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Illumina to Develop Genotyping BeadChip

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Illumina, Inc. has announced that it is collaborating with the Wellcome Trust Sanger Institute (WTSI) and the Wellcome Trust Case-Control Consortium (WT-CCC) on the design of a custom Sentrix® BeadChip that will enable researchers to study the impact of those SNPs that cause amino acid changes (non-synonymous), on a broad and deep range of disease samples. 

The WTSI will use the BeadChip to study four common disease phenotypes with common controls as part of the WT-CCC. 

The BeadChip configuration will enable the analysis of six samples simultaneously on one microarray, studying 15,000 SNPs apiece, using Illumina's Infinium™ assay.

The Infinium assay allows investigators to query the entire genome with call rates, reproducibility and related performance metrics comparable to Illumina's GoldenGate® assay protocol.

The Infinium assay enables virtually unconstrained, intelligent SNP selection for BeadChip array content.

Content for the Sentrix cSNP-6 BeadChip will be composed principally of non-synonymous, coding SNPs selected from the HapMap Project. 

Non-synonymous SNPs are located in the coding regions of genes and cause amino acid changes in the corresponding proteins. 

As a result, these candidates functional SNPs - as a category - are more likely to impact common disease susceptibility than the rest of genome (in addition to gene expression regulatory sequences that remain to be defined) and, therefore, have higher experimental value.

Given the ambitious scale and schedule of the non-synonymous SNP study, the WTSI has purchased additional scanners, automation and LIMS (laboratory information management system) capability to further increase sample throughput of the Institute's BeadLab, a production-scale, end-to-end genetic analysis laboratory that leverages Illumina's BeadArray™ technology. 

According to Dr. Panos Deloukas, Senior Investigator at the WTSI, “We plan to genotype over 5000 samples with the non-synonymous SNP BeadChip in a case-control study design.”

“Our schedule is to finish data production by the end of the year, a target made possible by Illumina's multi-sample chip.”

“Non-synonymous SNPs are likely to be a productive early target in our quest to understand the genetic component of these common diseases.”

Following the WTSI's completion of the project using the genotyping BeadChip, Illumina intends to turn the custom SNP product into a standard microarray offering, at which time the Company will make available detail about locus selection and sequence information. 

“We're very pleased to extend our longstanding relationship with the WTSI,” stated Jay Flatley, Illumina President and CEO. 

“Our jointly developed SNP array not only provides high experimental value, it also underscores the flexibility of our BeadArray Technology, and particularly the BeadChip format.”

“The non-synonymous SNP-6 Genotyping BeadChip will be the first multi-sample microarray product to leverage our Infinium assay.”