Netherlands-based Erasmus University Medical Center is tapping into the expertise of informatics firm Ingenuity Systems to help analyze its next-generation sequencing (NGS) data in the hunt for potential new disease-related genes. The collaboration has allowed Erasmus to use Ingenuity’s IPA® software and Ingenuity® Knowledge Base to map and contextualize genes and variants related to biological processes, functions, diseases, pathways, compounds, and relationships. The university claims the technology has already led to the discovery of a novel gene variant implicated in a specific disease field.
“Like many researchers, we faced the challenge of sifting through thousands of variants in order to rapidly identify the few that were the best candidates for follow-up studies and those most likely to be causal for our disease phenotype,” comments Erasmus professor Peter van der Spek, Ph.D. “IPA helped us overcome this challenge and discover a novel causal variant in a disease area of interest. 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.”
Ingenuity claims the success of the collaboration to date is validation of its technology. “We’re excited to see this validation of IPA’s role in NGS research and its ability to provide meaningful insights for researchers leveraging NGS data,” adds Doug Basset, Ph.D., CSO and CTO. “We’re looking forward to our ongoing collaboration and translating the results of this collaboration into new product capabilities.”
IPA is an all-in-one, web-based software application developed to allow users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, along with metabolomics and proteomics experiments, and other small-scale experiments that generate gene and chemical lists.
News of the Erasmus collaboration comes just a couple of weeks after Ingenuity announced an NGS partnership with GenomeQuest designed to support workflows specifically targeted for personalized medicine research. Through this collaboration the firms will integrate GenomeQuest’s Sequence Data Management platform with IPA, which will allow users to seamlessly exchange gene information, perform interactive analysis, and create and test hypotheses across the domains of genome sequencing and biological pathways.
The GenomeQuest partnership itself followed just a month after Ingenuity announced a collaboration with CLC bio that will provide interoperability between the two firms’ software solutions. Through this partnership Ingenuity and CLC bio aim to provide researchers with the ability to easily exchange data between CLC bio's enterprise and desktop solutions and Ingenuity's IPA software, for carrying out both array and next-generation sequencing data and knowledge analyses.