NEW YORK (GenomeWeb) – Newport, Va.-based bioinformatics firm Gataca is looking for researchers to test early versions of its flagship cloud-based products for the life science market as part of an ongoing beta, and is seeking investment partners to support its development and growth moving forward.
Specifically, Gataca — whose name is coined from DNA's constituent chemical moieties — is asking interested researchers and especially virologists from academia, clinical laboratories, and the pharmaceutical and biotechnology industries to test OneGenomeBox, its next-generation sequence data management solution; and HepCBase, its software for analyzing both Sanger- and NGS-generated genomic data from the hepatitis C virus (HCV). The company plans to launch OneGenomeBox at the end of the fourth quarter of this year, and to launch HepCBase in Q2 2015.
OneGenomeBox contains tools primarily for managing, storing, and visualizing data. Among other features, its tools let users evaluate raw read quality, as well as trim and filter reads based on parameters such as N content, log changes, and GC bias. It complements existing research workflows because it reduces the time bottleneck associated with large data uploads, taking hours instead of days, and once the files are in the system, they can easily be shared and explored, Gataca CEO Johanna Craig told BioInform. Users can move sequence files in and out of the system easily to perform tasks such as read alignment and variant calling using their preferred algorithms. Gataca is mulling adding both an alignment tool and variant caller to OneGenomeBox at a later date depending on customer demand, Craig said.
The company's other product, HepCBase, is a version of OneGenomeBox that is tailored for analyzing HCV sequence data. Among other features, it has tools for HCV genotyping, phylogenetic analysis, and analyzing and reporting genetic mutations; and will soon also include an alignment tool tailored to the mutation rate of the virus. The software has two modules; one designed for use with Sanger sequence, and a second specifically for exploring NGS data.
In the Sanger sequence module, when users import Hep C sequences or the entire roughly 9-kilobase viral genome, the system is able to recognize things like protein regions and motif structure, and it stores and displays the information to the user in a viewer. It also highlights DNA modifications such as phosphorylation sites, does multiple sequence alignments using HCV mutation rates as a variable, performs graphical pairwise alignments to show sequence similarities and differences, and more. The next-gen sequencing module, which is still being developed and currently has fewer HCV-specific capabilities than the Sanger module, includes tools for HCV genotyping and will soon include routines for assessing HCV strain diversity. The solution can be used for HCV testing and screening in clinical laboratories.
Although OneGenomeBox is nearer commercial launch, HepCBase was the initial product on which Gataca intended to build its business. The company launched in 2005 with plans to develop and sell software solutions specifically for virologists studying HCV, who at the time did not have computational solutions for analyzing HCV mutations and thus did much of that kind of analysis work manually, Craig explained. Armed with grants from the National Science Foundation, she and her team began developing a solution that would help virologists make sense of their data. But then sequencing technologies evolved and virologists started to use then-novel next-generation sequencing technology instead of traditional Sanger sequencing for which HepCBase was designed, and that meant rethinking and redesigning the software, she said.
Gataca secured additional grants from the National Institutes of Health's Small Business Innovation Research program and those funds have supported its development efforts to date, Craig said. Now in addition to running the beta, the firm is seeking investment partners to support its development moving forward as well as looking into expanding its employee headcount — right now Gataca has two employees and works with about 10 consultants.
The current beta is primarily to test OneGenomeBox, but Gataca is accepting applications to test the more embryonic HepCBase as well, Craig said. Ideally, researchers who want to try out the latter solution will choose to test one of the two modules and give specific feedback to guide development efforts on the solution since it does target a very specific market segment, she said. It is especially seeking testers for the Sanger module, which is further along in its development.
Gataca is also using the beta to determine which cloud infrastructure to use, to flesh out its commercialization plan, and to mull various competitive pricing models for its products — it is considering things like charging a licensing fee for a certain number of seats, and charging on an annual or per-project basis. Part of that involves exploring the HCV market opportunity in greater depth and areas where its software could confer the most benefit, Craig told BioInform.
Once the life cycle and genetic code of HCV was sussed out, pharmaceutical companies began developing new and more effective treatments for the virus such as Gilead's sofosbuvir (brand name Sovaldi), she said. But these specialty treatments are expensive — a 12-week sofosbuvir treatment, for example, costs $84,000 — and unsustainable in the long run, she pointed out. As such, researchers in academia are starting to look for less expensive therapies, developing vaccines to prevent the disease in the first place, and working on providing more tailored treatment options, all areas that the HepCBase software could help address, according to Craig. As such, "we really have a bigger market now than we did before," she said.
Separately, Gataca also offers software customization services — pricing is determined on a per-project basis — through which it can tailor OneGenomeBox to manage and analyze sequence data from viruses other than of HCV that are of interest to potential customers — HIV, dengue, and influenza, for example — as well as tweak its visualization and results reporting capabilities to fit clients' projects. In fact, the company plans to eventually do for HIV what it has done for HCV. On this front, Craig said that the company is working with the Forum for Collaborative HIV Research, a Washington, DC-based public/private partnership, on a pilot project using Gataca's software. It is also planning a similar offering for hepatitis B virus, Craig said, and is even exploring the possibility of working with the Ebola virus. The firm is also interested in working with patrons of its custom services to potentially commercialize targeted solutions developed as part of their projects, Craig said.