By Julia Karow
Illumina expects results from its ovarian cancer biomarker study in early 2012 and is working on capturing ovarian cancer cells from body fluids, a company executive said last week.
The company also asserted that the MiSeq platform, to be commercialized later this year, will be suitable for diagnostic applications in cancer and other areas.
Illumina started its Cancer Discovery Initiative two years ago, focusing initially on ovarian and gastric cancer. Earlier this year, it added colorectal cancer to the program. Using next-generation sequencing, the company aims to discover biomarkers for early disease detection and prediction of therapy response or relapse, and to develop these markers into diagnostic tests.
Earlier this year, Illumina president and CEO Jay Flatley said the company is in the midst of validating ovarian cancer genes detected in 25 tumor-normal pairs by targeted sequencing in about 300 samples, a project to be completed by mid-year, with results expected by the end of the year (IS 1/18/2011).
During Illumina's first-quarter earnings call last week, Flatley revised this timeline slightly, saying that validation should be mostly completed by the end of the third quarter, and analysis by the end of the year, so "somewhere probably in Q1 [of 2012], we'll know what we have there."
In addition, as part of an effort to translate the results to the clinic, the company is applying a rare cell capture technology to see if it can detect ovarian cancer cells in body fluids. Those studies are "a very important part" of Illumina's translational work in ovarian cancer, Flatley said.
Illumina developed the proprietary rare cell capture technology in house (IS 1/18/2011) and plans to start offering it to third parties through its sequencing service business in the second quarter, he added.
The firm's gastric cancer biomarker discovery project is "three to five months behind" the ovarian cancer project, with validation sequencing ongoing, while the colorectal cancer project is "in the initial sequencing phases now," he said.
MiSeq for Dx
Flatley also reiterated the firm's belief that the MiSeq sequencing platform, which will cost less than $125,000 and be able to generate results in as few as eight hours, will be suitable for clinical and diagnostic sequencing applications.
Cancer will likely be the first area where such tests will be developed. While much of the discovery work in cancer sequencing is currently conducted on the HiSeq platform, "I suspect that most of the end applications that come out of that cancer research would be more suited for deployment on the MiSeq platform," he said. Sequencing-based diagnostic panels comprising "between 40 and a few hundred" genes would be a "perfect application for the MiSeq platform."
But cancer is only one area with promising diagnostic applications for sequencing. "MiSeq is getting very broad attention in many other diagnostic circles," according to Flatley — for example, for immune system sequencing and for sequencing viruses and bacteria.
Illumina is not the only firm eyeing potential diagnostic applications for its sequencing platform: Roche's 454 Life Sciences recently launched an HLA-typing assay for research, the first of several disease-focused assays for the 454 platform, and Life Technologies has said it envisages clinical applications for its Ion Torrent sequencer.
Flatley cautioned, however, that not all genomic diagnostics will use sequencing. For diagnostic tests involving genomic regions that are not highly variable, "arrays are going to remain an important component," he said. "But sequencing is becoming cheap enough and versatile enough that I think more and more customers are looking to apply next-gen sequencing to these types of applications."
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