Emerging from stealth mode, newly minted Five3 Genomics is hoping to claim a share of the bioinformatics marketplace by providing cancer genome analysis services using tools developed at the University of California, Santa Cruz.
The startup was founded by three UCSC graduates about a year and a half ago to commercialize informatics technologies they developed as students under UCSC's David Haussler.
The company plans to offer cloud-based data processing and interpretation services to researchers, pharmaceutical companies, and healthcare organizations involved in developing and applying personalized cancer therapies.
Five3’s core infrastructure includes Transporter, a high-speed transfer client based on open source technologies that let users upload and encrypt genomic data in FASTQ and BAM files; Contraster, which identifies germline and somatic variants using a Bayesian approach, locates variants involved in protein alterations in cancer, and finds rearrangements associated with fusions and copy number alterations; and Paradigm, a molecular pathway modeling tool that is also currently being used in a $10 million, three-year prostate cancer initiative funded by Stand Up to Cancer, the Prostate Cancer Foundation, and the American Association for Cancer Research (BI 10/12/2012).
The company currently offers free genomic data processing and annotation services to academic researchers, including sequence alignment pipelines, tumor-normal comparisons to detect relevant genetic alterations in cancer, and web-based visualization tools for further analysis. Researchers also have space to store their data in the cloud and share their information with collaborators.
Five3 is working on a separate pipeline for commercial clients that will have some of the same capabilities it offers in its research service along with additional features that are currently in development, including tools for deep data mining as well as analyzing genomic data from large patient cohorts, CEO Steve Benz told BioInform this week.
When the commercial pipeline comes on the market mid-year 2013, customers from industry will be charged a yet-to-be-determined fee for service, he said.
For now, industry clients can access Five3’s research analysis service for free as part of an ongoing beta and can provide feedback that will fuel further development of the commercial offering, Benz said.
A third component of Five3’s portfolio is an analysis service offered in conjunction with NantHealth — the digital medicine subsidiary of Los Angeles, Calif.-based NantWorks — that is intended for clinical use.
Benz explained that the partners are working to develop and provide patient decision support tools for use by oncologists. They are also reaching out to insurance companies to discuss methods of providing genomic analysis for patients as well as how to handle reimbursement issues, he said.
Under the terms of the agreement, Five3 will provide services for processing and analyzing genomic data in clinical cancer cases, while NantHealth will provide a secure environment for handling patient data among other informatics solutions, Benz said.
The companies are preparing to kick off a pilot project with an undisclosed private payer and they will also handle the genomic analysis component of NantHealth’s partnership with Blue Shield of California — which aims to a establish a clinically based continuous learning center as part of a new accountable care organization that Blue Shield will create with Access Medical Group and Saint John’s Health Center in Santa Monica, Calif. (GWDN 10/2/2012).
“The NantHealth service is going to be driven primarily through partnerships with payors,” and so its launch date “really depends on the success of these pilots and when the payors want to move ahead with more widespread adoption,” Benz said. “We're hopeful it's going to be more widely available in the next year as we secure more partnerships.”
Pricing for the clinical service — which is also yet to be determined — will be set by NantWorks, Benz said.
A Sign of Things to Come
Five3 Genomics is among a number of recently launched bioinformatics firms that had their start in academia and not-for-profit research institutes.
That list includes Cypher Genomics — a spinout of the Scripps Translational Science Institute, Scripps Health, and the Scripps Research Institute — which was launched last year to commercialize an annotation pipeline developed by its founders to predict the impacts of variations in the genome (BI 10/7/2011).
Another startup, Personalis, was also formed last year to commercialize a variant detection computational pipeline developed by researchers at Stanford and Yale Universities. Personalis later released a free version of its pipeline for academic users only (BI 4/6/2012).
Also joining the roster is Bina Technologies, a Redwood City, Calif.-based company whose founder and CEO, Narges Bani Asadi, began developing the algorithms that underlie the company’s variant analysis pipeline and accompanying hardware appliance while she was as a doctoral student at Stanford University (BI 4/27/2012).
A more recent entrant is TeselaGen Biotechnology, which is developing a cloud-based version of j5, an automated DNA cloning tool that was developed by one of the company’s founders at the Joint BioEnergy Institute (See related story this issue).
For their part, Five3’s founders decided to commercialize their software in order to generate the resources needed to adapt it for clinical use and also to prevent the tools from going the way of the dodo when academic research dollars dry up, Benz told BioInform.
The ultimate goal is to improve cancer treatment by providing “better answers to what’s going on in individual tumors” and developing better drugs. Tools like Paradigm can help with that, however “you need to have the resources in order to turn them into full blown products,” he said. “That requires the resources of a company.”
Five3 Genomics offers similar services to that of Foundation Medicine, DNANexus, Knome, and Illumina’s BaseSpace cloud infrastructure, which offers access to externally developed bioinformatics apps (BI 8/24/12).
Five3 intends to distinguish itself by focusing its analysis and annotation services on the oncology community and offering in-depth analysis capabilities that “offer a more complete view of what’s going on in the tumors than we’ve been able to see before,” Benz said.
In addition, offering its research pipeline for free to not-for-profit groups should help it secure academic buy-in, he added.
“Illumina’s offering is sort of driving why we think we should be giving away this stuff to researchers for free because we want them on our platform and using our tools and being able to do the same stuff they can do on Illumina’s platform but more in-depth and more cancer-focused analysis,” he said.
The seven-person company is currently hiring bioinformaticians, developers, and systems administrators.
The company’s scientific advisors include Haussler, a professor of biomolecular engineering, and Joshua Stuart, a professor of bioinformatics, both at UCSC. Other board members are Patrick Soon-Shiong, the founder and CEO of NantHealth; and Margaret Tempero, deputy director and director of research programs at the UCSC Helen Diller Family Comprehensive Cancer Center.