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Cofactor Genomics Set to Offer Services in Exchange for Sequencer Trade-Ins

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St. Louis-based Cofactor Genomics is gearing up to kick off a sequencer exchange program that would see some customers trading in their up-to-date sequencing instruments in exchange for credits toward Cofactor services.

The scheme — conceived in part through discussions with current and past customers — is intended to appeal to those facing challenges in trying to meet sequencer scalability and/or read length targets using their current sequencing instruments.

Some of those interested in the sequencer exchange program "may have written that check for the next-gen machine, but … they may not have the protocols worked out" for front-end molecular work or post-sequencing analysis, Cofactor CEO Jarret Glasscock told In Sequence.

Others labs might be ready to ratchet up their sequencing output, he added, but may lack the staff, hardware, or investment needed to support a larger capacity instrument.

By designing a program that ups Cofactor's own sequencing capacity in exchange for services tailored to customers' specific research goals, "we want to try to help our clients and any new clients to move forward as quickly as possible in their research," added Jon Armstrong, Cofactor's chief operating officer.

Cofactor Genomics is currently working through around 150 samples each month, Glasscock explained. The company hopes to roughly double that output using instruments obtained through the sequencer exchange program.

"The platforms that we would be taking into consideration for the exchange program are current-style platforms — anything in the … Ion Torrent [PGM], [Illumina] HiSeq, [Illumina] MiSeq range," Armstrong noted.

The trade-in plan is intended to feed into Cofactor's so-called master alliance program, which allows researchers in academia or industry to purchase a set amount of sequencing capacity and/or services over a specific time frame, Glasscock said.

That capacity can then be applied to a number of small projects within that time frame, for instance, or a few larger projects, Glasscock explained. "With this type of program or structure that we've built, they're able to take advantage of volume pricing with the dedicated capacity to get quick turnaround," he said.

"What we wanted to do, with individuals who had a given amount of work for a year or two, was set up that structure once," he added. "Then we became basically dedicated outsourcing for them."

For the sequencer exchange program specifically, the company plans to parcel out the amount of this sequencing capacity — coupled with appropriate sample preparation and/or bioinformatics-based analyses in most instances — on a case-by-case basis following discussions with those interested in making the instrument-for-services trade.

"Depending on what their goals and what their needs are, we try to develop a menu so that we can achieve their goals in the next year or two and what they have planned in their pipeline," Glasscock said.

For some, that may mean scaling up their available sequencing capacity from the Illumina MiSeq to that offered by the HiSeq 2000, he explained. Others may be involved in projects that call for metagenomic sequencing on the Roche 454, while certain customers may be better served by having access to sequence data that can be turned around quickly on the Ion Torrent instrument.

Rather than offering a standardized package of sequencing and services in exchange for a given instrument, the company plans to discuss proposals with interested labs to come up with the combination of sequencing strategies and platform(s), sample preparation steps, and analyses that best fit the research problem at hand, said Armstrong.

Washington University pathology and immunology researcher Eric Duncavage told IS that, at first glance, the sequencer exchange program "seems like a good idea," particularly for smaller labs or those who'd prefer not to deal with sequencer service contracts.

"It's difficult for small projects to get sequencing done," he noted. "Cofactor can do smaller scale projects that aren't as attractive to large-scale operations like our own genome center."

Duncavage is not affiliated with Cofactor, but worked with Armstrong in the past at Washington University. He is also corresponding author on a 2012 Modern Pathology paper looking for prognostically informative mutations and translocations in leukemia-related genes, which relied on services done at Cofactor.

Though he and his colleagues did their own analyses for that study, Duncavage noted that Cofactor's wet lab expertise and assistance in designing hybrid capture probes were especially helpful, since such approaches weren't as widely used or well-established when experiments for the project were done around 2009.

"Their wet lab stuff is very good," Duncavage said. "Especially back in the day, when indexing and stuff like that was pretty new."

Founded by researchers with experience working at the the Genome Institute at Washington University, Cofactor began offering sequencing services in 2008 (IS 12/02/2008).

During the intervening years, the company has grown from two or three individuals to a staff of around 15 people and moved out of its initial 1,600 square-foot lab into a 9,000 square-foot facility.

Its sequencing capacity has grown, too. In its early days, the company relied on a lone Illumina GAII instrument. Cofactor now has a wide variety of platforms: at least one each of the Illumina HiSeq 2000, Illumina MiSeq, SOLiD 4, Ion Torrent PGM, Roche 454 GS FLX, and Roche 454 GS Junior instruments.

That repertoire is expected to expand further through the sequencer exchange program — offering variety that company representatives hope will appeal to labs having a tough time settling on a platform to purchase for a given project.

"One of the biggest areas of anxiety for people in the next-gen space is which platform to purchase," Glasscock said. "We choose the correct platform for the project — and sometimes we choose multiple platforms for a given project."

Representatives did not provide details on the number of sequencing machines the company currently has on hand, noting that the number of instruments can vary from one quarter to the next depending on whether the firm brings in additional instruments for a given collaboration.

Since 2008, Cofactor has also cast off the now-too-narrow description of "sequencing service provider." It now calls itself a "contract research organization" and has invested a considerable amount of research and development into sample preparation and bioinformatics, which Armstrong calls the "bookends" of the sequencing pipeline.

"Really our concentration isn't so much on just generating the data here," he said. "We don't think of how we derive our value for our clients as having sequencers in house, necessarily, or having more than competitor A, B, or C."

"The value is in our very critical eye on library construction, the [quality control] process that goes into library construction," Armstrong argued, "and also more complicated library construction like long insert mate-pairs, which can be extremely challenging to make, in some cases, especially from DNA that isn't of high quality."

So, while it was founded at a time when access to next-generation sequencing platforms and experienced staff to run them was more limited, Armstrong noted that Cofactor has continued to develop library construction, capture, and analysis protocols to keep pace with the current climate, in which far more people have access to sequence data.

An investment in R&D has helped Cofactor make some forays into product offerings. For instance, the company began marketing a bovine whole-exome capture kit last year and hopes to introduce additional products and service add-ons in the coming year.

"We enjoy R&D here, so a lot of those product offerings and a lot of those bolt-ons come out of our R&D efforts," Armstrong said.

Cofactor employees have been working on improvements on the software side, too, with an emphasis on RNA sequencing, differential expression, and de novo assembly.

Indeed, the company's library preparation and analytical services were among the draws for Cofactor customer Hongwei Yu, with Marshall University.

His group turned to Cofactor when it wanted to sequence and find SNPs in the genome of a biofilm-producing, opportunistic pathogen called Pseudomonas aeruginosa PAO579 — work published in the Journal of Bacteriology this past December.

Yu told IS that he has no plans to take advantage of the sequencer exchange program, since his lab does not have its own sequencing instrument, but said his team is "very happy" with Cofactor's service so far and plans to continue working with the company to assess several other additional P. aeruginosa strains.

"For me, I don't think it's economical to have a sequencer running in my lab," he explained. "I'd rather pay to have someone else do it for us."

Armstrong and Glasscock said that they have started discussions with a few customers who expressed interest in the sequencer exchange program, but declined to disclose their identities.

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