including its identity, its ancestry and its strengths and vulnerabilities. Scientists use this information to better understand the microbes living in a particular environment, as well as to develop diagnostic tools and treatments. But without accurate portable DNA sequencers, crucial genetic details could be missed when research is conducted out in the field or in smaller laboratories. 

So Ziels and his collaborators at Aalborg University created a unique barcoding system that can make long-read DNA sequencing platforms like the MinION over 1000 times more accurate. After tagging the target molecules with these barcodes, researchers proceed as they usually would -- amplifying, or making multiple copies of, the tagged molecules using the standard PCR technique and sequencing the resulting DNA.  

The researchers can then use the barcodes to easily identify and group relevant DNA fragments in the sequencing data, ultimately producing near-perfect sequences from fragments that are up to 10 times longer than conventional technologies can process. Longer stretches of DNA allow the detection of even slight genetic variations and the assembly of genomes in high resolution. 

"A beautiful thing about this method is that it is applicable to any gene of interest that can be amplified," says Ziels, whose team has made the code and protocol for processing the sequencing data available through open-source repositories. "This means that it can be very useful in any field where the combination of high-accuracy and long-range genomic information is valuable, such as cancer research, plant research, human genetics and microbiome science." 

Ziels is currently collaborating with Metro Vancouver to develop an expanded version of the method that permits the near-real-time detection of microorganisms in water and wastewater. With an accurate picture of the microorganisms present in their water systems, says Ziels, communities may be able to improve their public health strategies and treatment technologies -- and better control the spread of harmful microorganisms like SARS-CoV-2.
-end-


University of British Columbia

Related DNA Articles from Brightsurf:

A new twist on DNA origami
A team* of scientists from ASU and Shanghai Jiao Tong University (SJTU) led by Hao Yan, ASU's Milton Glick Professor in the School of Molecular Sciences, and director of the ASU Biodesign Institute's Center for Molecular Design and Biomimetics, has just announced the creation of a new type of meta-DNA structures that will open up the fields of optoelectronics (including information storage and encryption) as well as synthetic biology.

Solving a DNA mystery
''A watched pot never boils,'' as the saying goes, but that was not the case for UC Santa Barbara researchers watching a ''pot'' of liquids formed from DNA.

Junk DNA might be really, really useful for biocomputing
When you don't understand how things work, it's not unusual to think of them as just plain old junk.

Designing DNA from scratch: Engineering the functions of micrometer-sized DNA droplets
Scientists at Tokyo Institute of Technology (Tokyo Tech) have constructed ''DNA droplets'' comprising designed DNA nanostructures.

Does DNA in the water tell us how many fish are there?
Researchers have developed a new non-invasive method to count individual fish by measuring the concentration of environmental DNA in the water, which could be applied for quantitative monitoring of aquatic ecosystems.

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.

Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.

DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.

A new spin on DNA
For decades, researchers have chased ways to study biological machines.

From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.

Read More: DNA News and DNA Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.