After wrapping up a recent fundraising round involving an unnamed investor, informatics startup Station X is preparing to launch its first product for the clinical research market — a tool focused on biomarker discovery from genomic data, BioInformlearned this week.

The web-based software, called GenePool, was developed in partnership with molecular diagnostic firm Genomic Health and provides tools for storing, analyzing, and visualizing large-scale genomic data and is intended for use in biomarker discovery projects.

According to the Redwood City, Calif.-based firm, scientists can use GenePool to analyze whole-genome, exome, and RNA sequencing datasets, as well as compare variants across multiple genomes. The software can identify expression changes and sequence variants and it provides users with a series of statistical tools, sorting and filtering options, and annotation capabilities.

The company plans to offer customers the option to access GenePool via the Internet or as an in-house installation for customers who are concerned about data security, Richard Goold, the company’s CEO and co-founder, told BioInform.

He said that the company plans to make the first version of GenePool, called GenePool for Biomarker Discovery, broadly available by the end of the year although he could not give a definite timeline. It’s currently available on a limited basis.

Station X has also been tapped to provide a subset of GenePool’s capabilities as an app that will be sold on Illumina’s BaseSpace cloud (see related story this issue).

Station X hasn’t disclosed pricing for the standard version of GenePool or the app.

The company also plans to build on the core GenePool technology to create software applications for clinical trials and for the interpretation of genetic test panels.

With its focus on the clinical market, Station X will have to contend with offerings from informatics vendors such as NextBio, GenomeQuest, and Knome, which already offer software aimed at meeting clinical data interpretation needs (BI 12/22/2011). GenePool could also compete with a product from Integromics, dubbed OmicsOffice for clinics, which is under development and expected to launch in 2013 (BI2/10/2012).

Station X‘s differentiating factor is its emphasis on supporting users who need to integrate clinical and genomic data and metadata for clinical research, Goold said.

“We want to support the companies who are doing the discovery and development of biomarkers,” unlike some other vendors whose products are geared towards “personal interpretation of genomes,” he explained to BioInform.

As part of that effort, Station X also offers a set of services for clients in the translational research and clinical research sector who are looking to outsource their sequencing needs rather than attempt to familiarize themselves with rapidly changing sequencing technologies, he said.

These services include helping customers design their sequencing projects; identifying sequencing centers that meet their requirements; as well as doing the initial processing and analysis of the data, Goold said.

With the sequencing and initial analysis taken care of, these clients can focus their bioinformatics resources and expertise on the aspects of the research process that are pertinent to their businesses.

Station X developed GenePool in conjunction with Genomic Health, who provided the initial funding and has acted as an incubator for the informatics startup since its launch last year.

This recent round of funding was provided by a second investor, whose identity hasn’t been disclosed.

Genomic Health “has been both an investor and an alpha software partner,” meaning that “we, as the software company, developed our software with [Genomic Health] representing a … ‘prototypical’ customer,” Goold explained.

Under this arrangement, “we had access to their data and worked closely with their [research and development] team to understand the challenges they encountered in biomarker development using NGS,” he explained.

As a result, Genomic Health “has had influence over features and functionality as well as early access to our platform, which helps support and accelerate their R&D,” he said.

When GenePool is commercialized, “as an investor, they will share in our upside,” which is “a nice return for their early support and encouragement,” Goold said.

Genomic Health’s investment was part of multi-pronged strategy to ramp up its informatics efforts in order to keep pace with its sequencing activities, Randy Scott, executive chairman of Genomic Health's board, told BioInform in an interview earlier this year.

Genomic Health’s $2.8 million investment was split between Station X and a second firm, Locus Development, which offers clinical tools and services for personalized healthcare (BI 1/13/2012).

Genomic Health recently combined Locus Development with its InVitae clinical genomics subsidiary to form a new, independent entity called InVitae that will focus on integrating next-generation sequence data into medical practice (CSN 8/15/2012).