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Custom SNP Genotyping

96 to 1,000,000 investigator-chosen SNPs can be assayed per sample using Illumina’s technologies. Depending on the number of custom SNPs desired and the sample number to be assayed, the platform used is either VeraCode, GoldenGate or Infinium.

Supported Organisms

Human
Mouse
Other – please inquire about other organisms

Study Designs

Replication of Genome Wide Association study
Fine mapping
Positional or functional candidate gene

Custom Array Option Details

Investigator-defined density and location
Selection by investigator, assistance available
Mouse SNP selection resource: Genotypes for 480 mouse strains and >13,000 Illumina-validated SNPs are publicly available along with SNP selection tools at Wellcome-CTC Mouse Strain Genotype Set

Custom content can be added to all GWAS arrays and the Exome array. Please inquire for more information.

Please note the following important considerations when designing custom content:

Success rates:

Not all custom assays will work, even if they have high Illumina design scores or have worked in other experiments. For Golden Gate experiments, data for up to 10% of the SNPs will not be returned. This falls within Illumina's specifications. In our experience, data is returned on 90-98% of SNPs selected. For Infinium assays, there are two levels of failure. The first level is at manufacturing. Illumina only guarantees that 80% of SNPs will pass manufacturing and make it on the chips. In our experience the range has been between 81% and 92% of SNPs make it onto the chips. Once the SNP is on the chip, it is possible that it will not work well and we will not be able to return data on it. Those failure rates are similar to the Golden Gate assays. Because of these issues, we recommend that for regions absolutely critical to your analysis, you build in redundant SNPs, ie. chose SNPs that are in LD with your critical SNPs and add them to the SNP pool to insure that you will be able to analyze the data appropriately.

Beadtypes vs. SNPs:

When designing Infinium (iSelect) projects, you are paying for beadtypes, not SNPs. Some Infinium assays must have the two alleles attached to individual beads, instead of having both alleles on the same bead. This is true for A/T and G/C SNPs and for some historical assays. When you are designing your project, you must note the number of beadtypes, not the number of SNPs. This means that the actual number of SNPs you can use in your project will be less than the number of beadtypes. The number of beadtypes is listed in the header information of the assay design files returned by Illumina.

Efficient SNP selection:

The most efficient way to select your SNPs is to get Illumina design scores on all of your possible SNPs prior to narrowing down your list. You can submit lists of rs numbers, genes and regions and receive design scores on all possible SNPs prior to starting your selection. This will tell you if your favorite SNP has a chance of working in the project or not, and will allow you to select appropriate proxies, if necessary. The assay files returned by Illumina contain useful information in addition to design scores, such as MAF in different world populations, cross species conservation scores and gene region annotation (ie. 5'UTR, 3'UTR, intronic, non-synonomous, synonomous) which can aid in SNP selection. To obtain these lists you can work with Illumina directly or you can contact our SNP selection consultant, Roxann Ashworth [rashwor2@jhmi.edu; 410-614-0702], who can assist you. All SNP lists must be approved and ordered by us.

QC SNPs:

For most custom SNP projects you will be required to include a minimum of 20 and a maximum of 96 QC SNPs in your pool of SNPs. These SNPs are used to cross-check against our 96 SNP barcode sample pretesting panel to assure the integrity of sample and data tracking through our entire process. They are also useful as Ancestry Informative Markers (AIMs) and for checking genotypes in previous GWAS studies, if applicable.

Platform

SNPs
per
Sample

Factors to Consider

GoldenGate

96, 384, 1,536 or 3,072

Tolerant of lower quality DNA samples

Infinium

3,000 - 1,000,000

Not recommended for WGA or highly degraded DNAs. An option for highly degraded samples may be the Illumina Restore process.

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