Ingenuity Systems said this week that Erasmus Medical Center will use its pathway informatics tools to analyze next-generation sequence data for cancer research studies.
The partnership will serve as a "validation of IPA's role in NGS research and its ability to provide meaningful insights for researchers leveraging NGS data," Doug Basset, chief scientific officer and chief technology officer for Ingenuity, said in a statement.
Netherlands-based Erasmus will use the Ingenuity Pathway Analysis software and Ingenuity Knowledgebase to map and contextualize genes and variants related to biological processes, functions, diseases, pathways, compounds, and relationships to "obtain a more complete biological picture from the data," Ingenuity said. Furthermore, Bassett told BioInform that Erasmus scientists will work"collaboratively with us on new NGS product capabilities, including applying and validating these new capabilities in the context of their disease research."
The partnership with Erasmus is part of a "significant investment in the enabling of next-generation sequencing analysis" by Ingenuity, Bassett said. He noted that the field is a rapidly growing area for the pathway analytics firm, with increasing interest from customers.
In particular, he noted that next-gen sequencing is generating large quantities of information whose value can't be realized "without the ability to contextualize those datasets."
Ingenuity has "built up [a] knowledgebase of expert ... content, which includes millions of computable findings extracted from the literature and we can leverage that with our collaborators and our customers to contextualize these huge NGS datasets and help people get from hundreds of thousands to millions of variants coming out of their study ... down to the 30 to 50 that are most likely critical for follow up," he said.
Peter van der Spek, who heads the bioinformatics department at Erasmus, said in a statement that in the past IPA has helped the hospital's researchers discover a novel causal variant and that it "provides the critical biological context necessary to realize the full potential of NGS datasets, thanks to its high-quality, detailed biomedical content and powerful analysis capabilities."
As part of its bid to market its pathway analysis tools to NGS users, Ingenuity has recently forged commercial partnerships with other vendors in the space with more joint ventures to come, Bassett said. Meanwhile, the firm will continue to expand its knowledgebase to include even "richer information that’s applicable to variant analysis, discovery, and causal association with disease," he said.
Earlier this year, the firm unveiled plans to integrate IPA with GenomeQuest's sequence data management platform (GWDN 01/05/2011).
Last December, CLC Bio and Ingenuity integrated the CLC Genomics Server and CLC Genomics workbench with IPA (GWDN 12/09/2010). In November, the company announced integration plans with Geospiza's GeneSifter software to create a research workflow for NGS data analysis and visualization (BI 11/05/2010).
"We feel we have made the right investments in content, the quality of the content, [and] the content also being rooted and linked into the genome coordinate space so that you can contextualize variants that are observed in NGS datasets," Bassett said. "We have also been investing a lot in early-access partnerships in connections with groups like [Erasmus] to ensure that we are tightly aligned and engaged with the science and using our knowledgebase and analytics to solve the most critical pain points for our customers."
Van der Spek told BioInform that the hospital will use IPA and the data contained in Ingenuity Knowledgebase to identify locations in the genome where somatic mutations occur and to try to discover whether these mutations occur in genes that are currently associated with cancer or in new genes not previously linked to tumors. Furthermore, he said, after selecting candidate genes and variants, Erasmus researchers will use the platform to prioritize which mutations are the most likely cause of the particular cancer in question.
The results of their work could deliver a two-pronged benefit to patients, van der Spek said, because the data would provide an indication of the patient's prognosis and at the same time help attending physicians determine the most effective drug or combination of drugs and therapies for each patient.
"Prognostic information ... [is] based upon proper patient stratification," he explained. "We stratify patients based on molecular criteria so if they seem to have the same underlying defect then we try to group these patients and then we look at their particular characteristics, which are, for instance, indicative for the overall survival." Once patients have been classified into subgroups based on similar "molecular signatures," the physician can then select targeted treatments.
This kind of patient stratification would also be useful for pharmaceutical companies looking for trial participants. In fact, van der Spek said that the hospital plans to seek collaborations with pharmaceutical companies who have developed specific drugs that target genes linked to cancers of interest.
Erasmus, which is one of the largest hospitals in the Netherlands, studies different types of cancers and houses several biobanks containing tumor samples from breast, prostate, lung, and colon cancers. The center plans to use IPA to identify mutations in cancers such as leukemia, brain and blood cancers, which are currently its main focus areas, van der Spek said.
He also said that in addition to the Ingenuity tools, Erasmus has an Oracle-based database index of the reference genome that will play a role in its efforts to locate common and rare variants in patient samples.
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