NextBio recently released the results of two in-house studies it performed to provide proof of its ability to help pharma and clinical researchers mine publicly available genomic data in their translational research efforts.
At the American Society of Human Genetics meeting held earlier this month in Montreal, NextBio presented findings from two studies: one that explored the biological mechanisms involved in the toxicity of tibolone — a hormone replacement therapy for post menopausal women; and a second study in which the company's researchers found a potential cancer biomarker by analyzing publicly available data.
NextBio officials told BioInform that they hope the results of these studies will woo customers in the translational and clinical markets, where the company sees great opportunity for its platform.
Saeid Akhtari, NextBio's president and CEO, said that the company's findings should appeal to clinical research centers that are using omics data in their translational and personalized medicine efforts as well as in drug research and development.
The company has historically focused its flagship NextBio search engine on the research market, but "we are seeing there are emerging applications on the translational [side,] which means clinical trials, molecular profiling of genomic data, [and] population stratification for clinical trials," Akhtari said.
These new applications promise to expand NextBio's customer base beyond scientists in academic research centers and biopharma companies, he said.
In line with its translational research ambitions, NextBio plans to develop additional applications that will address these new markets, Akhtari said, adding that the company envisions building a suite of tools that would address different customer requirements.
For instance, a pharma company studying biomarkers would likely require a different set of applications from a physician at a hospital trying to select therapies for cancer patients based on their molecular profiles, he explained.
NextBio plans to release the first set of these new applications in a few months.
A Data-Driven Approach to Cancer
NextBio's software-as-a-service platform enables users to integrate, search, and share public and proprietary data. It includes a so-called "correlation engine" that pre-computes connections among public and private data so that researchers can mine and interpret it in real time.
Last year, the company included a sequence-centric module in the platform so that users could integrate and mine high-throughput array and second-generation sequencing data (BI 4/23/2011).
NextBio offers three versions of its platform: NextBio Public, which is a free web application that provides access to a curated, correlated database of public data, literature, clinical trials, and scientific news; NextBio Professional, which adds the ability to explore internally generated data; and NextBio Enterprise, which includes tools to integrate publicly available experimental data with proprietary experimental data.
Ilya Kupershmidt, NextBio's product vice president, told BioInform that although some customers are already using the company's platform for biomarker identification and drug toxicity and repositioning studies, privacy considerations have made it "difficult to share sensitive studies that are performed by customers and commercial clients."
He said that the firm conducted the two internal studies to draw attention to NextBio's "data-driven approach" to research as a fruitful way to come up with new biological and clinical insights.
NextBio’s platform connects public and proprietary data from gene expression, genome-wide association, epigenetic, and genome resequencing studies. This data forms "one ecosystem" that makes it possible for end users "to ask questions across thousands of datasets related to disease, drugs and various tissues and cell types," Kupershmidt explained.
Also, because users can integrate their own proprietary information, researchers aren’t limited to published data alone, he said.
In the study looking at tibolone toxicity, NextBio researchers analyzed publicly available data from studies that indicated that the drug could induce gene expression changes that were similar to those caused by an aggressive form of breast cancer.
The researchers used the NextBio platform to query datasets of drugs and different treatment options to identify a signature that marked patients with breast cancer and then looked for treatments that produced similar gene expression changes, Kupershmidt said.
The team found positive correlations between gene expression changes induced by tibolone and those in patients with breast cancer.
The NextBio researchers also analyzed data on gabapentin, which also treats hormonal changes in post menopausal women. They found that the drug caused gene expression changes that weren’t correlated with breast cancer, suggesting that it might be a better alternative to tibolone for patients with the more aggressive form of the cancer.
A separate clinical trial performed in 2009 that looked at patients' clinical information alone also found that women who were treated with tibolone had higher rates of breast cancer, further validating NextBio’s findings.
In the second study, the NextBio team analyzed public data about a gene on chromosome eight that has been linked to prostate cancer and other tumors in gene expression and GWAS studies. They discovered that the gene is also highly expressed in embryonic stem cells and in cells that become pluripotent, which is one of the markers of early cancer development.
NextBio plans to do some follow-up work on both studies and publish the findings on its website.
‘Chicken Wire and Duct Tape’
Privately held NextBio doubled its customer base over the course of 2011 and its renewal rates are at 100 percent, Akhtari said.
The firm also recently opened an office in the UK to support its European customers and it plans to open an office in Japan next year for its Asian clients.
NextBio's current headcount stands at 75 employees and it is looking to hire people in its bioinformatics and data curation departments as well as in its business development, marketing, sales, and sales support arms.
Akhtari said that NextBio doesn’t consider itself to have any direct competitors in the market.
While there are companies that offer some components of its platform — for example, vendors that sell pathway analysis software and data mining tools — there aren't any that offer a "complete" commercial solution like NextBio’s platform, he explained.
In fact, most of NextBio's competition comes from internal efforts that cobble together piecemeal solutions with “chicken wire and duct tape,” Akhtari said.
These systems often require in-house experts to create and run queries on the datasets and it can take weeks or months to get results back from these processes, he said. NextBio users, on the other hand, have access to resources to help them “hone [their] queries” and get results back faster.
NextBio is certainly not the only bioinformatics firm setting its sights on the clinical market, however. A number of companies that have traditionally served the research market — such as GenomeQuest, IDBS, and GenoLogics — are expanding their offerings to meet the demands of the translational and clinical markets. Meanwhile, a number of new firms, such as Cypher Genomics and Omicia, have launched with the specific aim of providing clinical interpretation of genomic data.
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