NEW YORK – A new product line from Element Biosciences will simplify and shorten sample preparation for whole-exome and other hybridization-based targeted sequencing, eliminating many of the steps required by existing workflows.
Dubbed Trinity, the new method requires only a hybridization step with target probes before the DNA is loaded onto Element’s Aviti sequencer, cutting several steps required for conventional hybridization-based library prep. At launch, it will be compatible with whole-exome panels from Twist Bioscience and Danaher’s IDT, though other panels, including custom ones, will also become available, Element Senior VP of Applications Shawn Levy said during a virtual launch event last week.
"The capture efficiency is high, and we maintain highly complex libraries," Levy told GenomeWeb, noting that the duplication rate is less than 1 percent while library complexity is three- to fourfold higher than previous workflows. The kits also have an option for a rapid hybridization step that takes only about an hour.
"Sequencing run metrics look excellent," Chris Frazar, a researcher at the University of Washington who participated in the early-access program for Trinity, said during a video segment played during the event. Average Phred scores were around Q40, he said, and the kit provided 900 million reads, enough to cover 12 exome samples.
The launch illustrates how sequencing technology developers are looking for new ways to make next-gen sequencing ever easier for their customers. Earlier this month, Illumina launched an updated low-throughput instrument that comes with several validated, push-button workflows, in addition to easier sample and reagent loading.
Element's Trinity should also save customers money, Levy said. Though the new kit is more expensive than a standard Element kit, customers will no longer have to buy blocking and other reagents, leading to savings of around 20 percent for a "typical" user workflow, he said.
The new technology is an extension of the R&D work Element has put into its surface chemistry, Levy said. "Think of it as a polony generation step that is also the capture step, as well," he said. "By taking advantage of the way Element does temperature control and the fluidics, we can make it happen all at once." There is "no material change" to sequencing run times, he added.
Targeted sequencing is "still a tremendous market," he said, especially custom capture panels. "We knew [it] wasn't going anywhere."
In her presentation, Element CEO and Cofounder Molly He noted that the company has received around 300 total orders for Aviti, with about 20 percent in the translational research market. Element also had William Lai, director of the Cornell University Epigenomics Core Facility, present data from his use of the firm's Teton multiomics chemistry to obtain a "finer resolution of cell state" based on protein and RNA in cell line samples.
In addition to selling Trinity kits, Element is offering the new workflow as a service to help sway customers. The product changes some of the considerations for experimental design, which the company can help with. "You have to think from the flow cell backwards, instead of from the library forward," Levy said. A 1 billion-read flow cell can fit around 24 exomes at 50X to 70X coverage, though other coverage levels can be accommodated by changing the number of samples.
Early next year, Element will be offering the ability to do smaller panels using the Trinity workflow, which could increase sample multiplexing to 192 samples per flow cells. It will also offer what it calls "Trinity Plus," a product that will enable sequencing a baseline library as well as enriching for certain targets. The primary use case appears to be a low-coverage whole genome plus enrichment on the exome. Levy said such an approach would have applications in ag-bio, including genotyping by sequencing.
Trinity should appeal to existing customers, including core labs, according to Levy, but also attract new customers, especially in ag-bio. "I think we even see an avenue that will allow us to be highly competitive against things like microarrays," he said.
Further down the road, RNA capture and methylation panels could also be done with the Trinity technology, he added.