By Julia Karow
This article was originally published Jan. 28.
As part of an internal oncology biomarker discovery project, Illumina has analyzed 11 ovarian cancer samples and normal controls with its sequencing technology, and expects to complete a set of 25 ovarian tumor/normal pairs by the end of March, according to a company official.
Early results indicate that the genomes analyzed so far are "highly rearranged," even though they were derived from early-stage tumors, and that there is "a lot of heterogeneity" between them, according to Greg Heath, senior vice president and general manager for Illumina's diagnostics business unit. Heath spoke at Illumina's R&D day for investors and analysts in Hayward, Calif., last month, which was webcast.
A year ago, Illumina announced that as part of its diagnostics strategy, it was planning an internal cancer biomarker discovery project for early-stage cancer detection, focusing on ovarian and gastric cancer (see In Sequence 1/20/2009).
The original plan was to analyze 25 ovarian and 25 gastric tumor/normal pairs by the end of 2009 using the company's Genome Analyzer, including whole-genome sequencing to at least 30-fold coverage, mRNA-seq, methylation sequencing, and chip genotyping. That timeline got delayed somewhat, and the company now expects to finish the ovarian tumors by the end of March and move into a validation phase, and then tackle the gastric cancer samples.
The delay was largely due to a longer-than-expected process of acquiring and qualifying the samples, Heath explained. For the ovarian cancer project, for example, he said the company was looking for stage I or II samples with a tumor content of at least 70 percent from non-smokers who did not have mutations in the BRCA 1 or 2 genes. He also said that the type of consent required for whole-genome sequencing is "quite a bit different from what is normally consented" and required the company, in some instances, to go back and ask for additional consent.
At the moment, he said, Illumina has 20 ovarian tumor samples in house, most of which it has qualified for the project, while another five samples are with a clinical collaborator. So far, it has analyzed 11 tumor/normal pairs, looking for single-base changes, insertions and deletions, structural variants, copy number changes, and loss of heterozygosity.
After teasing out the somatic variants that only occur in the tumor samples, the company submits the results to an ovarian cancer advisory board, which includes experts at the MD Anderson Cancer Center, the Fred Hutchinson Cancer Research Center, Massachusetts General Hospital, and the Dana Farber Cancer Institute.
Based on a list of candidate genes derived from the results, Illumina researchers are hoping to find cancer-specific pathways that could be targeted by existing drugs or become the starting point for new drug development; or to develop biomarkers.
"We will then take a subset of those candidate genes and move them into a validation phase, which we will do either on arrays or through targeted sequencing," Heath explained. If they find suitable markers, they then plan to launch them as lab-developed tests in Illumina's CLIA lab, and, ultimately, develop them as in vitro diagnostics.
Heath cautioned, though, that it might be difficult to find a common set of biomarkers among the samples. For example, he said that copy number changes differed a lot between six tumor/normal pairs analyzed so far, with some tumors having few, others a lot. "We might find that there is not a common set of biomarkers, but that each tumor is different and will need to be sequenced not only once, but several times on a monitoring basis," he said.
But discovering biomarkers is only one goal that Illumina is pursuing with this project. Another one is to develop experimental protocols and analytical tools that could be useful to its customers in large-scale cancer genome projects.
"We are learning a lot that we can apply and present to Illumina's customers," said Mark Ross, a researcher at Illumina, during a company seminar that was webcast last month. "Obviously, there is a huge interest outside Illumina in …studying very large numbers of tumors vs. normal genomes," he said, such as the International Cancer Genome Consortium and the Cancer Genome Atlas.
As a pilot for the ovarian and gastric cancer project, Ross said, Illumina and collaborators from the Wellcome Trust Sanger Institute sequenced a melanoma genome from a well-characterized cell line, a project that was recently published in Nature (see In Sequence 12/22/2009).
In that project, the researchers were able to cover more than 90 percent of the human reference genome and to call somatic substitutions with about 90-percent sensitivity and 97-percent specificity. In the meantime, the company has been improving the process of calling variants, including small insertions and deletions, Ross said.
Sequencing DNA derived from tumors rather than cell lines, he said, poses additional challenges in that they are contaminated with normal tissue and there is no karyotype information available.