Informatics startup Syapse said this week that it has raised $3 million in Series A venture capital funding to support continued development of software for use in next-generation sequencing-based diagnostics.
The funding round was led by the Social+Capital Partnership. As part of the investment, Social+Capital's founder, Chamath Palihapitiya, will occupy a seat on Syapse's board of directions.
Syapse, a Stanford University spinoff, will use the funds to hire between eight and 10 software developers who will help the company continue development of its flagship product, Syapse Discovery, a web-based tool intended for companies and labs running NGS-based diagnostics, Glenn Winokur, the company's cofounder and CEO, told BioInform.
The new hires will also help the company further develop its second product, dubbed Omics Medical Record, which is intended for use in hospitals. It will provide physicians with a way to track and access their patients' omics and clinical information.
Syapse was founded in 2008 to develop and commercialize software products for omics-based diagnostics based on ideas that were discussed in a class at Stanford where two of the company's co-founders met.
As a side project, “we were investigating how semantic knowledge representation technology could be used to improve critical business processes in life sciences and healthcare,” Jonathan Hirsch, Syapse's president and co-founder, explained to BioInform. “[We] decided to form Syapse to pursue it further.”
In the company’s early days, Hirsch said, "we spent quite a bit of time embedded with a number of biomedical companies" and saw "a lot of the problems that were arising both on the diagnostic side as a result of … next-generation sequencing and then the corresponding problems that the clinicians, physicians, [and] clinical sites were having using these mounds of data that were coming in from the diagnostic companies."
As a result of these interactions, Syapse's founders decided to work on tools that would support the diagnostic development process as well as software to help clinicians handle the results of sequencing tests, he said.
They began building a software prototype and launched Syapse Discovery last year following a beta run that began in the summer of 2011. The software-as-a-service offering helps diagnostic labs manage data and interact with tools and instruments they use in the testing process.
Syapse Discovery frees internal developers at diagnostic firms "to focus on more proprietary aspects of their business" rather than on "custom development of one-off systems," which Hirsch said is Syapse's main competition.
With the software, customers "receive a packaged, supported solution … that is configurable for their needs and interfaces with their internally developed proprietary systems," allowing them to focus on other projects such as algorithm development, he said.
Underlying Syapse Discovery is a semantic data structure that "essentially allows us to assemble a massive knowledge graph of all the biomedical information that gets stored in our application," Hirsch explained.
According to Hirsch, Discovery gathers information from medical and genomic ontologies such as ICD-9 and SNOMED codes, Entrez Gene, and the Catalogue of Somatic Mutations in Cancer, which it uses to structure data that is entered into it. This way, diagnostic developers have access to information about genes they are testing for, related diseases, drugs that impact the genes, variant information, and more, he said.
Furthermore, Discovery's structure makes it possible to reconfigure the forms used to enter data into the system to suit customers' needs, Hirsch said. This means that diagnostic companies are free to use internal methodologies and workflows which they are used to "and our application can configure itself and configure the data structure" as required, he said.
Syapse also offers an application programming interface that lets users incorporate external computational tools, sequencers, and annotation information into the Discovery platform as well, Hirsch said.
Customers of the Discovery system are using the tool to track data, metadata, and their lab processes as well as to generate electronic diagnostic reports that they send to physicians at the end of the testing process, Hirsch said.
Meanwhile, Syapse is working on a separate reporting system, Omics Medical Record, that will provide a more comprehensive picture of each individual patient that aggregates results from multiple diagnostic testing facilities, he said.
This way, if a patient being treated at the University of California, San Francisco, for example, has their genome sequenced by one company, then has their tumor tissue profile sequenced by a second firm, and does a diagnostic test with another lab, the treating physician can gather and track all that information in a single application, Hirsch explained.
Omics Medical Record is currently in beta testing and it's unclear how long that process will last and, by extension, when the product will launch, CEO Winokur said.
"We'd love to have something commercially available this year, but it's really too early to be able to predict that," he told BioInform.
Meanwhile, Syapse Discovery is currently available, and academic labs — with the exception of core facilities — have free access to the application. On the commercial side, Discovery is priced based on the number of users. Enterprises with fewer than 10 users are charged $18,000 per year while larger groups are charged $40,000 per year for each "seat pack" of 20 users.
Since it launched Discovery, Syapse has snapped up a few customers for the product including InVitae, a spinout from GenomicHealth; and GenapSys, a sequencing systems developer.
InVitae, Hirsch said, is using the software in its efforts to develop next-generation sequencing-based diagnostics. The company is using Discovery to track data as it collects and processes samples. He also said that the two companies are working on creating "advanced reporting mechanisms" that combine genomics and clinical information and present it to physicians in a more "digestible fashion."
GenapSys, on the other hand, is using Discovery in its efforts to develop its sequencing platform, Hirsch said. He explained that GenapSys has connected Discovery directly to its sequencer so that it can track runs as well as modify and optimize its analytics processes.
He also said that when the company launches its sequencer, it will be connected to Discovery so that data from the instrument can be streamed up to the application directly and combined with additional clinical and genomic information.
Hirsch wouldn't comment on whether Syapse's relationship with GenapSys would result in a co-selling agreement between the two firms.
"We will be announcing agreements like that in the coming months, but specifically with regards to GenapSys right now, we are not yet announcing that," he told BioInform.
GenapSys isn't the only sequencing vendor that Syapse is involved with; the software developer is also on the list of partner companies for BaseSpace, Illumina's cloud infrastructure for genomic data storage and processing (BI 11/2/2012 and BI 8/24/2012).