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KBioBox Targets CRISPR Market With New Search Apps; Plans to Launch Solutions for Pathogen ID


NEW YORK (GenomeWeb) – Bioinformatics startup KBioBox has launched two new applications based on its core proprietary search engine technology that are intended to help researchers in industry and academia design and run gene editing experiments.

The new apps available on the so-called KBioBox bioinformatics portal are the 3-click gene editing off-target analysis program and the 3-click gene edit biodesign program. The gene edit off-target analysis solution, as its name implies, is designed to help researchers come up with CRISPR designs and identify potential off-target sites in the genome.

The new gene edit design analysis solution generates a ranked list of 10 bio designs based on gene location, search type, and gene edit type. It lets customers who already have CRISPR designs check whether their designs could have unintended impacts on other regions of the genome. Both solutions return simple annotated reports that include visualizations and locus information. The company has also developed an app for identifying pathogens in human samples that it plans to launch at a later date.

Both applications leverage KBioBox's genomic search engine, which uses proprietary algorithms that are capable of scouring whole genomes in minutes. KBioBox founder and CEO Kryngle Daly told GenomeWeb that he developed the engine in response to a perceived need for tools for searching nextgeneration sequencing data that improve Blast searches. "How do you search through terabytes of data to find that needle in the haystack? Scientists have built a lot of really good quantitative algorithms to deal with [needles] once you find them and to get really good results but what is missing is the search power," he recently told GenomeWeb.

Compared to running a Blast search, for example, which can take up to a week to fully parse a full human genome, the BioEngine can get through a full genome in seconds. This not only means that bioinformaticists can search single and multiple genomes in greater depth and in shorter periods of time, Daly said. "What's neat about our system is, because we can search the entire genome so rapidly and exactly, we can do a full genome off-target scan for a CRISPR or any type of gene edit in under a minute," he said. "What you get back is not approximations or thermodynamic predictions. You actually get a list of all the actual potential off sites in that reference sequence." In addition to gene editing tasks, the BioEngine can also be used in oncology contexts to perform variant analysis and for annotating genomes.

KBioBox is now focused on developing additional applications for sale on its platform, such as the ones released for gene editing, that leverage its core technology. In addition to its in-house development efforts, the company is seeking third-party developers willing to contribute apps to the KBioBox platform, Daly said. "Currently, we are looking for scientists with existing bioinformatic algorithms, or ones in development, that would benefit from better searching capabilities," he said. For example, companies like CosmosID and One Codex that have developed good quantitative algorithms for pathogen detection and analysis can use the BioEngine to improve the searching abilities of their platforms so that they can provide even better reports to their users. Other apps could focus on providing highly specific variant analyses, conserved region identification, and cross-species homology searching.

Next year, KBioBox plans to begin offering a packaged version of the BioEngine that will include all of the functionality needed to build apps, Daly said. In the interim, researchers interested in implementing their apps on the company's BioEngine can do so directly on the KBioBox's web portal or build them on outside systems and link them to the portal.

Customers, meanwhile, have the option to access KBioBox via the web portal or use the company's application programming interface to integrate its solutions into their existing workflows. Customers can pay per analysis or they can license the software. For the gene edit off-target analysis app, KBioBox charges $595 for a single off-target analysis with discounts for analysis bundles — $1,595 for three off-target analyses and $2,380 for five analyses. For the gene edit design solution, the company charges $995 for a single design, $2,685 for three designs, and $3,980 for five designs.

The company also offers gene edit packages. One package that provides one gene edit design and three off-target analyses costs $2,495; a second package that covers three gene edit designs and five off-target analyses costs $4,695; and a third package that covers five gene edit designs and nine off-target analyses costs $7,195. Customers can access the company's apps directly or through partners, like Transposagen Biopharmaceuticals, who resell KBioBox's off-target analyses as part of their cell line packages.

Transposagen sells modified cell lines and rodent models that are used for pharmaceutical research. "With a lot of the technologies we work with, there is a risk for an off-target," Matthew Goodwin, a technical sales specialist at Transposagen, told GenomeWeb. "Our customers were concerned about this and at the time, we didn't really have any in-house expertise to provide that type of analysis."

As a result, his firm signed an agreement with KBioBox in 2014 to provide customers with access to tools to assess the risks of gene editing in their cell lines and also to check the results post editing. "I think it's an increasing requirement [for] a lot of companies and academic researchers," Goodwin said. As many research studies that use gene editing technologies move towards clinical trials, "that check before and after the editing of the CRISPR tech is going to be paramount for any kind of FDA approvals and things like that so to ensure their project is in compliance so a lot of companies have this requirement built in," he said. "In fact, we probably wouldn't have some of the business of our customers if we didn't have KBioBox to help us with that."

In addition to its off-the-shelf product, KBioBox can also tailor its tools to meet customers' needs. For example, they can be adapted to accommodate new gene editing chemistries, Daly said. "It only takes us half a week to get a new type of chemistry in there," he told GenomeWeb. "All we have to do is change a few parameters in the application, we don't have to change the BioEngine at all. We've done this for several customers at this point."

KBioBox plans to launch other applications on its platform but because the company is currently pursuing patent protection for some of its capabilities, Daly declined to provide details about most of the planned apps. He did say, however, that the company intends to release a third CRISPR app that expands on the capabilities of the gene edit off-target analysis app. It will provide a list of primers for each of the potential off-targets so that researchers can run test experiments to see if the predicted off-target interactions really do occur.

The company has also developed at least one other application that is designed to detect pathogens present in human samples that Daly hopes to be able to eventually offer in diagnostic contexts. However, the company won't release the app until the application obtains the necessary approvals for diagnostic use, Daly said.

"It's really a question of what resources we need to do that and when we need to do that," he explained. "It would be great if we could find some people or companies to partner with that have the resources and the experience dealing with the [Food and Drug Administration] or getting medical technologies out there, which we can't do at this point," he said. "With the right partner, we can really push that through quickly."