This story has been updated to include comments from a Roche NimbleGen service provider and a Roche spokesperson.
Roche's decision to discontinue the majority of NimbleGen's array portfolio by the end of the year has its customers asking questions about the future of their own array-based projects and offerings.
Last month, the company announced its plans to shutter its NimbleGen array portfolio, save its sequence capture products, and lay off the majority of Roche NimbleGen's staff if it cannot find a buyer capable of supporting the business(BAN 6/13/2012).
A spokesperson said this week that nothing has changed since the company first discussed the restructuring.
Some customers interviewed by BioArray News said that they feel "sad" and "helpless" about Roche's decision and now must evaluate other platforms for use, while others said they have moved on to next-generation sequencing-based projects, and will continue to use NimbleGen sequence capture products.
Patrick Law, scientific officer for the Chinese University of Hong Kong's core facilities, said it "would be a pity" if the arrays are discontinued. CUHK is a certified service provider of NimbleGen arrays, and Law said that the university has an "increasing number of customers" interested in using NimbleGen chips, which he described as "very good research tools."
Now faced with the potential discontinuation of the platform, Law said that CUHK is "feeling helpless" as it does not have the budget to switch to another platform. Instead, it is looking to find a vendor that supplies arrays that will run on NimbleGen's hybridization and scanning systems. In the meantime, Law said that CUHK hopes that "someone will buy NimbleGen, ASAP."
Jón Jóhannes Jónsson, medical director of the department of genetics and molecular medicine at the National University Hospital of Iceland, said he would continue to use NimbleGen arrays should they continue to be available.
"I think the NimbleGen microarrays are fine and I would continue to buy them if they would be still produced," Jonsson said. Still, he added that array technology is "developing rapidly and you need to further develop your product to stay competitive."
Jónsson said that his department maintains a fully equipped array lab, and that it has used NimbleGen arrays "with success" for various applications, both in research and diagnostics.
"I am sad that they are discontinuing their service and don't understand why," Jónsson said. "I still think there will be market for microarrays and they had a good product."
Whatever happens to NimbleGen's chips, Jónsson said that his department will continue to use arrays, but has yet to determine what platform it will adopt should NimbleGen arrays be discontinued.
Some customers were less troubled by the news. Patrick Schnable, director of the Center for Plant Genomics at Iowa State University, had previously used NimbleGen comparative genomic hybridization arrays to study maize, but recently transitioned to sequence capture and next-gen sequencing for the analysis of structural variation, "because we prefer the greater information content of the resulting data."
The center also switched from NimbleGen's array-based sequence capture approach to its liquid-phase sequence capture products, and Schnable said his team "prefers liquid phase capture due to the simplicity of its workflow." Overall, Schnable said that the center plans to stick with NimbleGen sequence capture "because we believe their design pipeline yields excellent probes and probe coverage."
Loren Rieseberg, professor of botany at the University of British Columbia, was the corresponding author on a paper published earlier this year that described the development of NimbleGen-made arrays for five different groups of weeds.
While "pleased" with the arrays, Rieseberg said that his lab has been moving to sequencing-based analysis of expression variation, and said that if NimbleGen arrays are discontinued, it "will not be a problem for us."
Whether or not Roche ultimately finds a buyer for its NimbleGen array portfolio, Ambry Genetics hopes to be ready.
Aliso Viejo, Calif.-based Ambry became a certified service provider of NimbleGen sequence capture, CGH, chromatin immunoprecipitation (ChIP)-on-chip, methylation, and expression arrays last year.
Ardy Arianpour, vice president of business development at Ambry, said that the firm is now working on recalibrating its Roche NimbleGen hardware in order to process other types of arrays.
"We have lots of arrays running at Ambry, and [making] our NimbleGen instruments capable of running other arrays is actually an advantage and a cost savings on additional capital equipment," Arianpour said.
Since learning of Roche's plan to discontinue the business, Arianpour said that Ambry is "taking proactive steps" in moving projects forward to other platforms that Ambry currently offers. Ambry is also a certified service provider of Agilent Technologies' arrays, and Agilent makes Ambry's internally designed CHO Cell Expression Array, StemArray, and CancerArray chips.
Arianpour said that most of the firm's offerings are on the Agilent platform, and that Roche NimbleGen arrays have been used by specific customers. He added that Ambry can "easily transition" these clients' future projects onto other platforms.
Echoing CUHK's Law, Arianpour said that "someone should buy NimbleGen" as it offers "great products." Still, he cautioned that Roche's decison to discontinue most of its NimbleGen array portfolio is a "perfect example of why you should not be married to just one platform."
Valerie Reeb, manager of the Carver Center for Genomics at the University of Iowa, had similar sentiments. The CCG has been a Roche NimbleGen service provider for several years, and Reeb said the academic center was "surprised" and "disappointed" with Roche's decision to discontinue NimbleGen arrays, citing a high "level of interest" across the "full complement" of NimbleGen's portfolio.
Despite the decision, the CCG is moving ahead with array-based projects, and is considering a move to the Agilent platform.
"With the number and variety of projects we have done for investigators not only from the University of Iowa but from universities all across the country, we believe there remains considerable interest and need for this [microarray] technique," Reeb told BioArray News.
"As such, we continue to be committed to providing researchers a source for obtaining high quality data from their microarray projects," she said.
Should CCG adopt Agilent, Reeb said the transition for the center would be "relatively easy with little downtime or impact on the quality of services." She also pledged that CCG will continue to offer services on the Roche NimbleGen platform through the end of 2012.