Responding to customers’ increasing appetite for next-generation sequencing, Agencourt Bioscience has acquired a second SOLiD sequencer from Applied Biosystems, the Beckman Coulter subsidiary said this week.
The instruments still pose challenges both on the front end and the back end but will not affect the company’s fleet of 35 Sanger sequencers in the short term, Agencourt said. However, they will probably replace some of them in the long run.
“At the moment, [the Sanger] machines are still humming full-time,” Lynn Doucette-Stamm, vice president of business development at Agencourt, told In Sequence this week. “But if you asked me, five years from now, will we be running all those Sanger machines? Probably not. But when is that switchover? I don’t know.”
Agencourt received its first SOLiD system in October and told its customers at the time that it was offering pilot projects on the system.
Since then, “the demand from folks wanting to try their samples on the instrument [has been] extremely high,” said Erick Suh, Agencourt’s director of genomic services. “We have more opportunities than we can handle right now [so] we decided it would be good to boost up our capacity.”
Among the applications customers want to run on the new platform is ChIP-sequencing, and Agencourt is currently developing protocols for this. “There are some challenges in working with those types of samples and getting sufficient quantities in the right size range,” Suh said.
Other projects customers have requested to be run on the SOLiD instruments are microbial genome resequencing and studies that involve sequencing methylated DNA.
Local ABI sales reps have been referring to Agencourt potential SOLiD customers who would like to run a service project and analyze the resulting data before they commit to buying an instrument. This set-up, Suh said, also increases the demand for Agencourt’s service work.
To be sure, the SOLiD still poses challenges at the sample-input and the data-output ends. For example, Agencourt has not yet determined how many samples customers can run on a single slide without overly compromising the data output.
“Technically, you are able to divide a slide up into eight individual sections. But every time you do that — put a partition between the sections — you lose some efficiency,” Suh explained. “Obviously, people are trying to cram as many samples as they can onto a slide and maximize the throughput.”
And on the data-output end, Agencourt is in the process of choosing a formal storage policy for the enormous amounts of data. The company can store “for weeks if not months” data generated by its fleet of 35 ABI Sanger sequencers, Suh said, but it’s another story with even a single SOLiD platform, which yields several terabytes of raw image files per run..
For customers who have a need for long-term storage, a third-party provider might be the solution, Doucette-Stamm said. “We are in a new realm now; we never had this problem before.”
Besides its SOLiD base, Agencourt owns a 454 Genome Sequencer FLX and is still looking for other next-gen platforms, existing as well as future ones. “Right now, we are concentrating on really getting the SOLiD firmly running, getting everything in place, so we are comfortable with it,” Doucette-Stamm said. “Then we will move on to the next one.”