This story was originally published July 18.
Life Technologies has notified customers of its SOLiD 3 sequencers that it will no longer supply reagents for the system after Oct. 1.
The decision, which the company made in order to simplify its manufacturing process, is not expected to impact many customers since most SOLiD 3 users have already upgraded to the company's SOLiD 4 or 5500xl platforms, according to a company official.
The move did surprise some clinical labs with validated SOLiD 3 workflows, however, who are now left with only a few months to upgrade their sequencers and revalidate their processes.
"We've given customers the opportunity to convert over at a relatively reasonable price," Mark Gardner, vice president and general manager for advanced genomic systems at the company, told Clinical Sequencing News.
The exception, he acknowledged, is "folks who have not converted over [who] have had some sort of validated protocols that have kept them on SOLiD 3."
He added that the company is working with these customers "on a transition plan."
Gardner conceded that CLIA labs and other groups that have built a validated sequencing workflow around the SOLiD 3 would be hesitant to make any changes to their protocols. "For them to revalidate, that's really their main cost," he said. "That's something we've been sensitive to and we've been providing most of those customers with the ability to pre-buy or bulk buy reagents for the transition."
He noted that a software upgrade is available for the SOLiD 3 that will allow it to run SOLiD 4 reagents. The list price for the upgrade is $10,000, but he said the company has various programs in place to help defray the cost. Likewise, Life Tech is running a "series of promotions" intended to encourage SOLiD 3 users to upgrade to the 5500xl, though he declined to provide further details.
Gardner said that SOLiD 4 users should not fear that the company will discontinue reagents for that system since they are essentially the same as the 5500 reagents, though the packaging is different.
That was not the case for the SOLiD 3, however. The reagents for that system are "degenerately synthesized," Gardner explained. "In other words, you make the first two bases individually and then afterwards it's a random mix."
The consequence of that, he said, "was that there were coverage gaps with SOLiD 3 that we addressed with SOLiD 4."
The SOLiD 4 reagents, by contrast, are "individually synthesized probes, which yields better coverage," Gardner said. "It doesn't make sense to make both sets of probes."
Labs in the Lurch
While the company did not provide figures on the current number of SOLiD 3 users, a recent survey by Cambridge Healthtech Institute indicates that they make up a minority of the SOLiD user base. Out of 430 respondents to the survey, only 9 users said they were still using a SOLiD 3, while 82 respondents said they were using the SOLiD 4. The survey did not report data on the 5500xl.
Even though the overall number of SOLiD 3 users is small, the impact on the few clinical labs who are still running the system is significant.
For example, Emory Genetics Laboratory, which installed a SOLiD 3 in early 2010 and began offering several sequencing-based tests for congenital disorders last spring (IS 5/25/2010), was surprised to find out that the company was discontinuing the reagents for the system.
"For clinical laboratory applications … it is important that laboratories are given enough notice to make the switch, as accredited laboratories such [as] we have to document and report all changes we make to procedures," Ephrem Chin, manager of Emory Genetics Laboratory, told Clinical Sequencing News via e-mail.
He noted that the decision doesn't leave the lab with much time to upgrade its system and revalidate its processes. In addition, he said that the upgrade and revalidation would "have an immediate effect on test cost and test pipeline," though he declined to provide additional details.
Likewise, Michael Friez, director of diagnostic laboratories at Greenwood Genetic Center, said that "groups like ours that perform clinical testing feel like we don’t have the same flexibility as other research-oriented labs to switch over to new platforms without some significant degree of validation work to ensure consistent quality of the results being generated."
Friez said he was "made aware of this likely discontinuation of reagents after committing to an upgrade to the SOLiD 5500xl and other surrounding equipment."
Even though Greenwood had already decided to upgrade to the 5500xl, "we had specific conversations about keeping the SOLiD 3 in operation so we could continue using it for different purposes, especially for collaboration with other groups in South Carolina that do not have access to such equipment."
However, "based on this new information, this does not appear to be an option for us."
The "big unknown," he said, "is really how much validation is needed" for the 5500xl.
The system "should function in the same capacity, if not better than, the SOLiD 3, so everyone probably has their own idea of how much validation is truly required." However, he added, "there are no standards to refer to in this regard."
For the time being, he said, "it appears that each lab will need to basically make a good faith effort to adequately validate their protocols on the new platform."
Chin added that the situation highlights a drawback of implementing next-gen sequencing in the clinical setting — the technology is advancing at a much more rapid pace than most clinical labs are accustomed to. Yet he noted that vendors should be aware of the unique needs of the sector — especially as they eye the clinical market as a growth area for next-gen sequencing.
"We understand that the technology and this field [are] dynamic but clinical laboratories' needs are different and more stringent," Chin said.
"If companies manufacturing and marketing NGS instruments truly want to be in the clinical space, these issues need to be considered."
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