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Custom SNP Genotyping

Affymetrix, Illumina and OpenArray technologies support custom genotyping. In addition, there is the option for genotyping-by-sequencing using amplicon sequencing. Each of these have a different minimum of samples required. Please inquire for more information.


Supported Organisms

Study Designs

Custom Array Option Details


Custom content can be added to most Illumina Infinium genotyping arrays. Please inquire for more information.


Illumina provides information to help figure out how much overlap there is for regions of interest with their standard array content. Please click on the link to be directed to their website.

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 onto 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, i.e. choose 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.



Affymetrix has an Axiom Cloud Database of validated markers that can be used. In addition, Affymetrix will work to create assays for SNPs that are currently not in their database.


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 (i.e. 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 [; 410-614-0702], who can assist you.  All SNP lists must be approved and ordered by us.


Genomic coverage results presented in this paper can be used to help design new genotyping arrays. If the design is intended to be focused on specific candidate variants or regions, while also providing a backbone for genome-wide imputation, one may begin with the existing HumanCore or Biobank variant set and then add candidate variants that are not already well imputed by the backbone variants in target ancestry group(s).



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 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.




Factors to Consider


up to 50,000 or up to 800,000

384 peg format supports up to 50,000 SNPs; 96 peg format supports up to 800,000 SNPs

Amplicon Sequencing


Tolerant of lower quality DNA samples


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.



12, 26, 60, 120, 180, 240

Each option has a different sample number minimum. Please inquire for more information.




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