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CCI Deal Offers First Look at NextBio's Offering for Genomic Data Interpretation in Clinics


This article has been updated to correct an error in the previously reported number of patients whose data is in NextBio's database. The correct number is 8000 not 800 as stated earlier.

A few months after launching a version of its informatics platform for clinical use, NextBio has announced a partnership with the Cancer Care Institute that demonstrates the newly minted tool's ability to integrate and interpret genomic and clinical data from oncology patients in a medical setting.

At the Bio-IT conference in April this year, Santa Clara, Calif.-based NextBio staked its claim in the burgeoning market for tools to bring genomic information into routine clinical practice with the launch of NextBio Clinical, a program that enables users to look for correlations in molecular and clinical data from patients in public and proprietary studies (BI 4/27/2012).

This week, the company said that CCI — a research and radiation therapy cancer center — has purchased a license to NextBio Clinical as well as its NextBio Research platform. CCI plans to use the tools to analyze oncology patient data for research studies as well as to select appropriate treatments for patients based on their molecular profiles.

NextBio Clinical provides access to a database of public and private clinical, molecular, and genomic data, as well as clinical trial results, experimental models, and interpretation and analysis tools.

Satnam Alag, NextBio's chief technology officer and vice president of engineering, told BioInform that the company pulls public content from resources such as The Cancer Genome Atlas; the European Genome-Phenome Archive; the Multiple Myeloma Research Consortium; Array Express; and the Gene Expression Omnibus among others.

Both open source and proprietary software underlie NextBio's infrastructure, according to Alag. For example, "for our analysis pipelines, we have leveraged some public domain algorithms such as BWA, GATK, and parallelized them with Hadoop for scale," he said via e-mail.

At the same time, "wherever appropriate we have developed our own algorithms, for example, for correlation of data and data interpretation," he said.

NextBio Clinical was tailored specifically for use in academic and medical clinics and provides tools to identify prognostic and predictive biomarkers that guide therapy selection; identify relevant clinical trials for patients; and select clinical trial participants based on their genetic profiles.

Users can also mine their own patient data and public data in order to locate biomarkers, correlate them with clinical outcomes; and conduct retrospective analysis of patient data as part of biomarker-based drug response studies.

The company also offers a tailored version of its clinical product for pharmaceutical and biotech companies. That offering lets users analyze public and private clinical and molecular data to find potential biomarkers or improve therapeutic regimens; run in silico trials to assess and validate biomarkers for use in companion diagnostics; appraise drug targets in the context of genomic data from cell lines, stem cells, and animal models; and retrospectively analyze clinical trial data to identify potential biomarkers.

Speaking with BioInform this week, Alpana Verma-Alag, NextBio's head of clinical development, said the clinical offering provides an "easy way" to work with molecular and clinical data.

Currently, NextBio, whose primary focus is in oncology, has access to more than 2,000 cancer cell lines and data about more than 40,000 compounds and drugs. It provides genetic information such as somatic mutations, DNA methylation, copy number variations, RNA expression, genes, and biomarkers. Clinical data includes age, gender, race, cancer stage, histopathology, and treatment history for 16 different kinds of cancer in more than 8000 patients.

This information "makes it so easy to look at drug sensitivities and drug response," she said. "We are also able to tie in the cell line data with the individual patient data," which makes it possible "to be able to say whether [a patient] would be responsive to a particular drug or not," she explained.

When new users license the tool, NextBio helps them customize it so that they can analyze their own proprietary biomarkers in the context of the platform's knowledge base, she said.

Additionally, NextBio works with clinical customers, including CCI, to integrate the clinical tool with their internal electronic medical record systems, which is expected to save clinicians time since they won't have to enter patient data into two separate systems, Verma-Alag said.

"Being able to pull clinical data and demographic data and patient identification data from the EMR makes perfect sense," she said. Each time a patient visits and their EMR is updated, data can "seamlessly come in from the EMR."

Although its primary focus until now has been on oncology, NextBio intends to extend its platform to enable the analysis of other diseases including autoimmune diseases, metabolic disorders, and cardiovascular diseases, Verma-Alag said.

She also said the company will add proteomic and metabolomic data to its curated content.

NextBio offers a single subscription for its clinical product, unlike the research tool, which has three options: NextBio Public, a free web application that provides access to the company's curated 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.

NextBio isn't disclosing pricing details for its products.

First Look

CCI is a radiation cancer center located on two campuses in San Jose and Morgan Hill, Calif., that focuses primarily on solid tumors, which includes colorectal, lung, and prostate cancers. The center integrates medical, surgical, and radiation oncology and is involved in research efforts with the National Cancer Institute and Radiation Therapy Oncology Group clinical trials.

In a statement, Morteza Dowlatshahi, CCI's medical director, described NextBio's clinical offering as “a powerful, easy-to-use way to interpret our patients’ genomic data to conduct research studies as well as identify optimal treatments."

It was that ease of use as well as the ability to integrate the tool with its EMR system that led CCI to select NextBio Clinical over other tools that the institute was considering, Dowlatshahi told BioInform.

"We are a busy clinic and inputting data two or three times into different systems causes a lot of headaches for us," he said "The fact that the EMR could be integrated and the patient data is easily abstracted [were] the big selling points for us."


Furthermore, "we...liked the fact that not only [does] NextBio allow us to pursue research with our own sets of patients, but then there is also the public data that’s available and that’s really a big deal for us," he said. "We may only have a certain number of patients but the addition of NextBio's public data really boosts our research capability."

CCI licensed both NextBio Clinical and NextBio Research. Dowlatshahi explained that the institute would use the former to analyze and integrate specific patient data as part of lung cancer studies, for example, as well as in drug response studies. The research tool, meantime, will enable the institute's investigators to explore studies similar to their own as well as to map biomarkers and explore disease pathways.

CCI is already looking into some possible uses for its new system. Ly Do, one of CCI's associate partners, told BioInform that a potential application for the tool would be in outcome studies based on genetics.

One potential scenario would be to build on a research study done by the RTOG, which analyzes data from patients with higher versus lower doses of radiation. CCI could take things a step further by using genetic data to "tease out patients that might be more sensitive to the radiation or not sensitive to radiation," he said.

Another application is in a pilot project, which is studying a cohort of young Asian patients who have been diagnosed with an aggressive type of lung cancer although they've never smoked, Do said.

"There is a lot of research that can be done ... in terms of possibly screening patients so that we ... can keep an eye on them prior to actually being diagnosed [and] can catch them earlier," he said. "Another thing that we can also do is see if they have any particular genes that we can accurately target in the future ... whether it be with radiation or other targeted agents."

Moving forward into treatment scenarios, if biomarkers are found that are indicators of sensitivity or resistance to radiation or chemotherapy, incoming patients' tumors could be tested for these markers and "we can shift the treatment algorithm" so that therapies that would have the best outcome are selected, Do said.

For example, "if they relay a biomarker that relays radiation resistance, then maybe we would have to increase the dose of radiation. Or if they relay a chemo-resistant biomarker then we would have to switch the agent that we would normally use," he explained.

The Road to the Clinic

Although CCI is the first NextBio Clinical customer that the company has made public, it isn't the only one. According to Verma-Alag, NextBio Clinical is being used in other clinical centers that she can't disclose at present.

Although this is its first major move in the clinical domain, NextBio has been eyeing the space for a number of years.

Saeid Akhtari, the company's co-founder, president, and CEO, said this week that “it has always been NextBio’s goal to serve the full spectrum of life sciences research, from the laboratory to translational research to the clinic."

The company first made mention of its intent to one day play in the clinical space shortly after launching its first product for the research market in 2006. At the time, Akhtari said that although the release was aimed at bench biologists, the company hoped to eventually appeal to clinicians. He also said that NextBio and Stanford University School of Medicine had begun working on integrating patient data into the company's platform (BI 10/20/2006).

After several years of updating and improving the platform for its research clientele, NextBio presented the findings of two in-house studies last October in an effort to show that it was to able bring its solution to the translational and clinical research markets (BI 11/28/2011).

NextBio will have to do battle with offerings from Knome, Omicia, Personalis, and Cypher Genomics who are early arrivals the genomic data interpretation space.

It isn't clear how NextBio will differentiate itself from all of its competitors, though Verma-Alag noted that its licensing model sets it apart from service-oriented genome interpretation firms.

These companies "collect samples, analyze the data, and then present the patient with a report, that’s very different from our model," she said. "Our goal is to work with physicians' offices, academic medical centers, and pharma companies to enable them to generate unique insights, research, [and] clinical care, so we provide them with all they need at their fingertips."

Access to tools and keeping data close to the chest is paramount to the doctors and researchers on NextBio's client list, she said.

"They are very conscious of the value of the data that they have from ... the genomic, proteomic, metabolomic tests that they run," she said. "And they want to keep that data in house. They want to be able to work with it [and] mine it over time, so that’s definitely a value proposition to them."

Furthermore, these users want to "sequence once and read often," she said. Therefore, "our goal is not to give people a report ... because that’s so static; it doesn’t reflect the changing science."

Instead, NextBio intends to give users the tools and information that they need so that once they've done the necessary diagnostic test or sequencing they can re-analyze the same data to glean new insights as the science advances and new discoveries are made.

This way, "the doctor can ...make a decision on what's new now for his patient and then have a conversation with the patient and say you might be at risk for this because a new gene was discovered and you actually have that gene," she said.

Meanwhile, a translational researcher can run a retrospective study or an entirely new project, "because of the new insights that are now available," she said. "I think that happens only when you have all of the data in house and can have the ability to work with it."

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