Customers of GenePool, Station X's newly launched software for genomic and clinical data management and analysis, said this week that factors such as its ease of use, ready access to cloud infrastructure, and its ability to analyze both large and small numbers of samples make it a good analysis option for genomics projects.
Station X developed GenePool with molecular diagnostic firm Genomic Health (BI 8/24/2012), and launched the software this week after completing a six-month early access program during which it was used in genomics-based projects at Genomic Health, Mount Sinai Hospital, and the National Cancer Institute among others.
According to the company, the new software, which runs on Amazon Web Services, lets users analyze DNA and RNA sequences and provides statistical tools for identifying candidate biomarkers for diseases and drug response. Other features include step-by-step workflows for comparing gene expression in tumor and normal tissue samples; capabilities for comparing data from drug responders and non-responders; and tools for analyzing trios in genetic disease studies.
"GenePool was central to our analysis of BRCA-negative pedigrees with high incidence of breast and ovarian cancers," John Martignetti, an associate professor of genetics and genomic sciences at Mount Sinai's Icahn School of Medicine, said in a statement. "The interactive, logical software interface allowed our collaborative groups to move quickly from exome sequences to a refined candidate gene list. Moreover, drilling down into the alignments of each candidate, reviewing the annotations, and selecting the best candidates for further validation using GenePool was intuitive and seamless."
Another early access user, Dominick Sinicropi, a staff scientist at Genomic Health, also highlighted GenePool's simplicity and user friendliness, as well as its ability to handle data from large cohorts, as key benefits of using the software.
Sinicropi and colleagues at Genomic Health used the software in a breast cancer study where they analyzed gene expression data from formalin-fixed paraffin-embedded tissue samples collected from136 breast cancer patients to find biomarkers associated with breast cancer recurrence risk. With the help of GenePool, "we were able to correlate the expression signatures [from the patients] with clinical outcomes," he told BioInform this week. Full details of the study were published in a Plos One paper last year.
Furthermore, since it runs on the cloud, it eliminates the need for in-house infrastructure, he noted. Rather than invest heavily in IT, it's much simpler to pull up a large cluster of processors on Amazon to really make GenePool work "efficiently in a seamless way," he said. Access to the cloud also makes it much easier to share data and results in collaborative research studies, he added.
Initially, Station X was going to offer both cloud-based and in-house GenePool installations but ultimately chose to focus on the former because customers in its target market have in recent years grown more comfortable with crowd infrastructure and have begun relying on it for their sequence analysis needs, Richard Goold, Station X's CEO and co-founder, told BioInform. This decision also let the company focus its efforts on developing a single product that offers possibly better security than in-house servers could, he said.
The company believes its offering has applications in both the clinical and translational research markets, with potential customers in clinical and academic institutions as well as pharmaceutical and biotechnology companies.
"We anticipate some of our customers are going to be multinational organizations that have groups working … and perhaps collaborating with people in different countries," Goold said. There are also potential opportunities to partner with other companies; for example, vendors offering genome interpretation services could include GenePool in their analysis pipelines. "We like that model a lot and we are working hard on making [application programming interfaces] so that even if its not something that we develop, we'll be able to make their product better by adding [GenePool] inside," he said.
Station X isn't disclosing GenePool's pricing directly but Aaron Solomon, senior vice president for commercial operations, told BioInform that the firm has adopted a pricing scheme based on the number of users and datasets stored that comes out to about $5,000 per person per year. The company also offers reduced pricing for academic customers, he said.