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


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Researchers have found a simple way to eliminate almost all sequencing errors produced by a widespread portable DNA sequencer, potentially enabling researchers working outside the laboratory to study and detect microorganisms such as the SARS-CoV-2 virus more efficiently.

Using special molecular labels, the team was able to reduce five to 1

5 percent error rates of Oxford Nanopore Technologies’ MinION device to less than 0.005 percent – even when sequencing many long stretches of DNA at a time.

“MinION has revolutionized the field of genomics by freeing DNA sequencing from the frontiers of large laboratories,” said Ryan Ziels, an assistant professor of civil engineering at the University of British Columbia and co-author of the study, which was published. this week in Natural methods. “But until now, researchers have not been able to trust the device in many settings because of its rather high out-of-the-box error rate.”

Genome sequences can reveal a great deal about an organism, including its identity, its origin, and its strengths and vulnerabilities. Researchers are using 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, important genetic details can be missed when conducting research in the field or in smaller laboratories.

So Ziels and his collaborators at Aalborg University created a unique bar coding system that can make long-read DNA sequencing platforms like MinION more than 1000 times more accurate. After labeling the target molecules with these barcodes, the researchers proceed as they normally would – amplify or make multiple copies of the tagged molecules using the standard PCR technique and sequencing of the resulting DNA.

The researchers can then use the barcodes to easily identify and group relevant DNA fragments into the sequencing data and ultimately produce 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 small genetic variations and the assembly of genomes in high resolution.

“A beautiful thing about this method is that it applies 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 archives. “This means it can be very useful in any field where the combination of high accuracy and far-reaching genomic information is valuable, such as cancer research, plant research, human genetics and microbiology.”

Ziels is currently collaborating with Metro Vancouver to develop an expanded version of the method that allows near-real-time detection of microorganisms in water and wastewater. With an accurate picture of the microorganisms present in their water systems, Ziels says, communities may be able to 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-accuracy, 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

Citation: New method helps pocket-sized DNA sequencer achieve near-perfect accuracy (2021, January 12) Retrieved January 13, 2021 from https://phys.org/news/2021-01-method-pocket-sized-dna- sequencer-near -perfekt.html

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