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NHGRI, Research Groups, Illumina Developing Single Chip For Rare Variants


BOSTON — The National Human Genome Research Institute and several other research partners have agreed to pool their patient samples to develop a single assay able to pick up new and rare variants in genetic risk association studies.

Research groups doing sequencing studies and genome-wide association studies in cardiovascular disease, obesity, and type 2 diabetes are working on a project with Illumina to develop a single chip, called Metabo-Chip, that can detect up to 50,000 SNPs associated with various diseases, NHGRI scientist Michael Erdos said this week at a conference here on consumer genetics.

“We struck a deal where we could reveal up to 50,000 SNPs, including all the association [identified] through our various disease [studies], plus all of these very rare variants that we’re picking up in one or two samples through single-gene studies, and [putting] them all on one chip,” Erdos said.

In exchange for Illumina developing the chip, the various research groups have agreed to genotype a certain number of patient samples. In total, the research groups would genotype 200,000 patients at $30 per sample. The NHGRI has taken on the responsibility of genotyping approximately 32,000 patient samples for this project.

Having planned and conducted numerous GWAS studies under NHGRI, Erdos emphasized at the conference that garnering genome-wide significance is not dependent on analyzing a large number of SNPs, but genotyping a large number of patient samples.

“This is something that no one group can do,” Erdos said. So, “we all pulled our resources together.” Among the numerous research institutions involved in the effort to genotype samples in developing the Metabo-Chip, is the Broad Institute and the Wellcome Trust, Erdos told Pharmacogenomics Reporter.

According to Erdos, the partners are in the midst of designing the Metabo-Chip and the assay metrics will likely be ready in the next year, although he admitted, “we don’t know how we’re going to pay for this yet."

After the design is completed and Illumina develops the chip, the assays will be delivered to the various partners who will genotype samples from patients with various diseases.

NHGRI will use the Metabo-Chip to validate variants identified in a genetic risk-association study for diabetes, called Finland-United States Investigation of NIDDM Genetics (FUSION), and possibly for other studies.

As reported previously in PGx Reporter sister magazine BioArray News, Illumina CEO Jay Flatley forecasted a "slowdown" in the growth rate of GWAS over the next few quarters as researchers await new content from sequencing projects such as the 1000 Genomes Project to be incorporated onto microarrays.

However, according to Flatley this “temporary” slowdown will pick up as the new content "drives a whole new round of rich genome-wide association studies" based on rare variant content [see BAN 04-28-2009].

“There will be chips that will come out that will have [an] increasing percentage of content that comes from these rare variation projects," Flatley previously said. "An ultimate chip might be two years away by the time people really get done discovering all these and screening them, but there will be products that contain increasing amount of rare-variant information."

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