Illumina will take advantage of a new agreement with the Wellcome Trust Sanger Institute and the Wellcome Trust Case-Control Consortium to develop a new custom BeadChip that will become commercially available after the Sanger completes its studies using the chip next year, Illumina said last week.
The custom Sentrix BeadChip will analyze so-called non-synonymous SNPs that cause amino acid changes in proteins. The chip, to be called the cSNP-6 BeadChip, will allow researchers to study 15,000 SNPs on six samples simultaneously, using Illumina's Infinium assay.
The chip's content will be derived from the HapMap project, of which Illumina and the WTSI are participants. Researchers at the WTSI plan to use the chips to genotype more than 5,000 samples by the end of the year to study four common disease phenotypes.
Bill Craumer, head of corporate communications at Illumina, said that rather than continue to release new assays on its flagship BeadChip platform, the company decided to add to its existing arsenal of the Infinium assay, the Golden Gate assay, "which is more appropriate for smaller sets of makers," and the DASL assay" for profiling gene expression in degraded RNAs," which launched in January.
"We have no other breakthrough assays in the works, but rather powerful extensions of our existing assay technologies that leverage inherent specificity and reproducibility. Examples would include assays for methylation and allele-specific expression, among others," Craumer said.
In addition to the new custom BeadChip being developed for use with the Infinium assay, Illumina added its whole-genome genotyping application to the Infinium assay over the summer.
The WGG method, as described in the April edition of Nature Genetics, is an array-based method for SNP genotyping developed by a team led by Illumina's senior scientist Kevin Gunderson. BioArray News spoke with Gunderson about the paper and the method in April (see BAN 4/20/2005).
According to Craumer, the "the WGG method is based on our Infinium assay and will be used with a range of different BeadChips including whole-genome genotyping chips" like the company's Human-1 BeadChip "and multi-sample chips with more focused content" like those the firm has developed for the Sanger studies and will eventually commercialize.
"The same assay protocol is used for each; it's just applied differently," Craumer said.
— Justin Petrone ([email protected])