Compendia Goes Clinical

A couple of years ago, Compendia Bioscience was talking up its research partnerships with pharma. Now the Ann Arbor, MI, bioinformatics company and its new owner are changing the conversation to focus on the clinical applications of Compendia's ever-growing database and analytical software in the not-too-distant future.

Life Technologies (Carlsbad, CA) purchased Compendia in October for an undisclosed sum. The California company—which had $259 million in cash in August according to its quarterly SEC filing—has been on a genomics buying spree, having also purchased Navigenics (Foster City, CA), a personal genomics company, and Pinpoint Genomics (San Francisco, CA), which makes genomic tests, this year.

Compendia cofounder and CEO Daniel Rhodes, PhD, who has taken a position at Life Technologies, says lessons learned in gene and drug discovery can be applied to clinical cancer diagnostics and treatment. The aim, he adds, is similar to that of Foundation Medicine, of Cambridge, MA, which recently launched a commercial service that combines sequencing of 200 genes with therapeutic and clinical trial information. “We believe, though, that our expertise in cancer genomic data and analysis in the pharma research space provides a competitive advantage,” says Rhodes.

Compendia is best known for Oncomine, a database that includes gene expression and biomarker data from 62,000 cancer patients and software to analyze the data. Rhodes describes it as “highly curated,” with a track record in research applications. In 2008, he and his colleagues used Oncomine to find the SPINK1 gene that is overexpressed in some prostate cancers. This year, Rhodes was part of a team that used the software to identify mutations in genes associated with metastatic castration-resistant prostate cancer.

Rhodes says Oncomine can help distinguish the drivers in cancer genomics from passenger abnormalities that are present but not causative. “In the case of somatic mutations, we look for statistical enrichment of ‘hotspot’ mutations across thousands of patients, which is characteristic of functional drivers, but not of passengers,” he says. “In the case of DNA copy number alterations, we can survey thousands of tumors to identify the ‘peaks’ of copy number gain. These genes tend to be the drivers, whereas passengers don't show this statistical enrichment.”

Ronnie Andrews, president of medical sciences at Life Technologies, says Compendia will be part of the “synthetic engine” that the expanding company expects will produce many products based on cancer genomics. In September, Life Technologies began selling Pervenio Lung RS, a PCR-based lung cancer test developed by Pinpoint Genomics that measures the expression of 14 genes, including KRAS, BRAF, ALK, and p53. In addition, the company says that next year it will launch a Web portal for physicians that will link patient molecular profiles generated by its tests to a menu of treatment strategies and clinical trial options.