Wellcome puts its trust in Illumina

SAN DIEGO—Illumina announced recently that it has partnered with UK-based Wellcome Trust Sanger Institute (WTSI) and Wellcome Trust Case-Control Consortium on an ambitious genomics and proteomics project. The goal: to enable Wellcome to better correlate genetic variation and gene function with particular disease states, thus enhancing drug discovery, allowing diseases to be detected earlier and permitting better choices of drugs for individual patients.

To make this possible, Illumina is developing a custom Sentrix BeadChip that will enable researchers to study the impact of the single nucleotide polymorphisms (SNPs) that cause non-synonymous amino acid changes on a range of disease samples.

The WTSI will use the new BeadChip specifically to study four common disease phenotypes—asthma, diabetes, cancer and heart disease—as part of the Wellcome Trust Case-Control Consortium, which has put more than 20 leading human geneticists to work analyzing thousands of DNA samples from patients suffering from different diseases to identify common genetic variations for each condition. The consortium's scope is larger than what Illumina is involved in, covering eight major disease areas.

"We plan to genotype over 5,000 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," reports Dr. Panos Deloukas, senior investigator at the WTSI. "Non-synonymous SNPs are likely to be a productive early target in our quest to understand the genetic component of these common diseases."

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

"One of the things we're good at is that our assay allows virtually unlimited ability to choose almost any SNP you like," says William Craumer, director of corporate communications for Illumina. The Infinitum assay features single-tube sample preparation and requires no PCR or ligation steps, he says, which cuts down on labor and errors related to sample handling.

"The assay also provides high call rates and accuracy with no constraints on locus selection," he says, adding the assay can be scaled to unlimited levels of multiplexing without compromising data quality, unlike many alternative PCR-dependent assays.

While the recognition of the company's technology by the Wellcome Trust is gratifying, the long-term goal is the potential to create a commercial product, Craumer notes.

Following the WTSI's completion of the project using the new genotyping BeadChip, Illumina intends to turn the custom SNP product into a standard microarray offering, says Jay Flatley, Illumina's president and CEO. At that time, the company also will make available details about locus selection and sequence information.