EdgeBio said last week that it has received CLIA certification for its next-generation sequencing operations and will offer a clinical exome sequencing test intended for large labs and hospitals that can do their own in-house interpretation of the results.
A number of commercial and academic labs — including Ambry Genetics; the University of California, Los Angeles; Washington University's School of Medicine; and Emory University — have recently begun offering clinical exome sequencing testing services that include interpretation of results (CSN 3/7/2012, CSN 2/29/2012, CSN 3/21/2012).
EdgeBio is taking a different approach, however, planning to supply only aligned sequencing data, which customers can then interrogate and interpret themselves. Because of this, the company will sidestep issues related to determining what results to return, CEO Dean Gaalaas told Clinical Sequencing News.
EdgeBio has been offering next-gen sequencing services and products since 2008. Gaalaas said the company already has two customers who are solidifying agreements for the new clinical exome testing service while negotiations with a third client are currently in the works. He declined to provide details about these initial contracts, but said at least one client would likely announce its participation in coming months.
He explained that EdgeBio is seeking customers for the service who are looking only for the clinical sequencing data, and plan to do interpretation and make decisions on how to return results to patients themselves.
"What we're not going to do is have the capability to provide genetic counseling or the ability to interpret data to make clinical or therapeutic recommendations," Gaalaas said. "That's not our job."
"Say you have a genetic group or a lab group that has that capability but doesn't have access to a sequencer, or doesn't have bioinformatics. They want to be able to send out samples, get exome data and have an aligned file. But [they] know how to mine [the data] and when [they] see mutations, [they] know how to deliver that result either back to the attending physician or to the patient themselves," he explained.
EdgeBio plans to offer clinical exomes using both the Life Technologies' SOLiD and Illumina HiSeq platforms. Gaalaas said the official turnaround time for the exome sequencing service will be eight weeks, but that the company believes it can also "do better than that."
According to Gaalaas, the choice of platform will depend somewhat on what individual customers want, but the bulk of clinical sequencing will likely be done on the Illumina going forward.
"We started out with SOLiD just because we have such experience running the SOLiD," he explained. "We've only had our Illumina now for maybe three, four months, so when we were building with CLIA we didn't have a preponderance of Illumina data to support our initial application so we did it all on SOLiD."
Gaalaas said the company is currently in the process of collecting data to extend its certification to the HiSeq.
He added, "I think it's fair to say that the market has spoken, particularly with exome sequencing, and the norm is doing paired-end 2x100 base pair sequences, and unfortunately the SOLiD platform just doesn't have that chemistry availability."
In a release announcing the company's CLIA certification, EdgeBio said that Sherri Bale, managing director of GeneDx, will serve as the laboratory director for EdgeBio CLIA operations. Gaalaas said that Bale is not leaving her position at GeneDx.
"GeneDx is literally across the parking lot from us, so given their proximity Sherri has agreed to be our laboratory director as well," he explained.
Moving forward with this service model, Gaalaas said EdgeBio plans to expand its clinical sequencing offerings, but only according to specific needs from customer labs and hospitals.
The company doesn't have additional sequencing tests in mind. Rather, it plans to offer new services based on which areas of need develop in its customer base.
"We're not a hospital … we're really more of a sequence provider," Gaalaas said. "So, while a typical genetic lab might specialize in certain things or have relationships with doctors or may have a focus in a particular field and that's how they drive that [test] menu, we don't have an agenda per se."
"We do want to add more tests but it's just going to be determined by our customer profile — who signs up first and what they specialize in," he said.
Gaalaas noted that the company also has an Ion Torrent PGM, which may be of interest to customers who want to use AmpliSeq cancer or custom panels, "but we're not sitting around [saying] we've really got to develop a panel for [specific] markers."
Because it isn't planning to interpret exome sequencing results, EdgeBio also won't be offering confirmation of results by Sanger sequencing, Gaalaas said, a situation he said early potential customers seem to be happy with.
"Again, because we're not making the calls, that'’s up to the customer," he said. "We have Sanger capability in house so we can do those types of validations, but some of the early customers we've talked to, they also have that capability in house."
That's not to say EdgeBio couldn't or wouldn't ever do such confirmation for a customer who asked, but "it's not part of the service," Gaalaas said.