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The new method helps the pocket DNA sequencer achieve almost perfect accuracy



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


Using special molecular markers, the team was able to reduce the error rate of 5 to 1

5 percent on Oxford Nanopore Technologies’ MinION device to less than 0.005 percent – even when very long stretches of DNA are performed sequentially at once.

“MinION has revolutionized genomics by freeing DNA sequencing from the confines of large laboratories,” said Ryan Zills, a civil engineering assistant at the University of British Columbia and co-author of the study, which was published this week in Natural methods. “But so far, researchers have not been able to rely on the device in many settings due to the rather high error rate outside the box.”

Genomic sequences can reveal much about an organism, including its identity, its origins, and its strengths and vulnerabilities. Scientists use this information to better understand microbes living in a particular environment, as well as to develop diagnostic tools and treatments. But without accurate portable DNA sequencers, key genetic details can be missed when conducting research in the field or in smaller laboratories.

So Ziels and his colleagues at the University of Aalborg have created a unique barcoding system that can make long-read DNA sequencing platforms like MinION more than 1,000 times more accurate. After labeling the target molecules with these barcodes, the researchers proceeded as usual to amplify or make multiple copies of the labeled molecules using standard PCR technique and sequencing of the resulting DNA.

Researchers can then use barcodes to easily identify and group the relevant DNA fragments in the sequencing data, resulting in near-perfect sequences of fragments that are up to 10 times longer than conventional technologies. Longer sections of DNA allow the detection of even slight genetic variations and the collection of high-resolution genomes.

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

Ziels is currently working with Metro Vancouver to develop an extended version of the method that allows the detection of microorganisms in water and wastewater in near real time. With an accurate picture of the microorganisms present in their water systems, Ziels says, communities can improve their public health strategies and treatment technologies – and better control the spread of harmful microorganisms such as SARS-CoV-2.


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More information:
Søren M. Karst et al, High-precision long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing, Natural methods (2021). DOI: 10.1038 / s41592-020-01041-y

Provided by the University of British Columbia

Quote: The new method helps a pocket DNA sequencer achieve near-perfect accuracy (2021, January 12), retrieved on January 12, 2021 from https://phys.org/news/2021-01-method-pocket-sized-dna-sequencer- near -perfect.html

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