New Life Tech Products Use Compendia Gene Database

By Bio-IT World Staff

April 4, 2013 | Life Technologies Corporation announced two new offerings this morning that give users access to the large genomics database compiled by Compendia Biosciences, which the company acquired in October 2012.

Oncomine Gene Browser is a web portal that pairs the Oncomine analytics tool, developed by Compendia, with the Compendia database, allowing users to dig into the database and characterize genes of interest across multiple parameters, including gene expression, DNA copy number and mutation data, from thousands of cancer patients’ genetic data (exomes and transcriptomes).

The tool is most appropriate for researchers working with a small number of genes that need a comprehensive gene summary at a moderate price point, Life Technologies says.

“Oncomine Gene Browser is a new product for the academic and smaller pharma scientist that will enable them to be competitive in research and drug development,” said Dan Rhodes, head of medical bioinformatics for Life Technologies in a statement. “These investigators will now have access to data that have been collected and curated over the course of a decade, drawing from hundreds of clinical studies and representing millions of dollars worth of experiments, which will allow them to design more focused experiments and make faster progress.”

The second offering, Ion Reporter Oncomine Workflow, combines the Oncomine analytics platform with Ion Reporter software, which provides simple tools for mapping, calling, and annotating variants. The workflow can process variants from the Ion Torrent sequencer and provide access to curated next generation sequencing data from 4,000 matched tumor and normal pairs. When used with Life Technologies’ cancer panels, researchers can move from sample to sequence to driver mutations in a day, rather than weeks or months, the company says.

The Ion Reporter Oncomine Workflow will be available at no charge for an introductory period, making this premier cancer bioinformatics capability accessible to any scientist.

“This is a major advance because cancer sequencing experiments often yield hundreds of variants, among which only a small fraction are true cancer driver mutations,” said Dan Rhodes, head of Medical Science Informatics for Life Technologies in a statement. “Previously researchers were faced with cumbersome literature searches or complex bioinformatics approaches to discern drivers from passenger mutations. The thousands of patient tumor samples driving the Oncomine Analysis provide both context and confidence for the Gain of Function or Loss of Function classification. This allows any cancer researcher to immediately identify likely driver mutations in their sample."

“Next-generation sequencing of cancer samples identifies many potentially important variants, particularly if matched germline DNA is not sequenced in parallel,” said Scott Tomlins, assistant professor, Department of Pathology, University of Michigan in the same statement. “The addition of Oncomine annotations to Ion Reporter Software provides the best way to prioritize those mutations that are likely cancer drivers, based on well-curated supporting evidence across cancer types.”