Agilent this week released an expanded version of its SureSelect XT target-enrichment kit that can capture 34 megabases of genomic regions for next-generation sequencing on the Illumina, Roche 454, and Life Technologies SOLiD platforms.
The new custom kit, which represents a five-fold increase over the company's previous custom target enrichment offering, will allow researchers to conduct whole-exome sequencing studies for animals, micro-organisms, plants, and other organisms for which there are currently no commercial target-capture offerings, Fred Ernani, director of marketing for the SureSelect platform, told In Sequence last week at the annual meeting of the American Association for Cancer Research in Orlando, Fla.
"This custom kit will allow those who are doing more esoteric genomes to use the power of our technology in their studies," Ernani said.
In addition, Ernani said that the expanded kit would be of interest for researchers who would like to design targeted sequencing studies that look at the conserved regions within a genome or other regions for which a catalog kit is not available. "They can go ahead and make that in addition to the exome and combine the data sets," he said.
Researchers can use the company's online eArray design software to create their enrichment kits, and Ernani said that the turnaround time is six weeks or less. The SureSelect offering now encompasses a range from less than 200 kilobases to more than 34 megabases, and customers can order the kits in quantities ranging from 10 to 5,000 reactions. All kits arrive in a single tube.
Agilent has not disclosed pricing for the new kits but Ernani said the price depends on the amount of content and the size of the order and there's "a nice volume discount." He added that the expanded offering is "much more cost effective" than it would be to order five of the current 6.8-megabase kits.
Ernani said that the offering grew out of customer requests for targeted kits on the order of 30 megabases or more. Agilent provided the expanded kits for these customers under early-access agreements, though Ernani could not disclose the identities of any of these groups since they have not yet published their studies.
"You wouldn't believe how many people have come to us asking for exome designs for a whole variety of different organisms," he said. "It's obvious that exome sequencing has been seen as a very powerful tool for discovery, looking at the expressed genome."
He added that some early-access customers have designed kits to capture more than 60 megabases, and the company has not yet identified an upper end for the amount of genomic regions it can capture with its technology.
"We haven't seen the limit," Ernani said. "You'd think that at some point there will be a limit, but the way we design our kits, the baits are in molar excess so the kits are very concentrated. They become almost quantitative in their capture, so you can almost capture every target that you're trying to capture," he said.
"We haven't seen the limit yet and we're going pretty large."
Ernani said that Agilent is currently working to make kits that are compatible with the Pacific Biosciences and Ion Torrent sequencers.
In the company's collaboration with Pac Bio, for example, the single-molecule sequencing company modified the protocol for Agilent's SureSelect kinome RNA capture kit to target more than 600 genes in cancer cell lines and esophageal cancer samples.
In a presentation at AACR, PacBio CSO Eric Schadt discussed the kinome RNA work, which was done in collaboration with researchers at the University of California, San Francisco. He said that the researchers were able to detect KRAS mutations and splice variants with the kit.
Furthermore, he noted that the long reads of the PacBio system made it possible to cover the entire transcript length of any given gene with a single-molecule read — a capability that enables unambiguous detection of alternative splicing, he said.