The research team develops software that reduces the time and cost of gene sequencing

A team of researchers from Johns Hopkins University has developed new software that could revolutionize the way DNA is sequenced, making it much faster and cheaper to map everything from yeast genomes to cancer genes.

The software, detailed in a document published in Natural biotechnologies, can be used with portable sequencing devices to accelerate the ability to conduct genetic testing and provide diagnoses outside the laboratory. The new technology targets, collects and sequences specific genes without sample preparation and without having to map the surrounding genetic material as standard methods require.

“I think this will forever change the way DNA sequencing is performed,” said Michael C. Schatz, Bloomberg Distinguished Associate Professor of Computer Science and Biology and senior author of the paper.

The new process reduces the time it takes to profile gene mutations, from 15 days or more to just three. This allows scientists to understand and diagnose conditions almost immediately, saving time and money by eliminating additional preparation and analysis.

“In cancer genomics, there are a few dozen genes known to increase cancer risk, but with a standard sequencing run, you’d have to sequence the entire genome just to read those few genes,” Schatz said, adding that adaptive sequencing allows researchers to “pick and choose which molecules we want to read and which ones can be skipped.”

To give an idea of ​​how much this invention speeds sequencing, Schatz links it to looking for a movie on Netflix. The old standard method of sequencing would require someone to watch every second of every movie on Netflix to find what they want. Instead, adaptive sequencing eliminates hours of watching irrelevant content by quickly recognizing unwanted movies and skipping to the next item.

The open source software algorithm was written by lead author Sam Kovaka, a PhD student at Johns Hopkins. Its acronym name, UNCALLED, stands for Utility for Nanopore Current Alignment to Large Expanses of DNA.

It took two years to code, develop, and test the software and another year to perfect it enough to produce publication-worthy results, Kovaka said.

“UNCALLED allows unprecedented flexibility in targeted sequencing,” he added. “The fact that it is purely software-based means that researchers can target any genomic region at no additional cost to a normal sequencing run, and they can easily switch targets by simply running a different command.”

The process identifies DNA molecules as they pass through tiny electrified holes, or “nanopores,” inside devices called nanopore sequencers, which are smartphone-sized versions of the bulky machines used in labs. The software reads the data and compares it to the reference sequence of a specified genome within a fraction of a second. The desired molecules can pass through the pore to be fully mapped. But if an undesirable molecule is detected, the software reverses the voltage in the nanopore, physically ejecting the molecule to make room for the next one.

“It’s like a nightclub porter who lets the guests you want on a list enter while rejecting the rest with a Taser,” explains Schatz.

The research team performed two demonstrations of UNCALLED.

The first showed that the software was able to improve the sequencing of 148 genes known to increase cancer risk by rapidly and accurately profiling all of their variants with a single analysis through a portable sequencer. The software enabled real-time cataloging of dozens of complex structural mutations in cancer genes that a standard run would have missed.

Then the team demonstrated how the software can selectively sequence certain species collected from an environment, such as microbes living on the skin or those in pond water. By rejecting molecules from known microbes (such as E. coli), the software was able to efficiently sequence the remaining molecules, revealing a less understood yeast genome.

UNCALLED can operate on standard hardware used for nanopore sequencing without requiring special reagents or accelerators. The selection of genes or genomes to be sequenced is entirely software-controlled and can be changed at any time.