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Custom Illumina Genotyping Arrays at Center of Ongoing iCOGS Consortium's Cancer Studies


Illumina genotyping arrays are at the heart of an ongoing research effort that seeks to identify the heritability and genetic risk profiles of several cancers and their related subtypes.

Members of the EU-funded international Collaborative Oncological Gene-environment project, or iCOGS, presented their findings last week in 13 studies published in five research journals. For this first round of the project, which focused on breast, prostate, and ovarian cancers, the researchers used a custom-designed, 200,000-marker Illumina iSelect BeadChip dubbed the iCOGS array.

The consortium has also designed a second-generation chip containing 600,000 markers, called the OncoChip, which it plans to use in a further round of studies.

Though Illumina offers a variety of whole-genome genotyping arrays, many of which have been used in prior cancer studies, the first round of this project required a custom array because it needed to "type sets of markers that were not available on any one chip," said Douglas Easton, a professor of genetic epidemiology at the University of Cambridge.

Easton, who is senior author on the consortium's primary breast cancer study in Nature Genetics, told BioArray News that the iCOGS array was designed to genotype "a very high density of markers across more than 50 regions known to be involved in cancer susceptibility," a capability that "no standard array" would have provided.

"Even if there had been a standard array with all the markers we wanted, it would likely have had several million markers, and would have been prohibitively expensive to use for this size of study," Easton said.

In addition to obtaining a suitable price on the iSelect platform, which can process 12 different samples on each chip, iCOGS decided to work with Illumina because the "main genotyping centers involved were all set up to genotype at high throughput with Illumina so there was no other way of getting the genotyping done in a reasonable timeframe," Easton said.

According to an article describing the array design process, the researchers selected markers for the iCOGS array with a number of goals in mind. One was to follow up the results from many genome-wide association studies by "selecting all SNPs showing even quite weak evidence of association and still being able to genotype all these variants in a very large replication study."

A second aim was to enable genotyping across studies for multiple different cancers, in order to "explore in much greater depth than before the overlapping susceptibilities between them."

The researchers also claim that they designed the iCOGS array to provide a basis for risk profiling. As the array includes a large panel of SNPs selected from GWAS, they believe it is possible to develop risk profiles "based not just on the established risk loci but also using larger panels, including variants with disease associations that fall below traditional genome-wide significance levels."

Altogether, about 200,000 samples were genotyped using the iCOGS chip and the results of this phase of the project have been portrayed by participants as a success. In the papers published this week, the authors reported an increase in the number of genetic associations for breast, ovarian, and prostate cancer – nearly doubling the number of known susceptibility regions. They also reported insights into the differences between subtypes of cancer, including those revealed from comparisons of estrogen receptor-positive and estrogen receptor-negative breast cancers, as well as the pathways and mechanisms involved in susceptibility to these common cancers.

The publications and related articles are currently available online through a Nature Genetics portal.

New Studies, New Chip

Jennifer Stone, Illumina's cancer genomics marketing manager, told BioArray News that the iCOGS array is just one of many consortia-designed genotyping arrays the San Diego vendor manufactures. She said that genotyping panels based on the company's BeadChip platform are the foundation of "more than 25 different consortia products, with new groups being formed every year."

One example of such a consortium-designed, Illumina-manufactured array is the Metabochip, which tests approximately 200,000 SNPs identified through GWAS for metabolic and atherosclerotic/cardiovascular diseases and traits. Researchers presented findings made with the Metabochip in several papers last year (BAN 8/28/2012).

Another similar tool is the Cardiochip, a custom array that contains 50,000 SNPs found across 2,000 genes associated with cardiovascular disease, and has been used in more than 60 studies (BAN 10/16/2012).

Typically, consortia select the content for these arrays, though, in regards to the iCOGS project, Stone said that that Illumina assisted with the array's design to "ensure the iCOGS BeadChip included the highest quality content." She added that delivery of the chips to the consortium, from final design to shipping of the first of the arrays, was "well within our standard guidelines of 12 weeks for a project of this size."

While each consortium retains the right to make its array design available to non-affiliated research groups, Easton said that iCOGS has selected to share the iCOGS array with "several" interested parties. Stone said that Illumina also offers researchers the ability to "deploy similar content" onto a standalone iSelect array or as an add-on set of content to one of Illumina's many standard arrays.

According to Easton, though, the iCOGS array used in the first round of studies is no longer being made by Illumina. He said that the first-generation iCOGS array has been superseded by the higher-density OncoChip, which the consortium will use in a second round of studies targeting two additional cancers: colorectal and lung.

The OncoChip will include approximately 600,000 SNPs and will include fine mapping of all the new susceptibility regions identified with the iCOGS array, as well as associated variants identified through whole-genome, whole-exome, or targeted sequencing studies, Easton said.

"All of these require a larger chip, and fortunately as the technology has improved it is possible now to genotype many more markers on a chip for a similar cost as the iCOGS," he noted.

The main projects in the second round will be "similar in design" to the first round of the iCOGS project, and will consist of large case-control studies to examine the associations between the markers and risk, Easton said.

In addition, "there will be more focus on studies with extensive clinical data, to look for associations between the markers and treatment response and disease outcome," he said. "We will also include more studies which are drawn from prospective cohorts," Easton added. "This will be potentially important for analyzing the combined effects of genetic markers and other non-genetic risk factors for determining risk."

According to Easton, iCOGS hopes to genotype "at least 400,000 samples" with the OncoChip.

Some researchers outside the consortium have already expressed interest in buying the OncoChip, according to Easton, though he described its use in these other projects as "tentative." According to Easton, these other groups would like to use the OncoChip as part of prevention programs, such as identifying women at higher risk of breast cancer for chemoprevention studies.

Regardless of where those discussions go, Easton pledged that the OncoChip will also become available to outside groups after an initial period.