Sentrix® BeadChip and BeadArray Technology (Illumina, Inc.)

The BeadChip microarray platform can analyze several samples on the same device at the same time. BeadChips are manufactured with very flexible microelectronic mechanical systems-based technology. This makes it possible to create any number of microfabricated wells clustered into discrete regions (arrays) on a slide-shaped substrate. They can be used for low-to-medium sample throughput requirements or dense, whole-genome applications.

Illumina’s Sentrix® HumanHap500 Genotyping BeadChip makes it possible to do whole-genome genotyping of more than 555,000 tag SNP markers derived from the International HapMap Project on a single BeadChip. This BeadChip contains 555,000 tag SNP loci that offer comprehensive genomic coverage across different populations. The product can be used for whole-genome association studies and loss-of-heterozygosity/copy number studies. Because tag SNPs serve as proxies for other SNPs, this BeadChip provides higher genomic coverage with fewer SNPs than whole-genome genotyping strategies that use randomly selected SNPs.

The BeadArray genotyping system combines very high throughput and accuracy with low cost per SNP analysis. The technology uses three-micron silica beads that self-assemble in microwells on fiber-optic bundles or planar silica slides. Each bead is covered with several hundred thousand oligonucleotide copies that act as the capture sequences in one of Illumina’s assays. BeadArray can be used to analyze genetic variation through SNP genotyping, profile gene expression at the RNA level, and conduct proteomics research.

BeadArray technology is used in Illumina’s Beadlab and BeadStation systems for several DNA and RNA analysis applications. The BeadLab production SNP genotyping systems can generate 800,000 to 1.3 million genotypes per day. The BeadStation enables a wide range of sample throughput and several applications for genetic analysis. The system can be used manually for both RNA- and DNA-based applications. The process can also be automated using Tecan liquid handlers and robot controls. As research needs change or new applications become available, additional applications or automation can easily be added to an existing system.

The BeadArray platforms and BeadLab and BeadStation processing systems can be used to rapidly conduct genotyping analyses on large numbers of samples, which may be used clinically to identify cancer susceptibility genes in patients. The products can also be used to rapidly evaluate the expression of genes from a whole human genome panel, which may be used to identify new molecular targets for cancer detection or therapeutic interventions.

Two series of IMAT SBIR awards to Illumina supported the development of the bead technology. Mark Chee was the PI for both sets of awards (CA081952 and CA083398).

The goal of the Phase I IMAT R43 SBIR award (CA081952) was to develop genome-profiling analysis tools. The research funded by the Phase I award showed the feasibility of the genome-expression array and methods to determine the identity of sequences (i.e., array decoding), the development of arrays, and quality control of manufacturing. Successful completion of the research under the Phase I (R43) IMAT SBIR award resulted in the funding of a Phase II (R44) award. The Phase II research resulted in the validation of the technology’s ability to accurately determine the identity of sequences (i.e., decoding), sample preparation and hybridization procedures, and validation of the products.

This support from the IMAT Program resulted in the development and commercialization of the 96-well fiber-optic matrix array system and the silicon wafer BeadChip system. BeadArray became commercially available before the SBIR grant period expired, and two BeadChips were commercialized after the grant period ended—the Sentrix® Human RefSeq Genome Expression BeadChip, permitting analysis of ~24,000 genes, and the Sentrix® Whole Human Genome Expression BeadChip, permitting analysis of ~48,000 genes.

In the Parallel Array Processor awards (the R43 and R44 CA083398 awards), Illumina made progress in developing components for a new parallel array processor and protocols for genotyping, RNA profiling, and genomic DNA analyses. The overall goal of this work was to develop an automated, high-throughput genotyping and RNA profiling system. With support from the CA083398 IMAT awards, Illumina improved the software, sample handling, and detection systems and integrated these capabilities into devices. The company then evaluated these devices for performance in automatically processing large numbers of arrays. The investigators also developed procedures for RNA profiling and quantitative genomic DNA experiments.

The BeadLab system was made commercially available by the conclusion of the grant funding period. A lower cost, lower throughput genotyping station for smaller research laboratories was developed during this grant. After the grant ended, Illumina made this genotyping station, BeadStation 500, commercially available.

Illumina recently introduced a flexible, high-throughput DNA methylation profiling technology, GoldenGate®, that can be used with BeadArray to perform genome-wide methylation profiling across several areas, including cancer and human embryonic stem cell research. The first standard panel using the combined technologies covers 1,505 methylation sites over 800 cancer genes.

PubMed lists 15 publications, including one on cancer, that involve the use of BeadChip technology. An additional 18 publications report on research involving BeadArray technology. Of these, 5 address cancer research. Two more publications mention the BeadStation.