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Illumina Starts Validating Ovarian, Gastric Cancer Genes from Discovery Project; Adds Colorectal Cancer


By Julia Karow

This article was originally published January 13.

As part of its Cancer Discovery Initiative, Illumina is validating genes discovered by sequencing ovarian and gastric cancer samples in larger sample sets and expects to have results for ovarian cancer in the latter half of the year, according to a company executive. It has also embarked on a third cancer type, colorectal cancer.

The aim of the initiative, which Illumina launched two years ago (IS 1/20/2009), is to use sequencing to discover biomarkers for early disease detection and to predict response to therapy or relapse. Eventually, the firm wants to develop new diagnostics on the BeadXpress platform. According to its website, Illumina is partnering with "leading cancer research institutions" for the project.

The company chose to tackle ovarian and gastric cancer first, where survival rates are poor if the disease is detected late. Also, for ovarian cancer, most diagnoses are currently made at a late stage. The aim is to discover biomarkers for early detection and to predict resistance to platinum therapy. Last fall, Illumina reported that it had completed sequencing the genomes, methylomes, and transcriptomes of 25 tumor/normal ovarian cancer samples (IS 11/2/2011), and had found about 40 "significant genes," half of which had not previously been implicated in the disease. It had also completed sequencing 25 tumor/normal gastric cancer samples.

At the JP Morgan Healthcare Conference in San Francisco last week, Illumina CEO Jay Flatley said that the company is currently validating the ovarian cancer genes — along with some additional related genes — by targeted sequencing in 300 samples. The project is expected to be completed mid-year, and in the second half of the year, "we'll determine what's come out of this cancer discovery activity," Flatley said.

For gastric cancer, he said, company researchers have discovered three "very important genes," and are beginning to validate those in a set of 250 samples.

The company has also selected colorectal cancer as a third cancer type to investigate. Half of colorectal cancers that are treated with surgery alone relapse, according to the firm's website, and therapies selected by stage of diagnosis are not well associated with the likelihood of response. The goal, thus, is to discover biomarkers for disease prognosis and relapse. "Sequencing on those cancer samples is just now beginning," Flatley said. He did not mention the number of samples to be analyzed.

According to the website, if validation pans out, Illumina plans to offer diagnostic services for ovarian cancer in its CLIA lab. Ultimately, it wants to run prospective trials on these markers and gain regulatory clearance for diagnostics developed on its BeadXpress platform, which received 510(k) clearance from the US Food and Drug Administration last year.

Have topics you'd like to see covered in In Sequence? Email the editor at jkarow [at] genomeweb [.] com.