A new study, published in Nature Biotechnology, reveals scientists from the Broad Institute have found a way to examine any human virus more efficiently, cost-effectively and on large scales than previously known.
The CATCH method (Compact Aggregation of Targets for Comprehensive Hybridization), as it is known, allows scientists to create “baits” for known viruses and strains, even those traditionally low in abundance during clinical samples. Users can design custom sets of probes to capture genetic material of any combination of microbial species, providing a potential boost to the capabilities of even small sequencing centers throughout the world.
The study was led by MIT graduate student Hayden Metsky and postdoctoral researcher Katie Siddle.
“We wanted to rethink how we were actually designing the probes to do capture,” Metsky said. “We realized that we could capture viruses, including their known diversity, with fewer probes than we’d used before. To make this an effective tool for surveillance, we then decided to try targeting about 20 viruses at a time, and we eventually scaled up to the 356 viral species known to infect humans.”
Users of CATCH can input genomes from all forms of all human viruses currently in the National Center for Biotechnology Information’s GenBank sequence database. It, in turn, selects the best set of probes for the job. Those probe sequencing lists can then be sent to one of a few companies that synthesize probes for research, which the scientists can use for their work.
In testing, these CATCH-designed probe sets revealed themselves to provide 18 times more of the sequencing data than before enrichment. Metsky and Siddle have also made all probes they have designed through CATCH readily available to the public, flying in the face of probe designs’ traditional proprietary nature.