The BeadXpress system from Illumina offers a cost effective platform for assaying 96 or 384 SNPs in essentially any number of individuals. The BeadXpress platform primarily uses the Golden Gate SNP genotyping assay that we currently use in conjunction with the iScan (formally the Bead Array Reader). For more information on Golden Gate, see our Illumina Golden Gate genotyping web page. The main advantages of the BeadXpress platform compared to the iScan are that the costs/SNP are lower than on the iScan, particularly at the 96 SNP/sample level, and that variable numbers of samples can be more easily assayed since the readout is not entirely dependent on maintaining samples in a 96 well format (with the caveat that labor costs are very similar regardless of the number of samples processed, up to a full plate).
The BeadXpress Platform
As with the Bead Array reader, the starting experimental material is output from the Illumina Golden Gate assay–Cy3 and Cy5 labeled PCR extension products containing different Illumicode address sequences. In BeadXpress, these products are allowed to hybridize to small glass rods that are coupled to oligos complementary to the Illumicodes. The glass rods (the so-called VeraCode “beads”) also contain etched bar codes which correspond to a specifc Illumicode address sequence. The hybridization between the beads and PCR products takes place in suspension for several hours (as opposed to the iScan platform, in which the the PCR sample is applied to BeadChips for overnight hybridization), then the beads are washed, resuspended, and loaded onto the reader. The reader sucks up eight samples at a time (a column of a 96 well plate) and distributes them into a grooved plate. Red and green lasers scan the plate and detect the bar code on each bead as well as the relative Cy3 and Cy5 fluorescent signal. Each bar code corresponds to a specific Illumicode address which corresponds to a specific genomic sequence provided in the SNP design file, thus the relative Cy3 and Cy5 signals provides the genotype data for that SNP. Data visualization and software manipulations are as described for the iScan.
Starting a BeadXpress Project
As with iScan based genotyping projects, the first step is to create a file that contains your desired SNPs. This is described in more detail on the Illumina Golden Gate genotyping web page. Once in its final form, the oligonucleotide (“OPA”) file is provided to us and we submit it to Illumina as part of an order containing all the reagents for the assay. You will be billed right away for the oligonucleotide pool and other Illumina reagents, but will only be billed for the other materials as we process your samples. The ordering process for BeadXpress is distinct in that the reagents and materials are have to be ordered at the same time as the oligonucleotide pool, whereas for iScan based projects the oligonucleotide can be ordered separately. This has relevance for your project design in one respect only–price breaks are available for projects ordered in multiples of 5, especially at the 15 plate level.
In every other way, sample preparation, software, and data interpretation the platform mirrors our existing Illumina system, the iScan. Please consult that Illumina Golden Gate genotyping web page for more details and other links. Of course, we want to talk to you as well if you have specific questions about how this platform could work for you.