The BeadXpress system from Illumina is an ideal platform for assaying 96 to >3000 SNPs in essentially any number of individuals because it yields very accurate and high-throughput data with costs of $0.07-$0.25 per genotype.

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How Does This Work?

The Basics

The BeadXpress platform utilizes the Illumina Golden Gate assay technology, which is a robust, multiplexed, PCR extension and amplification method that allows a quantitative comparison of biallelic SNPs.

Enough with the hype though... in the most straightforward terms, the assay enables us to very specifically amplify the sequence around a particular SNP and label the two amplified alleles with a different fluorescent dye (Cy3 and Cy5). We can include up to 384 SNPs in one reaction well, for each DNA sample, a process called “multiplexing”.

Then, these amplified alleles are hybridized to and immobilized on a special substrate built by Illumina, called a VeraCode bead. From here, the Illumina BeadXpress machine can automatically determine the identity of PCR primer hybridized to the VeraCode beads, and measure and quantify the fluorescent signal (thus indicating the genotype) for each amplified SNP.

For a more detailed description of the mechanics and chemistry, we recommend that you consult the Illumina web site.

How to Get Started

Our clients have a choice in this. Either, they develop their target SNP list and flanking oligos independently, or they choose to have our bioinformatics specialists assist them in this process.

Once a SNP and oligo list has been created, this file is provided to Illumina as one part of the order.   Illumina will use the SNP and oligo list to create an OPA (oligo pool array) which is actually the list of which VeraCode beads will match to which SNP oligos.

Illumina then sends the OPA and associated reagents to our laboratory. We combine these with your DNA samples, and generate your data.