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Cofactor Genomics’ Small-Lab Sequencing Service Uses Second-Gen Tools Exclusively

Sensing demand among small research labs for large-scale sequencing, a new service provider called Cofactor Genomics has set up shop in St. Louis, banking exclusively on second-generation sequencing technology.
The startup, founded earlier this year by three scientists who previously worked with second-gen sequencing platforms at the Washington University Genome Center and backed with angel funding, began offering services in May on a single Illumina Genome Analyzer II. Next year, it plans to add 454 and SOLiD sequencing services.
Cofactor, which targets small customers and focuses on projects that require specialty libraries, said it differs from other commercial service providers and academic core facilities by not only delivering sequence data but by also providing customers with experimental design, library construction, and custom bioinformatics services.
It is also among the first sequencing-service shops that offers no Sanger sequencing.
“We realized that with next-gen, it does not take a whole genome center to do this kind of work, and that it can bring a lot of value even to the small labs,” CEO Ryan Richt recently told In Sequence.
However, he and his colleagues also realized that “one of the biggest problems small labs had — besides not having access to next-gen — was about the analysis, … and none of the other service providers were clearly focused on providing custom bioinformatics even to small labs.”
Previously, Richt and co-founders Matt Hickenbotham and Jarret Glasscock each spent several years at the WashU Genome Center, where they “were involved with next-gen sequencing from the beginning,” he said. All three have worked with Elaine Mardis, co-director of the center, on developing and testing new sequencing platforms and analysis tools.
Richt is quick to point out that the five-person company is no longer affiliated with the Genome Center or its researchers, but the experience he and his colleagues have gained “really makes a difference” for operating the instrument and analyzing the data.
Also, he said, they “still have ongoing relationships with many of the next-gen instrument manufacturers and other lab equipment manufacturers.”
Cofactor, which is funded by an undisclosed amount from the founders and an angel investor, is located “down the street” from the WashU Medical School in an old building with wooden floors and exposed brick walls that it shares with other tenants that include photographers, designers, and architects.

“None of the other service providers were clearly focused on providing custom bioinformatics even to small labs.”

The firm decided to start with a single Illumina system because “we had been working with them practically from the beginning of Solexa, and it represented the smallest initial investment when you consider the total cost of ownership,” according to Richt. However, he said, “we had always planned to support and integrate all three [second-generation] platforms to exploit their unique advantages.”
One way the company differs from most other service providers is that it posts pricing information on its website. Prices range from just under $3,000 for a partial lane of sequencing that yields 68 megabases of data to $52,600 for three flowcells, which generate 8.16 gigabases of data.
According to Richt, prices are all-inclusive, covering assistance with experimental design, library preparation, sequencing, custom data analysis, and a fast hard drive to mail the data back to customers.
“There are no hidden fees,” he said. “The whole process of getting a quote makes people feel like they are getting unfair prices — and they probably are — and we just wanted to completely remove that uncertainty and have people know upfront.”
Users can also check online when sequencing capacity is available. The company currently has a project turnaround time of about a month, Richt said.
Most of the company’s current customers are academic labs. While such customers could also use services from academic core facilities, many of these — including one at WashU — do not include computational analysis services and require users to make their own sequencing libraries, according to Richt.
That is one reason why the company focuses on “specialty libraries” that are more difficult to generate than genomic libraries, for applications such as RNA-Seq, bisulfite sequencing for methylation analysis, or microRNA analysis.
For the data analysis, Cofactor Genomics uses a combination of alignment and assembly tools developed elsewhere, and analysis, visualization, and statistical software it developed in-house, including a graphical visualization software called “Gentuition” that allows customers to “zoom from the whole genome all the way down to the primary reads,” Richt said.
Until recently, the company sold licenses to this software separately, but starting in January it will bundle a new version of the tool with customer projects.
The company, which has received advice on its strategy from the WashU Olin Business School, also plans to increase its staff, including “a very experienced lead sales rep,” and to expand its sequencing instrumentation.
Early next year, it will start offering 454 sequencing and analysis services through a partnership with MOgene, another St. Louis-based firm that focuses on microarray-based services.
Probably “even before that,” Cofactor Genomics plans to purchase a SOLiD sequencer from Life Technologies “to take advantage of [its] extensive barcoding options and [its] incredibly quick library preps for RNA-Seq and microRNAs — which turn out to be the most popular applications by far,” Richt said.
In addition, it has new library preps for the Illumina platform as well as new software under development, though Richt did not provide details on these.

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