Cofactor Genomics has moved into new 10,000 square foot headquarters, which will enable it to double its sequencing capacity. The firm is also launching a new RNA sequencing service, dubbed RNA-seq Dx, and it expects its facilities to become CLIA certified around the second quarter of 2014.
CEO Jarret Glasscock told In Sequence that in the last six months, the St. Louis, Mo.-based services firm has signed more three- to five-year contracts than it has in its entire five-year existence. While more laboratories own next-gen sequencing instruments than ever before, Glasscock said that the demand for services is not waning. Additionally, clients are now looking not just for sequencing services, but also for a partner to work with them from sample preparation and experiment design all the way through analysis and interpretation.
Cofactor offers services on all commercially available sequencing platforms, but does not disclose how many of each system it owns or leases. It offers de novo whole-genome sequencing and assembly, RNA-seq, micro RNA-seq, and targeted sequencing like exomes or panels for SNP analysis.
By far, its most popular service is RNA-seq, Glasscock said. Because of that, he said the firm has focused on honing that service, funneling around 90 percent of its R&D budget into developing better protocols for RNA-seq.
The result is a new offering dubbed RNA-seq Dx, a service that includes extensive quality controls and measurements of sensitivity, specificity, and accuracy. The service includes "molecular spike-ins for QC and normalization in combination with the correct design for sequencing count, read length, and the appropriate analysis," Glasscock said.
Despite its name, the service is not diagnostic, but it "brings molecular-based standards, very similar to what's present in arrays" to RNA-seq, Glasscock said.
Aside from RNA-seq, Glasscock said that customers look to Cofactor for its bioinformatics capabilities and help choosing the appropriate sequencing platform or platforms. He said that many projects employ a combination of short- and long-read technologies.
"Using mixed platform approaches, we can give the best bang for the buck," he said. "Using a long-read approach combined with a much deeper, higher count, short-read approach allows us to see into what the complexities are."
Sometimes, the two platforms will be used to create hybrid assemblies, he said. But the long-read sequencing technology can also be used in RNA sequencing when looking at specific isoforms.
Glasscock told IS that the firm serves three primary customer bases, — the pharmaceutical, agriculture, and biofuels industries — and that industry customers are increasingly using next-gen sequencing services. He also said that RNA-seq is popular among all three customer bases.
Pharmaceutical clients tend to use the service in very early discovery stages to identify where they are going to focus their candidates and to understand the biology of the phenotype, he said. Additionally, RNA-seq can also be used to understand drug sensitivity and resistance at the gene expression level.
Often, pharmaceutical companies will want to follow up the RNA-seq study with an exome or targeted panel to understand how the changes in gene expression correlate with specific SNPs, Glasscock said. He added that becoming CLIA certified will help drive the company's exome sequencing business, particularly among pharmaceutical companies looking to implement sequencing as part of a clinical trial or as a follow on to RNA-seq.
Agbio clients typically use RNA-seq to understand how different environmental stresses impact gene expression and to understand host/pathogen relationships, including which genes are expressed when a plant is infected.
Moving forward, Glasscock said that the firm aims to develop protocols similar to its RNA-seq Dx offering for DNA sequencing applications, in order to provide those measures of sensitivity, specificity, and accuracy to all of its sequencing services.