SAN DIEGO—Representing its second deal in six months with Cancer Research UK, an independent charity dedicated to cancer research, Illumina has inked a nearly $7-million contract to conduct large-scale genotyping for United Kingdom-based research groups that are studying the molecular basis of prostate cancer. The ultimate goal is to design and validate biomarkers associated with prostate cancer susceptibility and disease progression and to improve discovery and development work on potential therapies.
Phase one of the work will involve conducting whole-genome genotyping—classified as having greater than 550,000 SNPs per sample—for at least 4,000 well-classified prostate patients and controls. Phase two will involve development of a custom, 12-sample BeadChip that will enable analysis of 24,000 SNPs per sample and be used to genotype at least 8,000 samples.
Both phases will use Illumina's Sentrix BeadChips and Infinium Assay, with the option to employ related assay methods.
The previous deal between Illumina and Cancer Research UK was structured very similarly, notes Jay Flatley, Illumina's president and CEO, except that under the November 2005 deal, the target is colorectal cancer and phase two was set to genotype more 10,000 samples using a BeadChip enabling analysis of 20,000 SNPs per sample.
Cancer Research UK is extending its relationship with Illumina to perform a second genotyping study because the quality of the data has been high so far for the work that began in November, says Harpal Kumar, COO of Cancer Research UK, and the organization expects that to be the case here as well.
Kumar notes that the work is important because prostate cancer is the most common cancer among men but not much is known about the molecular mechanism of the disease's development.
"Complicating our understanding of prostate cancer is the fact that it tends to cause few symptoms in its early stages," he adds. "But early diagnosis is a key part of successful treatment."
In the United Kingdom, more than 275,000 persons are diagnosed with cancer annually, Cancer Research UK reports. Prostate cancer is one of four types—along with breast cancer, lung cancer and colorectal cancer—that account for more than half of all new cancer cases.
SNP content for the BeadChips is derived largely from what Flatley calls "high-value tagSNPs" that were identified in the recently completed HapMap Project.
"TagSNPs deliver high statistical value to researchers because they can serve as proxies for larger groups of SNPs," Flatley notes. Researchers can analyze human populations comprehensively and efficiently by examining between 250,000 and 500,000 tagSNPs, he says, instead of the entire set of more than 10 million SNPs, thus opening doors to genome-wide disease association studies such as those being conducted by Cancer Research UK.
Sentrix HumanHap BeadChips are the only whole-genome genotyping arrays with tagSNP-centric content, Flately asserts.
In addition to identifying potential biomarkers as a result of the deal with Illumina, Cancer Research UK will evaluate the genotype data to detect and analyze chromosomal aberrations such as copy number changes and loss of heterozygosity, with an eye toward identifying clues to genetic mechanisms underlying cancer development.
