New Method Helps Pocket DNA Sequencer Achieve Near-Perfect Precision

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

Using special molecular labels, the team was able to reduce the 5-15% error rate of the Oxford Nanopore Technologies MinION device to less than 0.005%, even when sequencing many long segments of DNA at a time.

“MinION has revolutionized the field of genomics by freeing DNA sequencing from the confines of large laboratories,” says Ryan Ziels, assistant professor of civil engineering at the University of British Columbia and co-lead author of the ‘study, which was published this week in Nature’s Methods. “But so far, researchers have not been able to rely on the device in many settings due to its fairly high out-of-the-box error rate.”

Genomic sequences can reveal a lot about an organism, including its identity, ancestry, and 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 precise portable DNA sequencers, crucial genetic details could be missed when research is conducted in the field or in smaller labs.

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

Researchers can then use the barcodes to easily identify and cluster relevant DNA fragments in the sequencing data, ultimately producing near-perfect sequences from fragments 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 nice thing about this method is that it is applicable to any gene of interest that can be amplified,” says Ziels, whose team made available the code and protocol for processing the sequencing data via open source repositories. “This means that it can be very useful in all areas where the combination of high precision and long range genomic information is valuable, such as cancer research, plant research, human genetics and science. of the microbiome. ”

Ziels is currently working with Metro Vancouver to develop an expanded version of the method that enables 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 might be able to improve their public health strategies and treatment technologies and better control the spread of harmful microorganisms like SARS-CoV-2.