Custom Genotyping Products:
SNP panels may be tailored to your specific research needs. Two different chemistries are used depending on the number of SNPs to be assayed. Lower numbers of SNPs are generally assayed using the Golden Gate chemistry, SNPs numbering over 6000 are generally assayed using the Infinium chemistry. See below for details.
We offer a SNP selection service or you may select SNPs yourself, after consultation with our staff to learn proper selection criteria. Not every SNP will work with the Illumina system. To determine which SNPs are suitable, SNPs may be submitted to Illumina for scoring. You may submit a list of rs numbers from dbSNP, a list of HUGO approved gene names, a list of NM numbers from Genbank or SNPs which you have identified. For file formats for each of these types of data, please contact Roxann Ashworth [410-859-3085]. Illumina s scores can then be combined with other criteria to select the set of SNPs most likely to give optimal information. Once the final set of SNPs is selected, it is returned to Illumina (by the SNP Center) for oligo synthesis. A poster describing our experience with SNP selection is available here. When submitting a list for scoring, be sure to specify if the list is for Golden Gate or Infinium chemistry.
Clients are able to design custom SNP assays for any species for which SNP data is available. Illumina currently supports mouse, rat, cow and horse genomes in addition to the human genome, but other genomes are possible as well. Please contact us for details.
Custom Golden-Gate Genotyping:
Golden-Gate chemistry is Illumina's original genotyping chemistry, carried out on fiber optic bundles in a 96 well format. More information can be found on Illumina's website. It can be used to assay SNP panels of 96, 384, 768, 1536, or multiples of 1536 SNPs.
Costs for genotyping vary by panel size. If assaying more than 3072 SNPs on more than 1100 samples, pricing will generally be cheaper using the Infinium chemistry on 6000 SNPs. See pricing page for details.
iSelect Infinium BeadChips:
The Infinium technology is the same technology as used for the Genome Wide Association Chips. Custom panels are deployed on a 12 sample per chip format. For more information, please see Illumina's website These custom panels can be created using between 6000 and 60,000 SNPs. The minimum number of samples for this to be cost-effective is 1,100.
Pricing on this product is based on increments of both SNP numbers and sample numbers. When selecting SNPs for this platform, one should select as many SNPs as possible within the appropriate increment, as Illumina estimates up to 20% of the selected SNPs will fail the manufacturing process and will not be placed on the custom chip. The SNP number calculations are further complicated by the fact that there are two different forms of the Infinium chemistry, one of which requires two bead types, the other of which requires only one. Bead types need to be counted when the final number of SNPs in selected. This information is provided by Illumina when the SNP selection files are returned. Please contact Roxann Ashworth [410-859-3085] for detailed information on pricing and SNP selection.
Oligo Ordering:
Oligos must be ordered in quantities of 96, 384, 768 or 1536 SNPs for each panel. Custom Infinium chips must be ordered with a minimum of 6000 SNPs. Costs vary based on the scale desired. For a price quote, please contact Roxann Ashworth [410-859-3085]. Unless prearranged, all oligo orders must be placed through the SNP Center.
Analysis software: If you wish to use Illumina's Bead Studio software to analyze your data, licenses are available for internal JHU customers for $2,000 each. This does not include the methylation module.